commit 1aa9dc381ff8201ae17b9d7c2117dccbde2eb724 Merge: 19706fb0 2d7a646b Author: Mahesh Natarajan Date: Mon Jun 1 14:30:56 2026 -0700 Nyx 26.06 release Update AMReX submodule for June 2026 release commit 2d7a646b430563f1f5fd00424417e218d7dc1b67 Author: nataraj2 Date: Mon Jun 1 13:10:03 2026 -0700 Update AMReX submodule for June 2026 release subprojects/amrex commit 19706fb0651c1dbf1dabaf24c1e74da5ecfa0561 Merge: 699f8cc6 c4815a0d Author: Jean M. Sexton Date: Tue May 26 13:55:50 2026 -0700 Merge pull request #114 from nataraj2/matter_pk Updating `docs.yml` commit c4815a0d25b0fa822f515371ec3e70a9cff48493 Author: nataraj2 Date: Tue May 26 11:41:12 2026 -0700 Updating docs.yml .github/workflows/docs.yml commit 699f8cc68d59e0f7786503d1a9b1ea692882bcaa Merge: 12f16a1a f165d459 Author: Jean M. Sexton Date: Tue May 26 06:18:27 2026 -0700 Merge pull request #113 from nataraj2/matter_pk Updating yml files for build and deploy commit f165d45977df537fb496ff02c143d8fb5ecdc337 Author: nataraj2 Date: Sun May 24 17:04:26 2026 -0700 Removing unwanted nvcc .github/workflows/dependencies/dependencies_nvcc_2404.sh commit 8db4cc5b0024f285dd7e5be759f6455740bf3da8 Author: nataraj2 Date: Sun May 24 06:39:45 2026 -0700 Trying to fix nvcc error .github/workflows/dependencies/dependencies_nvcc.sh commit 9ec05440d5331a2618d295e942177e8d1ce2f969 Author: nataraj2 Date: Sun May 24 05:36:26 2026 -0700 Trying to fix nvcc error .github/workflows/dependencies/dependencies_nvcc.sh commit 1294ef63e61bc1ad9836a731d1271f6dee306f9e Author: nataraj2 Date: Sat May 23 20:39:51 2026 -0700 Updating cmake CMakeLists.txt commit 7ae8cd71b436b4d86c242466c90fa5bf8a51c134 Author: nataraj2 Date: Sat May 23 19:25:40 2026 -0700 Make nvcc dependency script executable .github/workflows/dependencies/dependencies_nvcc.sh .github/workflows/linux.yml commit 1f982e25f0421a5080ee588c79c54f8b38cbc8be Author: nataraj2 Date: Sat May 23 19:13:59 2026 -0700 Make nvcc dependency script executable .github/workflows/dependencies/dependencies_nvcc_2404.sh commit f74defe63b10b7cd71133c8df64fde8e714f69f9 Author: nataraj2 Date: Sat May 23 19:09:54 2026 -0700 Correcting nvcc dependencies .github/workflows/dependencies/dependencies_nvcc_2404.sh .github/workflows/linux.yml commit f261d2a3c5e98733a6c14d2ea1935a581bbc3ba7 Author: nataraj2 Date: Sat May 23 18:47:16 2026 -0700 Updating hip dependencies .github/workflows/dependencies/dependencies_hip.sh commit 65b1594f8bbc080f060461f9a8bfbe2f67beb8b2 Author: nataraj2 Date: Sat May 23 18:42:43 2026 -0700 Updating to check .github/workflows/linux.yml commit 36f7d5c07ceaaee1f9b4d9277bd35a439617a581 Author: nataraj2 Date: Sat May 23 18:37:13 2026 -0700 Updating to check .github/workflows/linux.yml commit 1f271e2f58c0691f796623cebb4a79c48b8368e1 Author: nataraj2 Date: Thu May 7 00:34:32 2026 -0700 Turning off openmp for mac build .github/workflows/macos.yml commit 393f307092dd9ba6f91e7630e3dfa1d53f172d33 Author: nataraj2 Date: Thu May 7 00:27:46 2026 -0700 Updating to python3-setuptools .github/workflows/dependencies/documentation.sh commit 24b0197e619aba604ebdaea1f3ba4df167cf77d2 Author: nataraj2 Date: Wed May 6 17:14:22 2026 -0700 Updating yml files for build and delpoy .github/workflows/docs.yml .github/workflows/draft-pdf.yml .github/workflows/linux.yml .github/workflows/macos.yml commit 12f16a1a1f19dd1908adea4285c3318885920aa5 Merge: 9268adc6 b38a70c9 Author: Jean M. Sexton Date: Tue May 5 17:22:27 2026 -0700 Merge pull request #112 from nataraj2/matter_pk Adding guards for FFT routines commit b38a70c96461a6168eb732e3522bf3d7b55fa5f3 Author: nataraj2 Date: Tue May 5 16:35:44 2026 -0700 Adding guards forfft routines Source/DerivedQuantities/ParticleDerive.cpp commit 9268adc6c3abca12d7b43991de72c3efe9dc9511 Merge: f4b50a67 46846c91 Author: Jean M. Sexton Date: Tue May 5 15:49:07 2026 -0700 Merge pull request #110 from nataraj2/matter_pk Adding routines for matter Pk using AMReX FFT commit 46846c9189868a22e2c9e2a57b1f8c4b11de3131 Author: nataraj2 Date: Tue May 5 15:20:17 2026 -0700 Correcting comments Source/DerivedQuantities/ParticleDerive.cpp commit c222ed535bcf33f6284f48335462843fba06bf06 Author: nataraj2 Date: Sat May 2 19:58:44 2026 -0700 Update submodule to latest development subprojects/amrex commit c510f7edee83fa8d0c57eb9b62b016d2a19216e6 Author: nataraj2 Date: Sat Apr 25 00:13:29 2026 -0700 Correcting compilation error Source/Driver/Nyx.H commit 11ddf3f437998752565175a69b7a27b4d421ce33 Author: nataraj2 Date: Fri Apr 24 15:25:37 2026 -0700 Adding missing namespace Source/DerivedQuantities/ParticleDerive.cpp commit f44e91f8f4fca83c21cbfe6d366c953abbf2b8b0 Author: nataraj2 Date: Fri Apr 24 12:42:44 2026 -0700 Including missing headers Source/DerivedQuantities/ParticleDerive.cpp commit b6a4f45d769b353ddcb31ede2e748c95a7f7a14b Author: nataraj2 Date: Fri Apr 24 12:38:34 2026 -0700 Adding routines for matter spectrum coputation with amrex fft Source/DerivedQuantities/ParticleDerive.cpp Source/Driver/Nyx.H commit f4b50a672375ef197f6d5284f78b048ef064be23 Merge: 8b5a29f3 70e8fc88 Author: Andrew Myers Date: Tue Apr 21 20:57:28 2026 -0700 Merge pull request #109 from atmyers/remove_gp_redist_overload Remove the special overload of RedistributeGPU commit 70e8fc888768f7af4f09f6944839f7629b8e38e5 Author: Andrew Myers Date: Mon Apr 20 11:13:26 2026 -0700 Remove the special overload of RedistributeGPU Exec/ParticleFilterTest/NyxParticleContainer.H Source/Particle/NyxParticleContainer.H commit 8b5a29f34096d014ab4ab054b82584f86179eade Merge: e14ce39c ff1ae8cf Author: Weiqun Zhang Date: Wed Jan 28 08:29:57 2026 -0800 Merge pull request #107 from WeiqunZhang/fix_array4_begin_end Update due to recent changes in amrex::Array4 commit ff1ae8cf93faa21b4c1e49cb88c8f4a5a3209564 Author: Weiqun Zhang Date: Wed Jan 28 08:26:21 2026 -0800 Update due to recent changes in amrex::Array4 Source/Particle/NeutrinoParticles_K.H commit e14ce39c08e3cda7055bdde043a3af3d90448e46 Merge: 0851590d 95c6e8ec Author: Jean M. Sexton Date: Wed Dec 10 07:39:17 2025 -0800 Merge pull request #106 from nataraj2/docs Update docs commit 95c6e8ec036b756ac9ef709b983a6c4d25f700c6 Author: Mahesh Natarajan Date: Mon Dec 8 20:23:59 2025 -0800 Adding halo inputs Docs/sphinx_documentation/source/NyxInputs.rst commit 3f7e40688a7ba8550d52e6b4342261a20bbf2e7c Author: Mahesh Natarajan Date: Mon Dec 8 16:08:25 2025 -0800 Adding references to conf.py Docs/sphinx_documentation/source/conf.py commit 57befa17f20b99327d5d7caecff9606d69dd2b7b Author: Mahesh Natarajan Date: Mon Dec 8 16:06:28 2025 -0800 Updating docs Docs/sphinx_documentation/source/NyxInputs.rst commit 69ce909f4ca4cb24234f0a5d1802f8742114a396 Author: Mahesh Natarajan Date: Mon Dec 8 15:59:56 2025 -0800 Updating docs Docs/sphinx_documentation/source/NyxInputs.rst commit 0851590d457f4455bfd463b04056cacff49bb7ea Merge: d1efec0a b781354c Author: Jean M. Sexton Date: Mon Dec 8 13:04:29 2025 -0800 Merge pull request #105 from nataraj2/checkpoint_now Writing checkpoint files at user defined redshift values commit b781354c1ee11eaf26bbdf31d09d98582b7af821 Author: Mahesh Natarajan Date: Fri Dec 5 13:32:19 2025 -0800 Minor comments correction Source/Driver/comoving.cpp commit fd8b2a551bff567342b502b7d9e9289b399c4a8b Author: Mahesh Natarajan Date: Fri Dec 5 13:29:58 2025 -0800 Minor correction Source/Driver/Nyx.cpp commit f88ea0b91702758f83b577be0423618793c23819 Author: Mahesh Natarajan Date: Fri Dec 5 13:17:13 2025 -0800 Adding routines for checkpoint now Source/Driver/.comoving.cpp.swp commit bbddf9c201d98c63e982d743bec344257ebbdfc1 Author: Mahesh Natarajan Date: Fri Dec 5 13:16:44 2025 -0800 Adding routines for checkpoint now Source/Driver/.comoving.cpp.swp Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Driver/comoving.cpp commit d1efec0ac9dc915c7127d9409cd14f37c5061309 Merge: 51a5f8e5 5c8d6a3a Author: Jean M. Sexton Date: Tue Dec 2 11:43:23 2025 -0800 Merge pull request #104 from nataraj2/reeber_issues_fix All reeber issues fix commit 5c8d6a3ab6d782fc164edb8c39be2a735fb0d813 Author: Mahesh Natarajan Date: Sat Nov 29 20:29:57 2025 -0800 Fix all reeber issues Source/Driver/.Nyx.cpp.swp commit eeb5a19f8f8b9479f748ad1988dd9feec47a9826 Author: Mahesh Natarajan Date: Sat Nov 29 20:28:51 2025 -0800 Fix all reeber issues Source/Driver/.Nyx.cpp.swp Source/Driver/Nyx.H Source/Driver/Nyx.cpp Util/reeber/src/reeber.cpp commit 51a5f8e55ef70ac488b13a376629e9027bc2e5d6 Merge: eade1ebd d84b1dfa Author: Jean M. Sexton Date: Thu Jan 9 10:06:19 2025 -0800 Merge pull request #100 from 'n8xm/fix-reeber-doublefree' into development commit eade1ebd1e87cb38c41640256c5275da5f0277f2 Author: Jean M. Sexton Date: Thu Jan 9 09:57:02 2025 -0800 Minor fixes for github actions, update submodules .github/workflows/linux.yml subprojects/amrex subprojects/sundials commit 9e8d785e9f3affce0feb304d59cc6831daef7b16 Merge: f41af9d1 3b5bbde1 Author: Jean M. Sexton Date: Thu Jan 9 09:34:06 2025 -0800 Merge pull request #99 from 'nataraj2/LightConeBinary' into development commit f41af9d1909b077194b763630ecd502c49fe84ac Merge: d8a5c6e2 c9eab0d6 Author: Jean M. Sexton Date: Thu Jan 9 09:31:26 2025 -0800 Merge pull request #97 from 'n8xm/fix-reeber-build' into development commit d8a5c6e28da5dbe3be00baf67af482f2c8d77a08 Merge: 0686860f 9c21da6b Author: Jean M. Sexton Date: Thu Jan 9 09:29:55 2025 -0800 Merge pull request #92 'n8xm/feature-extend-gitignore' into development runlog, tags, compile_commands.json in gitignore commit 0686860f99789d96f6bbb91e3a5a887da9670bcb Author: Jean M. Sexton Date: Thu Jan 9 08:45:36 2025 -0800 Update Nyx gpu sundials compile docs Docs/sphinx_documentation/source/NyxGettingStarted.rst Docs/sphinx_documentation/source/getting_started/NyxSundials.rst commit 46f39f065538127ab1e7fa632855e9978f5c48d4 Merge: 708f578d e129c065 Author: Jean M. Sexton Date: Thu Jan 9 08:21:40 2025 -0800 Merge pull request #91 from n8xm/fix-sundials-doc-typo commit 3b5bbde19e9cd0c7e9b697a95866b94ef3965874 Author: Mahesh Natarajan Date: Thu Jan 2 12:38:28 2025 -0800 Correcitng reduce command error Exec/ParticleFilterTest/LightConeParticle.cpp commit 2f550c9ee84ffa830c32701a431b8ac602fbb1d1 Author: Mahesh Natarajan Date: Thu Jan 2 12:12:14 2025 -0800 Adding inputs for 128^3 and 768^3 simulations Exec/ParticleFilterTest/inputs_128x128x128 Exec/ParticleFilterTest/inputs_768x768x768 commit 070013bebd93936cb30c1b6f1f5cbb0123decd5d Author: Mahesh Natarajan Date: Thu Jan 2 12:06:35 2025 -0800 Replacing MPI functions with AMReX wrappers wherever possible Exec/ParticleFilterTest/LightConeParticle.cpp commit d84b1dfa6464fef1639bbbb616c93fcdc0a1110e Author: Nathan X. Marshak Date: Fri Dec 20 19:23:09 2024 -0500 Ascent volume rendering of density, xh Exec/LyA/ascent_actions.yaml commit 5bb2b09db2b4cda1af8a3d300593d3bbba0f64a8 Author: Nathan X. Marshak Date: Fri Dec 20 14:58:20 2024 -0700 Use non-owning pointer to avoid double free Util/reeber/src/reeber.cpp commit c9eab0d63a07b3c2ac5219651d1b7f5f46af3113 Merge: 24346b6c bdec354e Author: Nathan X. Marshak Date: Fri Dec 20 15:45:40 2024 -0500 Merge branch 'fix-insitu-halo-finding' into fix-reeber-build commit 2e5144adb0e79368edd0c39797b016415c70a935 Author: Mahesh Natarajan Date: Wed Dec 4 09:55:11 2024 -0800 Removing unwanted file Exec/ParticleFilterTest/Nyx_advance_TryMPIButFail.cpp commit 6b3bdccdcdfda1ffbcfa2e0450a6abd7f220e743 Author: Mahesh Natarajan Date: Wed Dec 4 09:52:06 2024 -0800 Writing binary files for lightcones Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp Exec/ParticleFilterTest/LightConeParticle.H Exec/ParticleFilterTest/LightConeParticle.cpp Exec/ParticleFilterTest/Make.package Exec/ParticleFilterTest/Nyx_advance.cpp Exec/ParticleFilterTest/temp.H commit 6a55d0264aa4fca287c00c8183cd51ddc99ee065 Author: Mahesh Natarajan Date: Sun Nov 17 12:02:19 2024 -0800 Simple binary files for particle data and python script to read Exec/ParticleFilterTest/DarkMatterParticleContainer.H Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp Exec/ParticleFilterTest/GNUmakefile Exec/ParticleFilterTest/Nyx_advance.cpp Exec/ParticleFilterTest/Nyx_advance_TryMPIButFail.cpp Exec/ParticleFilterTest/Read_BinarySimple.py Exec/ParticleFilterTest/temp.H commit 5ae5c6c50bc30fbc09c228c11dae26253a262208 Author: Mahesh Natarajan Date: Sat Nov 16 12:31:55 2024 -0800 Test: Writing CSV file for single proc works Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp Exec/ParticleFilterTest/GNUmakefile Exec/ParticleFilterTest/Make.package Exec/ParticleFilterTest/Nyx_advance.cpp Exec/ParticleFilterTest/temp.H commit bdec354ee9dc812125da73c39979d954c33f3288 Author: Nathan X. Marshak Date: Fri Oct 18 17:53:09 2024 -0600 Fixed compile of in situ halo finding code. Source/IO/Nyx_output.cpp commit 24346b6c8b55156da7604b3096a83a6df69ee2cf Author: Nathan X. Marshak Date: Fri Sep 20 17:50:14 2024 -0600 Fix compile error when Reeber is enabled Util/reeber/src/reeber.cpp commit 708f578d729dad03a40e5b5b7c210e563e224529 Merge: d470edeb e9155337 Author: Jean M. Sexton Date: Thu Sep 5 16:52:25 2024 -0700 Merge pull request #95 from nataraj2/HDF5_Lightcone Minor change commit e91553370f55a24ee6be294f97389a9eb4f3e703 Author: Mahesh Natarajan Date: Thu Sep 5 15:44:00 2024 -0700 Minor change Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit d470edeb1bd5348d731f30d4f4feb429d4d10a1f Author: Jean M. Sexton Date: Thu Sep 5 05:25:30 2024 -0700 Tweak seperate tiles Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit 92e46c4743921cdf6010a4cc81a4e8d6664a866a Author: Jean M. Sexton Date: Thu Sep 5 05:13:27 2024 -0700 Change store function to track duplicates and use it Exec/ParticleFilterTest/DarkMatterParticleContainer.H Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit cd29ecc466f49d50e33e8e79e936e5978a67b476 Author: Jean M. Sexton Date: Wed Sep 4 16:06:48 2024 -0700 Make push_back option for cpu-only build Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit a440f28f983bf7c450e4b27507e0d637258dca80 Author: Jean M. Sexton Date: Wed Aug 28 08:58:23 2024 -0700 Minor spacing fixes and remove zlen checking in new filters Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit 3abfcc909055aa5277c9b32787ce267c4769fb2c Author: Jean M. Sexton Date: Wed Aug 28 08:56:56 2024 -0700 Revert changes in order to use src.m_aos Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit 5d4f38bcb835c3554fea512d529f4165d589592e Merge: e4193fdb 68d1003b Author: Jean M. Sexton Date: Wed Aug 28 10:56:13 2024 -0500 Merge pull request #94 from nataraj2/HDF5_Lightcone Correcting compilation errors with HDF5 commit 68d1003b9958bd815acc1163eacc11ecd0399f16 Author: Mahesh Natarajan Date: Sat Aug 17 21:01:54 2024 -0700 Correcting compilation errors with HDF5 Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit e4193fdbfc4adecec4aae8acb35ac36b95248b1a Merge: 1c8adeb9 1cdbfcf0 Author: Jean M. Sexton Date: Wed Aug 14 15:58:10 2024 -0700 Merge branch 'development' into filter_structs commit 1c8adeb97ca47f0680f26bb62b4f85a8428f09ed Author: Jean M. Sexton Date: Wed Aug 14 15:57:21 2024 -0700 Add HDF5 stubs Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit d37e18ad50d27329023ade755aa82ea3f6aee8f8 Author: Jean M. Sexton Date: Wed Aug 14 15:48:42 2024 -0700 Fixes from call with Andrew and Mahesh Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit 1cdbfcf00b054a6f7d7504f8c17b04ca4705f3a9 Merge: 05fb655d a2b87f43 Author: Jean M. Sexton Date: Tue Aug 13 16:23:47 2024 -0700 Merge branch 'Lightcone' into development commit 05fb655da415a5c2ea0684e957c07a4cacd7bf12 Merge: fe575b5a afbd9f2b Author: Jean M. Sexton Date: Tue Aug 13 16:18:57 2024 -0700 Merge branch 'filter_structs' into development commit afbd9f2b583af1877e5bd5995b397f2c705e5422 Author: Jean M. Sexton Date: Tue Aug 13 14:02:38 2024 -0700 Change particletile to particletiledata for passing in src Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit c3095ce68902b823bb488166b1164976eec3719f Author: Jean M. Sexton Date: Tue Aug 13 10:54:41 2024 -0700 Fix predicate Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit a2b87f4390847f1b5a2f11ee6da92ac199003b07 Author: Mahesh Natarajan Date: Tue Aug 13 09:58:15 2024 -0700 Removing print Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit f0b9fca112df6db14686cbd50c0d369696c9d77c Author: Mahesh Natarajan Date: Tue Aug 13 09:57:28 2024 -0700 Reverting back to original if check Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp Exec/ParticleFilterTest/Nyx_advance.cpp commit b9747961d123beab878208a221c6eb0a22eb1dd9 Author: Mahesh Natarajan Date: Tue Aug 13 09:56:04 2024 -0700 Removing commented lines Exec/ParticleFilterTest/Nyx_advance.cpp commit 9f3d85efc13f0f1e5a44f8bf1f4d52d55c2860cc Author: Jean M. Sexton Date: Tue Aug 13 08:54:40 2024 -0700 New filter structs compile Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp Exec/ParticleFilterTest/GNUmakefile Exec/ParticleFilterTest/Nyx_advance.cpp Exec/ParticleFilterTest/inputs commit 5ff9bfe6d74fd0b1d3900d8be4e623b9ed8ffa00 Author: Mahesh Natarajan Date: Sat Aug 10 20:19:08 2024 -0700 Changes to particle intersections Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp Exec/ParticleFilterTest/Nyx_advance.cpp commit fe575b5ad24d64f82ac0c7d6a2e4b2f275462921 Author: Jean M. Sexton Date: Tue Jul 30 05:58:47 2024 -0700 Minor tweak to use more specific ParIter Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit a91f4b05bcc262e4a280b6e8f075d3c69f659aae Author: Jean M. Sexton Date: Mon Apr 22 17:25:43 2024 -0700 Update workflow .github/workflows/dependencies/dependencies_hip.sh .github/workflows/dependencies/dependencies_nvcc10.sh .github/workflows/linux.yml commit 2b48b4a35cf439682a8182b9703716aab95bdb7c Author: Jean M. Sexton Date: Mon Apr 22 17:05:43 2024 -0700 Update sundials submodule and make Exec/Make.Nyx Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp subprojects/sundials commit 7fd667ed93ec176904dab8f95a2b04535b22e40c Author: Jean M. Sexton Date: Mon Apr 22 16:22:06 2024 -0700 Update AMReX submodule subprojects/amrex commit 9c21da6b4567be36d7b67ebbc40d312c5d1f2cbd Author: Nathan X. Marshak Date: Thu Apr 11 12:17:17 2024 -0600 runlog, tags, compile_commands.json in gitignore .gitignore commit e129c065927006ffc9c9269d7be86b57160f57f8 Author: Nathan X. Marshak Date: Thu Apr 11 12:14:15 2024 -0600 Updated Sundials version to match rest of docs Docs/sphinx_documentation/source/NyxGettingStarted.rst commit 05ccb5950c4fc9979dec253b89319ae5ae58bac8 Author: Jean M. Sexton Date: Fri Feb 2 11:02:26 2024 -0800 Account for storing pos in rdata Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit 10c45adb8b1ce61c88aac98fac9aaafd0ed01e7a Author: Jean M. Sexton Date: Fri Feb 2 10:52:37 2024 -0800 Change position checking Exec/ParticleFilterTest/DarkMatterParticleContainer.H Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit 20edad4a0f5726898d00d79231dc0f15b82ff1e9 Author: Jean M. Sexton Date: Fri Feb 2 08:31:41 2024 -0800 Update this and ShellPC pointers and use Define Exec/ParticleFilterTest/DarkMatterParticleContainer.H Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit 5c96147b86fd2dffebb0ec457942ec898d7fd57f Author: Jean M. Sexton Date: Wed Jan 31 15:59:44 2024 -0800 Account for center Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit c6a84d6ec182a724e5aa62684613c576f4e6125a Author: Jean M. Sexton Date: Wed Jan 31 15:55:07 2024 -0800 Use spherical coords lightcone Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit dd14b228f01fe0d6eb6dac6b74b98eb38847b471 Author: Jean M. Sexton Date: Wed Jan 31 14:05:53 2024 -0800 Add flag for lightcone_start_z Exec/ParticleFilterTest/Nyx.H Exec/ParticleFilterTest/Nyx.cpp Exec/ParticleFilterTest/Nyx_advance.cpp Exec/ParticleFilterTest/Nyx_advance_particles.cpp commit 920062555df94be2e2acd4fe5a0c59bf556aaa63 Author: Jean M. Sexton Date: Wed Jan 31 10:26:55 2024 -0800 Also scale by a in additional places Exec/ParticleFilterTest/comoving.cpp commit 094bea982a645c888642263b025b6f6fc080b021 Author: Jean M. Sexton Date: Mon Jan 29 17:38:56 2024 -0800 Changes to integrate radius Exec/ParticleFilterTest/DarkMatterParticleContainer.H Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp Exec/ParticleFilterTest/Nyx.H Exec/ParticleFilterTest/NyxParticleContainer.H Exec/ParticleFilterTest/Nyx_advance.cpp Exec/ParticleFilterTest/Nyx_advance_particles.cpp Exec/ParticleFilterTest/comoving.cpp commit 2f382fc2bc1e367cacf8d00a4074939f658b0376 Author: Jean M. Sexton Date: Mon Jan 29 13:09:34 2024 -0800 Change center from corner of domain to center Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit fa60f54cc96e4c07ae1d728c4e5cc3d24d75c0b0 Merge: 5a6e7aa5 fb5216c7 Author: Jean M. Sexton Date: Mon Jan 29 11:06:52 2024 -0800 Merge branch 'development' into filter_lightcone commit 5a6e7aa516ef6afbb9af6b4bba3ce34370572682 Author: Jean M. Sexton Date: Fri Jan 26 08:45:47 2024 -0800 Make lightcone output filename a function of z Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit 62d15234a3557e3e3f7582d845880810bc8d2cc4 Author: Jean M. Sexton Date: Fri Jan 26 08:31:54 2024 -0800 Remove prints Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit e5e282283c6fd17cbdf56e0e06780da8c3f4db8c Author: Jean M. Sexton Date: Fri Jan 26 08:21:54 2024 -0800 Change this to Shell Exec/ParticleFilterTest/DarkMatterParticleContainer.H Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit 11d19645cc69eea37784e7dd406754c9dc6f057c Author: Jean M. Sexton Date: Fri Jan 26 07:53:52 2024 -0800 test Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit fb5216c7cb8789a773b38931ff576f2eb178c79f Merge: 810ef725 e27ceb3f Author: Weiqun Zhang Date: Sun Jan 21 11:46:23 2024 -0800 Merge pull request #88 from WeiqunZhang/amrex_prefix Prepare for amrex changes commit e27ceb3f410b39a72beeddfaa6a5d4598f40c5d0 Author: Weiqun Zhang Date: Sun Jan 21 10:30:39 2024 -0800 Prepare for amrex changes Source/AGN/AGN_halos.cpp Source/DerivedQuantities/ParticleDerive.cpp Source/Driver/Nyx.cpp Source/Gravity/Gravity.cpp Source/Hydro/strang_hydro.cpp Source/Initialization/Nyx_setup.cpp Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NyxParticleContainer.H Source/TimeStep/Nyx_enforce_minimum_density.cpp commit 7b853b84fc5cccc0a73f35ccf3fb89929ce73399 Author: Jean M. Sexton Date: Fri Nov 3 10:33:48 2023 -0700 Fix ParIter Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp commit 4c040261f6bb7d5ad2a69cccd13184c2ee29ca4e Author: Jean M. Sexton Date: Thu Nov 2 09:22:05 2023 -0700 Make LightConeTest Exec/ParticleFilterTest/32.nyx Exec/ParticleFilterTest/64sssss_20mpc.nyx Exec/ParticleFilterTest/CMakeLists.txt Exec/ParticleFilterTest/DarkMatterParticleContainer.H Exec/ParticleFilterTest/DarkMatterParticleContainer.cpp Exec/ParticleFilterTest/GNUmakefile Exec/ParticleFilterTest/Make.package Exec/ParticleFilterTest/NeutrinoParticleContainer.H Exec/ParticleFilterTest/Nyx.H Exec/ParticleFilterTest/NyxParticleContainer.H Exec/ParticleFilterTest/NyxParticles.cpp Exec/ParticleFilterTest/Nyx_advance.cpp Exec/ParticleFilterTest/Nyx_advance_particles.cpp Exec/ParticleFilterTest/Prob.cpp Exec/ParticleFilterTest/Prob_error.cpp Exec/ParticleFilterTest/TREECOOL_middle Exec/ParticleFilterTest/ascent_actions.yaml Exec/ParticleFilterTest/ascent_actions_nohydro.yaml Exec/ParticleFilterTest/ascent_actions_slicefile.yaml Exec/ParticleFilterTest/inputs Exec/ParticleFilterTest/inputs.rt Exec/ParticleFilterTest/inputs.rt.garuda Exec/ParticleFilterTest/inputs_nohydro.rt commit 810ef725f71a395013d9d86cf9e133b6cf233cd8 Author: Jean M. Sexton Date: Thu Aug 24 09:12:06 2023 -0700 Use diag_eos directly when inhomogeneous on Source/HeatCool/f_rhs_struct.H commit cc6bfd365ef6d392e7a61f09f5da73725516b375 Author: Jean M. Sexton Date: Wed Aug 16 15:27:04 2023 -0700 Second pass at ghost update for subcycle Source/Particle/DarkMatterParticleContainer.cpp commit 54d216baf16666d88d505d832436b71499279342 Author: Jean M. Sexton Date: Wed Aug 16 15:07:27 2023 -0700 First pass at ghost particle fix Source/Particle/DarkMatterParticleContainer.cpp commit b51682d98dbbe61459c5a8e5161b7421893a7a89 Author: Jean M. Sexton Date: Tue Aug 15 15:47:50 2023 -0700 Add warning or abort for forcing with managed Source/Forcing/Forcing.cpp commit 7a8ba99df880a20e55112ce34ae5bea1b96f88d2 Author: Jean M. Sexton Date: Tue Aug 15 15:24:53 2023 -0700 Revert "First pass at forcing edits device arena" This reverts commit dc78ee569f11d6c2a8f0e485c22ac528de28a687. Exec/DrivenTurbulence/Nyx_sources.cpp Source/Forcing/Forcing.cpp commit dc78ee569f11d6c2a8f0e485c22ac528de28a687 Author: Jean M. Sexton Date: Thu Jul 27 15:22:08 2023 -0700 First pass at forcing edits for device arena Exec/DrivenTurbulence/Nyx_sources.cpp Source/Forcing/Forcing.cpp commit d00eb7d7c3ffd113a3b7540f6cd7ecd92aef8218 Author: Jean M. Sexton Date: Thu Jul 27 12:24:32 2023 -0700 Update total particle derive to use ParallelFor Source/DerivedQuantities/ParticleDerive.cpp commit 8613f29b7a83298582c14b966f8a6a8210dc903a Merge: 76bffaa3 2cb1ace2 Author: Jean M. Sexton Date: Wed Apr 19 15:37:35 2023 -0700 Fixes for new API associated with SoA-only particlesMerge pull request #87 from atmyers/soa_particle_fix Fixes for new API associated with SoA-only particles commit 2cb1ace2d92dcfc939d7f7d51808650513eefa48 Author: Andrew Myers Date: Tue Apr 18 10:25:19 2023 -0700 Updating AMReX version subprojects/amrex commit e96699e78d2c605f2673ac2f172a796220e8b426 Author: Andrew Myers Date: Tue Apr 18 08:39:38 2023 -0700 Fixes for new API associated with SoA-only particles Source/Particle/NyxParticleContainer.H commit 76bffaa317c8974b76c6e761e7eb74a0e896cb47 Author: Ann Almgren Date: Mon Apr 17 16:15:07 2023 -0700 update yml files .github/workflows/linux.yml .github/workflows/macos.yml commit b483c23f7196b1af9622314c27ad9e308fa3cc7a Author: Ann Almgren Date: Mon Apr 17 16:10:15 2023 -0700 update amrex_basics Docs/sphinx_documentation/source/getting_started/amrex_basics.rst commit d94beaf5759740a82205e45b4087038c3584b6a3 Author: Ann Almgren Date: Mon Apr 17 16:05:17 2023 -0700 add some basic amrex documentation Docs/sphinx_documentation/source/NyxGettingStarted.rst Docs/sphinx_documentation/source/getting_started/amrex_basics.rst commit d32083e0e9b674619af9c9ea7094b8619def3dfe Merge: efb3b05f 8c0232c9 Author: Jean M. Sexton Date: Mon Nov 7 16:29:25 2022 -0800 Merge pull request #86 from WeiqunZhang/bndrydata MacBndry -> BndryData commit 8c0232c9a3fe048726acbcf90aaa2c791788853c Author: Weiqun Zhang Date: Mon Nov 7 16:04:13 2022 -0800 MacBndry -> BndryData MacBndry is no longer being used. Source/Gravity/Gravity.H commit efb3b05f77fe3eed02312469470e8e3f1fc858ee Author: Jean M. Sexton Date: Fri Nov 4 18:05:18 2022 -0700 Minor fixes for SAVE_REACT Exec/LyA/GNUmakefile Exec/Make.Nyx Source/Driver/Nyx.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/HeatCool/integrate_state_with_source_3d_stubs.cpp commit b9386fad75a900534a57c5abe5bd6fc616ff43e7 Author: Jean M. Sexton Date: Fri Nov 4 17:40:19 2022 -0700 Add SAVE_REACT compile option Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp commit cb7dd4fdc2bcda4ebc04acde370b9e8155e3a3fa Author: Jean M. Sexton Date: Tue Oct 11 17:34:40 2022 -0700 Update cuda dependencies for CI .github/workflows/dependencies/dependencies_nvcc10.sh .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/linux.yml commit 1efee02e97a6f14f77d8074b11bfc320f54dded5 Author: Jean M. Sexton Date: Tue Oct 11 17:17:49 2022 -0700 Add notes for heat cool outputs and testing Exec/HeatCoolTests/example_setup.sh Source/HeatCool/f_rhs_struct.H subprojects/amrex subprojects/sundials commit e8285ce2aab00bedc68d2e666fa48660f64453a8 Author: Jean M. Sexton Date: Wed Aug 31 16:36:03 2022 -0700 Make H_reion_z index dependent Co-authored-by: Hyunbae Park Source/HeatCool/f_rhs_struct.H commit fc999702478b8b66dfb7b4b5795424601e3e1286 Author: Jean M. Sexton Date: Thu May 19 18:49:11 2022 -0400 Add ascent version printing to Nyx describe function, and cleanup crusher make flags Exec/LyA/GNUmakefile.ascent Source/IO/Nyx_output.cpp commit 08c88a88e4a1daca4551dd9fc0e94292ec68d57b Author: Jean M. Sexton Date: Thu May 19 08:01:37 2022 -0700 Fix printing and uncomment SUNProfiler reset Source/HeatCool/integrate_state_with_source_3d.cpp commit 65d618de9a9434d135cdc687c288186314c1392d Author: Jean M. Sexton Date: Mon May 16 16:38:00 2022 -0700 Add describe functionality similar to Castro Source/Driver/Nyx.H Source/Driver/nyx_main.cpp Source/IO/Nyx_output.cpp commit 3aa5e69ad6e303e9d3236dac422ab8de81379dfa Author: Jean M. Sexton Date: Mon May 16 15:47:56 2022 -0700 Update tags for ascent, amrex, sundials versions Exec/LyA/GNUmakefile.ascent subprojects/amrex subprojects/sundials commit 2cd11f30ddadba50b939c814038a09cd9304921d Author: Jean M. Sexton Date: Mon May 16 15:39:24 2022 -0700 Update ascent defaults and seperate out make options Exec/LyA/GNUmakefile.ascent Exec/LyA/ascent_actions.yaml Exec/LyA/ascent_options.json commit 74737652214e0593c3c669fdabee60f53f858f0b Author: Jean M. Sexton Date: Mon May 16 15:00:07 2022 -0700 Add more file checking Source/EOS/atomic_rates.H commit 4aa2d65a4901f449d8fa40315001652fee071293 Author: Jean M. Sexton Date: Mon May 16 14:59:50 2022 -0700 Fix inhomog reion input flag order and add some file checking Source/EOS/atomic_rates.H Source/HeatCool/f_rhs_struct.H Source/Initialization/Nyx_initdata.cpp commit c5f431cfefe3ce915e28cb3114ab28ba3003852c Author: Jean M. Sexton Date: Wed Mar 30 16:25:45 2022 -0400 Use std namespace Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/ParticleDerive.cpp Source/Driver/Nyx.cpp Source/Driver/comoving.cpp Source/Driver/sum_integrated_quantities.cpp Source/EOS/atomic_rates.H Source/EOS/eos_hc.H Source/HeatCool/f_rhs.H Source/HeatCool/f_rhs_struct.H Source/Hydro/Godunov.H Source/Hydro/Godunov.cpp Source/Hydro/Riemann.H Source/Hydro/trace_ppm.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Particle/NeutrinoParticles_K.H Source/Particle/NyxParticleContainer.H subprojects/amrex commit 81b59ef9ce06c3c5e804c1836a67d0862ddb9fd4 Merge: a3391588 49420a6d Author: Jean M. Sexton Date: Fri Mar 18 15:24:27 2022 -0400 Merge branch 'development' into test_hip_omp commit 49420a6d2a69cdfedf1cc473a9ca0f23ab1c6111 Author: Jean M. Sexton Date: Mon Feb 7 17:03:12 2022 -0800 Remove redundant flags to further build cleanup CMakeLists.txt Exec/Make.Nyx Source/CMakeLists.txt Source/Driver/Nyx.cpp Source/HeatCool/integrate_state_with_source_3d.cpp cmake/NyxSetupSUNDIALS.cmake commit cf9f821dd210d9466e5601b1cbbf82b1cfe2959e Merge: d76dc286 49b74184 Author: Jean M. Sexton Date: Mon Feb 7 18:34:52 2022 -0800 Merge pull request #85 from sundials-codes/sundials-updates Sundials updates Add an option to switch between atomic and LDS reductions with the HIP vector Print profiling data when SUNDIALS is built with profiling enabled Add some nonlinear solver stats output Fix cmake build commit 49b74184887b5ebd411c1f4446e3d53bc2cd155d Author: David J. Gardner Date: Mon Feb 7 20:12:43 2022 -0500 include AMReX_Config.H Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp commit fbd70744ad62d001cf43348bd69f89575d55e5c0 Author: David J. Gardner Date: Fri Feb 4 01:19:06 2022 -0500 build fixes Exec/Make.Nyx Source/CMakeLists.txt Source/Driver/Nyx.cpp commit 1599ceb2795217d57417530b09d7fcdceab6a102 Author: David J. Gardner Date: Thu Feb 3 15:16:17 2022 -0500 update to amrex 22.02 subprojects/amrex commit 201fe9f2769f66b65662183cd3baecd1d4e25b3f Author: David J. Gardner Date: Thu Feb 3 15:04:52 2022 -0500 use pointers for exec policies, add atomic/LDS option for CUDA Source/Driver/Nyx.cpp Source/HeatCool/integrate_state_with_source_3d.cpp commit cdd48d596de337b3afa29b960b3adf022fa4fd70 Author: David J. Gardner Date: Wed Feb 2 23:35:24 2022 -0800 timer for full integrate function Source/HeatCool/integrate_state_with_source_3d.cpp commit 6282d01d3acc1666d673c8c4b8b495c13a249f32 Author: David J. Gardner Date: Wed Feb 2 23:34:55 2022 -0800 print timings Source/HeatCool/integrate_state_with_source_3d.cpp commit abb6c02d2029e2f2ed3add09b5ab5c156b108239 Author: David J. Gardner Date: Wed Feb 2 23:32:09 2022 -0800 fix alignment Source/HeatCool/integrate_state_with_source_3d.cpp commit 21ebabb21a152f30c9249129c16015b10cae00df Author: David J. Gardner Date: Wed Feb 2 23:31:41 2022 -0800 update cvode stats output Source/HeatCool/integrate_state_with_source_3d.cpp commit 7556b3564a0e4ac5b6d9c1370863cc751ac055ed Author: David J. Gardner Date: Wed Feb 2 23:31:03 2022 -0800 add atomic reduction option Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/HeatCool/integrate_state_with_source_3d.cpp commit d76dc286a10b5e455e21018bfa469e2bff9dd5a3 Author: Jean M. Sexton Date: Fri Jan 14 05:44:54 2022 -0800 Move cmake statements into HIP if cmake/NyxSetupSUNDIALS.cmake commit 64d4cc2fdab9126902aae0473e3fd23c92f817bd Author: Jean M. Sexton Date: Fri Jan 14 05:35:29 2022 -0800 Update Docs to reference Sundials 6 Docs/sphinx_documentation/source/getting_started/NyxSundials.rst commit a00cf5f1799e0eabb0ab671245f55c6ae77facb5 Author: Jean M. Sexton Date: Fri Jan 14 05:35:14 2022 -0800 Further tweaks to CMake header inclusion for Sundials HIP Source/HeatCool/integrate_state_with_source_3d.cpp cmake/NyxSetupSUNDIALS.cmake commit aeff4074c6cafe0619e15482b60564944d0d712b Author: Jean M. Sexton Date: Thu Jan 13 15:16:00 2022 -0500 Fix superbuild for GitHub action and add HIP fusing libraries CMakeLists.txt Exec/LyA/GNUmakefile cmake/NyxSetupAMReX.cmake cmake/NyxSetupSUNDIALS.cmake commit d1b99e7a5fe54af35538ec58a4f8f5e1e9f7cbcf Merge: ffb60f2f 77062064 Author: Jean M. Sexton Date: Thu Jan 13 13:29:30 2022 -0500 Merge branch 'sundials-codes-development' into development commit 77062064fefc8f071d3757c974bdf784b678d737 Author: Balos, Cody Joe Date: Thu Jan 13 08:44:24 2022 -0800 update submodules .gitmodules commit 3b7961ba045e125dbf5677ca6f21671e42f706a8 Author: Balos, Cody Joe Date: Thu Jan 13 08:42:49 2022 -0800 update submodules .gitmodules commit 4f5c462c2ae3c9a8e663bb46ca1547fae6212f46 Author: Balos, Cody Joe Date: Thu Jan 13 08:42:32 2022 -0800 update submodules subprojects/amrex subprojects/sundials commit 18740668c308251258b3a4c0db2a2c0875364bbf Author: Balos, Cody Joe Date: Tue Dec 28 17:47:16 2021 -0800 update code to sundials 6 Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp commit b1066047451f8cf1af216ce5ba2efa151d4e96c9 Author: Balos, Cody Joe Date: Tue Dec 28 15:55:43 2021 -0800 update submodules .gitmodules subprojects/amrex subprojects/sundials commit ffb60f2fd244ee8c2cc9133f8f3867dd2938b573 Author: Jean M. Sexton Date: Mon Nov 29 06:30:39 2021 -0800 Fix logical condition on creating directories for hctest Source/HeatCool/integrate_state_with_source_3d.cpp commit 22e143b7fc6170eeccba77ca783051157deb9bac Author: Jean M. Sexton Date: Thu Nov 11 15:57:20 2021 -0800 Update converter to explicitly use std namespace for string Util/Converters/Plotfile2HDF5_grids/AmrDerive.cpp commit f25d5ab189c8e514be0ea8418d23019aa9d9f49e Author: Jean M. Sexton Date: Tue Nov 2 06:15:54 2021 -0700 Fix HeatCoolTests created edge cases Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/Initialization/Nyx_setup.cpp commit 24069ced27073af2d8f0682fe28375d1695042db Author: Jean M. Sexton Date: Mon Nov 1 17:48:51 2021 -0700 Remove unneeded sphinx package requirements.txt commit 1b69c0cadda127e74100e39236b515b28674a53c Author: Jean M. Sexton Date: Mon Nov 1 17:16:15 2021 -0700 Fixes for Github CI failures HIP, remove verbose, add HC compile guards .github/workflows/dependencies/dependencies_hip.sh Source/HeatCool/f_rhs_struct.H Source/TimeStep/Nyx_advance.cpp commit 9dc28dd753aaacec08eafb2dc72560e153f0820c Author: Jean M. Sexton Date: Mon Nov 1 17:08:04 2021 -0700 Fix example Exec/HeatCoolTests/example_setup.sh commit 3746f76b22bbb598c635d0d947f2f01a84912dfc Author: Jean M. Sexton Date: Mon Nov 1 16:48:04 2021 -0700 Fixes for Github CI failures .github/workflows/dependencies/dependencies_hip.sh Source/HeatCool/f_rhs_struct.H Source/Initialization/Nyx_setup.cpp commit 2892ff6729b683ec5c4fca93a9f5e75cc9e550ad Author: Jean M. Sexton Date: Mon Nov 1 15:43:58 2021 -0700 Add cmake example Exec/HeatCoolTests/example_setup.sh commit 946d70ca5e520b2b7dbfd5626827c0def6d92cfc Author: Jean M. Sexton Date: Mon Nov 1 15:43:44 2021 -0700 Move file Exec/HeatCoolTests/example_setup.sh commit 1da60cb9503c923e9dd8f4dee3d141bbde276543 Author: Jean M. Sexton Date: Mon Nov 1 15:32:58 2021 -0700 Update Heating Cooling documentation with new flags Docs/sphinx_documentation/source/NyxHeatCool.rst commit 639655edd7899ef6bbc817e932afbe26e3f11b5a Author: Jean M. Sexton Date: Mon Nov 1 13:21:39 2021 -0700 Add extra redistribute after moveKickDrift for neutrino_cfl>1 Source/TimeStep/Nyx_advance.cpp Source/TimeStep/Nyx_advance_particles.cpp commit bc980580d66caa39459ad8c082134c4639da78ab Author: Jean M. Sexton Date: Mon Nov 1 13:08:48 2021 -0700 Change std::isnan to amrex::isnan for HC Source/HeatCool/f_rhs.H Source/HeatCool/f_rhs_struct.H commit d6b1905a29e97e74f8ae757c5bccdf71b2f83d22 Author: Jean M. Sexton Date: Mon Nov 1 13:06:59 2021 -0700 Add readme example for HeatCoolTests Exec/HeatCoolTests/README.md commit 3a52f80a574583f2ab49b39715355acc0d58e2db Author: Jean M. Sexton Date: Mon Nov 1 12:57:00 2021 -0700 Make file paths come from input file Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/TimeStep/Nyx_advance.cpp commit cb56198b82b745f5631e57af24f2b53e327523e0 Author: Jean M. Sexton Date: Tue Oct 19 18:01:15 2021 -0700 Change which procs write Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp commit 7abb038b8e9b5ba80d2a333e789f45a1bb293acd Author: Jean M. Sexton Date: Mon Oct 18 17:29:02 2021 -0700 Make a read for HeatCoolTest that works for 1 MPI, 1 OpenMP LyA Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/TimeStep/Nyx_advance.cpp commit 043d1b1c252d4be4ba16b84b4d3909db1bde2a0a Author: Jean M. Sexton Date: Mon Oct 18 15:03:09 2021 -0700 Add write and read to source, and useful edge cases to hackily use existing reads Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/Particle/NyxParticles.cpp Source/TimeStep/Nyx_advance.cpp commit b73ae078728532212f4be50893979223d52b5878 Author: Jean M. Sexton Date: Mon Oct 18 15:02:13 2021 -0700 Try seperate heatcooltest Exec/HeatCoolTests/GNUmakefile Exec/HeatCoolTests/Make.package Exec/HeatCoolTests/Prob.cpp Exec/HeatCoolTests/Prob_error.cpp Exec/HeatCoolTests/TREECOOL_middle Exec/HeatCoolTests/nyx_main.cpp commit 8a77935f901ed35ce2e6d367e1fe4d5fe0351af0 Author: Jean M. Sexton Date: Mon Oct 18 13:13:35 2021 -0700 Add input info Source/HeatCool/integrate_state_with_source_3d.cpp commit 93fb7e63231bfd4456f7f6663defb61a7d3300ba Author: Jean M. Sexton Date: Wed Oct 13 12:16:32 2021 -0700 Use seperate setup Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/HeatCool/integrate_state_with_source_3d.cpp Source/Initialization/Nyx_setup.cpp commit abaa48a8e956ac02ca3922e8c516ee3b4eb5837c Author: Jean M. Sexton Date: Tue Oct 12 10:36:54 2021 -0700 First pass at writing out multifab info Source/HeatCool/integrate_state_with_source_3d.cpp commit 12af915774c48fe93aa2b1fc6828632d8f6c241b Author: Jean M. Sexton Date: Mon Oct 4 13:17:25 2021 -0700 Update subprojects for 21.10 subprojects/amrex subprojects/sundials commit 2a4721be27945763736af5e0179efd78758f544d Author: Jean M. Sexton Date: Thu Sep 9 21:55:54 2021 -0700 Fix particle_initrandom_mass_total scaling to use whole domain Source/Particle/NyxParticles.cpp Source/TimeStep/Nyx_advance.cpp commit 0aa9b2a0e1b5ba1b09acd147950109ef84990e93 Author: Jean M. Sexton Date: Sun Sep 5 12:55:36 2021 -0400 Make github hip workflow more similar to amrex workflow .github/workflows/linux.yml commit 4c52fd03a3992ad6400aa4d4031a9f1ba39e0e0c Author: Jean M. Sexton Date: Sun Sep 5 12:02:25 2021 -0400 Update HIP CI to use ROCM 4.3 .github/workflows/dependencies/dependencies_hip.sh .github/workflows/linux.yml commit 6c5774addc74efa05763227b56de5c308c3633c1 Author: Jean M. Sexton Date: Sun Sep 5 11:53:38 2021 -0400 Fix print statements in heating-cooling Source/HeatCool/integrate_state_with_source_3d.cpp Source/HeatCool/sdc_reactions.cpp commit aeb12e5329858207dcd38e15fad4cf5472b65971 Author: Jean M. Sexton Date: Sun Sep 5 11:46:11 2021 -0400 Fix header file include to match make Source/HeatCool/integrate_state_vec_3d.cpp commit 3ae7b51673a517cd489de897c99ee0a974a53222 Author: Jean M. Sexton Date: Fri Sep 3 17:45:40 2021 -0400 Update AMReX submodule subprojects/amrex commit 97acb037a1695a7d7937288be6909b754d58a0f9 Author: Jean M. Sexton Date: Fri Sep 3 17:29:30 2021 -0400 Add Scaling input flag option for total particle mass Docs/sphinx_documentation/source/ICs.rst Exec/Scaling/inputs Source/Driver/Nyx.H Source/Particle/NyxParticles.cpp commit f633a1b4dcff16dccf7de52d4884cc945974773d Author: Jean M. Sexton Date: Fri Sep 3 16:31:43 2021 -0400 Update Scaling inputs file Exec/Scaling/inputs commit 88ef3bf9188fa360188424cd453e86d26d82fe96 Author: Jean M. Sexton Date: Tue Aug 17 20:56:17 2021 -0400 Switch to AMReX 21.08 subprojects/amrex commit def1540d51dcd552c4384416a95615112165cee9 Author: Jean M. Sexton Date: Tue Aug 17 20:01:20 2021 -0400 Add back in explicit synchronize() for minimize_memory Source/Hydro/Hydro.cpp commit a3391588b1c3e29b13ecd1d64ee91e39e5388ecc Author: Jean M. Sexton Date: Fri May 28 13:44:02 2021 -0400 Add example script Exec/LyA/test_spock_hip_omp.sh commit 88c22e43143095d2bfe275baef0b4a90d8c431ad Author: Jean M. Sexton Date: Fri May 21 17:52:06 2021 -0400 Second pass adding hip with omp Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/ParticleDerive.cpp Source/Driver/Nyx.cpp Source/Driver/comoving.cpp Source/Driver/sum_integrated_quantities.cpp Source/EOS/atomic_rates.H Source/EOS/eos_hc.H Source/HeatCool/f_rhs.H Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp Source/Hydro/Godunov.H Source/Hydro/Godunov.cpp Source/Hydro/Riemann.H Source/Hydro/trace_ppm.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Particle/NeutrinoParticles_K.H Source/Particle/NyxParticleContainer.H commit 354fe4d840ac1e6dff1ede33589a9e9aec983c83 Author: Jean M. Sexton Date: Thu May 20 14:01:15 2021 -0400 First pass at adding omp with hip Exec/Make.Nyx commit 8dd3a6771a73016db61ac3f7dba601336bd55635 Author: Jean M. Sexton Date: Fri May 28 13:46:15 2021 -0400 Update documentation for runs with Sundials and Hip Docs/sphinx_documentation/source/getting_started/NyxSundials.rst commit 0aae9171f0cd4be233eee7a1c521182de6ba8fbc Author: Jean M. Sexton Date: Fri May 28 12:36:22 2021 -0400 Revert "Test Nyx CI with amrex PR 1800" This reverts commit 636371e2df64f13fbe300422e3c0acec9004c143. .gitmodules subprojects/amrex commit b1361a026c6f8ff199252db8f4eaa7cf615d11a2 Author: Jean M. Sexton Date: Thu May 27 16:16:13 2021 -0700 Fix Copy -> Parallel Copy in ParticleDerive Source/DerivedQuantities/ParticleDerive.cpp commit 636371e2df64f13fbe300422e3c0acec9004c143 Author: Jean M. Sexton Date: Thu May 27 15:28:38 2021 -0400 Test Nyx CI with amrex PR 1800 .gitmodules subprojects/amrex commit 0985311bcccd812eccfe50180ae2f05af16574aa Author: Jean M. Sexton Date: Thu May 27 14:46:32 2021 -0400 Add CMake compile option for SunMemory CMakeLists.txt Source/CMakeLists.txt cmake/NyxSetupAMReX.cmake commit ad29ffcbaac13d7f9692d22afbd9114dd99a24ae Author: Jean M. Sexton Date: Thu May 27 18:33:28 2021 +0000 CI fixes .github/workflows/dependencies/dependencies_hip.sh cmake/NyxSetupAMReX.cmake commit 0d7e0c7936a9d7d8cc788f9cfbf1e52344c06ff1 Author: Jean M. Sexton Date: Thu May 27 18:16:36 2021 +0000 Rearrange ifdefs for clarity on GPU type Source/HeatCool/integrate_state_with_source_3d.cpp commit 59980b45ccc3eb9013d4dfd021a10b279cc708eb Author: Jean M. Sexton Date: Thu May 27 18:14:53 2021 +0000 Change header order for Sundials Sycl CMake superbuild Source/HeatCool/integrate_state_with_source_3d.cpp commit c03af74a0886e8f7b974ee9978e15b26aa7163d4 Author: Jean M. Sexton Date: Thu May 27 02:57:38 2021 -0400 Add rocprim to HIP CI .github/workflows/dependencies/dependencies_hip.sh commit 0aec1b3f9f3ebc31a6f1378d86733876905b1850 Author: Jean M. Sexton Date: Thu May 27 02:46:40 2021 -0400 Update override and deprecated copy to fix warnings Source/DerivedQuantities/ParticleDerive.cpp Source/Driver/Nyx.H Source/Gravity/Gravity.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Particle/AGNParticleContainer.cpp Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NeutrinoParticleContainer.cpp commit 96f2b46d97af070ed34213e0458eaa23d44a27ea Author: Jean M. Sexton Date: Wed May 26 20:17:43 2021 -0400 Change submodule to development. Make default sundials_alloc_type nonempty .gitmodules Source/Driver/Nyx.cpp subprojects/amrex commit cf55ea9a32b7bd2acf9edf1afe3f54bef93c60d4 Merge: 75b5f3f0 8e2812c7 Author: Jean M. Sexton Date: Wed May 26 16:59:23 2021 -0400 Merge branch 'gpu_feature' into development commit 8e2812c7261ee1f562ca6f1e8a64d59b52515f5e Author: Jean M. Sexton Date: Wed May 26 16:54:30 2021 -0400 Add compile flag to exclude SUNMemoryHelper Exec/Make.Nyx Source/HeatCool/integrate_state_with_source_3d.cpp commit 32162ac657dafe7831cb4702bd5d05baae741ea2 Author: Jean M. Sexton Date: Wed May 26 12:15:45 2021 -0400 Add back in instantaneous heating from reionization Source/EOS/eos_hc.H Source/HeatCool/f_rhs_struct.H commit 75b5f3f00653a8be3ae06664b66e3137697ef304 Author: Jean M. Sexton Date: Fri May 7 14:46:19 2021 -0400 Add cublas for Sundials CI .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/dependencies/dependencies_nvcc9.sh commit 1635bf90e14b9b4c51a458faf7324c1606c8f4f1 Author: Jean M. Sexton Date: Fri May 7 13:56:41 2021 -0400 Add cusolver for Sundials CI .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/dependencies/dependencies_nvcc9.sh .github/workflows/linux.yml commit e420d8e8acd20b0e4647c6b0e35912c9836ca978 Author: Jean M. Sexton Date: Fri May 7 13:03:24 2021 -0400 Add print statements to CI .github/workflows/linux.yml commit bf60fd51c8a2a0a5ad0e71a0bac820c2d3c8591f Author: Jean M. Sexton Date: Fri May 7 01:02:56 2021 -0400 Fix example script Util/Converters/assign_particle_vels/test_script_summit.sh Util/Converters/assign_particle_vels/test_script_summit_jobindex.sh commit 0b2b94e691924ed3df22f46ff77e500553e3ef6a Author: Jean M. Sexton Date: Thu May 6 18:51:52 2021 -0400 Make append option for dark matter hdf5 Util/Converters/Plotfile2HDF5_grids/AmrDerive.cpp Util/Converters/assign_particle_vels/inputs.rt Util/Converters/assign_particle_vels/nyx_main.cpp Util/Converters/assign_particle_vels/test_script_summit.sh commit f8c2fde4c1c1099a607e469606e3e927dd6a824e Author: Jean M. Sexton Date: Wed May 5 22:08:38 2021 +0000 Update default DPCPP Sundials alloc Source/Driver/Nyx.cpp Source/HeatCool/integrate_state_with_source_3d.cpp commit d7a1aa4a2bb8da620f7bec14845f6a8579fe29ac Author: Jean M. Sexton Date: Wed May 5 22:07:18 2021 +0000 Fix argument order for Sycl and first pass at cmake update Source/HeatCool/integrate_state_with_source_3d.cpp cmake/NyxSetupAMReX.cmake commit 1d988da5efd25f1c88bbfe4a72d73a72e1ad5386 Author: Jean M. Sexton Date: Wed May 5 20:51:03 2021 +0000 Test SunMemory PR .gitmodules Source/Driver/Nyx.cpp subprojects/amrex commit 7b492a59a3e30f4cf9dd146f25d9364c2c3b5ac6 Merge: 78fdf6d6 9c5ce3f2 Author: Jean M. Sexton Date: Wed May 5 19:54:27 2021 +0000 Merge branch 'development' into gpu_feature commit 9c5ce3f2622077b09d702ea14d1e920145c6ddbb Author: Jean M. Sexton Date: Wed May 5 12:41:09 2021 -0700 Add cusparse to CI and remove noexcept from ReduceMin .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/dependencies/dependencies_nvcc9.sh .github/workflows/linux.yml Source/Driver/Nyx.cpp commit 7b91175d5be9f9c6c555119de71e2c85ff1081d2 Author: Jean M. Sexton Date: Wed May 5 10:42:07 2021 -0700 Make Cuda 9 CI path absolute .github/workflows/linux.yml commit a9113b1c98ad569c3376dac458828689aa976929 Author: Jean M. Sexton Date: Wed May 5 10:38:12 2021 -0700 Fix spacing .github/workflows/linux.yml commit 85177f0e4676e9ec1231cb555d3001739fb8da58 Author: Jean M. Sexton Date: Wed May 5 10:21:53 2021 -0700 Update Cuda CI flags and locations .github/workflows/dependencies/dependencies_nvcc9.sh .github/workflows/linux.yml commit 030b26219c3142ff0a24ee644a742b54bab5d4bb Author: Jean M. Sexton Date: Wed May 5 10:20:20 2021 -0700 Update Cuda CI release targets and names .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/dependencies/dependencies_nvcc9.sh .github/workflows/linux.yml commit b80343873cdeb30fa50c51369e7563818270a71e Author: Jean M. Sexton Date: Wed May 5 10:01:15 2021 -0700 Update Cuda CI compiler .github/workflows/linux.yml commit 0ae81aa31494069dc26678ae17dd67bbc577b140 Author: Jean M. Sexton Date: Wed May 5 09:54:41 2021 -0700 Rename CI file .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/dependencies/dependencies_nvcc9.sh .github/workflows/linux.yml commit 93152613c41bfcfde6ff989c4ca583ee4b3a3b73 Author: Jean M. Sexton Date: Wed May 5 09:23:04 2021 -0700 Update Cuda tests in Github CI .github/workflows/dependencies/dependencies_nvcc.sh .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/linux.yml commit 3ae4c7958f5bc2f1bce8fe014170f0577d1e64d3 Author: Jean M. Sexton Date: Tue May 4 17:26:13 2021 -0700 Change package name for CI .github/workflows/dependencies/dependencies_nvcc.sh commit 2d225323f2a8334effd36941070184080483c57b Author: Jean M. Sexton Date: Tue May 4 17:23:46 2021 -0700 Change spacing for CI .github/workflows/linux.yml commit 1583034ab8dc7a7b73d222da53db1850baeba8af Author: Jean M. Sexton Date: Tue May 4 17:16:54 2021 -0700 First pass at Github CI update .github/workflows/linux.yml CMakeLists.txt Source/CMakeLists.txt cmake/NyxSetupSUNDIALS.cmake commit 78fdf6d6dfc9fdb6431d88824547a131206f40f4 Author: Jean M. Sexton Date: Mon May 3 19:00:00 2021 -0500 Tweak default sundials memory alloc flags Source/Driver/Nyx.cpp commit b8b86344e33efaa0520ed556f4fc36de641a0c59 Merge: 2a390f60 66ac35a1 Author: Jean M. Sexton Date: Tue May 4 12:28:01 2021 -0500 Merge branch 'gpu_feature' into gpu_feature_cuda_only commit 66ac35a1326767d28065490fa93b57a9b82c1505 Author: Jean M. Sexton Date: Tue May 4 17:26:16 2021 +0000 Manual merge of HeatCool Source/HeatCool/integrate_state_with_source_3d.cpp commit 47e545409421680235255097c6c5c0ae4332a698 Author: Jean M. Sexton Date: Tue May 4 10:15:29 2021 -0700 Update Sod and MiniSB max_grid_size and blocking_factor Exec/HydroTests/inputs.regtest.sod Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Exec/MiniSB/inputs.analysis commit 061bf1a2c1a3e039ff6d3c4bb7834d59199b09f7 Author: Jean M. Sexton Date: Fri Apr 30 19:57:01 2021 -0700 First pass at creating particle assign grid quantities from restart Source/Particle/NyxParticles.cpp Util/Converters/assign_particle_vels/GNUmakefile Util/Converters/assign_particle_vels/Make.package Util/Converters/assign_particle_vels/Prob.cpp Util/Converters/assign_particle_vels/Prob_error.cpp Util/Converters/assign_particle_vels/README Util/Converters/assign_particle_vels/inputs.rt Util/Converters/assign_particle_vels/nyx_main.cpp commit 5dc611da6807a641cb627cd306129a973c882ecb Merge: c1ee73e7 e2065728 Author: Jean M. Sexton Date: Mon May 3 15:38:19 2021 -0500 Merge branch 'gpu_feature' of https://github.com/amrex-astro/Nyx into gpu_feature commit 2a390f60f077c4af9edc476e6541a9385ef1cda0 Author: Jean M. Sexton Date: Mon May 3 14:18:46 2021 -0500 Revert fused assumption for LyA compiled with Hip Exec/LyA/GNUmakefile commit 2afdddfd1af1e457253b41259ef66ed00b36a8ff Author: Jean M. Sexton Date: Thu Apr 29 20:03:19 2021 -0500 Add Hip sundials allocation and fusing test Exec/LyA/GNUmakefile Exec/Make.Nyx Source/Driver/Nyx.cpp Source/HeatCool/integrate_state_with_source_3d.cpp commit 862d863bdbb985323125f37c3eee0226ea42d922 Author: Jean M. Sexton Date: Sat Apr 10 20:39:18 2021 -0700 Add timers Source/HeatCool/integrate_state_with_source_3d.cpp commit c79819b3bd3e72a0fdbaf80f6f01d5d35c6c8dc8 Merge: 8cc8acae 1ebcfa26 Author: Jean M. Sexton Date: Sat Apr 10 20:38:40 2021 -0700 Merge branch 'gpu_feature_cuda_only' into development commit 8cc8acae4f4b4900153e6b0c70e973919544d989 Author: Jean M. Sexton Date: Fri Apr 9 13:27:19 2021 -0700 OMP hacking for sundials test Source/Driver/sum_utils.cpp Source/HeatCool/integrate_state_with_source_3d.cpp Source/Particle/DarkMatterParticleContainer.cpp commit 5070453779fef820e97ad054be0b6ca52eb73b43 Author: Jean M. Sexton Date: Fri Apr 9 11:40:09 2021 -0400 Fix typo Exec/LyA/inputs Exec/LyA/inputs.rt Exec/LyA/inputs.rt.garuda Exec/LyA/inputs.summit Exec/LyA/inputs_nohydro.rt commit e20657285e2635f59a17f5134a5928fded150db5 Merge: cf4d6af2 daa1556a Author: Jean M. Sexton Date: Fri Apr 2 11:53:40 2021 -0500 Merge branch 'development' into gpu_feature commit daa1556abae72345cc9757a965828e166121af61 Merge: ecdf2987 8f1ecbf1 Author: Jean M. Sexton Date: Fri Apr 2 09:51:42 2021 -0700 Merge branch 'development' of https://github.com/amrex-astro/Nyx into development commit ecdf2987b5a209271c150562a0dfdd76fe3a7718 Author: Jean M. Sexton Date: Mon Mar 29 13:16:11 2021 -0700 Recharacterize default MLPoisson object reuse Exec/LyA/inputs Exec/LyA/inputs.rt Exec/LyA/inputs.rt.garuda Exec/LyA/inputs.summit Exec/LyA/inputs_nohydro.rt Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Gravity/Gravity.cpp commit 8f1ecbf1368bbf7f240f2f97b935d4c347222a11 Author: Jean M. Sexton Date: Mon Mar 29 14:16:31 2021 -0500 Add timer regions on reductions Source/Driver/Nyx.cpp Source/Driver/sum_utils.cpp Source/IO/Nyx_output.cpp commit bc0d91f1847723648a6f626c83aa5848fdf427be Author: Jean M. Sexton Date: Mon Mar 29 14:13:45 2021 -0500 Add Real enforcement for PRECISION=FLOAT example Source/Driver/constants_cosmo.H Source/EOS/eos_hc.H Source/Forcing/Forcing.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp Source/Hydro/Godunov.H Source/Hydro/Utilities.cpp Source/Initialization/Nyx_initdata.cpp Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NyxParticleContainer.H commit 6dcb75c8b0109553e151beb4a5d308f3f591ad31 Author: Jean M. Sexton Date: Fri Mar 26 21:39:14 2021 -0500 Make MultiplyParticleMass use ParallelFor Source/Particle/NyxParticleContainer.H commit 0e295fbb77eff3ef6679ab0939271cfefd74e223 Author: Jean M. Sexton Date: Fri Mar 26 21:38:48 2021 -0500 Prefer using non-managed HIP Sundials Vector, since we never access it on the host Source/HeatCool/integrate_state_with_source_3d.cpp commit c1ee73e71e8b3a968de0fd4cf62f7468220480d1 Author: Jean M. Sexton Date: Fri Mar 26 11:11:09 2021 -0500 Add DPCPP compile guard, change managed type for HIP Source/HeatCool/integrate_state_with_source_3d.cpp commit ede223c063f698b11083a8cf52c82d745759f300 Merge: cf4d6af2 92f47966 Author: Jean M. Sexton Date: Tue Mar 23 20:39:23 2021 -0500 Merge branch 'development' into gpu_feature commit 92f47966a5c280b458662546374830224eb31ee2 Author: Jean M. Sexton Date: Tue Jun 11 06:54:32 2019 -0700 Test moving MLPoission define to post_regrid instead of every timestep Source/Driver/Nyx.cpp Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit 3a5866d5d2f1d18c73b011989b90cb606aad3626 Merge: 048a26bd 593446f4 Author: jmsexton03 Date: Thu Mar 18 12:42:55 2021 -0700 Merge pull request #77 from maxpkatz/levelbld Update for new Amr constructor that takes a LevelBld commit 593446f43fc399b5611fedebf8e4378feb8f7598 Author: Max Katz Date: Thu Mar 18 05:52:23 2021 -0700 Update AMReX subprojects/amrex commit 79fcabfaadea56f92cd772569438b39a510f606b Author: Max Katz Date: Mon Mar 15 20:30:30 2021 -0700 Update for new Amr constructor that takes a LevelBld Source/Driver/nyx_main.cpp commit cf4d6af23abdd90ec7b2c45fbac4ed9f7e3d7068 Author: Jean M. Sexton Date: Wed Mar 10 22:21:48 2021 +0000 Second pass DPC++ SUNMemory Source/HeatCool/integrate_state_with_source_3d.cpp commit 3bd7b2e232434eda3d61db063610582b1c5ecf02 Author: Jean M. Sexton Date: Tue Mar 9 21:55:08 2021 +0000 First pass at HIP / DPC++ SUNMemory Source/HeatCool/integrate_state_with_source_3d.cpp commit 1ebcfa264eef1d1f8c38d98dfd9e7a800fb17bee Author: Jean M. Sexton Date: Mon Mar 8 15:36:16 2021 -0500 First pass at SUNMemory Exec/Make.Nyx Source/HeatCool/integrate_state_with_source_3d.cpp commit fd0a6cd374ce943aae8d4aa2aa406442064caa7e Author: Jean M. Sexton Date: Mon Mar 8 15:06:36 2021 -0500 Revert "Replace Elixir" This reverts commit 678f509d7b1461a981d27f4ea927c2ee3b257202. Source/Hydro/Godunov.cpp Source/Hydro/Hydro.cpp commit 31fae8b0bff05502ff914bb2336d139ef9720adb Merge: 678f509d 048a26bd Author: Jean M. Sexton Date: Mon Mar 8 14:53:08 2021 -0500 Merge branch 'development' into gpu_feature commit 048a26bdae232868105444685180816617b8ba3e Author: zarija Date: Thu Mar 4 11:42:15 2021 -0800 Statement of need Docs/paper/paper.md commit 89113c201be72b96be83f3c7ce87bf0e63cfb0e0 Author: Jean M. Sexton Date: Thu Mar 4 09:57:59 2021 -0800 Update statement of need in paper Docs/paper/paper.md commit 678f509d7b1461a981d27f4ea927c2ee3b257202 Author: Jean M. Sexton Date: Tue Mar 2 12:02:36 2021 -0500 Replace Elixir Source/Hydro/Godunov.cpp Source/Hydro/Hydro.cpp commit 23c36ec8b5f34f04aca68eba75f76e2139cff890 Author: Jean M. Sexton Date: Tue Mar 2 13:10:06 2021 -0500 Replace Elixir Source/Hydro/Godunov.cpp Source/Hydro/Hydro.cpp commit cc42454b20cbc753df10f37aa812300aedf6aa13 Author: Jean M. Sexton Date: Mon Jul 12 11:04:57 2021 -0700 Add Zenodo DOI badge to README README.md commit 5fae8f01e239a80e24a10e9433f476a696200df8 Author: Jean M. Sexton Date: Mon Jul 12 11:02:14 2021 -0700 Add JOSS badge to README README.md commit c48a90600d2132e8aaaff2ac7e0d1c2bcfb07742 Merge: 07dd713a 4a32bfcf Author: jmsexton03 Date: Tue Jul 6 09:27:23 2021 -0700 Merge pull request #83 from dfm/patch-1 Updating GADGET-4 reference to published version commit 4a32bfcf6208181727245ac241c10c329dfcc80a Author: Dan Foreman-Mackey Date: Tue Jul 6 12:23:35 2021 -0400 Updating GADGET-4 reference to published version Docs/paper/paper.bib commit 07dd713a44e94b2be84887fd81425345edb3ea7b Author: Jean M. Sexton Date: Thu Jul 1 22:57:46 2021 -0700 Nyx 21.07 commit 28475d0eb39e6e234a4683976fece89cbb559b2d Author: Jean M. Sexton Date: Thu Jul 1 19:03:34 2021 -0700 Fix make bug Exec/Make.Nyx commit e0e212cfd2e41a8526a39519f3424df56d51edda Author: Jean M. Sexton Date: Thu Jul 1 17:17:50 2021 -0700 Update to 21.07 * Update to 21.07 AMReX submodule * Fix sundials namespace include order * Make OpenMP+GPU less compiler-specific Exec/Make.Nyx Source/HeatCool/integrate_state_with_source_3d.cpp subprojects/amrex commit 19cb30604a541dde66720e8a86b4b069fa2b81d9 Merge: 9114eb2b 564f9905 Author: jmsexton03 Date: Thu Jul 1 10:47:17 2021 -0700 Merge pull request #82 from dfm/joss-edits Minor typographic edits for JOSS manuscript commit 564f9905c3d0c93902428375fef42905bb916010 Author: Dan F-M Date: Fri Jun 25 12:54:21 2021 -0400 minor typographic edits for JOSS manuscript Docs/paper/paper.bib Docs/paper/paper.md commit 9114eb2bb5fcb056e8308c75fd5f06c6cfca476c Author: Jean M. Sexton Date: Mon Jun 21 17:52:47 2021 -0700 Fix spacing Docs/sphinx_documentation/source/NyxCitation.rst Docs/sphinx_documentation/source/NyxGettingStarted.rst commit 3059644407dc2986c60a11cbf8a19fdaa6743f8c Author: Jean M. Sexton Date: Mon Jun 21 17:47:50 2021 -0700 More character encoding fixes Docs/paper/paper.bib commit 0d6e100985f8edf0f33ab8ea154f905c1e1bce69 Author: Jean M. Sexton Date: Mon Jun 21 17:31:34 2021 -0700 CI and UTF-8 fix .github/workflows/dependencies/dependencies_mac.sh Docs/paper/paper.bib commit cd71f29da8a6492b0724534445bce264c0a19ce5 Author: Jean M. Sexton Date: Mon Jun 21 14:22:55 2021 -0700 Tweak build documentation to include AMReX build link .github/workflows/dependencies/dependencies_mac.sh .github/workflows/macos.yml Docs/sphinx_documentation/source/NyxGettingStarted.rst Docs/sphinx_documentation/source/getting_started/BuildingGMake.rst Exec/Make.Nyx cmake/NyxSetupAMReX.cmake commit e1e31a9bcefa92c10a087eaac58f6b19192d02cd Author: Jean M. Sexton Date: Mon Jun 21 14:13:27 2021 -0700 Update bibtex references syntax Docs/paper/paper.bib commit d410b563f26980bfa3cd786a7433228ed8a5520f Author: Jean M. Sexton Date: Mon Jun 21 13:37:55 2021 -0700 Remove ASCL references and convert non-unicode chars Docs/paper/paper.bib commit e2f0f04b745c706f2c2143951364a8e16a5ba28f Author: Jean M. Sexton Date: Mon Jun 21 13:27:01 2021 -0700 Add citations for cosmo codes Docs/paper/paper.bib Docs/paper/paper.md commit e5b9cad659b406fa7671eaf0e1454e36ba06c208 Author: Jean M. Sexton Date: Mon Jun 14 14:04:54 2021 -0700 Syntax cleanup Docs/paper/paper.md commit 4d4c224022c0c71b27d01e879ccf8e1f8786d211 Author: zarija Date: Tue Jun 8 09:14:45 2021 -0700 Small changes to the paper Docs/paper/paper.bib Docs/paper/paper.md commit 3808f00f7dff7d7d6605a37f69aa71cbe20eb3de Author: Ann Almgren Date: Mon Jun 7 13:24:41 2021 -0700 Make default for AMREX_HOME point to Nyx/subprojects/amrex Exec/AMR-density/GNUmakefile Exec/AMR-density/GNUmakefile.cuda Exec/AMR-zoom/GNUmakefile Exec/DrivenTurbulence/GNUmakefile Exec/GravityTests/MacLaurin/GNUmakefile Exec/GravityTests/zeldovich_dm/build/GNUmakefile Exec/Henson/amr-info/GNUmakefile Exec/Henson/extract-particles/GNUmakefile Exec/Henson/sample-analysis/GNUmakefile Exec/HydroTests/GNUmakefile Exec/LyA/GNUmakefile Exec/LyA/GNUmakefile.summit Exec/LyA_Neutrinos/GNUmakefile Exec/MiniSB/GNUmakefile Exec/ParticleMeshTest/GNUmakefile Exec/ParticleOnlyTest/GNUmakefile Exec/SantaBarbara/GNUmakefile Exec/Scaling/GNUmakefile commit b39b3ac83b26d7777288ea1fed4bcce85953295f Author: Jean M. Sexton Date: Thu Jun 3 18:58:24 2021 -0700 Flags for tile_size hydro and heating-cooling Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp Source/Hydro/Hydro.cpp commit 4b5a153af8d8b6e36cc8f328ae9a4fccfe5046da Author: Jean M. Sexton Date: Wed Jun 2 20:45:52 2021 -0400 Update amrex submodule for Sundials interface subprojects/amrex commit 2b8c3a11bdca83dcb2b218324008a828efff5313 Merge: e3d92489 2783cf82 Author: Jean M. Sexton Date: Wed Jun 2 15:37:35 2021 -0700 Merge branch 'development' of github.com:amrex-astro/Nyx into development commit e3d92489fad7b70efaf976f1634ffb509e053b7f Author: Jean M. Sexton Date: Wed Jun 2 15:36:43 2021 -0700 Move plotfile write in order to use write_particle_density_at_init and call Nyx functions directly Util/Converters/Plotfile2HDF5_grids/AmrDerive.cpp Util/Converters/assign_particle_vels/NyxParticles.cpp Util/Converters/assign_particle_vels/nyx_main.cpp commit 2783cf822107ff426c78db3a8759910f0c06f13c Author: Jean M. Sexton Date: Wed Jun 2 13:54:26 2021 -0700 Update additional / modified input flag docs Docs/sphinx_documentation/source/ICs.rst Docs/sphinx_documentation/source/NyxHeatCool.rst Docs/sphinx_documentation/source/conf.py Docs/sphinx_documentation/source/getting_started/BuildingGMake.rst commit a2c675676f49d10a148ffcc814736edba15a04a7 Author: Jean M. Sexton Date: Wed Jun 2 12:44:17 2021 -0700 derive plotfile use new jobinfo, the_parameters This makes the plotfile to hdf5 converter aware of universe metadata like comoving_h seperately from other flags, and writes the _gridDM plotfile based on the newest inputs Util/Converters/Plotfile2HDF5_grids/AmrDerive.cpp Util/Converters/assign_particle_vels/nyx_main.cpp commit 36fda820aab2a6500a3f4d3e10d501394207b066 Author: Jean M. Sexton Date: Sat May 29 16:21:19 2021 -0400 Add more header files for clarity and ordering Source/HeatCool/integrate_state_with_source_3d.cpp commit f2b0a37bc19c39a3558b1a52e91332dbb232ea2f Author: Jean M. Sexton Date: Fri May 28 16:46:59 2021 -0400 GPU and OpenMP picky about sundials includes order Fix typo in make Sunmemory compile guard Exec/Make.Nyx Source/HeatCool/integrate_state_with_source_3d.cpp commit ed79cac32e708b28858970739b16f5c8afa44f4c Author: Jean M. Sexton Date: Mon Mar 1 14:02:11 2021 -0500 Add strang restart from sdc workaround Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/TimeStep/Nyx_advance.cpp commit 4faa5073bab19a9979d3768a7662195f662909db Author: Jean M. Sexton Date: Tue Feb 16 09:03:14 2021 -0800 Update dois and references Docs/paper/paper.bib commit 563fb6618a8cc1ecdefa000d1ec7f2a746bdab2c Author: Jean M. Sexton Date: Fri Feb 12 17:14:35 2021 -0800 Minor paper rearrangement Docs/paper/paper.md commit 58ae6bb2dda061d219b523ce4447076acb27d824 Merge: e339d5a0 bd8020b4 Author: zarija Date: Fri Feb 12 16:21:22 2021 -0800 Add Chris and info on IGM physics in Nyx commit e339d5a057ca16d6ca01db1a401b90418fb45f97 Author: zarija Date: Fri Feb 12 16:18:39 2021 -0800 Add Chris and info on IGM physics in Nyx Docs/paper/paper.bib Docs/paper/paper.md commit bd8020b4fbc024269c4fb760f73a1d964e85b01d Author: Ann Almgren Date: Fri Feb 12 15:56:24 2021 -0800 Adding Chris Docs/paper/paper.md commit 5ce14fa74f9d3a4e0fcd8de4a011c5e8c2588567 Author: Ann Almgren Date: Fri Feb 12 15:01:20 2021 -0800 Add Brian Friesen Docs/paper/paper.md commit 981e04637873bf00f8c4783a73ee30c12efe4d5d Author: Jean M. Sexton Date: Fri Feb 12 14:24:19 2021 -0800 Add gamma, nghost_state, more IC types to docs Docs/sphinx_documentation/source/ICs.rst Docs/sphinx_documentation/source/NyxInputs.rst commit 4fd1bbbe2c8a9089fc5f9927bf9fd653135921ec Author: Jean M. Sexton Date: Fri Feb 12 14:00:52 2021 -0800 Add initialization, timestep, and gamma flags to docs Docs/sphinx_documentation/source/ICs.rst Docs/sphinx_documentation/source/NyxInputs.rst commit 0e03b66a0ade3cce84e1da5b57a71ef47015cfaa Author: Jean M. Sexton Date: Fri Feb 12 12:55:44 2021 -0800 Add plot variable descriptions Docs/sphinx_documentation/source/NyxInputs.rst commit c168f02f77740402c6db2ec132a4253baa025404 Author: Jean M. Sexton Date: Fri Feb 12 12:23:34 2021 -0800 Fix paper citation Docs/paper/paper.md commit d40c63a742293e8d9bfa71b571d946ab7a37b661 Author: Jean M. Sexton Date: Fri Feb 12 12:18:57 2021 -0800 Add Open Journals PDF Generator Action for JOSS paper .github/workflows/draft-pdf.yml commit b910d23f6d583265444ef4ecb5178e6f8f64dcac Author: Jean M. Sexton Date: Fri Feb 12 12:07:56 2021 -0800 Fix CMake auxilary input files list Exec/LyA/CMakeLists.txt commit dc5aa700bcb03f462a7213bda6c8654ba2238b9d Author: Jean M. Sexton Date: Fri Feb 12 11:49:23 2021 -0800 Add memory and load balancing flags Docs/sphinx_documentation/source/NyxInputs.rst commit d86a096261b22e5b503de7575e73cb5438019490 Author: Jean M. Sexton Date: Fri Feb 12 11:19:08 2021 -0800 Add Ascent documentation and links Docs/sphinx_documentation/source/InSitu.rst commit dfc54dec8e06d7399754e186f994380ae6586094 Author: Jean M. Sexton Date: Fri Feb 12 13:13:58 2021 -0500 Update summit make example Exec/LyA/GNUmakefile.summit Exec/LyA/ascent_actions_slicefile.yaml Exec/LyA/ascent_options.json Exec/LyA/inputs.summit commit 730fd5ea23ec81b46874da675250f1837884253f Author: Jean M. Sexton Date: Fri Feb 12 11:49:40 2021 -0500 Update make and inputs names Exec/LyA/GNUmakefile.cuda Exec/LyA/GNUmakefile.summit Exec/LyA/inputs.summit commit 723b1283c3ca8cab8cf8d5e3be43688d67cd5930 Author: zarija Date: Thu Feb 11 16:27:33 2021 -0800 missing reionization parameter Docs/sphinx_documentation/source/NyxInputs.rst commit a09f9c2750504757b53d09c2a79aea2f5a69ef39 Author: Jean M. Sexton Date: Thu Feb 11 16:12:04 2021 -0800 Fix warnings Source/Initialization/Nyx_initdata.cpp Source/Particle/NyxParticles.cpp commit af18b6fca9ffc340e4e3e17adf525e29d51582e7 Author: Jean M. Sexton Date: Thu Feb 11 16:08:20 2021 -0800 Fix comoving_type default Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Particle/NyxParticles.cpp commit 1b82f54eff40535e9ecee2f4c6a3a1125ae37d7e Author: Jean M. Sexton Date: Thu Feb 11 15:52:56 2021 -0800 Update LyA and cuda build documentation Docs/sphinx_documentation/source/getting_started/BuildingCMake.rst Docs/sphinx_documentation/source/getting_started/BuildingGMake.rst Docs/sphinx_documentation/source/getting_started/RunningTheCode.rst commit c96d0499d05c9c5f8c50bac524fc0af1b2ec8283 Author: Jean M. Sexton Date: Thu Feb 11 15:07:25 2021 -0800 Remove unused simd vector Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Driver/nyx_main.cpp Source/Initialization/Nyx_setup.cpp commit b5df8f346240f819f89cc9d38929e56107bf1537 Author: Jean M. Sexton Date: Thu Feb 11 14:39:39 2021 -0800 Remove particle_launch_ics, add reference link Docs/sphinx_documentation/source/NyxUnits.rst Source/Initialization/Nyx_initdata.cpp commit eb3a9dc448d76d28fc282c0921685543ebd30d77 Author: Jean M. Sexton Date: Thu Feb 11 14:38:52 2021 -0800 Fix scope issue for comoving_type Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Driver/comoving.cpp commit 83f038b8d6bc9168f4c48827122bdac4a499fcbc Author: Jean M. Sexton Date: Thu Feb 11 13:45:52 2021 -0800 Remove comoving_type flag Exec/ParticleMeshTest/Prob.cpp Exec/ParticleMeshTest/inputs.2line Exec/ParticleMeshTest/inputs.2line.restarttest Exec/ParticleMeshTest/inputs.mass.nosub Exec/ParticleMeshTest/inputs.mass.sub Exec/ParticleOnlyTest/Prob.cpp Exec/ParticleOnlyTest/inputs.2line Exec/ParticleOnlyTest/inputs.2line.restarttest Exec/ParticleOnlyTest/inputs.mass.nosub Exec/ParticleOnlyTest/inputs.mass.sub Source/Driver/Prob.H Source/Driver/comoving.cpp commit df32a07240b5473213210764d3c392411e53ab2a Author: Jean M. Sexton Date: Thu Feb 11 13:40:58 2021 -0800 Make comoving_type only apply for specific tests Exec/HydroTests/Prob.cpp Exec/ParticleMeshTest/inputs.2line Exec/ParticleMeshTest/inputs.2line.restarttest Exec/ParticleMeshTest/inputs.mass.nosub Exec/ParticleMeshTest/inputs.mass.sub Exec/ParticleOnlyTest/inputs.2line Exec/ParticleOnlyTest/inputs.2line.restarttest Exec/ParticleOnlyTest/inputs.mass.nosub Exec/ParticleOnlyTest/inputs.mass.sub Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Driver/Prob.H Source/Driver/comoving.cpp commit 0e8a385edd46047f1bb3245fea81ec00d8fc23c6 Author: Ann Almgren Date: Thu Feb 11 11:40:53 2021 -0800 Add Weiqun to paper.md Docs/paper/paper.md commit c0d9f4101bbc5e28da5bfff0dccb95b46956c6c0 Author: Ann Almgren Date: Thu Feb 11 11:38:31 2021 -0800 Remove "strict_subcycling" -- it was always 0 Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/TimeStep/Nyx_advance.cpp Source/TimeStep/Nyx_advance_particles.cpp commit 5a327be5aa62ea85af628e3ccefac0938905a9ca Author: Ann Almgren Date: Thu Feb 11 11:34:55 2021 -0800 1) make Riemann use same "small" as Godunov was using 2) Keep small = 1.e-6 but don't allow it to be reset at run-time Source/Driver/Nyx.cpp Source/Hydro/Riemann.H commit 5fc6c1e5a5237169ffa3ad6c512729779cfad544 Author: Ann Almgren Date: Thu Feb 11 11:20:55 2021 -0800 add "plot_rank" to list of inputs in table about plotfile generation Docs/sphinx_documentation/source/NyxInputs.rst commit 446c5ab081ef713a7687ba88d6ff491aa43ee2e9 Author: Ann Almgren Date: Thu Feb 11 11:18:11 2021 -0800 Remove "how" from nyx_main.cpp -- it wasn't used anyway Source/Driver/nyx_main.cpp commit d1fb47a2d63a0d2e1a0c39feceaffde5923d8918 Author: Ann Almgren Date: Thu Feb 11 11:12:36 2021 -0800 Remove plot_X and slice_* as inputs parameters and code they controlled Source/Driver/Nyx.cpp Source/IO/Nyx_output.cpp commit 65cfcf07edd9ca115452c1bdb181961b2c5d64ed Author: Ann Almgren Date: Thu Feb 11 10:42:37 2021 -0800 remove Nrep as run-time option -- it only worked with reading in ascii particle files Source/Driver/Nyx.H Source/Particle/NyxParticles.cpp commit 46df038956b57b3480bf756b5af83c81a03b4132 Author: Ann Almgren Date: Thu Feb 11 10:29:06 2021 -0800 fix typo in comment Source/Initialization/Nyx_initcosmo.cpp commit c49eae0638756f0d8479f179887dd78493d6152a Merge: 834afcb3 3156838b Author: Ann Almgren Date: Thu Feb 11 10:22:45 2021 -0800 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development commit 834afcb3db2e230b1a9d89caf76e7cb5d4d3d5dd Author: Ann Almgren Date: Thu Feb 11 10:22:36 2021 -0800 clean up Docs/sphinx_documentation/source/NyxInputs.rst commit 3156838b065060114c2397b7c0327a5806228098 Author: Jean M. Sexton Date: Thu Feb 11 10:16:29 2021 -0800 Update dt_binpow and some Cmake documentation Docs/sphinx_documentation/source/NyxGettingStarted.rst Docs/sphinx_documentation/source/NyxInputs.rst Docs/sphinx_documentation/source/getting_started/BuildingCMake.rst commit f1632910e2df688ac4ef70121f223fe60509a484 Merge: 1051f2e9 91e779a0 Author: Jean M. Sexton Date: Thu Feb 11 10:15:42 2021 -0800 Merge branch 'development' of ssh://github.com/amrex-astro/Nyx into development commit 91e779a0fd70c674bc181bb9613456af232c9848 Author: mic84 Date: Thu Feb 11 10:10:28 2021 -0800 CMake: disable OpenMP when accelerators are on (#75) CMakeLists.txt commit 1051f2e96a59d91fe09cedf02ee9f3504adaa2d8 Author: Jean M. Sexton Date: Thu Feb 11 09:10:35 2021 -0800 Remove unused strang hydro and heat-cool functions Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Hydro/strang_hydro.cpp Source/Hydro/strang_hydro_fuse.cpp commit 61a8116a14a380b41431c96582d46af62caf48e8 Author: Jean M. Sexton Date: Thu Feb 11 08:08:49 2021 -0800 Fix spacing warnings, ref Gravity inputs Docs/sphinx_documentation/source/NyxGravity.rst Docs/sphinx_documentation/source/NyxInputs.rst commit 843b04208e34b80dded4a52f62a3ed2b239f6711 Author: zarija Date: Wed Feb 10 23:42:00 2021 -0800 Description of parameters Docs/sphinx_documentation/source/NyxInputs.rst Docs/sphinx_documentation/source/PostProcessing.rst commit 6633f16aa0fe99afa9394985ff25da6e5f492725 Author: zarija Date: Wed Feb 10 19:50:09 2021 -0800 In situ / postprocessing Docs/sphinx_documentation/source/ICs.rst Docs/sphinx_documentation/source/InSitu.rst Docs/sphinx_documentation/source/PostProcessing.rst Docs/sphinx_documentation/source/index.rst commit f2ed2405adb46fbbb278dfd58daabaf28bd4f6f6 Author: zarija Date: Wed Feb 10 09:41:00 2021 -0800 Add C++ example code for writing a binary IC file Docs/sphinx_documentation/source/ICs.rst commit be8f035cd9a16508a58c758ee1fb82049b370cb3 Author: Jean M. Sexton Date: Wed Feb 10 05:48:36 2021 -0800 Insert ifndef NO_HYDRO for forcing calls, since forcing is defined on the mesh Source/Driver/Nyx.cpp Source/Forcing/Make.package Source/IO/Nyx_output.cpp commit 1039d9a85aff2a27c542a66fa477a516af3cb620 Author: zarija Date: Tue Feb 9 19:13:05 2021 -0800 Work in progress section and small changes Docs/sphinx_documentation/source/Development.rst Docs/sphinx_documentation/source/ICs.rst Docs/sphinx_documentation/source/PostProcessing.rst Docs/sphinx_documentation/source/conf.py Docs/sphinx_documentation/source/index.rst commit 4c1c85713e75bb13dd60cad44644126292bc4372 Author: zarija Date: Tue Feb 9 18:25:14 2021 -0800 ICs clarifications Docs/sphinx_documentation/source/ICs.rst commit 1e82321344c8cdcd45277ea4fce11a5b5a37cc13 Author: zarija Date: Tue Feb 9 16:45:33 2021 -0800 Initial conditions description Docs/sphinx_documentation/source/ICs.rst Docs/sphinx_documentation/source/index.rst commit 697a8a3b3e7ebd4e7479723f43027c39bd726757 Merge: 5fec3ce2 ea29eb2c Author: zarija Date: Tue Feb 9 16:16:38 2021 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 5fec3ce27db4bf22e7d3078279b8e103c3f02f55 Merge: 667401d6 21ce738b Author: zarija Date: Tue Feb 9 16:16:22 2021 -0800 Fix table commit ea29eb2cbe8aee643c7430b667518d575a31e5b9 Author: Ann Almgren Date: Tue Feb 9 15:57:16 2021 -0800 Get rid of last traces of USE_CGS Exec/DrivenTurbulence/GNUmakefile Source/Driver/Make.package commit 667401d6d193daa63f92a4eb3dccccf114e25654 Author: zarija Date: Tue Feb 9 15:53:07 2021 -0800 Small fixes... Docs/sphinx_documentation/source/NyxUnits.rst commit 21ce738b27a4289501d0935376b6354c01856893 Author: Ann Almgren Date: Tue Feb 9 15:52:33 2021 -0800 fix table and typo Docs/sphinx_documentation/source/NyxUnits.rst commit 92e1238bdd479632f08f94c0fe31ffedc0b66e21 Merge: d880be29 84cc8775 Author: zarija Date: Tue Feb 9 15:36:27 2021 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit d880be292e7cc3f115f17664a8a38929258620cb Author: zarija Date: Tue Feb 9 15:36:11 2021 -0800 Units page Docs/sphinx_documentation/source/NyxUnits.rst commit 84cc87757b28ba83330a5223b810a19d763794ed Author: Jean M. Sexton Date: Tue Feb 9 15:16:32 2021 -0800 Add LyA fused note to gmake Docs/sphinx_documentation/source/getting_started/BuildingGMake.rst Docs/sphinx_documentation/source/getting_started/NyxSundials.rst commit bae4bb9a064780301b8d3934bd0b55091217bc9a Author: Jean M. Sexton Date: Tue Feb 9 14:48:40 2021 -0800 Start adding LyA docs Docs/sphinx_documentation/source/NyxGettingStarted.rst Docs/sphinx_documentation/source/getting_started/BuildingGMake.rst Docs/sphinx_documentation/source/getting_started/NyxSundials.rst Docs/sphinx_documentation/source/getting_started/RunningTheCode.rst commit 7b33c18534219bf7b7c08f7c2bb4bde90f79cd41 Author: mic84 Date: Tue Feb 9 11:46:01 2021 -0800 CMake: few fixes (#74) 1) Get rid of Nyx_FORCING option (replaced by run-time option) 2) Set Nyx_HYDRO=YES by default 3) Better warnings when a directory in Exec are excluded from the build CMakeLists.txt Docs/sphinx_documentation/source/getting_started/BuildingCMake.rst Exec/CMakeLists.txt Exec/DrivenTurbulence/CMakeLists.txt Source/CMakeLists.txt commit 1c869e8f969faba5a1dcf721580a1d5ee063d94b Author: Ann Almgren Date: Tue Feb 9 11:27:49 2021 -0800 Remove reference to USE_FORCING as compile-time option Docs/sphinx_documentation/source/NightlyTests.rst commit a8997685a3b4d6bcd83b3a516bedf1e85a30f954 Author: Ann Almgren Date: Tue Feb 9 11:19:24 2021 -0800 Remove USE_FORCING as compile-time flag -- we will always include the files in Source/Forcing, and whether or not forcing is used is completely controlled by the run-time do_forcing flag (which defaults to 0) Exec/DrivenTurbulence/GNUmakefile Exec/DrivenTurbulence/Nyx_sources.cpp Exec/Make.Nyx Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Driver/sum_integrated_quantities.cpp Source/Forcing/Make.package Source/IO/Nyx_output.cpp Source/Initialization/Nyx_setup.cpp Source/TimeStep/Nyx_advance.cpp Source/TimeStep/Nyx_sources.cpp commit db3549343e22d9c86592677a732dc8f834b6e4d5 Author: Ann Almgren Date: Mon Feb 8 16:34:38 2021 -0800 Add Andrew Myers Docs/paper/paper.md commit 976b4700c2ece83d05f6ad84b808de161a5ce6c3 Author: Ann Almgren Date: Mon Feb 8 16:21:17 2021 -0800 Hard-wise "strt_time" to 0 Source/Driver/nyx_main.cpp commit 901faf85297c73f71462155a28430a1dcc924c39 Author: Ann Almgren Date: Mon Feb 8 16:03:40 2021 -0800 don't parmparse dump_old - it defaults to false and let's leave it that way Source/Driver/Nyx.cpp commit 448a2bcf5bf2c9903b5b68f146c8222a20c75c5c Author: Ann Almgren Date: Mon Feb 8 16:00:33 2021 -0800 1) remove "use_analriem" -- it wasn't used 2) remove the option to turn off refluxing from the inputs file Source/Driver/Nyx.H Source/Driver/Nyx.cpp commit c63fde86814794075900b343da25b7e0c68cd500 Author: Ann Almgren Date: Mon Feb 8 15:50:59 2021 -0800 Remove vorticity as a tagging criterion Source/Driver/Nyx.cpp Source/Driver/Nyx_error.cpp commit d0faf65ea60d50fd1ee86e72200ad4de682a41d4 Author: Ann Almgren Date: Mon Feb 8 15:19:51 2021 -0800 Add "nyx.do_forcing" to forcing docs and fix formatting in particle docs Docs/sphinx_documentation/source/NyxForcing.rst Docs/sphinx_documentation/source/Particles.rst commit ff02b90d8f9e56d4169f67e894cd7a1ca22a9533 Author: Ann Almgren Date: Mon Feb 8 14:43:22 2021 -0800 Add missing inputs from Gravity.cpp Docs/sphinx_documentation/source/NyxInputs.rst commit 502f7d13ad0b2156264705ee8a12afdcf1c5b5c1 Author: zarija Date: Mon Feb 8 12:14:04 2021 -0800 Keep DM particles section to algorithm without ICs Docs/sphinx_documentation/source/Particles.rst commit d3bc365fbb53547e41cb372487b2ba45e0574932 Author: zarija Date: Mon Feb 8 10:52:58 2021 -0800 Splitting in situ and postprocessing in the docs Docs/sphinx_documentation/source/InSitu.rst Docs/sphinx_documentation/source/PostProcessing.rst Docs/sphinx_documentation/source/Visualization.rst Docs/sphinx_documentation/source/index.rst commit 12c6e233b8cd8451a065c8ac12854d2c4275f1c9 Author: zarija Date: Mon Feb 8 00:25:34 2021 -0800 Remove separate AGN version Exec/LyA_AGN/32.nyx Exec/LyA_AGN/64sssss_20mpc.nyx Exec/LyA_AGN/CMakeLists.txt Exec/LyA_AGN/GNUmakefile Exec/LyA_AGN/Make.package Exec/LyA_AGN/Prob.cpp Exec/LyA_AGN/Prob_error.cpp Exec/LyA_AGN/TREECOOL_middle Exec/LyA_AGN/inputs Exec/LyA_AGN/inputs.rt commit feed3fda0307599d4899242ed57b6309e9cd61b2 Author: zarija Date: Mon Feb 8 00:24:34 2021 -0800 Halo finder in LyA Exec/LyA/GNUmakefile Exec/LyA/inputs commit da29fe1c1ef000b7ca2ad1801508ddadbef5430e Author: mic84 Date: Fri Feb 5 11:34:48 2021 -0800 CMake: random fixed (#72) * CMake: bump up amrex version * CMake: missing input file for MiniSB case Exec/MiniSB/CMakeLists.txt subprojects/amrex commit fada26a314870177500ea02b6ace1271185ce3c8 Author: Jean M. Sexton Date: Thu Feb 4 12:50:35 2021 -0800 Make tables numbered, add references Docs/sphinx_documentation/source/NyxUnits.rst Docs/sphinx_documentation/source/conf.py commit 1d29bb5369ca2d8047a113e9eabde4868827d59c Author: Jean M. Sexton Date: Thu Feb 4 12:13:16 2021 -0800 W/tables use pandoc --columns=360 --wrap=preserve Docs/sphinx_documentation/source/NyxUnits.rst commit 0f6dac1b27cf0e2798a22d9351e98a3a3b4859bd Author: Jean M. Sexton Date: Tue Feb 2 11:02:08 2021 -0600 Remove print statements, change sdc condition for HIP hc functions Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp commit 68f71bdd02c8d1253dea9d28c9ac8177dc8ac316 Author: Jean M. Sexton Date: Tue Feb 2 10:44:04 2021 -0600 Add print statements, force using sdc funtions Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp commit 6c87aa696f46ca12bd6ec7f71018d1d363e49341 Author: Jean M. Sexton Date: Tue Feb 2 09:53:22 2021 -0600 Add prints Source/HeatCool/integrate_state_with_source_3d.cpp commit 4c286afbc1bc6e894ca6cc5daa5c2e5b359bc680 Author: Jean M. Sexton Date: Mon Feb 1 12:00:11 2021 -0800 Update documentation for forcing and large_temp Docs/sphinx_documentation/source/NyxEquations.rst Docs/sphinx_documentation/source/NyxForcing.rst Docs/sphinx_documentation/source/NyxUnits.rst commit 79b991dea38ff7d815856bf32dfa25dfb20d550d Author: Jean M. Sexton Date: Mon Feb 1 11:14:21 2021 -0800 Update Sundials documentation to reflect new release Docs/sphinx_documentation/source/NyxSundials.rst commit 8de8acdca020505676134efe8ee2e394287033ca Author: Jean M. Sexton Date: Mon Feb 1 09:15:22 2021 -0800 Update amrex and sundials release subprojects/amrex subprojects/sundials commit 3ae4d1ee13cbb2069247a6840204000b425fb90d Merge: b2419469 69b3ff78 Author: Andrew Myers Date: Fri Jan 29 11:48:36 2021 -0800 Merge pull request #70 from atmyers/remove_init_comso Remove unused InitCosmo and InitCosmo1ppc functions from Nyx commit b2419469654df36d2c2ade898f2d97a70a7fa5ec Author: Jean M. Sexton Date: Fri Jan 29 11:27:32 2021 -0800 Use MPROTON/BOLTZMANN instead of mp_over_kb / e_to_cgs Source/EOS/eos_hc.H commit 234c9ea0996fee9cd6eae47006e5d3439ca9d39e Author: Jean M. Sexton Date: Fri Jan 29 16:58:40 2021 +0000 Revert define hack and use constexpr Source/EOS/atomic_rates_data.H commit 624e699a4d06d22749ba7898871bf82c4c6f5191 Author: Jean M. Sexton Date: Fri Jan 29 16:24:00 2021 +0000 Remove print statements Source/Driver/Nyx.cpp Source/EOS/eos_hc.H commit 6e3bc729ab69c7366284dc92fe733ab4227107dd Author: Jean M. Sexton Date: Fri Jan 29 16:02:10 2021 +0000 Add print for LyA/inputs STEP 158 failure Source/EOS/eos_hc.H Source/HeatCool/sdc_reactions.cpp commit bc5a23f7410a40a16c937ed7daccea7b7516f66c Author: Jean M. Sexton Date: Fri Jan 29 00:55:03 2021 +0000 DPC++ works better with passing by reference Source/Driver/Nyx.cpp Source/EOS/atomic_rates_data.H Source/EOS/eos_hc.H Source/HeatCool/f_rhs.H Source/HeatCool/f_rhs_struct.H commit 7857e02e0718de73861d4008e4c6d3c626094b7b Author: Jean M. Sexton Date: Fri Jan 29 00:54:09 2021 +0000 fcompare works on async_out with fewer input flags Exec/LyA/inputs commit 3f04c6133a938b23a588bf2608d66bbc2b9b0f04 Author: Jean M. Sexton Date: Tue Jan 26 12:02:40 2021 -0800 Add enforece_min_density to algo doc Docs/sphinx_documentation/source/NyxSplitting.rst commit c6537510616e2d4dfa45f0d7037b09710e23e820 Author: Jean M. Sexton Date: Tue Jan 26 09:50:57 2021 -0800 Fix typo Source/TimeStep/Nyx_enforce_minimum_density.cpp commit d7f5381f1d5de229f7acf7e192ae8db47816fca1 Author: Jean M. Sexton Date: Tue Jan 26 09:47:10 2021 -0800 Remove override since function prototype different Source/Driver/Nyx.H commit afc727c8ad96421159dbc3e84237bf8c128be5a0 Author: Jean M. Sexton Date: Tue Jan 26 09:45:46 2021 -0800 Fix hydro_src for SDC when enforcing minimum density Source/Driver/Nyx.H Source/TimeStep/Nyx_enforce_minimum_density.cpp Source/TimeStep/Nyx_update_state_with_sources.cpp commit 04fc27acffb39b960521b7596e2e847a08df1895 Author: Jean M. Sexton Date: Tue Jan 26 07:44:04 2021 -0800 Add override specifier Source/Driver/Nyx.H commit 69b3ff78edea5dfaf65aabb262ee43adc79ae498 Author: Andrew Myers Date: Mon Jan 25 11:52:01 2021 -0800 revert sundials submodule change subprojects/sundials commit daba23b7217a5923488dfa24e70bfd7c6bfa204c Author: Andrew Myers Date: Mon Jan 25 11:39:06 2021 -0800 remove unused InitCosmo and InitCosmo1ppc functions from Nyx Source/Particle/DarkMatterParticleContainer.H Source/Particle/DarkMatterParticleContainer.cpp subprojects/sundials commit 8281c000a9f8e2e5ecc295ab66453259e5734d68 Author: Jean M. Sexton Date: Fri Jan 22 15:17:28 2021 -0800 Add particle load balancing documentation Docs/sphinx_documentation/source/LoadBalancing.rst Docs/sphinx_documentation/source/Particles.rst commit d420636a83473486bf47c09d869c2feae090a215 Author: Jean M. Sexton Date: Fri Jan 22 15:11:05 2021 -0800 Add debugging print, change input levels Exec/ParticleOnlyTest/inputs.load Source/Driver/Nyx.cpp commit 63d4e986afdaee7b49bb404e91bb77774f1ec6e3 Author: Jean M. Sexton Date: Fri Jan 22 15:00:32 2021 -0800 Use level-specific pointer Source/Driver/Nyx.cpp commit 31b6b62f72599557fda8c2172db1b29f9b4a5ce5 Author: Jean M. Sexton Date: Fri Jan 22 14:51:29 2021 -0800 Lost all particles Exec/ParticleOnlyTest/64sssss_20mpc.nyx Exec/ParticleOnlyTest/inputs.load Source/Driver/Nyx.cpp Source/TimeStep/Nyx_advance_particles.cpp commit 1bb44d86bfa9408d7f038c963d32463e9a89f177 Author: Jean M. Sexton Date: Thu Jan 21 22:48:22 2021 +0000 Update sundials submodule subprojects/sundials commit 3d272d785042eb96d141f4a321a5df872de4c18a Author: Jean M. Sexton Date: Thu Jan 21 22:48:42 2021 +0000 Add N_VNewManaged_Sycl for sdc DPCPP Exec/Make.Nyx Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp commit 79267d1ee3eea4d721e9ba93e50f80fa1609ba6d Author: Jean M. Sexton Date: Thu Jan 21 15:50:43 2021 -0600 Add N_VNewManaged_Hip for sdc HIP Exec/Make.Nyx Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp commit ed504e109bce821059dcedbf5836a0d79fb8e8f3 Author: Jean M. Sexton Date: Thu Jan 21 08:32:11 2021 -0800 Remove emphasis, use specific notation for ahalf Docs/sphinx_documentation/source/NyxSplitting.rst commit b02bb196815ba9fc4233f7f3afbfd16d13e71a4e Author: Jean M. Sexton Date: Thu Jan 21 08:12:42 2021 -0800 Fix math block scoping in rst Docs/sphinx_documentation/source/NyxSplitting.rst commit 75befeb12dc70043061567e62b46c9fd0a64ce4d Author: Jean M. Sexton Date: Thu Jan 21 07:58:50 2021 -0800 Remove comments Docs/sphinx_documentation/source/NyxSplitting.rst commit 900509cbecd2287cb68559e9d67018e9d20cd84d Author: Jean M. Sexton Date: Thu Jan 21 07:55:14 2021 -0800 Change emphasis Docs/sphinx_documentation/source/NyxSplitting.rst commit 7c7b858f9af0718e685c407f8f5e459f0822115e Author: Jean M. Sexton Date: Thu Jan 21 07:26:58 2021 -0800 First pass at sdc pandoc conversion Docs/sphinx_documentation/source/NyxSplitting.rst Docs/sphinx_documentation/source/index.rst Docs/sphinx_documentation/source/refs.bib commit f81f54aaa62ffdbec82eaf5ab64c311460005c43 Author: Jean M. Sexton Date: Wed Jan 20 14:10:33 2021 -0800 Update HeatCool documentation Docs/sphinx_documentation/source/NyxHeatCool.rst commit 6eb10ff71e6635cc6043c8ba40006c1e5090676e Author: Jean M. Sexton Date: Wed Jan 20 11:35:59 2021 -0800 Use Clone for OpenMP Sundials vectors Source/HeatCool/integrate_state_with_source_3d.cpp commit 652ee8f8d878f0e58650edb3899f7578ce916dc9 Author: Jean M. Sexton Date: Wed Jan 20 11:09:26 2021 -0800 Use N_VClone Source/HeatCool/integrate_state_with_source_3d.cpp commit 37350e803d7744153de648eda90cfa18dd472604 Author: Jean M. Sexton Date: Fri Jan 15 14:53:18 2021 -0800 Add initial comments on gravity, update refs Docs/paper/paper.bib Docs/paper/paper.md commit abcec3355eb8d0ff6a71d99e0cc6db06bcab743b Author: Jean M. Sexton Date: Fri Jan 15 11:12:50 2021 -0800 Fix linking warning, remove unneeded code Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/LoadBalancing.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst Docs/sphinx_documentation/source/NyxSundials.rst Docs/sphinx_documentation/source/Visualization.rst commit 1603cb6d63bb9791e15984dda0f2e81536f7a1ad Author: Jean M. Sexton Date: Fri Jan 15 10:25:32 2021 -0800 Remove TARGET_FOLDER since we want to deploy to root .github/workflows/docs.yml commit 6f33ba070d3e5f35b407ab7d6084e6bcf6e3d400 Author: Jean M. Sexton Date: Fri Jan 15 10:07:31 2021 -0800 Change directory and skip latexpdf build_docs.sh commit 1a120772d21014668667900a16ec826f89e50503 Author: Jean M. Sexton Date: Fri Jan 15 10:01:31 2021 -0800 Update to use correct Doxyfile build_docs.sh commit fe5c0c00dc858e3fa8671ac2b846b4b3b293fca6 Author: Jean M. Sexton Date: Fri Jan 15 09:54:46 2021 -0800 Fix yaml spacing3 .github/workflows/docs.yml commit 29137ad436a067c643cb16524e0fe8e865034d99 Author: Jean M. Sexton Date: Fri Jan 15 09:53:29 2021 -0800 Fix yaml spacing2 .github/workflows/docs.yml commit c99e215f0ab0e234621ce0502573aad2216794a5 Author: Jean M. Sexton Date: Fri Jan 15 09:52:14 2021 -0800 Fix yaml spacing .github/workflows/docs.yml commit 46ded0bde3148e0ae234dc6558b237cd7537509b Author: Jean M. Sexton Date: Fri Jan 15 09:47:40 2021 -0800 Fix spacing .github/workflows/docs.yml commit 1bdbedb28f99a7a6bebd897975ece846d5bd706b Author: Jean M. Sexton Date: Fri Jan 15 09:44:56 2021 -0800 Add python dependencies again for docs .github/workflows/docs.yml commit 91d13ef4327a59505c6bc7ee3d4a34c722746cf7 Author: Jean M. Sexton Date: Fri Jan 15 09:14:12 2021 -0800 Update dependancies, remove Travis script .github/workflows/dependencies/documentation.sh build_and_deploy.sh commit c869b12edf3c5396eedc076cde2e00ca7feca81b Author: Jean M. Sexton Date: Fri Jan 15 09:04:35 2021 -0800 Fix table spacing Docs/sphinx_documentation/source/NyxInputs.rst commit f41bf6c88efee85cc7c5b540f8fd771d63b116b7 Author: Jean M. Sexton Date: Fri Jan 15 09:00:18 2021 -0800 Use gh-pages .github/workflows/docs.yml commit c3340c1840c31967b88f6b56d41e5e81091638d3 Merge: ed21ea30 abc7aa71 Author: Jean M. Sexton Date: Fri Jan 15 08:55:12 2021 -0800 Merge branch 'dev_doc' into development commit ed21ea306932c5e4defb5e8e2c4f178cd840c4ae Author: Jean M. Sexton Date: Thu Jan 14 10:48:57 2021 -0800 Make ext_src in a launch region by default Source/Hydro/strang_hydro.cpp commit c1268a002c19a13113712d03ffe1019dc871d045 Author: Jean M. Sexton Date: Thu Jan 14 10:34:50 2021 -0800 Use RunOn::Device, fix OMP and Elixir in Gravity Source/Driver/sum_utils.cpp Source/Gravity/Gravity.cpp commit c6eb9709b8941206a2b923c8b78180033f5f8133 Author: Jean M. Sexton Date: Thu Jan 14 12:04:33 2021 -0500 Remove most LaunchSafeGuard and setLaunchRegion Source/Driver/Nyx.cpp Source/Driver/nyx_main.cpp Source/Driver/sum_integrated_quantities.cpp Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp Source/HeatCool/sdc_reactions.cpp Source/HeatCool/strang_reactions.cpp Source/Hydro/sdc_hydro.cpp Source/Hydro/strang_hydro.cpp Source/Hydro/strang_hydro_fuse.cpp Source/IO/Nyx_output.cpp Source/Initialization/Nyx_initdata.cpp Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NyxParticleContainer.H Source/Particle/NyxParticles.cpp Source/TimeStep/Nyx_advance.cpp Source/TimeStep/Nyx_advance_particles.cpp commit d476b9f61419c93d7c5cb93c07c10d2e483b0276 Author: Jean M. Sexton Date: Wed Jan 13 12:45:33 2021 -0800 Make post_regrid use same grav_vec_new logic as post_restart, make debug statement more verbose Source/Driver/Nyx.cpp Source/TimeStep/Nyx_enforce_minimum_density.cpp commit 0ebfe7f73ce071b11aa439b7f63e5c4e32806609 Author: Jean M. Sexton Date: Wed Jan 13 07:19:16 2021 -0800 Clarify comments Source/Hydro/Hydro.cpp Source/Initialization/Nyx_initdata.cpp commit ddf15da65bfbbce149d9c56f6059d3d767ba5d10 Author: Jean M. Sexton Date: Tue Jan 12 16:59:51 2021 -0800 Revert "Replace LaunchSafeGuard with empty lines" This reverts commit a2c11f564f26c34c7e0170c43c8a655506e5d0c3. Source/Driver/Nyx.cpp Source/Driver/nyx_main.cpp Source/Driver/sum_integrated_quantities.cpp Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp Source/HeatCool/sdc_reactions.cpp Source/HeatCool/strang_reactions.cpp Source/Hydro/sdc_hydro.cpp Source/Hydro/strang_hydro.cpp Source/Hydro/strang_hydro_fuse.cpp Source/IO/Nyx_output.cpp Source/Initialization/Nyx_initdata.cpp Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NyxParticleContainer.H Source/Particle/NyxParticles.cpp Source/TimeStep/Nyx_advance.cpp Source/TimeStep/Nyx_advance_particles.cpp commit a2c11f564f26c34c7e0170c43c8a655506e5d0c3 Author: Jean M. Sexton Date: Tue Jan 12 13:17:26 2021 -0800 Replace LaunchSafeGuard with empty lines Source/Driver/Nyx.cpp Source/Driver/nyx_main.cpp Source/Driver/sum_integrated_quantities.cpp Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp Source/HeatCool/sdc_reactions.cpp Source/HeatCool/strang_reactions.cpp Source/Hydro/sdc_hydro.cpp Source/Hydro/strang_hydro.cpp Source/Hydro/strang_hydro_fuse.cpp Source/IO/Nyx_output.cpp Source/Initialization/Nyx_initdata.cpp Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NyxParticleContainer.H Source/Particle/NyxParticles.cpp Source/TimeStep/Nyx_advance.cpp Source/TimeStep/Nyx_advance_particles.cpp commit 038faaeddf42a32c939969bc2f824a1bb48772bc Merge: 0f6d2f02 5d9c1dae Author: asalmgren Date: Mon Jan 11 13:38:24 2021 -0800 Merge pull request #69 from atmyers/particleinit_warnings Fix compiler warnings associated with ParticleInit. commit 5d9c1dae6b02a7175c8139b9d1936488caa420eb Merge: 0e63b73c 0f6d2f02 Author: Andrew Myers Date: Mon Jan 11 13:15:11 2021 -0800 Merge branch 'development' into particleinit_warnings commit 0e63b73c0bcdd3b21807294712fd94abfeb21294 Author: Andrew Myers Date: Mon Jan 11 13:15:06 2021 -0800 update submodule subprojects/amrex commit abc7aa71aafa812003eb0626d5d292c48d34ed79 Author: Jean M. Sexton Date: Fri Jan 8 11:00:52 2021 -0800 Add documention Github Action workflow .github/workflows/dependencies/documentation.sh .github/workflows/docs.yml build_docs.sh commit 0f6d2f02023aba3319405a4788cc3609b126d56b Author: Ann Almgren Date: Mon Jan 11 12:19:34 2021 -0800 eliminate one more compiler warning Exec/MiniSB/Prob.cpp commit a6656e82ea14d2d575d528ba7b6ae84c75dd14eb Author: Ann Almgren Date: Mon Jan 11 11:19:32 2021 -0800 update amrex submodule subprojects/amrex commit e58bcdecf74e5f136fbc4da9f9f736b941234c15 Author: Andrew Myers Date: Mon Jan 11 10:59:04 2021 -0800 fix compiler warnings associated with ParticleInit Source/Particle/NyxParticles.cpp subprojects/amrex commit e69f94e6d73639396dbb9350288fbc99427f2f2e Author: Ann Almgren Date: Sat Jan 9 12:26:00 2021 -0800 Restore one line needed for NO_HYDRO to compile, and eliminate a few more compiler warnings Source/Initialization/Nyx_initdata.cpp commit eabae500690242c1f21d661b23d70f4207bac26b Author: Ann Almgren Date: Sat Jan 9 11:17:56 2021 -0800 just formatting Source/Driver/Nyx.cpp commit 8c6d512c5ec500d39e33f43b1c0d9eea8e2cf329 Author: Ann Almgren Date: Sat Jan 9 11:08:50 2021 -0800 1) clean up forcing -- replace num_modes_ext by simply num_modes 2) initialize new PhiGrav_Type to 0 even though it isnt used since it will be written in the checkpoint file Source/Driver/Nyx.cpp Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp commit db735cbddd16a2eda13ae92c870a86c921c03bfb Author: Ann Almgren Date: Sat Jan 9 11:01:17 2021 -0800 Remove print statement Source/IO/write_info.cpp commit 7a67f989372e40d607db3e56b333da4a4165f46f Author: Ann Almgren Date: Sat Jan 9 10:25:36 2021 -0800 Remove more compiler warnings Exec/GravityTests/zeldovich_dm/run_hydro/runlog Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Initialization/Nyx_initdata.cpp Source/Particle/NyxParticleContainer.H commit 9ff044a8347448f7b560e9307ed3916c6d1c1442 Author: Jean M. Sexton Date: Sat Jan 9 05:51:12 2021 -0800 Cleanup of Nyx_initdata warnings Source/Initialization/Nyx_initdata.cpp commit 6f1e76470ec6e6ce6d2035dc8511b1b30c7c322e Author: mic84 Date: Fri Jan 8 21:47:59 2021 -0800 CMake: update (#68) * Fix Prob.cpp to work when NO_HYDRO=TRUE * Move Prob.H to Source/Driver * CMake: define myxcore object library * CMake: fix CUDA builds * CI: fix dpcpp runner * CI: update dpc++ runner * Lets try this * Change not -> ! else dpcpp errors * Replace logical operands with standard form * More logical operands replacements * CI: remove Fortran * CMake: various improvements in handling exe-specific options * Fix stuff * Fix corner cases * Try this * Ooops - I did it again * CMake: re-organize structure * CMake: fix broken CUDA compilation CMakeLists.txt Exec/LyA_Neutrinos/CMakeLists.txt Source/AGN/CMakeLists.txt Source/CMakeLists.txt Source/Driver/CMakeLists.txt Source/Particle/CMakeLists.txt Source/TimeStep/CMakeLists.txt Source/TimeStep/Nyx_enforce_minimum_density.cpp cmake/NyxSetupExecutable.cmake commit 5c89086571b5bb02184bc9d1a71add2a109d219c Author: Ann Almgren Date: Fri Jan 8 20:59:55 2021 -0800 remove unused variables Source/Gravity/Gravity.cpp commit d0121de9e1f62604c84fb69a8cec67451d68ce53 Author: Ann Almgren Date: Fri Jan 8 20:05:38 2021 -0800 More cleanup based on compiler warnings Exec/AMR-density/Prob.cpp Exec/DrivenTurbulence/Nyx_sources.cpp Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/Derive_forcing.cpp Source/DerivedQuantities/ParticleDerive.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/bc_fill.cpp Source/Particle/NyxParticleContainer.H Source/Particle/NyxParticles.cpp Source/TimeStep/Nyx_sources.cpp commit 5cbcc754184cfae0e9fdc9ab2438f60b8296d7e2 Author: Ann Almgren Date: Fri Jan 8 20:02:19 2021 -0800 Comment why we need S_old Source/Hydro/strang_hydro.cpp commit c7875357fb41718e864874b58ba893492d53f53b Author: Ann Almgren Date: Fri Jan 8 20:00:59 2021 -0800 Put S_old back ... Source/Hydro/strang_hydro.cpp commit 7fd14afd28c0a0eb6043770fb49fbb992b2684b5 Author: Ann Almgren Date: Fri Jan 8 19:13:17 2021 -0800 Fix typo Source/Forcing/Forcing_init.cpp commit 5b641488fc1f6f418af9efec81079a3020d66638 Author: Ann Almgren Date: Fri Jan 8 19:03:44 2021 -0800 num_modes_ext --> num_modes in Stochastic Forcing init routine. Source/DerivedQuantities/ParticleDerive.cpp Source/Driver/Nyx.cpp Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp commit 723c30dc9287cbbf949d2739eef95341761e5066 Author: Ann Almgren Date: Fri Jan 8 17:49:32 2021 -0800 Remove more compiler warnings Exec/AMR-density/Prob.cpp Source/Forcing/Forcing.cpp Source/HeatCool/integrate_state_vec_3d_stubs.cpp Source/HeatCool/strang_reactions.cpp Source/Hydro/strang_hydro.cpp Source/IO/Nyx_output.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Particle/DarkMatterParticleContainer.cpp Source/TimeStep/Nyx_sources.cpp commit b817017055b2b3c5e753e6d97ac62bc6412a86ab Author: Jean M. Sexton Date: Fri Jan 8 14:34:17 2021 -0800 Fix changed enforce_minimum_density_floor prototype Source/Particle/NyxParticles.cpp commit a2706bd9b341e0766e19cf72cdb1eba22f903b31 Author: Ann Almgren Date: Fri Jan 8 13:11:14 2021 -0800 fix oops in last commit Source/Hydro/Hydro.cpp commit df42cdf9d1dcbb462597f0c9f3e25a6be925e360 Author: Ann Almgren Date: Fri Jan 8 12:59:00 2021 -0800 More clean-up of compiler warnings, I think we've finished all of Hydro and Timestep diretories Source/Driver/Nyx.H Source/Driver/comoving.cpp Source/Hydro/Godunov.H Source/Hydro/Godunov.cpp Source/Hydro/Hydro.H Source/Hydro/Hydro.cpp Source/Hydro/Riemann.H Source/Hydro/Utilities.H Source/Hydro/sdc_hydro.cpp Source/Hydro/strang_hydro.cpp Source/Hydro/trace_ppm.cpp Source/TimeStep/Nyx_enforce_minimum_density.H Source/TimeStep/Nyx_enforce_minimum_density.cpp Source/TimeStep/Nyx_sources.cpp Source/TimeStep/Nyx_update_state_with_sources.cpp commit a31a4d35bebf0e450d6801b5caf99c325e9a812f Author: Ann Almgren Date: Fri Jan 8 12:06:16 2021 -0800 More cleanup of compiler warnings Source/Driver/Nyx_error.cpp Source/Driver/comoving.cpp Source/TimeStep/Nyx_advance.cpp Source/TimeStep/Nyx_advance_particles.cpp commit 39fa2aa9682e503944a51bd4ab2d5a29b3a14f2a Author: Ann Almgren Date: Fri Jan 8 11:42:53 2021 -0800 Cleaning up compiler warnings .... Exec/DrivenTurbulence/Prob.cpp Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Driver/Prob.H Source/EOS/eos_adiabatic.H Source/Particle/NyxParticleContainer.H commit 8c4550dc7e8c718df8d4d6d6016736a7f35c6b17 Author: mic84 Date: Thu Jan 7 14:37:29 2021 -0800 CMake: update to account for changes to Prob.H (#67) * Fix Prob.cpp to work when NO_HYDRO=TRUE * Move Prob.H to Source/Driver * CMake: define myxcore object library * CMake: fix CUDA builds * CI: fix dpcpp runner * CI: update dpc++ runner * Lets try this * Change not -> ! else dpcpp errors * Replace logical operands with standard form * More logical operands replacements * CI: remove Fortran * CMake: various improvements in handling exe-specific options * Fix stuff * Fix corner cases .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_clang6.sh .github/workflows/dependencies/dependencies_dpcpp.sh .github/workflows/dependencies/dependencies_hip.sh .github/workflows/dependencies/dependencies_nvcc.sh .github/workflows/linux.yml CMakeLists.txt Exec/AMR-density/CMakeLists.txt Exec/AMR-density/Prob.cpp Exec/AMR-zoom/CMakeLists.txt Exec/AMR-zoom/Prob.cpp Exec/DrivenTurbulence/CMakeLists.txt Exec/DrivenTurbulence/Prob.cpp Exec/HydroTests/CMakeLists.txt Exec/HydroTests/Prob.cpp Exec/LyA/CMakeLists.txt Exec/LyA/Prob.cpp Exec/LyA_AGN/CMakeLists.txt Exec/LyA_AGN/Prob.cpp Exec/LyA_Neutrinos/CMakeLists.txt Exec/LyA_Neutrinos/Prob.cpp Exec/MiniSB/CMakeLists.txt Exec/MiniSB/Prob.cpp Exec/ParticleMeshTest/Prob.cpp Exec/SantaBarbara/Prob.cpp Exec/Scaling/Prob.cpp Source/AGN/CMakeLists.txt Source/CMakeLists.txt Source/DerivedQuantities/CMakeLists.txt Source/Driver/CMakeLists.txt Source/Driver/Make.package Source/Driver/Nyx.cpp Source/Driver/Prob.H Source/EOS/CMakeLists.txt Source/Forcing/CMakeLists.txt Source/Gravity/CMakeLists.txt Source/HeatCool/CMakeLists.txt Source/Hydro/CMakeLists.txt Source/Hydro/Utilities.cpp Source/IO/CMakeLists.txt Source/Initialization/CMakeLists.txt Source/Initialization/Nyx_initdata.cpp Source/Monitors/CMakeLists.txt Source/Particle/CMakeLists.txt Source/Particle/DarkMatterParticleContainer.cpp Source/TimeStep/CMakeLists.txt Source/TimeStep/Nyx_enforce_minimum_density.H Source/TimeStep/Nyx_enforce_minimum_density.cpp Source/TimeStep/Nyx_time_center_sources.cpp Util/zhi_converter/main.cpp cmake/NyxSetupExecutable.cmake subprojects/amrex commit c2b5e573d16ad6f2b71444100974fdb954af9b1b Author: Ann Almgren Date: Thu Jan 7 13:30:00 2021 -0800 Oops -- didn't mean to commit Nyx_enforce_minimum_density.cpp.ann! Source/TimeStep/Nyx_enforce_minimum_density.cpp.ann commit fc47f59b3d24b1181ec5277eb6e0c5d4f97b8739 Author: Ann Almgren Date: Thu Jan 7 13:27:49 2021 -0800 Pass h_species in to enforce_minimum_density_floor rather than hard-wiring it Source/TimeStep/Nyx_enforce_minimum_density.H Source/TimeStep/Nyx_enforce_minimum_density.cpp Source/TimeStep/Nyx_enforce_minimum_density.cpp.ann commit 2d533324cc846d094e59511676a6ee251d810111 Author: Ann Almgren Date: Thu Jan 7 13:15:53 2021 -0800 removing tab from f_rhs_struct.H Source/HeatCool/f_rhs_struct.H commit 5336329a8a12fb51057592c7deaefa5b62c9b73f Author: Jean M. Sexton Date: Thu Jan 7 11:43:54 2021 -0800 Remove XHYDROGEN and YHELIUM from strang Source/HeatCool/f_rhs.H Source/HeatCool/integrate_state_vec_3d.cpp commit 883fc69bcda40998eecc22d616ee0d487a1867e9 Author: Jean M. Sexton Date: Wed Jan 6 10:22:29 2021 -0800 Update h_species and YHELIUM to use input parameters in eos_hc and f_rhs_struct Source/Driver/constants_cosmo.H Source/EOS/eos_hc.H Source/HeatCool/f_rhs.H Source/HeatCool/f_rhs_struct.H commit 208d11bcf04bc9645906e10d8167224d344b06dd Author: Jean M. Sexton Date: Wed Jan 6 10:01:29 2021 -0800 Apply uvb_density from input flags and update inhomog JH and JHe Source/HeatCool/f_rhs_struct.H commit a4462950e6403c235663ada2b0275c62b1f72e0d Author: Jean M. Sexton Date: Wed Jan 6 09:47:38 2021 -0800 Use stored mean_rhob Source/HeatCool/f_rhs.H Source/HeatCool/f_rhs_struct.H commit 2defd4d1c351fe7df549ea079cc7472433f492c4 Author: Ann Almgren Date: Mon Jan 4 20:30:34 2021 -0800 fix runlog_precision stuff Source/IO/write_info.cpp commit a84d11192473a4882a698920f7236a400d1dcf2e Author: Ann Almgren Date: Mon Jan 4 20:22:33 2021 -0800 fix typo in runlog_precision type Source/IO/write_info.cpp commit 7683f216b5106098fed19d62fe39bb2454b76203 Author: Ann Almgren Date: Mon Jan 4 18:53:04 2021 -0800 Make the terse parameter be the min of the input terse parameter and the regular Source/IO/write_info.cpp commit d90c6ee92b48d4a41413d1eaa803fe324a13ff00 Author: Ann Almgren Date: Mon Jan 4 18:51:54 2021 -0800 Add a second parameter that controls the runlog precision so we can have different columns have different precisions. Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/IO/write_info.cpp commit d2c5304e82c75a556229db1244ee6056a62bb3a1 Author: Ann Almgren Date: Mon Jan 4 14:48:37 2021 -0800 1) Clean up hydro more 2) replace BL_SPACEDIM by AMREX_SPACEDIM Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Driver/Nyx_error.cpp Source/Gravity/Gravity.cpp Source/Hydro/Hydro.H Source/Hydro/Hydro.cpp Source/Hydro/sdc_hydro.cpp Source/Hydro/strang_hydro.cpp Source/Hydro/strang_hydro_fuse.cpp Source/IO/Nyx_output.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/read_plotfile.cpp Source/Particle/AGNParticleContainer.H Source/Particle/DarkMatterParticleContainer.H Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NeutrinoParticleContainer.H Source/Particle/NyxParticleContainer.H Source/Particle/NyxParticles.cpp Source/TimeStep/Nyx_advance.cpp Source/TimeStep/Nyx_advance_particles.cpp Source/TimeStep/Nyx_correct_gsrc.cpp commit 31e138332f03715ef0869f0d339e68478e4b3dae Author: Ann Almgren Date: Mon Jan 4 11:18:17 2021 -0800 fix typo Source/Hydro/Hydro.cpp commit bdfede0f800e62033cf44e1bce1eee3f7cb9d36b Author: Ann Almgren Date: Mon Jan 4 09:44:36 2021 -0800 Move two lines from pc_ext_flx into Hydro.cpp Source/Hydro/Hydro.H Source/Hydro/Hydro.cpp commit 8d7592e14f1ace6c5c3df0f02160c2d02cb62df8 Author: Ann Almgren Date: Mon Jan 4 09:20:30 2021 -0800 Replace XHYDROGEN by h_species in eos_hc.H -- h_species was already passed in Source/EOS/eos_hc.H commit 137f88325aa50840a4ccd0c06227880406914af2 Author: Ann Almgren Date: Sun Jan 3 20:15:40 2021 -0800 Revert "Clean up hydro -- combine pc_ext_flx and pc_ext_flx_dt and remove" This reverts commit 533a16597971ba088f3e5e3df400b566385267cf. Source/Hydro/Hydro.H Source/Hydro/Hydro.cpp commit 533a16597971ba088f3e5e3df400b566385267cf Author: Ann Almgren Date: Sun Jan 3 17:55:43 2021 -0800 Clean up hydro -- combine pc_ext_flx and pc_ext_flx_dt and remove these and pc_update as separate functions Source/Hydro/Hydro.H Source/Hydro/Hydro.cpp commit e90631202b4ed776277d512360d4281c37c9fd71 Author: Ann Almgren Date: Sat Jan 2 13:04:52 2021 -0800 More Prob.H --> Prob.cpp Add changes to source files to go with last commit Exec/Henson/amr-info/Make.package Exec/Henson/amr-info/Prob.cpp Exec/Henson/amr-info/Prob_error.cpp Exec/Henson/extract-particles/Make.package Exec/Henson/extract-particles/Prob.cpp Exec/Henson/extract-particles/Prob_error.cpp Exec/Henson/sample-analysis/Make.package Exec/Henson/sample-analysis/Prob.cpp Exec/Henson/sample-analysis/Prob_error.cpp Source/Initialization/Nyx_initdata.cpp Source/Particle/NyxParticles.cpp commit 7f7dfcf6395f3b11ccc61ed7a0f8ddfa32802086 Author: Ann Almgren Date: Sat Jan 2 12:59:41 2021 -0800 Replace a Prob.H in each Exec subdirectory by Exec/Prob.H and Prob*cpp in each run directory. Exec/AMR-density/Make.package Exec/AMR-density/Prob.cpp Exec/AMR-density/Prob_error.cpp Exec/AMR-zoom/Make.package Exec/AMR-zoom/Prob.cpp Exec/AMR-zoom/Prob_error.cpp Exec/DrivenTurbulence/Make.package Exec/DrivenTurbulence/Prob.cpp Exec/DrivenTurbulence/Prob_error.cpp Exec/HydroTests/Make.package Exec/HydroTests/Prob.cpp Exec/HydroTests/Prob_error.cpp Exec/LyA/Make.package Exec/LyA/Prob.cpp Exec/LyA/Prob_error.cpp Exec/LyA_AGN/Make.package Exec/LyA_AGN/Prob.cpp Exec/LyA_AGN/Prob_error.cpp Exec/LyA_Neutrinos/Make.package Exec/LyA_Neutrinos/Prob.H Exec/LyA_Neutrinos/Prob.cpp Exec/LyA_Neutrinos/Prob_error.cpp Exec/Make.package Exec/MiniSB/Make.package Exec/MiniSB/Prob.cpp Exec/MiniSB/Prob_error.cpp Exec/ParticleMeshTest/Make.package Exec/ParticleMeshTest/Prob.cpp Exec/ParticleMeshTest/Prob_error.cpp Exec/ParticleOnlyTest/Make.package Exec/ParticleOnlyTest/Prob.H Exec/ParticleOnlyTest/Prob.cpp Exec/ParticleOnlyTest/Prob_error.cpp Exec/Prob.H Exec/Prob_param.H Exec/SantaBarbara/GNUmakefile Exec/SantaBarbara/Make.package Exec/SantaBarbara/Prob.cpp Exec/SantaBarbara/Prob_error.cpp Exec/Scaling/Make.package Exec/Scaling/Prob.cpp Exec/Scaling/Prob_error.cpp Source/AGN/AGN_halos.cpp commit afbc2430dc5b66603dd6ef6c0b49d4d311d5b199 Author: Ann Almgren Date: Sat Jan 2 09:47:09 2021 -0800 Clean-up -- shouldn't change any answers Source/Hydro/trace_ppm.cpp commit b426208e16a8d8f1c033a4dee6ec25f44ceb5980 Author: Ann Almgren Date: Sat Jan 2 08:18:24 2021 -0800 Do "fix" in trace_ppm for all cases, not just when rho_pred < 1/2 rho_ref. This should affect all solutions with both hydro and sources. Source/Hydro/trace_ppm.cpp commit 2f018c591840f6b9cdfc222d956330f7f443236c Author: Ann Almgren Date: Fri Jan 1 19:43:33 2021 -0800 Fix DrivenTurbulence/Prob.H Exec/DrivenTurbulence/Prob.H commit 8422184f5f9cb41e6389445639b651c5312efd32 Author: Ann Almgren Date: Fri Jan 1 19:10:24 2021 -0800 Fix oops in parmparsing in HydroTests/Prob.H Exec/HydroTests/Prob.H commit 77def5c61f8ec48e10b2918630ec8d0920fdc537 Author: Ann Almgren Date: Fri Jan 1 18:41:33 2021 -0800 Comment out print statements in trace_ppm Source/Hydro/trace_ppm.cpp commit 0740cf89b95c7c365f244f226995f06351ef304c Author: Ann Almgren Date: Fri Jan 1 16:41:34 2021 -0800 Don't hardwire the species in Prob.H -- use h_species and he_species from the inputs file instead Exec/AMR-density/Make.package Exec/AMR-density/Prob.H Exec/AMR-zoom/Make.package Exec/AMR-zoom/Prob.H Exec/DrivenTurbulence/Prob.H Exec/GravityTests/MacLaurin/Make.package Exec/GravityTests/zeldovich_dm/build/Prob.H Exec/Henson/amr-info/Prob.H Exec/Henson/extract-particles/Prob.H Exec/Henson/sample-analysis/Prob.H Exec/HydroTests/Make.package Exec/HydroTests/Prob.H Exec/LyA/Prob.H Exec/LyA_AGN/Prob.H Exec/LyA_Neutrinos/Prob.H Exec/Make.Nyx Exec/Make.package Exec/MiniSB/Prob.H Exec/ParticleMeshTest/Prob.H Exec/ParticleOnlyTest/Prob.H Exec/Prob_param.H Exec/SantaBarbara/Make.package Exec/SantaBarbara/Nyx_error.cpp Exec/SantaBarbara/Prob.H Exec/Scaling/Prob.H Source/Driver/Nyx.H Source/EOS/eos_hc.H Source/Initialization/Nyx_initdata.cpp Source/Particle/NyxParticles.cpp commit 878495a37a2a0c0a6b602f23bea7d4810b896e3d Author: Ann Almgren Date: Fri Jan 1 08:51:25 2021 -0800 Remove enforce_minimum_energy_cons since it didnt' appear to work Source/Driver/Nyx.H Source/TimeStep/Nyx_enforce_minimum_density.cpp commit 390292963462d61a24746a015d31ad74f0b6ee48 Author: Ann Almgren Date: Thu Dec 31 14:26:57 2020 -0800 fix typo Source/Hydro/trace_ppm.cpp commit 2a19e9f08fdafe7b02fe49da74ff4dd597db5fb4 Author: Ann Almgren Date: Thu Dec 31 14:00:21 2020 -0800 Just some cleanup of trace_ppm -- shouldn't change results Source/Hydro/trace_ppm.cpp commit 7a9b657122fa6780052fdb6d44de28a34397fe15 Author: Ann Almgren Date: Sun Dec 27 16:02:38 2020 -0800 This version of the PPM tracing has the same fix for the pressure/energy source terms as we had previously added for the gravity source terms. Currently these fixes are only applied when the rho traced to faces < 1/2 rho_ref, but we believe it should always be done. This should be tested as soon as possible. Source/Hydro/trace_ppm.cpp commit 81b6cfd39b8829c962dca2e334edc60768ef743e Author: Ann Almgren Date: Sat Dec 26 08:52:33 2020 -0800 Add option to not do reduction in compute_rho_temp with OpenMP (for regression testing) Source/Driver/Nyx.cpp commit 25538c23ce58d7765b96ce0ca9cfa0ed1fe2e226 Author: Ann Almgren Date: Mon Dec 21 21:20:53 2020 -0800 one last fix Exec/LyA_Neutrinos/Prob.H commit 5004b72e2bec37ed7a4999b449694b7c33e353b5 Author: Ann Almgren Date: Mon Dec 21 20:34:17 2020 -0800 only include NumSpec ifndef CONST_SPECIES Source/Hydro/Godunov.H Source/Hydro/Godunov.cpp Source/Hydro/Hydro.cpp Source/Hydro/PLM.H Source/Hydro/trace_ppm.cpp Source/Initialization/Nyx_initdata.cpp commit f32ff2e31f68a896dcaca6d86003f03c1a7d3e75 Author: Ann Almgren Date: Mon Dec 21 19:37:30 2020 -0800 CONST_SPEC --> CONST_SPECIES Exec/MiniSB/Prob.H commit 89417c066e00fdb60c85c3a0d48ef479a5328608 Author: Ann Almgren Date: Mon Dec 21 18:29:45 2020 -0800 Get rid of tabs Source/Gravity/Gravity.cpp Source/Particle/DarkMatterParticleContainer.cpp Source/TimeStep/Nyx_enforce_minimum_density.cpp commit 506b9b4605ebafed11840d5b0f0d4327e798f302 Author: Ann Almgren Date: Mon Dec 21 18:27:35 2020 -0800 Update Nyx_sources.cpp in DrivenTurbulence Exec/DrivenTurbulence/Nyx_sources.cpp commit 381a057c49eebb772e1c7a2d7afe24782b6eaa4b Author: Ann Almgren Date: Mon Dec 21 18:00:58 2020 -0800 More transition since we only define FirstSpec_comp when CONST_SPECIES not defined Exec/HydroTests/Prob.H Source/Hydro/Godunov.H Source/Hydro/Godunov.cpp Source/Hydro/Hydro.H Source/Hydro/IndexDefines.H Source/Hydro/PLM.H Source/Hydro/Utilities.H Source/Hydro/trace_ppm.cpp Source/Initialization/Nyx_initdata.cpp Source/TimeStep/Nyx_enforce_minimum_density.H Source/TimeStep/Nyx_enforce_minimum_density.cpp commit 1f00527d5d37003909cb84078fd85a6703530da7 Author: Ann Almgren Date: Mon Dec 21 17:04:47 2020 -0800 oops -- missed some in last commit Exec/HydroTests/Prob.H commit 1b8108b36cd4f62c74755c424c189b3a84463e9a Author: Ann Almgren Date: Mon Dec 21 16:32:23 2020 -0800 Consolidate so {URHO,Density} --> Density_comp, and analogously for the other indices Exec/AMR-density/Prob.H Exec/AMR-zoom/Prob.H Exec/DrivenTurbulence/Nyx_sources.cpp Exec/DrivenTurbulence/Prob.H Exec/GravityTests/zeldovich_dm/build/Prob.H Exec/Henson/amr-info/Prob.H Exec/Henson/extract-particles/Prob.H Exec/Henson/sample-analysis/Prob.H Exec/HydroTests/Prob.H Exec/LyA/Prob.H Exec/LyA_AGN/Prob.H Exec/LyA_Neutrinos/Prob.H Exec/MiniSB/Prob.H Exec/ParticleMeshTest/Prob.H Exec/ParticleOnlyTest/Prob.H Exec/Scaling/Prob.H Source/AGN/AGN_halos.cpp Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/ParticleDerive.cpp Source/Driver/Nyx.cpp Source/Driver/sum_integrated_quantities.cpp Source/EOS/reset_internal_e.H Source/Forcing/Forcing.cpp Source/Gravity/Gravity.H Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/Godunov.H Source/Hydro/Godunov.cpp Source/Hydro/Hydro.H Source/Hydro/IndexDefines.H Source/Hydro/PLM.H Source/Hydro/Utilities.H Source/Hydro/Utilities.cpp Source/Hydro/sdc_hydro.cpp Source/Hydro/trace_ppm.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/read_plotfile.cpp Source/Particle/NyxParticles.cpp Source/TimeStep/Nyx_correct_gsrc.cpp Source/TimeStep/Nyx_enforce_minimum_density.H Source/TimeStep/Nyx_enforce_minimum_density.cpp Source/TimeStep/Nyx_sources.cpp Source/TimeStep/Nyx_time_center_sources.cpp Source/TimeStep/Nyx_update_state_with_sources.cpp commit 1fa7e58f5c2fdd27f295edf941930822c5fbcce4 Author: Ann Almgren Date: Sun Dec 20 15:53:55 2020 -0800 Remove sections on tracing and the SGS Model since that is no longer maintained. Docs/sphinx_documentation/source/NyxEquations.rst commit 0c1b6f21649d3fe7d5c08f2e6061af916f80e394 Author: Ann Almgren Date: Sun Dec 20 15:48:27 2020 -0800 fix the table in the forcing section Docs/sphinx_documentation/source/NyxForcing.rst commit e16816b85a04d277bdbf280c477ca510a5f4c8b8 Author: Ann Almgren Date: Sun Dec 20 15:06:00 2020 -0800 fix typos in previous commit Source/Driver/Nyx.H Source/HeatCool/integrate_state_vec_3d.cpp commit f4b67d13f32da4962bb28b50bcbd27614656ed57 Author: Ann Almgren Date: Sun Dec 20 14:53:44 2020 -0800 Add run-time option sundials_use_tiling that defaults to true but allows us to turn off tiling at runtime for sundials loops Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp commit 27a61bf66190365215892877af5823bd62cc4afc Author: Ann Almgren Date: Sun Dec 20 10:07:16 2020 -0800 fix typo: "paricles" --> "particles" Docs/sphinx_documentation/source/Particles.rst commit 377eeeb1edbe15337cec04d7c30a4be08348fc39 Author: Ann Almgren Date: Sun Dec 20 09:37:38 2020 -0800 Update particle section of docs to reflect we only do move-kick-drift algorithm Docs/sphinx_documentation/source/Particles.rst commit 3d44e58737c17031a9d35fc5f2a3d55f979ea5a7 Author: Ann Almgren Date: Sun Dec 20 08:39:25 2020 -0800 Fix formatting to make it easier to read Source/HeatCool/integrate_state_with_source_3d.cpp commit e1e4ccfaca49811f8af60a5a89478957a3c614eb Author: Ann Almgren Date: Sun Dec 20 08:35:23 2020 -0800 remove particle_move_type from all inputs files Exec/AMR-density/inputs Exec/AMR-density/inputs.cuda Exec/AMR-density/inputs.rt Exec/AMR-density/inputs_nohydro.rt Exec/AMR-zoom/inputs Exec/GravityTests/zeldovich_dm/run/inputs Exec/GravityTests/zeldovich_dm/run/inputs_hydro Exec/GravityTests/zeldovich_dm/run/inputs_wmap7 Exec/GravityTests/zeldovich_dm/run_hydro/inputs_hydro Exec/LyA/inputs Exec/LyA/inputs.cuda Exec/LyA/inputs.rt Exec/LyA/inputs.rt.garuda Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA/inputs_nohydro.rt Exec/LyA_AGN/inputs Exec/LyA_AGN/inputs.rt Exec/LyA_Neutrinos/inputs Exec/LyA_Neutrinos/inputs.no_hydro_64 Exec/LyA_Neutrinos/inputs.rt Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Exec/MiniSB/inputs.analysis Exec/ParticleMeshTest/inputs.2line Exec/ParticleMeshTest/inputs.2line.restarttest Exec/ParticleMeshTest/inputs.mass.nosub Exec/ParticleMeshTest/inputs.mass.sub Exec/ParticleOnlyTest/inputs.2line Exec/ParticleOnlyTest/inputs.2line.restarttest Exec/ParticleOnlyTest/inputs.mass.nosub Exec/ParticleOnlyTest/inputs.mass.sub Exec/SantaBarbara/inputs Exec/Scaling/inputs Exec/Scaling/inputs.256.noreduceverb Exec/Scaling/inputs_short commit 5e77d75821fd3da42ad5f0a242236c43e2ef24a9 Author: Ann Almgren Date: Sun Dec 20 08:27:44 2020 -0800 Remove the option for particles to move randomly -- they now only move "gravitationally" Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Particle/NyxParticles.cpp Source/TimeStep/Nyx_advance.cpp Source/TimeStep/Nyx_advance_particles.cpp commit b818008e73f66f07f50962460fbfaf92c294f7fe Author: Ann Almgren Date: Sat Dec 19 11:39:37 2020 -0800 Remove extra declarations of int ncomp Source/Gravity/Gravity.cpp commit 2a05ea0b1fd0c9db6960b04ae05bfb35d578ceee Merge: d0dd1837 70673dca Author: jmsexton03 Date: Tue Dec 15 15:18:33 2020 -0500 Merge pull request #66 from zingale/github_attributes add a .gitattrbutes so github does a better job with language detection commit 70673dca4f1b86653e1eed768c525cb8e62598b3 Author: Michael Zingale Date: Tue Dec 15 13:43:40 2020 -0500 add a .gitattrbutes so github does a better job with language detection .gitattributes commit d0dd183748e85615e32c327004d540d6ad3069c7 Author: Jean M. Sexton Date: Tue Dec 15 07:48:27 2020 -0800 Fix location of IR_new in Initialization, add if guard for do_hydro Source/Initialization/Nyx_initdata.cpp commit 7d61540b2a836e2d3696bf27c629747254a0e949 Author: Jean M. Sexton Date: Tue Dec 15 07:14:23 2020 -0800 Fix typo in ordering of arguments in strang Source/Hydro/strang_hydro.cpp commit afb54ba63d0a54b42dc032d38f473708fbc23358 Author: Jean M. Sexton Date: Mon Dec 14 20:46:04 2020 -0800 Move USE_RPATH to before include of Make.defs Exec/Make.Nyx commit 5dde6c0973c53631b07cdb8b7acd7473ccebb305 Author: Jean M. Sexton Date: Mon Dec 14 23:40:48 2020 -0500 Revert LIBRARIES -> libraries change, add back rpath Exec/Make.Nyx commit 67e0bcfd17c57dd7807f71359281e8f84b69176e Author: Jean M. Sexton Date: Mon Dec 14 17:34:02 2020 -0500 Use energy enforce for small_rhoe Source/TimeStep/Nyx_enforce_minimum_density.cpp commit cee745c8101e6c383dcbc3abcff27fa66f7bee5b Author: Jean M. Sexton Date: Mon Dec 14 17:31:59 2020 -0500 Make ascent compile with sundials 5.6.0 Exec/LyA/GNUmakefile.cuda-ascent Exec/Make.Nyx commit c656bfd492559c3a71c421d49b4c1f042ecffd8a Author: Jean M. Sexton Date: Mon Dec 14 13:33:40 2020 -0800 Fix OMP bounds for strang Source/HeatCool/integrate_state_vec_3d.cpp commit 50c55ba6de21d691feb711d185edbc3e3f3619e5 Author: Ann Almgren Date: Mon Dec 14 12:55:31 2020 -0800 Now actually call enforce_min_energy_cons from enforce_min_density_cons Source/TimeStep/Nyx_enforce_minimum_density.cpp commit c886070a7f96bc8001d14ae6d79dc2c59456ce12 Author: Ann Almgren Date: Mon Dec 14 12:50:01 2020 -0800 Add code to enforce that (rho e) > small_rhoe in addition to enforcing small density Source/Driver/Nyx.H Source/TimeStep/Nyx_enforce_minimum_density.H Source/TimeStep/Nyx_enforce_minimum_density.cpp commit cbaeabe014226cabff656ba2a8b7e2ef5296c35f Author: Jean M. Sexton Date: Sun Dec 13 21:25:16 2020 -0500 Fixes for compiling and testing OMP+CUDA Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp Source/Initialization/Nyx_initdata.cpp Source/Particle/NyxParticleContainer.H commit 079952f0b795828c17e21a5a2d800c6a71689556 Author: Jean M. Sexton Date: Sun Dec 13 18:41:05 2020 -0500 Respect reset_internal_e hard reset Source/EOS/reset_internal_e.H commit 67f3eadd9c224f1f65068381f27dd98e7007b0c1 Author: Jean M. Sexton Date: Sun Dec 13 17:55:36 2020 -0500 Fold enforce_min_density updates to rho_e into reset_e_src for sdc fix Source/Driver/Nyx.H Source/EOS/reset_internal_e.H Source/HeatCool/sdc_reactions.cpp Source/Hydro/sdc_hydro.cpp Source/Hydro/strang_hydro.cpp Source/TimeStep/Nyx_enforce_minimum_density.cpp Source/TimeStep/Nyx_update_state_with_sources.cpp commit 92ac7448ddc85eb279a76834007c3674b8e49b3c Author: Jean M. Sexton Date: Sun Dec 13 17:10:58 2020 -0500 Revert "Remove trace_ppm test" This reverts commit dc4f9dc8dac1c76c74a23c12472a4dab9d35fbe2. Revert "Add fix for I_R in enforce_min_density" This reverts commit 14131cb27812c56e1859750405003adf4dc2de88. Source/Hydro/trace_ppm.cpp Source/TimeStep/Nyx_enforce_minimum_density.cpp commit 17ec500ae5c386455d0ac5fa72722a4015e60e2d Merge: dc4f9dc8 ba165089 Author: Jean M. Sexton Date: Sun Dec 13 16:59:55 2020 -0500 Merge branch 'development' of github.com:amrex-astro/Nyx into development commit ba165089dbf6c23fa2eeab3f0ea9628a2e9f34f6 Merge: 15a26236 0e1b58cd Author: Ann Almgren Date: Fri Dec 11 16:58:14 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 15a2623641f004eb1bb464f1f2dfabbfbb720b39 Author: Ann Almgren Date: Fri Dec 11 16:57:33 2020 -0800 Fix ngrow that is used for the gravity solve in post_regrid Source/Driver/Nyx.cpp commit dc4f9dc8dac1c76c74a23c12472a4dab9d35fbe2 Author: Jean M. Sexton Date: Wed Dec 9 19:28:11 2020 -0500 Remove trace_ppm test Source/Hydro/trace_ppm.cpp commit 14131cb27812c56e1859750405003adf4dc2de88 Author: Jean M. Sexton Date: Wed Dec 9 16:31:04 2020 -0500 Add fix for I_R in enforce_min_density Source/TimeStep/Nyx_enforce_minimum_density.cpp commit 0e1b58cd46fde8da9250144d12114dfc60cd9873 Author: Jean M. Sexton Date: Tue Dec 8 18:09:13 2020 -0800 Add FillBoundary for sanity Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NyxParticleContainer.H commit d5ad14448b9baec3a12136dca90ed64619cd58c1 Author: Jean M. Sexton Date: Tue Dec 8 18:00:50 2020 -0800 Add conditionals to check for ParallelCopy with load balancing Source/DerivedQuantities/ParticleDerive.cpp Source/Driver/Nyx.cpp Source/Gravity/Gravity.cpp Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NyxParticleContainer.H commit 48f43a51da30fc52ea93ff84b33fcde3c1c3e14c Author: Jean M. Sexton Date: Mon Dec 7 13:06:30 2020 -0800 Use new Getting Started docs structure Docs/sphinx_documentation/source/NyxGettingStarted.rst Docs/sphinx_documentation/source/NyxGettingStarted_new.rst Docs/sphinx_documentation/source/getting_started/BuildingCMake.rst Docs/sphinx_documentation/source/getting_started/RunningTheCode.rst Docs/sphinx_documentation/source/index.rst commit 7f1a5d04195afd947a5cfc5e036701a052814d95 Merge: 03a68959 d70cb444 Author: Jean M. Sexton Date: Mon Dec 7 11:08:54 2020 -0800 Merge branch 'mr/cmake-doc' into development commit 03a68959886238a43f09768fde752ae0b66e7f7f Author: zarija Date: Mon Dec 7 01:32:56 2020 -0800 git mv paper into Docs Docs/paper/paper.bib Docs/paper/paper.md commit 7021b54d5f437b3263316f4b4be0820a63e4083b Author: zarija Date: Mon Dec 7 01:12:29 2020 -0800 Adding .py particle converter from a private repo... Util/Converters/plotfile2HDF5_particles_amr.py commit d6c70744eaf5f73739dc8ca060dbe8110c5718ef Author: zarija Date: Mon Dec 7 01:06:42 2020 -0800 Delete depreciated converters Util/convert_all_fields/AmrDerive.cpp Util/convert_all_fields/GNUmakefile Util/convert_all_fields/Make.package Util/convert_lyaf/AmrDerive.cpp Util/convert_lyaf/GNUmakefile Util/convert_lyaf/Make.package Util/convert_nbody/AmrDerive.cpp Util/convert_nbody/GNUmakefile Util/convert_nbody/Make.package commit be5e3ed6718b0f47476f785e1ec029fdc138c18f Author: zarija Date: Mon Dec 7 01:04:54 2020 -0800 Keep AMR converter too Util/Converters/convert_amr/AmrElements.cpp Util/Converters/convert_amr/GNUmakefile Util/Converters/convert_amr/Make.package Util/Converters/convert_amr/README Util/Converters/convert_amr/inputs commit d348029fd4ce9ecb74954c1edfe228b0583fd244 Author: zarija Date: Mon Dec 7 01:02:04 2020 -0800 Clean hdf5 grids converter Util/Converters/Plotfile2HDF5_grids/AmrDerive.cpp Util/Converters/Plotfile2HDF5_grids/GNUmakefile Util/Converters/Plotfile2HDF5_grids/Make.package commit 3a9b72e45dfc29dbf13ba4e58b73d5ecffb34714 Author: Ann Almgren Date: Sat Dec 5 13:18:25 2020 -0800 Update to refer to CONTRIBUTING.md README.md commit 4841acb2515a1f200857ec5ee1e8d4b5f08b35fa Author: Ann Almgren Date: Sat Dec 5 12:35:35 2020 -0800 Add CONTRIBUTING.md file that tells how to use forks and PRs CONTRIBUTING.md commit 2f67463ed9601830c26402c6ba3b03171470bf78 Author: Jean M. Sexton Date: Fri Dec 4 10:51:12 2020 -0800 Remove doxygen-related documentation files Docs/sphinx_documentation/source/class/classAGNParticleContainer.rst Docs/sphinx_documentation/source/class/classDarkMatterParticleContainer.rst Docs/sphinx_documentation/source/class/classGravity.rst Docs/sphinx_documentation/source/class/classMemInfo.rst Docs/sphinx_documentation/source/class/classNyx.rst Docs/sphinx_documentation/source/class/classNyxBld.rst Docs/sphinx_documentation/source/class/classNyxParticleContainer.rst Docs/sphinx_documentation/source/class/classNyxParticleContainerBase.rst Docs/sphinx_documentation/source/class/classStochasticForcing.rst Docs/sphinx_documentation/source/classlist.rst Docs/sphinx_documentation/source/conf.py Docs/sphinx_documentation/source/file/AGNParticleContainer_8H.rst Docs/sphinx_documentation/source/file/AGNParticleContainer_8cpp.rst Docs/sphinx_documentation/source/file/AGN__sources_8cpp.rst Docs/sphinx_documentation/source/file/DarkMatterParticleContainer_8H.rst Docs/sphinx_documentation/source/file/DarkMatterParticleContainer_8cpp.rst Docs/sphinx_documentation/source/file/Derive__F_8H.rst Docs/sphinx_documentation/source/file/Forcing_8H.rst Docs/sphinx_documentation/source/file/Forcing_8cpp.rst Docs/sphinx_documentation/source/file/Forcing__init_8cpp.rst Docs/sphinx_documentation/source/file/Gravity_8H.rst Docs/sphinx_documentation/source/file/Gravity_8cpp.rst Docs/sphinx_documentation/source/file/Gravity__F_8H.rst Docs/sphinx_documentation/source/file/MemInfo_8H.rst Docs/sphinx_documentation/source/file/MemInfo_8cpp.rst Docs/sphinx_documentation/source/file/MersenneTwister_8cpp.rst Docs/sphinx_documentation/source/file/NeutrinoParticleContainer_8H.rst Docs/sphinx_documentation/source/file/NeutrinoParticleContainer_8cpp.rst Docs/sphinx_documentation/source/file/NyxBld_8cpp.rst Docs/sphinx_documentation/source/file/NyxParticleContainer_8H.rst Docs/sphinx_documentation/source/file/NyxParticles_8cpp.rst Docs/sphinx_documentation/source/file/Nyx_8H.rst Docs/sphinx_documentation/source/file/Nyx_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__F_8H.rst Docs/sphinx_documentation/source/file/Nyx__advance_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__error_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__error__F_8H.rst Docs/sphinx_documentation/source/file/Nyx__halos_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__initcosmo_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__initdata_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__output_8H.rst Docs/sphinx_documentation/source/file/Nyx__output_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__setup_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__sources_8cpp.rst Docs/sphinx_documentation/source/file/ParticleDerive_8cpp.rst Docs/sphinx_documentation/source/file/advance__particles_8cpp.rst Docs/sphinx_documentation/source/file/agn__F_8H.rst Docs/sphinx_documentation/source/file/comoving_8cpp.rst Docs/sphinx_documentation/source/file/compute__hydro__sources_8cpp.rst Docs/sphinx_documentation/source/file/dm__F_8H.rst Docs/sphinx_documentation/source/file/main_8cpp.rst Docs/sphinx_documentation/source/file/nyx__main_8cpp.rst Docs/sphinx_documentation/source/file/read__plotfile_8cpp.rst Docs/sphinx_documentation/source/file/sdc__hydro_8cpp.rst Docs/sphinx_documentation/source/file/sdc__reactions_8cpp.rst Docs/sphinx_documentation/source/file/strang__hydro_8cpp.rst Docs/sphinx_documentation/source/file/strang__reactions_8cpp.rst Docs/sphinx_documentation/source/file/sum__integrated__quantities_8cpp.rst Docs/sphinx_documentation/source/file/sum__utils_8cpp.rst Docs/sphinx_documentation/source/file/testMemInfo_8cpp.rst Docs/sphinx_documentation/source/file/update__state__with__sources_8cpp.rst Docs/sphinx_documentation/source/file/write__info_8cpp.rst Docs/sphinx_documentation/source/filelist.rst Docs/sphinx_documentation/source/index.rst Docs/sphinx_documentation/source/namespace/namespace_0D20.rst Docs/sphinx_documentation/source/namespace/namespace_0D35.rst Docs/sphinx_documentation/source/namespace/namespace_0D39.rst Docs/sphinx_documentation/source/namespace/namespace_0D7.rst Docs/sphinx_documentation/source/namespace/namespaceamrex.rst Docs/sphinx_documentation/source/namespacelist.rst Docs/sphinx_documentation/source/runtime_parameters.rst Docs/sphinx_documentation/source/zreferences.rst commit e1bd5811c126d54288bbce971de8725b0bc9090a Author: Jean M. Sexton Date: Fri Dec 4 11:14:12 2020 -0800 Fix merge resolution Source/Driver/Nyx.cpp commit dd9b03d379eac68f4776e30e29e58acf20680e01 Author: mic84 Date: Fri Dec 4 10:51:53 2020 -0800 CMake: use AMReX default flags if none is provided (#65) * CMake: some clean-up * CMake: use AMReX default flags if none is provided * CMake: bump AMReX version Source/CMakeLists.txt Source/Driver/Nyx.cpp Source/Driver/nyx_main.cpp Source/Particle/NyxParticleContainer.H cmake/NyxSetupAMReX.cmake cmake/NyxSetupExecutable.cmake commit f1f1d87f76284cc93acfac6806f71f77c590bb07 Merge: c8d884eb a2baf771 Author: Ann Almgren Date: Fri Dec 4 08:25:59 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit c8d884eb31c6799170d41bab7956a814d5e5c71e Author: Ann Almgren Date: Fri Dec 4 08:25:44 2020 -0800 Fix to yesterday's oops Source/Driver/comoving.cpp commit a2baf77169a6a850627e9979fae2c86a771cd1fd Author: Jean M. Sexton Date: Thu Dec 3 18:41:23 2020 -0800 Change AMR-density to use 1.1 instead of 8 for tagging Exec/AMR-density/inputs.rt commit 90a1ce92d64c3f1bfbcf7e2bdda21fbf3269ced0 Author: Ann Almgren Date: Thu Dec 3 16:58:28 2020 -0800 Rename "xacc" so it doesn't get confused with the "xacc" in the EOS stuff. We now call these "small_dt_fac" and "small_a_fac" Source/Driver/comoving.cpp commit b394dadd09e4012a5b9c258b0a96f9a7503895a3 Author: Ann Almgren Date: Thu Dec 3 16:49:59 2020 -0800 Replace "Real average_gas_density" declaration by "int average_gas_density" -- this may change runlog. Source/Driver/Nyx.cpp commit 1a2f3bca1d908c87f0f356c7edc9b15c0de9aaa2 Author: Zarija Date: Thu Dec 3 14:33:44 2020 -0800 Remove (depreciated) HPGMG Util/hpgmg/LICENSE Util/hpgmg/README Util/hpgmg/finite-volume/README Util/hpgmg/finite-volume/local.mk Util/hpgmg/finite-volume/source/Make.package Util/hpgmg/finite-volume/source/Makefile Util/hpgmg/finite-volume/source/README Util/hpgmg/finite-volume/source/TODO Util/hpgmg/finite-volume/source/call_hpgmg_setup.c Util/hpgmg/finite-volume/source/compile Util/hpgmg/finite-volume/source/defines.h Util/hpgmg/finite-volume/source/hpgmg-fv.c Util/hpgmg/finite-volume/source/hpgmg_setup.c Util/hpgmg/finite-volume/source/level.c Util/hpgmg/finite-volume/source/level.h Util/hpgmg/finite-volume/source/local.mk Util/hpgmg/finite-volume/source/mg.h Util/hpgmg/finite-volume/source/mg_hpgmg.c Util/hpgmg/finite-volume/source/operators.27pt.c Util/hpgmg/finite-volume/source/operators.7pt.c Util/hpgmg/finite-volume/source/operators.fv2.c Util/hpgmg/finite-volume/source/operators.fv4.c Util/hpgmg/finite-volume/source/operators.h Util/hpgmg/finite-volume/source/operators.old.c Util/hpgmg/finite-volume/source/operators.old/aggregate.mpi/chebyshev.c Util/hpgmg/finite-volume/source/operators.old/aggregate.mpi/gsrb.c Util/hpgmg/finite-volume/source/operators.old/aggregate.mpi/jacobi.c Util/hpgmg/finite-volume/source/operators.old/apply_op.c Util/hpgmg/finite-volume/source/operators.old/chebyshev.c Util/hpgmg/finite-volume/source/operators.old/gsrb.c Util/hpgmg/finite-volume/source/operators.old/iterators.c Util/hpgmg/finite-volume/source/operators.old/jacobi.c Util/hpgmg/finite-volume/source/operators.old/misc.c Util/hpgmg/finite-volume/source/operators.old/residual.c Util/hpgmg/finite-volume/source/operators.old/symgs.c Util/hpgmg/finite-volume/source/operators/apply_op.c Util/hpgmg/finite-volume/source/operators/blockCopy.c Util/hpgmg/finite-volume/source/operators/boundary_fd.c Util/hpgmg/finite-volume/source/operators/boundary_fv.c Util/hpgmg/finite-volume/source/operators/chebyshev.c Util/hpgmg/finite-volume/source/operators/exchange_boundary.c Util/hpgmg/finite-volume/source/operators/gsrb.c Util/hpgmg/finite-volume/source/operators/interpolation_p0.c Util/hpgmg/finite-volume/source/operators/interpolation_p1.c Util/hpgmg/finite-volume/source/operators/interpolation_p2.c Util/hpgmg/finite-volume/source/operators/interpolation_v2.c Util/hpgmg/finite-volume/source/operators/interpolation_v4.c Util/hpgmg/finite-volume/source/operators/jacobi.c Util/hpgmg/finite-volume/source/operators/misc.c Util/hpgmg/finite-volume/source/operators/problem.fv.c Util/hpgmg/finite-volume/source/operators/problem.p4.c Util/hpgmg/finite-volume/source/operators/problem.p6.c Util/hpgmg/finite-volume/source/operators/problem.sine.c Util/hpgmg/finite-volume/source/operators/rebuild.c Util/hpgmg/finite-volume/source/operators/residual.c Util/hpgmg/finite-volume/source/operators/restriction.c Util/hpgmg/finite-volume/source/operators/symgs.c Util/hpgmg/finite-volume/source/solvers.c Util/hpgmg/finite-volume/source/solvers.h Util/hpgmg/finite-volume/source/solvers/bicgstab.c Util/hpgmg/finite-volume/source/solvers/cabicgstab.c Util/hpgmg/finite-volume/source/solvers/cacg.c Util/hpgmg/finite-volume/source/solvers/cg.c Util/hpgmg/finite-volume/source/solvers/matmul.c Util/hpgmg/finite-volume/source/timers.c Util/hpgmg/finite-volume/source/timers.h Util/hpgmg/finite-volume/source/timers/mpi.c Util/hpgmg/finite-volume/source/timers/omp.c Util/hpgmg/finite-volume/source/timers/x86.c commit 7f13c51b7957258ed501d7ddb06d56743fba4ef1 Author: Ann Almgren Date: Thu Dec 3 14:27:34 2020 -0800 max_temp_dt should be defined as int not real; other than that just fixing formatting Source/Driver/Nyx.cpp commit 2c8e9a4e51bd9a8923bded13ba3ddadb8d95db38 Author: Ann Almgren Date: Thu Dec 3 14:13:35 2020 -0800 replace tabs by spaces Source/Gravity/Gravity.cpp Source/HeatCool/f_rhs_struct.H Source/IO/Nyx_output.cpp Source/Initialization/Nyx_initdata.cpp Source/TimeStep/Nyx_advance.cpp commit a7fa3480adae2d11d701bbb4596c7dd2fd78ade2 Author: Zarija Date: Thu Dec 3 14:01:45 2020 -0800 Fix typo Util/Diagnostics/README.md commit d685bfbd53c5a529415aaac3e5ace0ed6b0336fe Author: Zarija Date: Thu Dec 3 13:57:57 2020 -0800 Diagnostics cleanup Diagnostics/README Util/Diagnostics/AmrDerive.cpp Util/Diagnostics/GNUmakefile Util/Diagnostics/Make.package Util/Diagnostics/README.md Util/Diagnostics/inputs commit d2e6c21a8d6b0caa7d954cf1b4e1035901ddec4b Author: Ann Almgren Date: Thu Dec 3 13:51:50 2020 -0800 Move S_old back to where it was Source/Hydro/strang_hydro.cpp commit 06e05f1bb34fda9f3d25f7308dd70c53cc316d33 Author: Ann Almgren Date: Thu Dec 3 13:01:11 2020 -0800 Code cleanup to quiet at least some compiler warnings Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Driver/comoving.cpp Source/Driver/sum_integrated_quantities.cpp Source/Hydro/Hydro.cpp Source/Hydro/strang_hydro.cpp Source/Initialization/Nyx_initdata.cpp Source/Particle/NyxParticles.cpp Source/TimeStep/Nyx_correct_gsrc.cpp Source/TimeStep/Nyx_enforce_minimum_density.cpp Source/TimeStep/Nyx_sources.cpp Source/TimeStep/Nyx_time_center_sources.cpp Source/TimeStep/Nyx_update_state_with_sources.cpp commit 57818b6680544c2cf16385f167e445ea91ac10ff Author: Jean M. Sexton Date: Thu Dec 3 15:50:00 2020 -0500 Remove debugging statement Source/Particle/NyxParticles.cpp commit 9ccbb1646c20ecc1074e11e1dfa21ee1e0fc7937 Merge: 7e8bf889 a3647ea8 Author: Ann Almgren Date: Thu Dec 3 12:21:40 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 7e8bf889e66a2cd688fac6aadac2a42751328493 Author: Ann Almgren Date: Thu Dec 3 12:21:22 2020 -0800 amrex::Real FirstSpec --> int FirstSpec Exec/AMR-density/Prob.H Exec/AMR-zoom/Prob.H Exec/DrivenTurbulence/Prob.H Exec/GravityTests/zeldovich_dm/build/Prob.H Exec/Henson/amr-info/Prob.H Exec/Henson/extract-particles/Prob.H Exec/Henson/sample-analysis/Prob.H Exec/HydroTests/Prob.H Exec/LyA/Prob.H Exec/LyA_AGN/Prob.H Exec/LyA_Neutrinos/Prob.H Exec/MiniSB/Prob.H Exec/Scaling/Prob.H commit a3647ea8407812cf50fd72e1d40813e1113bfc83 Author: Jean M. Sexton Date: Thu Dec 3 12:09:48 2020 -0800 Update Scaling GNUmakefile, all inputs to default to correct heat_cool_type Exec/AMR-density/inputs.cuda Exec/LyA/inputs.cuda Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA_AGN/inputs.rt Exec/LyA_Neutrinos/inputs.no_hydro_64 Exec/Scaling/GNUmakefile Exec/Scaling/inputs Exec/Scaling/inputs_short commit 7e27ba078ea648a0cbafe0dc43abc75f16602c04 Author: Ann Almgren Date: Thu Dec 3 11:56:40 2020 -0800 Remove volume multifab -- replae by vol = dx * dy * dz Source/Hydro/Hydro.H Source/Hydro/Hydro.cpp commit 5158ec1de459f8dcf16734351f969452f776779a Author: Ann Almgren Date: Thu Dec 3 11:37:14 2020 -0800 Remove area multifab -- replace by area[AMREX_SPACEDIM] Source/Hydro/Hydro.H Source/Hydro/Hydro.cpp commit 5e05b5a5e751958abe1ce8b1e672509610aeb6ba Author: Jean M. Sexton Date: Thu Dec 3 09:55:54 2020 -0800 Remove incorrect OpenMP pragma Source/Gravity/Gravity.cpp commit f049c971f2a8f77b6b01b2c31368157b545b6e73 Author: Jean M. Sexton Date: Thu Dec 3 09:38:08 2020 -0800 Fix incorrect filename use Source/Particle/NyxParticles.cpp commit 609f7c272b7a9cfc51f48f7614664b02bfe53512 Author: Zarija Date: Thu Dec 3 00:49:18 2020 -0800 Banner added README.md Util/banner.jpeg commit 366b741ef82cdca89ed00e7452c65607dbe431bd Author: Jean M. Sexton Date: Wed Dec 2 22:55:57 2020 -0800 Add enforce minimum density_floor in init_santa_barbara Source/Particle/NyxParticles.cpp commit ae6e440ff5fa0eb57303734950e39823c5d1f98a Author: Jean M. Sexton Date: Wed Dec 2 22:54:28 2020 -0800 Add OpenMP pragmas to MFIter loops, change tiling option Source/Driver/Nyx.cpp Source/Driver/sum_utils.cpp Source/Gravity/Gravity.cpp Source/Initialization/Nyx_initdata.cpp Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NeutrinoParticleContainer.cpp Source/TimeStep/Nyx_correct_gsrc.cpp Source/TimeStep/Nyx_enforce_minimum_density.cpp Source/TimeStep/Nyx_sources.cpp Source/TimeStep/Nyx_time_center_sources.cpp commit d70cb4442bcd4289adab535cbc2f0e71a00d5e5a Author: Michele Rosso Date: Wed Dec 2 20:21:23 2020 -0800 Doc: add CMake build infos Docs/sphinx_documentation/source/NyxGettingStarted.rst Docs/sphinx_documentation/source/NyxGettingStarted_new.rst Docs/sphinx_documentation/source/getting_started/BuildingCMake.rst Docs/sphinx_documentation/source/getting_started/BuildingGMake.rst Docs/sphinx_documentation/source/getting_started/RunningTheCode.rst Docs/sphinx_documentation/source/getting_started/Structure.rst Docs/sphinx_documentation/source/index.rst commit 73e3a056f18fdea0990b026a5ca20dcf82ee9f47 Author: Jean M. Sexton Date: Wed Dec 2 16:44:37 2020 -0800 Fix indexing bug related to uninitialized variables Exec/HydroTests/Prob.H commit c0b0a460563fd6b2a58cdc6941e1df42ee12d3cb Author: Zarija Date: Wed Dec 2 14:59:30 2020 -0800 Fix heat_cool_type in example problems Exec/LyA/inputs Exec/LyA_AGN/inputs commit e68f3efae3bd7d5254b9f62ff87e4bac63238b85 Author: Jean M. Sexton Date: Wed Dec 2 14:55:00 2020 -0800 Change int to round for Real parameters that are secretly int Exec/HydroTests/Prob.H commit 411bf6064bed2d5927db9f1ed4a1209db26287ad Author: Zarija Date: Wed Dec 2 14:51:09 2020 -0800 Make Sundials instructions compiler-independent Docs/sphinx_documentation/source/NyxSundials.rst commit c46a1718cd2853d9140238ffd3eb9ac4dfc2ad66 Author: Jean M. Sexton Date: Tue Dec 1 22:41:02 2020 -0800 Fix empty advance call particles-only Source/Driver/Nyx.cpp Source/TimeStep/Nyx_advance.cpp commit c9b070eacbee8f6d0d3052595c2f110ddc473b67 Author: mic84 Date: Tue Dec 1 21:51:16 2020 -0800 CMake for Nyx (#64) * CMake: begin CMake-fying Nyx * CMake: continue with cmake-fication process * CMake: change the logic of the whole cmake setup * CMake: upgrade to latest amrex * CMake: add more executables to the CMake * Add hidden folder for github ci * CMake: begin adding support for sundials * CMake: now we can build sundials and link against it * CMake: add more nyx exes * CMake: fix option * CMake: disable Lya_AGN cause it's broken * CMake: small improvements * fix workflows for cmake * fix cuda command * don't error on shadow * add mpi to clang depends * CMake: add support for GPU backends * add OpenMP to depends for clang * properly turn on HIP and DPC++ * fix openmp * fewer errors * remove -Werror for clang * no need to make install * CMake: update CMake to reflect changes in the dir structure * CMake: fix CUDA compilation * CMake: Nyx_PARTICLES available on if Nyx_GRAVITY is enabled * CMake: set NEUTRINO related option for Lya_Neutrinos only * CMake: bump up AMReX version * CMake: refactor the options * CI: remove options Nyx_SUNDIALS * CMake: more improvements to the options * CMake: update filenames for Heatcool dir * CMake: fix some options * CMake: Nyx_MPI is now a dependent option * CI: do no enable OMP for GPU builds for now * CMake: update CMakeLists.txt in Heatcool dir Co-authored-by: Andrew Myers .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_clang6.sh .github/workflows/dependencies/dependencies_dpcpp.sh .github/workflows/dependencies/dependencies_hip.sh .github/workflows/dependencies/dependencies_nvcc.sh .github/workflows/linux.yml CMakeLists.txt Exec/AMR-density/CMakeLists.txt Exec/AMR-zoom/CMakeLists.txt Exec/CMakeLists.txt Exec/DrivenTurbulence/CMakeLists.txt Exec/HydroTests/CMakeLists.txt Exec/LyA/CMakeLists.txt Exec/LyA_AGN/CMakeLists.txt Exec/LyA_Neutrinos/CMakeLists.txt Exec/MiniSB/CMakeLists.txt Source/AGN/CMakeLists.txt Source/CMakeLists.txt Source/DerivedQuantities/CMakeLists.txt Source/Driver/CMakeLists.txt Source/Driver/Nyx.H Source/EOS/CMakeLists.txt Source/Forcing/CMakeLists.txt Source/Gravity/CMakeLists.txt Source/HeatCool/CMakeLists.txt Source/Hydro/CMakeLists.txt Source/IO/CMakeLists.txt Source/Initialization/CMakeLists.txt Source/Initialization/Nyx_setup.cpp Source/Monitors/CMakeLists.txt Source/Particle/CMakeLists.txt Source/TimeStep/CMakeLists.txt cmake/NyxSetupAMReX.cmake cmake/NyxSetupExecutable.cmake cmake/NyxSetupSUNDIALS.cmake subprojects/amrex commit accdb9c4c6651cb370c6d39a222b4b0241c0b7be Author: Jean M. Sexton Date: Tue Dec 1 17:49:53 2020 -0800 Update HeatCool final stats and case where USE_SDC=FALSE Source/HeatCool/Make.package Source/HeatCool/integrate_state_with_source_3d.cpp commit e2b7b7a261c8d01c38cea1a4e6a550cf0d3ff38b Author: Zarija Date: Tue Dec 1 16:35:23 2020 -0800 Fix citation CITATION.md Docs/sphinx_documentation/source/NyxCitation.rst commit 0d2212aee7dd96d61e51b1daf3835fcf0fa3ab7f Author: Zarija Date: Tue Dec 1 15:10:28 2020 -0800 Citation CITATION Docs/sphinx_documentation/source/NyxCitation.rst Docs/sphinx_documentation/source/NyxPapers.rst Docs/sphinx_documentation/source/index.rst commit 056aaa190028e0e42136354f67cbdf1f095e60c5 Author: Jean M. Sexton Date: Tue Dec 1 14:11:44 2020 -0800 Typo, forgot eos fields Exec/DrivenTurbulence/inputs.regtest commit 08fb74a5de87f20fb75af8c483067925491aeb13 Author: Jean M. Sexton Date: Tue Dec 1 13:34:42 2020 -0800 Fix DrivenTurbulence inputs.regtest Exec/DrivenTurbulence/inputs.regtest commit 27d608bf59e42bc77d175dd58bbacd73b29a0942 Author: Ann Almgren Date: Tue Dec 1 11:41:24 2020 -0800 fix typo ("was ran" --> "was run") README.md commit 8d71471c1cffe88251e654f91bc6dca0da2bf299 Author: Zarija Date: Tue Dec 1 11:12:00 2020 -0800 README update README.md commit 3a234f23a4b70dcdc48eb30887876b248c9d1777 Author: Jean M. Sexton Date: Tue Dec 1 09:50:55 2020 -0800 Remove print statement, fix typo Source/Driver/Nyx.cpp Source/EOS/eos_hc.H commit e8f870aae5827bbf9e6301d3e01bf4f398e53b04 Merge: 0e0dd65d bc11e4f0 Author: Jean M. Sexton Date: Mon Nov 30 19:34:01 2020 -0800 Merge branch 'development' of github.com:amrex-astro/Nyx into development commit 0e0dd65d490f1594b6ff8dab74df5cfc046e44c7 Author: Jean M. Sexton Date: Mon Nov 30 19:33:06 2020 -0800 Clean up unused HeatCool options Source/Driver/Nyx.cpp Source/EOS/eos_hc.H Source/HeatCool/Make.package Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_vec_3d_stubs.cpp Source/TimeStep/Nyx_time_center_sources.cpp commit 98b7ca9e085b5e66847b5daec596d175be3152fa Author: Jean M. Sexton Date: Mon Nov 30 19:12:37 2020 -0800 HeatCool cleanup Source/HeatCool/Make.package Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_cell_3d.cpp Source/HeatCool/integrate_state_exact_3d.cpp Source/HeatCool/integrate_state_exact_3d_stubs.cpp Source/HeatCool/integrate_state_vec_3d_stubs.cpp commit 94886db57ffef9e047094222eea4343ee41543e3 Author: Jean M. Sexton Date: Mon Nov 30 19:04:29 2020 -0800 Update refinement doc examples Docs/sphinx_documentation/source/Refinement.rst commit bc11e4f06d6d6a26361fd691c3d05841ed3cda66 Author: Ann Almgren Date: Mon Nov 30 18:54:36 2020 -0800 Remove "ifdef GRAVITY" from source code since it's always true now Source/DerivedQuantities/ParticleDerive.cpp Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Driver/sum_integrated_quantities.cpp Source/Hydro/sdc_hydro.cpp Source/Hydro/strang_hydro.cpp Source/Hydro/strang_hydro_fuse.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Particle/NyxParticles.cpp Source/TimeStep/Nyx_advance.cpp Source/TimeStep/Nyx_advance_particles.cpp Source/TimeStep/Nyx_correct_gsrc.cpp commit 101c341405e9482cba6689b5c5b33cb27e655391 Author: Jean M. Sexton Date: Mon Nov 30 18:20:17 2020 -0800 Fix SDC Amr init Source/Driver/Nyx.cpp commit ebc920c5cf6c2eddce6318b896c262786daf2aa6 Author: Ann Almgren Date: Mon Nov 30 16:31:56 2020 -0800 Add "nyx.do_grav = 0" to all inputs files in Exec/HydroTests Exec/HydroTests/inputs-sod-x Exec/HydroTests/inputs-sod-y Exec/HydroTests/inputs-sod-z Exec/HydroTests/inputs-test2-x Exec/HydroTests/inputs-test2-y Exec/HydroTests/inputs-test2-z Exec/HydroTests/inputs-test3-x Exec/HydroTests/inputs-test3-y Exec/HydroTests/inputs-test3-z Exec/HydroTests/inputs.3d.sph.sedov Exec/HydroTests/inputs.3d.sph.testsuite.sedov Exec/HydroTests/inputs.regtest.sedov Exec/HydroTests/inputs.regtest.sod Exec/HydroTests/inputs.regtest.test2 Exec/HydroTests/inputs.regtest.test3 Exec/HydroTests/inputs.restarttest.test2 commit 64bfbe2df8fc8cc810dff5bae5221245c6c642f8 Author: Jean M. Sexton Date: Mon Nov 30 19:22:02 2020 -0500 Make USE_PARTICLES and USE_GRAV default Exec/Make.Nyx commit a59153d0632d66597433ca0aa0deafa4f3030ca1 Author: Jean M. Sexton Date: Mon Nov 30 19:17:03 2020 -0500 Fix ifdef and if scope Source/TimeStep/Nyx_advance.cpp commit b157b28ff4eee81467919674da012daed0413cba Author: Ann Almgren Date: Mon Nov 30 15:57:27 2020 -0800 Add section on refinement criteria Docs/sphinx_documentation/source/Refinement.rst Docs/sphinx_documentation/source/index.rst commit 64e39776ca203cdafbd1b0b59749207f3088ba64 Author: Ann Almgren Date: Mon Nov 30 15:52:45 2020 -0800 Remove reference to setting USE_PARTICLES = TRUE Docs/sphinx_documentation/source/Particles.rst commit 499b34517dad34896e55824d0cef2e6060f20d4d Author: Ann Almgren Date: Mon Nov 30 15:51:59 2020 -0800 Remove references to setting USE_GRAV = TRUE Docs/sphinx_documentation/source/NyxGravity.rst Docs/sphinx_documentation/source/NyxInputs.rst commit 4def402911e411f72af3e2366ac573c63b4a475f Author: Jean M. Sexton Date: Mon Nov 30 15:38:15 2020 -0800 Fix if ordering Exec/Make.Nyx commit 2e89e1bd2b8b83de9db93991f95765909d123469 Merge: a1e7d9b8 bbfab7f4 Author: Ann Almgren Date: Mon Nov 30 15:34:44 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit a1e7d9b8ecc740d7a7cd1c5e6b09fb3af76d647f Author: Ann Almgren Date: Mon Nov 30 15:34:08 2020 -0800 Update info about nightly regression tests Docs/sphinx_documentation/source/NightlyTests.rst commit bbfab7f4a02f5998cee6f03a3039d62134b88980 Author: Jean M. Sexton Date: Mon Nov 30 15:29:40 2020 -0800 Remove USE_GRAV from GNUmakefile and default to true Exec/AMR-density/GNUmakefile Exec/AMR-density/GNUmakefile.cuda Exec/AMR-zoom/GNUmakefile Exec/DrivenTurbulence/GNUmakefile Exec/HydroTests/GNUmakefile Exec/LyA/GNUmakefile Exec/LyA_AGN/GNUmakefile Exec/LyA_Neutrinos/GNUmakefile Exec/Make.Nyx Exec/MiniSB/GNUmakefile Exec/ParticleMeshTest/GNUmakefile Exec/ParticleOnlyTest/GNUmakefile Exec/SantaBarbara/GNUmakefile Exec/Scaling/GNUmakefile commit d4c77b553d0e8e0de6eb3f3900b85d8d214fe5d5 Author: Jean M. Sexton Date: Mon Nov 30 10:59:12 2020 -0800 Fix duplicate Nyx_sources.cpp include Source/TimeStep/Make.package commit d9672206aafe4d074d5956757da838d2c810d971 Author: Jean M. Sexton Date: Wed Nov 25 14:23:11 2020 -0800 Make HydroTests use top-level Make.Nyx Exec/HydroTests/GNUmakefile Exec/HydroTests/Make.Nyx Exec/Make.Nyx commit 9b0c8dff62e13b9a6cd497d7f9ebbfb13f704f97 Author: Jean M. Sexton Date: Wed Nov 25 14:16:44 2020 -0800 Add ifdefs on AMREX_PARTICLES Exec/HydroTests/Make.Nyx Source/DerivedQuantities/ParticleDerive.cpp Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/IO/Nyx_output.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/TimeStep/Nyx_advance.cpp commit 50210167b58bcc82c8c4ae91e054a9cb22a57689 Author: Ann Almgren Date: Sun Nov 29 14:00:16 2020 -0800 Set default for agglomeration and consolidation to 1. Docs/sphinx_documentation/source/NyxInputs.rst Source/Gravity/Gravity.cpp commit 2fc9ada43169e1b6b243b7950ff97fda7472e805 Author: Ann Almgren Date: Sat Nov 28 19:26:36 2020 -0800 This fix should take care of the cases where the tracing in PPM was creating densities that were far too small. For now it is only used as a fix for cases where the density goes noticeably too small (i.e. drops by factor of 1/2, which includes all cases that previously were getting floored), but in the long run we think we may want to do this everywhere Source/Hydro/trace_ppm.cpp commit 6df6070b399357f4ffc21c7946828d48fe12955e Author: Ann Almgren Date: Sat Nov 28 18:26:15 2020 -0800 This is fix to previous commit -- getting rid of grav_source_type Source/TimeStep/Nyx_correct_gsrc.cpp commit ef23b271d3e9c7be3e79bc6fade3e465e80a8549 Author: Ann Almgren Date: Sat Nov 28 16:39:46 2020 -0800 Remove grav_source_type as parameter since it was hard-wired to 1 Docs/sphinx_documentation/source/NyxGravity.rst Source/Driver/constants_cosmo.H Source/TimeStep/Nyx_correct_gsrc.cpp Source/TimeStep/Nyx_update_state_with_sources.cpp commit ff5cc7859961f140fafce0d6c62da03da21593b4 Author: Ann Almgren Date: Fri Nov 27 13:56:13 2020 -0800 Remove all tabs! README.md Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Driver/Nyx_error.cpp Source/Driver/comoving.cpp Source/Driver/constants_cosmo.H Source/Driver/sum_integrated_quantities.cpp Source/EOS/atomic_rates.H Source/EOS/reset_internal_e.H Source/HeatCool/f_rhs.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/HeatCool/integrate_state_with_source_3d_stubs.cpp Source/Hydro/Hydro.cpp Source/TimeStep/Nyx_advance.cpp Source/TimeStep/Nyx_enforce_minimum_density.H UsersGuide/AGN/AGN.tex UsersGuide/AMR/AMR.tex UsersGuide/Classes/classes.eps UsersGuide/Classes/classes.fig UsersGuide/ComovingHydro/Equations.tex UsersGuide/ComovingHydro/sgs.bib UsersGuide/EOSNetwork/EOSNetwork.tex UsersGuide/Equations/Equations.tex UsersGuide/FlowChart/FlowChart.tex UsersGuide/Forcing/NyxForcing.tex UsersGuide/Forcing/force.bib UsersGuide/GNUmakefile UsersGuide/GettingStarted/NyxGettingStarted.tex UsersGuide/Gravity/NyxGravity.tex UsersGuide/Gravity/gr.bib UsersGuide/HeatCool/NyxHeatCool.tex UsersGuide/HeatCool/heatcool.bib UsersGuide/Inputs/NyxInputs.tex UsersGuide/Introduction/NyxIntroduction.tex UsersGuide/ManagingJobs/managingjobs.tex UsersGuide/NyxUserGuide.tex UsersGuide/Particles/Particles.tex UsersGuide/PostProcessing/NyxPostProcessing.tex UsersGuide/Scaling/Scaling.tex UsersGuide/Suggestions/Suggestions.tex UsersGuide/UnitsAndConstants/NyxUnits.tex UsersGuide/Visualization/NyxVisualization.tex commit 66c5204f89b4960908f188948d710c765df02670 Author: Ann Almgren Date: Fri Nov 27 13:48:41 2020 -0800 Add AGN info and restructure introure intro Docs/sphinx_documentation/source/NyxPapers.rst Docs/sphinx_documentation/source/NyxPreface.rst Docs/sphinx_documentation/source/NyxUnits.rst Docs/sphinx_documentation/source/index.rst commit f232a096b064a6eee49d875936e249ed1fe57b36 Author: Ann Almgren Date: Fri Nov 27 13:45:45 2020 -0800 Add AGN model Docs/sphinx_documentation/source/AGN.rst Docs/sphinx_documentation/source/index.rst commit f0b7465e9062bf2baca5959827ab37d1637e113c Author: Ann Almgren Date: Fri Nov 27 13:30:19 2020 -0800 Update info about inputs Docs/sphinx_documentation/source/NyxGettingStarted.rst Docs/sphinx_documentation/source/NyxInputs.rst commit f0d75b458a26de64022302e4755b02b0d26d2e97 Author: Ann Almgren Date: Fri Nov 27 13:23:42 2020 -0800 fix typo Docs/sphinx_documentation/source/NyxInputs.rst commit aac58d3d33412ff2e6a11e0fdaa8f2f9aab08ede Author: Ann Almgren Date: Fri Nov 27 13:22:55 2020 -0800 Add debugging section to docs -- just some helpful hints ... Docs/sphinx_documentation/source/Debugging.rst Docs/sphinx_documentation/source/NyxInputs.rst Docs/sphinx_documentation/source/index.rst commit ec2057f8e96f4228020778e3dfcbec76d2f9e95c Author: Ann Almgren Date: Fri Nov 27 13:10:33 2020 -0800 Remove nyx.allow_untagging from source and docs - it wasn't being used Docs/sphinx_documentation/source/NyxInputs.rst Source/Driver/Nyx.H Source/Driver/Nyx.cpp commit 2b339dfbc3dfcde3e459710ea9b8c271bcee61c3 Author: Ann Almgren Date: Fri Nov 27 13:05:15 2020 -0800 1) Update formatting of docs 2) Remove use_flattening flag -- default behavior is always to do flattening Docs/sphinx_documentation/source/NyxInputs.rst Exec/MiniSB/inputs.analysis Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Hydro/Godunov.H Source/Hydro/Godunov.cpp Source/Hydro/Hydro.H Source/Hydro/Hydro.cpp Source/Hydro/PLM.H Source/Hydro/trace_ppm.cpp commit a959da0f22677147c92e63ad9776c22b841fc016 Author: Ann Almgren Date: Fri Nov 27 12:39:02 2020 -0800 formatting fix Docs/sphinx_documentation/source/NyxInputs.rst commit 1046c51485a872f946a45e848302d78f366ec889 Author: Ann Almgren Date: Fri Nov 27 12:37:52 2020 -0800 Remove "do_special_tagging" from source and docs -- it wasn't used anywhere Docs/sphinx_documentation/source/NyxInputs.rst Source/Driver/Nyx.H Source/Driver/Nyx.cpp commit 15ed725eddfcc09a56fad5aafcc4d747a8ad02d9 Author: Ann Almgren Date: Fri Nov 27 11:31:09 2020 -0800 fix table formatting Docs/sphinx_documentation/source/NyxInputs.rst commit 0243f8a545485d68b131a9b72c9a94e6d63e64b1 Author: Ann Almgren Date: Fri Nov 27 11:03:31 2020 -0800 update the multigrid inputs and put them in the same section as the other inputs Docs/sphinx_documentation/source/InputsMultigrid.rst Docs/sphinx_documentation/source/NyxInputs.rst Docs/sphinx_documentation/source/index.rst commit b0dc3b191fcbc34b612c868fc7e0d0e970e6ed83 Author: Ann Almgren Date: Fri Nov 27 10:47:43 2020 -0800 Add ppm_type and enforce_min_density_type to the documentation Docs/sphinx_documentation/source/NyxInputs.rst commit 3be40a9bd4e8d84980ad645d6ce34c266eafce55 Author: Ann Almgren Date: Fri Nov 27 10:33:30 2020 -0800 add some more comments Source/TimeStep/Nyx_enforce_minimum_density.cpp commit abcbb93331c883dd7c9780425ef45436e0432985 Author: Ann Almgren Date: Fri Nov 27 10:28:51 2020 -0800 Add the conservative option for enforcing minimum density, and a flag (enforce_min_density_type with default to "floor") that decides which routine to use. This should not change the default behavior. Docs/sphinx_documentation/source/NyxIntroduction.rst Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/TimeStep/Make.package Source/TimeStep/Nyx_enforce_minimum_density.H Source/TimeStep/Nyx_enforce_minimum_density.cpp commit f8a2dca88c9a398a26ee07e64dc1d6fcb14442c9 Author: Ann Almgren Date: Fri Nov 27 09:40:02 2020 -0800 remove use_exact_gravity flag which wasn't being used Source/Driver/Nyx.H Source/Driver/Nyx.cpp commit 8d8329193e1a094c9448435f74f8358dff538626 Author: Ann Almgren Date: Fri Nov 27 09:34:06 2020 -0800 Reformat the call to enforce_minimum_density in preparation for adding the conservative option Source/Driver/Nyx.H Source/TimeStep/Make.package Source/TimeStep/Nyx_advance_particles.cpp Source/TimeStep/Nyx_enforce_minimum_density.cpp Source/TimeStep/Nyx_update_state_with_sources.cpp commit eded4b8bd8e6168eeb249d690cdad5593615f775 Merge: 5e92e802 02ff3395 Author: Ann Almgren Date: Tue Nov 24 19:19:25 2020 -0800 Merge branch 'development' of https://github.com/amrex-astro/Nyx into development commit 5e92e8028f0e31d513f073a6932883802ccfa346 Author: Ann Almgren Date: Tue Nov 24 19:19:13 2020 -0800 do_react isn't used so remove any reference to it Docs/sphinx_documentation/source/NyxInputs.rst Exec/DrivenTurbulence/inputs Exec/DrivenTurbulence/inputs.regtest Exec/HydroTests/inputs-test2-y Exec/HydroTests/inputs-test2-z Exec/HydroTests/inputs-test3-x Exec/HydroTests/inputs.3d.sph.sedov Exec/HydroTests/inputs.3d.sph.testsuite.sedov Exec/HydroTests/inputs.regtest.sedov Exec/HydroTests/inputs.regtest.test3 commit 02ff3395ec3f703531ae42aa7ef059b97b1cc031 Author: Jean M. Sexton Date: Tue Nov 24 17:06:45 2020 -0800 Remove namelist from sphinx, move Sundials doc Docs/sphinx_documentation/source/NyxGettingStarted.rst Docs/sphinx_documentation/source/NyxSundials.rst Docs/sphinx_documentation/source/index.rst commit 48bac113d98843885c039c2875a9850485b54bf8 Author: Ann Almgren Date: Tue Nov 24 14:47:57 2020 -0800 Remove gravity_type since it can only be PoissonGrav Exec/AMR-density/inputs Exec/AMR-density/inputs.cuda Exec/AMR-density/inputs.rt Exec/AMR-density/inputs_nohydro.rt Exec/AMR-zoom/inputs Exec/GravityTests/MacLaurin/inputs Exec/GravityTests/zeldovich_dm/run/inputs Exec/GravityTests/zeldovich_dm/run/inputs_hydro Exec/GravityTests/zeldovich_dm/run/inputs_wmap7 Exec/GravityTests/zeldovich_dm/run_hydro/inputs_hydro Exec/LyA/inputs Exec/LyA/inputs.cuda Exec/LyA/inputs.rt Exec/LyA/inputs.rt.garuda Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA/inputs_nohydro.rt Exec/LyA_AGN/inputs Exec/LyA_AGN/inputs.rt Exec/LyA_Neutrinos/inputs Exec/LyA_Neutrinos/inputs.no_hydro_64 Exec/LyA_Neutrinos/inputs.rt Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Exec/MiniSB/inputs.analysis Exec/ParticleMeshTest/inputs.2line Exec/ParticleMeshTest/inputs.2line.restarttest Exec/ParticleMeshTest/inputs.mass.nosub Exec/ParticleMeshTest/inputs.mass.sub Exec/ParticleOnlyTest/inputs.2line Exec/ParticleOnlyTest/inputs.2line.restarttest Exec/ParticleOnlyTest/inputs.mass.nosub Exec/ParticleOnlyTest/inputs.mass.sub Exec/SantaBarbara/inputs Exec/Scaling/inputs Exec/Scaling/inputs.256.noreduceverb Exec/Scaling/inputs_short Source/Driver/Nyx.cpp Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit 64b319a097f1ca742c84649a5e673c1a390ecd8b Author: Jean M. Sexton Date: Tue Nov 24 11:59:59 2020 -0800 Move sundials make variables for heat-cool Exec/Make.Nyx commit c3a5d2e154e5acb18685e99683ac06f9d83b6a3e Author: Jean M. Sexton Date: Mon Nov 23 18:27:18 2020 -0500 Fix missing flag Exec/Make.Nyx commit fe10745b4b0523f022d522299c0e96e24d61e1cc Author: Jean M. Sexton Date: Mon Nov 23 14:20:35 2020 -0800 Remove fortran sundials references Docs/sphinx_documentation/source/NyxSundials.rst Exec/Make.Nyx commit 53f41f4e9c3501fd4d74ae9f5c5404b4ed6c1abd Author: Jean M. Sexton Date: Mon Nov 23 14:15:12 2020 -0800 Add Sundials build instructions Docs/sphinx_documentation/source/NyxSundials.rst Docs/sphinx_documentation/source/index.rst commit eb99cc756f73322b77150e76170b94c77fcb6ee0 Author: Jean M. Sexton Date: Mon Nov 23 13:59:33 2020 -0800 Move USE_SUNDIALS to Nyx GNUmake Exec/AMR-density/GNUmakefile Exec/LyA/GNUmakefile Exec/Make.Nyx commit a0925aede1fbab9a3cc01744d83681333b4d1b34 Author: Ann Almgren Date: Mon Nov 23 14:07:34 2020 -0800 More updating of tables Docs/sphinx_documentation/source/NyxInputs.rst commit bda3cd20183507045be4c2ea6e16b4bd78436807 Author: Ann Almgren Date: Sun Nov 22 18:45:19 2020 -0800 more formatting fixes Docs/sphinx_documentation/source/NyxInputs.rst commit 588369d6c37edb6cc043420ecc8eaf7f4a2e6196 Author: Ann Almgren Date: Sun Nov 22 18:33:48 2020 -0800 fix formatting Docs/sphinx_documentation/source/NyxInputs.rst commit 9e7b3888c87cde00ce38a691590d637550d6a59d Author: Ann Almgren Date: Sun Nov 22 17:48:52 2020 -0800 More clean up of Gravity inputs and documentation of inputs Docs/sphinx_documentation/source/InputsMultigrid.rst Docs/sphinx_documentation/source/NyxInputs.rst Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit 44aa2b5adb94b45cb6a6d02beaa202962c8ddd01 Author: Ann Almgren Date: Sun Nov 22 17:15:32 2020 -0800 Before this commit, the inputs "mg.v" and "mg.bottom_solver" were not being read. 1) We now read mg.v to define "Gravity::mg_verbose" which is passed into the MLMG solver using mlmg.setVerbose(mg_verbose). The default mg_verbose = 0. 2) We now read mg.bottom_solver as a string instead of an integer, and pass the correct string into the mlmg solver using mlmg.SetBottomSolver. The default bottom solver is BiCG. No expected change to current regression tests. Exec/AMR-density/inputs Exec/AMR-density/inputs.cuda Exec/AMR-density/inputs.rt Exec/AMR-density/inputs_nohydro.rt Exec/AMR-zoom/inputs Exec/GravityTests/MacLaurin/inputs Exec/GravityTests/zeldovich_dm/run/inputs Exec/GravityTests/zeldovich_dm/run/inputs_hydro Exec/GravityTests/zeldovich_dm/run/inputs_wmap7 Exec/GravityTests/zeldovich_dm/run_hydro/inputs_hydro Exec/LyA/inputs Exec/LyA/inputs.cuda Exec/LyA/inputs.rt Exec/LyA/inputs.rt.garuda Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA/inputs_nohydro.rt Exec/LyA_AGN/inputs Exec/LyA_AGN/inputs.rt Exec/LyA_Neutrinos/inputs Exec/LyA_Neutrinos/inputs.no_hydro_64 Exec/LyA_Neutrinos/inputs.rt Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Exec/MiniSB/inputs.analysis Exec/ParticleMeshTest/inputs.2line Exec/ParticleMeshTest/inputs.2line.restarttest Exec/ParticleMeshTest/inputs.mass.nosub Exec/ParticleMeshTest/inputs.mass.sub Exec/ParticleOnlyTest/inputs.2line Exec/ParticleOnlyTest/inputs.2line.restarttest Exec/ParticleOnlyTest/inputs.mass.nosub Exec/ParticleOnlyTest/inputs.mass.sub Exec/SantaBarbara/inputs Exec/Scaling/inputs Exec/Scaling/inputs.256.noreduceverb Exec/Scaling/inputs_short Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit 209e284570559a4a12223040fbd1094f268e463c Author: Ann Almgren Date: Sat Nov 21 17:27:19 2020 -0800 Remove print_fortran_warnings form all inputs file -- this is no longer used. Exec/AMR-density/inputs Exec/AMR-density/inputs.cuda Exec/AMR-density/inputs.rt Exec/AMR-density/inputs_nohydro.rt Exec/AMR-zoom/inputs Exec/GravityTests/zeldovich_dm/run/inputs Exec/GravityTests/zeldovich_dm/run/inputs_hydro Exec/GravityTests/zeldovich_dm/run_hydro/inputs_hydro Exec/LyA/inputs Exec/LyA/inputs.cuda Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA_AGN/inputs Exec/LyA_Neutrinos/inputs Exec/LyA_Neutrinos/inputs.no_hydro_64 Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Exec/ParticleOnlyTest/inputs.2line Exec/Scaling/inputs Exec/Scaling/inputs.256.noreduceverb Exec/Scaling/inputs_short commit cc7d8eb423d569244f1f86d9ac5e1cd3c51c3141 Author: Jean M. Sexton Date: Fri Nov 20 18:23:45 2020 -0500 Fix normalize_species_fluxes near-zero case (gh-63) Source/Hydro/Hydro.H commit 29c63ec81e35de6e841ff420de2915f99a03cc8b Author: Jean M. Sexton Date: Fri Nov 20 14:56:15 2020 -0500 Add input flag tagging_base for overden for different sizes Source/DerivedQuantities/ParticleDerive.cpp Source/Driver/Nyx.H Source/Driver/Nyx.cpp commit 4762ae66147420b088d4d924eeebebc1c83dace9 Merge: c8db344d 9cc7ffd8 Author: Ann Almgren Date: Mon Nov 16 15:44:41 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit c8db344d87350e0f06296c9802fc393d1f2630a8 Author: Ann Almgren Date: Mon Nov 16 15:44:31 2020 -0800 update to intro Docs/sphinx_documentation/source/NyxInputs.rst Docs/sphinx_documentation/source/NyxIntroduction.rst Docs/sphinx_documentation/source/NyxPreface.rst commit 9cc7ffd8bd0fcffd2cd439e8c15fabd5031a0d55 Author: Jean M. Sexton Date: Mon Nov 16 15:31:04 2020 -0800 Add if guards for AtomicRates, fix typo Source/Driver/Nyx.cpp commit 02d1ebf30d1c6bb2a2b21f5334e6ef57d9f477c7 Merge: 92f518ad 7ab20175 Author: mic84 Date: Mon Nov 16 15:18:38 2020 -0800 Merge pull request #62 from mic84/mr/more-fixes-2 Some more fixes commit 7ab20175b913eb75b6424b66fa58f4be1d69438e Author: Michele Rosso Date: Mon Nov 16 15:15:14 2020 -0800 Some more fixes Source/DerivedQuantities/Derive.cpp Source/Driver/Make.package commit 92f518adc4da7b5fcabfbb70c3ce936d5fb8fda9 Merge: 79dd54e3 57373c81 Author: mic84 Date: Mon Nov 16 15:04:22 2020 -0800 Merge pull request #61 from mic84/mr/gnumake-fix GNUMake: remove sources located elsewhere commit 57373c81fb1702d8d9e487bbcd110472fc5c2801 Author: Michele Rosso Date: Mon Nov 16 15:02:42 2020 -0800 GNUMake: remove sources located elsewhere Source/Driver/Make.package commit 79dd54e39bd3f65348dc14eef275e4a1f864a4c5 Author: Ann Almgren Date: Mon Nov 16 14:52:19 2020 -0800 Reorder the gravity docs section Docs/sphinx_documentation/source/NyxGravity.rst commit 2f0041aa79d7fb125e6b2e10e834fbaa403474dc Merge: c1fbd685 8bb4fd05 Author: Ann Almgren Date: Mon Nov 16 14:45:50 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit c1fbd68584352d601629a65598e94998cb290b04 Author: Ann Almgren Date: Mon Nov 16 14:44:16 2020 -0800 Update particle documentation. Docs/sphinx_documentation/source/Particles.rst UsersGuide/Particles/Particles.tex commit 8bb4fd051a7ed056a1c3ba7da07427ce2ad171c7 Author: Jean M. Sexton Date: Mon Nov 16 14:12:28 2020 -0800 Migrate Inputs, Forcing, and HeatCool Docs/sphinx_documentation/source/NyxForcing.rst Docs/sphinx_documentation/source/NyxInputs.rst Docs/sphinx_documentation/source/index.rst Docs/sphinx_documentation/source/refs.bib Docs/sphinx_documentation/source/zreferences.rst UsersGuide/Forcing/NyxForcing.tex UsersGuide/HeatCool/NyxHeatCool.tex UsersGuide/Inputs/NyxInputs.tex commit f865339d3720c8f58781993424725d437274de69 Author: Ann Almgren Date: Mon Nov 16 13:53:16 2020 -0800 Refer to online documentation. UsersGuide/GettingStarted/NyxGettingStarted.tex commit 0fca0f9a4f5b11ac8335062abe2ece8d42ad35f7 Author: Ann Almgren Date: Mon Nov 16 13:52:19 2020 -0800 1) update docs for how to run 2) add ic_sb_32.ascii to the repo so a new user can "just run" the MiniSB problem Docs/sphinx_documentation/source/NyxGettingStarted.rst Exec/MiniSB/ic_sb_32.ascii commit 8cc669ae6992bb113eaaaa4fcc332abf35d7caf4 Author: Jean M. Sexton Date: Mon Nov 16 13:40:55 2020 -0800 Update Prob.H to have valid NO_HYDRO option Exec/AMR-density/Prob.H Exec/AMR-zoom/Prob.H Exec/Henson/amr-info/Prob.H Exec/Henson/extract-particles/Prob.H Exec/Henson/sample-analysis/Prob.H Exec/LyA/Prob.H Exec/LyA_AGN/Prob.H Exec/LyA_Neutrinos/Prob.H Exec/MiniSB/Prob.H Exec/ParticleMeshTest/Prob.H Exec/ParticleOnlyTest/Prob.H Exec/Scaling/Prob.H commit 867b0dcea953c373f2e4241673c9e600fedcc3a8 Author: Jean M. Sexton Date: Mon Nov 16 13:28:43 2020 -0800 Rename files and rearrange Source/DerivedQuantities/Derive_nohydro.cpp Source/DerivedQuantities/Make.package Source/DerivedQuantities/ParticleDerive.H Source/DerivedQuantities/ParticleDerive.cpp Source/Initialization/Nyx_setup.cpp commit 77a9f30c1bc6de340f4be4cf5b143ccd8b575573 Author: Jean M. Sexton Date: Mon Nov 16 13:18:47 2020 -0800 Change NO_HYDRO behavior for EOS and Derive Do not compile EOS or set hydro-related small values Do not compile derived functions not included in no_hydro_setup Source/DerivedQuantities/Derive.H Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/Derive_nohydro.H Source/DerivedQuantities/Derive_nohydro.cpp Source/DerivedQuantities/Make.package Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/EOS/Make.package Source/Hydro/IndexDefines.H Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp commit 6af23ca19dca2f8aa1907c75b4a1c58aa8b6e420 Author: Ann Almgren Date: Mon Nov 16 10:45:30 2020 -0800 Move include of bc_fill.H from Nyx.H to Nyx_setup.cpp Source/Driver/Nyx.H Source/Initialization/Nyx_setup.cpp UsersGuide/Equations/Equations.tex UsersGuide/PostProcessing/NyxPostProcessing.tex UsersGuide/Visualization/NyxVisualization.tex commit b13fd788991ed20562fb64d7b0710c56584d58f5 Author: Ann Almgren Date: Sun Nov 15 16:41:22 2020 -0800 refer to online documentation UsersGuide/ComovingHydro/Equations.tex commit b699002c80cd5f9601316e1ff6f5fc42ea3795d6 Author: Ann Almgren Date: Sun Nov 15 16:36:05 2020 -0800 Replace the https links UsersGuide/Gravity/NyxGravity.tex commit ffa3461228cc912f4ad6e48f5172b07b23fcfcbc Author: Ann Almgren Date: Sun Nov 15 16:27:29 2020 -0800 Point to online documentation. UsersGuide/Gravity/NyxGravity.tex commit 248522ee2acc0567549d08776767bbf37fb29f54 Author: Ann Almgren Date: Sun Nov 15 16:24:38 2020 -0800 refer to the online documentation UsersGuide/Equations/Equations.tex commit 9b873985b0ec477a03d20228f49ce42379973992 Author: Ann Almgren Date: Sat Nov 14 09:40:02 2020 -0800 Replace user guide chapter by pointer to online docs UsersGuide/PostProcessing/NyxPostProcessing.tex commit 92778534e583c4b02c2f6b251bb8f40a76132c96 Author: Ann Almgren Date: Sat Nov 14 09:39:13 2020 -0800 Migrate more text from UserGuide to online docs Docs/sphinx_documentation/source/PostProcessing.rst Docs/sphinx_documentation/source/index.rst commit 6cdeb4c3f96a03bb02dcca598a4bc30e306e5d38 Author: Ann Almgren Date: Sat Nov 14 09:32:21 2020 -0800 Replace Visualization.tex with link to online docs UsersGuide/Visualization/NyxVisualization.tex commit 30025caeaf3e7e878d5ff85334871053baa4dfd6 Author: Ann Almgren Date: Sat Nov 14 09:29:18 2020 -0800 Add Visualization chapter (with link to AMReX docs) Docs/sphinx_documentation/source/Visualization.rst Docs/sphinx_documentation/source/index.rst commit b134fc616dc062a305ec543b9e5e99d4729bc470 Merge: 893e6c65 02a9d199 Author: Ann Almgren Date: Fri Nov 13 18:04:29 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 893e6c658e0da5d6c71ba1578094ff65ace01e50 Author: Ann Almgren Date: Fri Nov 13 18:04:19 2020 -0800 clean up the bc routines Exec/HydroTests/bc_fill.cpp Source/Driver/Make.package Source/Driver/bc_fill.H Source/Driver/bc_fill.cpp Source/Initialization/Make.package Source/Initialization/Nyx_setup.cpp Source/Initialization/bc_fill.H Source/Initialization/bc_fill.cpp commit 02a9d199c3c243978c53144d54ea7f8e793f4ff0 Author: Jean M. Sexton Date: Fri Nov 13 15:46:10 2020 -0800 Remove unused fortran files Exec/AMR-density/Tagging_3d.f90 Exec/AMR-density/probdata.f90 Exec/AMR-density/rhsfn.f90 Exec/DrivenTurbulence/Derive_prob_3d.f90 Exec/DrivenTurbulence/Tagging_3d.f90 Exec/DrivenTurbulence/ext_src_3d.f90 Exec/DrivenTurbulence/probdata.f90 Exec/SantaBarbara/Prob_3d.f90 Exec/SantaBarbara/Tagging_3d.f90 Exec/SantaBarbara/probdata.f90 commit 90a17f90bfa098dfbcf9cde0929791ccea747966 Author: Ann Almgren Date: Fri Nov 13 15:32:08 2020 -0800 Take IndexDefines out of Nyx.H Source/Driver/Nyx.H Source/Driver/bc_fill.H Source/EOS/reset_internal_e.H Source/Hydro/Utilities.cpp commit 2cdf2a3279e2f885a78c1c08e1b5cfa7778a4004 Author: Ann Almgren Date: Fri Nov 13 12:04:56 2020 -0800 Fix non-SDC compile Source/Driver/Nyx.H commit 44e97f159f923f98d4b56e80559329feb0fd3bb1 Author: Jean M. Sexton Date: Fri Nov 13 10:27:22 2020 -0800 Fix Make.package typo Source/HeatCool/Make.package commit 212cd4004c883892837bcd68fe646e530a8f9e7b Author: Ann Almgren Date: Thu Nov 12 16:57:50 2020 -0800 Change the order in which we read the inputs Source/Driver/Nyx.cpp commit be5c401bd2a15d4b0f8d2c1b0bbc8ebfb2301542 Author: Ann Almgren Date: Thu Nov 12 13:29:10 2020 -0800 Fix includes... Source/HeatCool/Make.package commit 6130a2090ec6e77ea119a9fbd9561b1b5ba2f752 Author: Ann Almgren Date: Thu Nov 12 13:09:33 2020 -0800 Make sure the right flags are read in under the right circumstances Source/Driver/Nyx.cpp Source/HeatCool/Make.package Source/TimeStep/Nyx_advance.cpp commit fd1c655bbda3fdb1a4f882231dd117d522cfa31d Author: Ann Almgren Date: Wed Nov 11 13:42:11 2020 -0800 Fix Hydro/Make.package Source/Hydro/Make.package commit a6e63279d4530d909389e369651df4751f6586c3 Author: Ann Almgren Date: Wed Nov 11 13:20:30 2020 -0800 Fix HeatCool/Make.package Source/HeatCool/Make.package commit a7eb90da87b123b986409152d188b7565a90d807 Merge: 896ea1e8 5962ecb3 Author: Ann Almgren Date: Wed Nov 11 12:58:57 2020 -0800 Merge branch 'development' into reorg commit 5962ecb351eabd01064c6b8f2ef335412cfb8182 Author: Jean M. Sexton Date: Wed Nov 11 12:36:11 2020 -0800 Add synchronize for forcing Exec/DrivenTurbulence/Nyx_sources.cpp commit 896ea1e8322610a9fd194bfb4ddeaceb861f68bd Author: Ann Almgren Date: Wed Nov 11 11:49:37 2020 -0800 Reorg and clean-up Exec/HydroTests/Make.Nyx Exec/Make.Nyx Exec/ParticleOnlyTest/GNUmakefile Source/Constants/Make.package Source/Driver/Make.package Source/Driver/Nyx.H Source/Driver/Nyx.cpp Source/Driver/NyxBld.cpp Source/Driver/Nyx_error.cpp Source/Driver/Nyx_halos.cpp Source/Driver/bc_fill.H Source/Driver/bc_fill.cpp Source/Driver/comoving.cpp Source/Driver/constants_cosmo.H Source/Driver/main.cpp Source/Driver/nyx_main.cpp Source/Driver/sum_integrated_quantities.cpp Source/Driver/sum_utils.cpp Source/EOS/eos_adiabatic.H Source/HeatCool/Make.package Source/HeatCool/sdc_reactions.cpp Source/HeatCool/strang_reactions.cpp Source/Hydro/Godunov.H Source/Hydro/Godunov.cpp Source/Hydro/Hydro.H Source/Hydro/Hydro.cpp Source/Hydro/IndexDefines.H Source/Hydro/Make.package Source/Hydro/PLM.H Source/Hydro/PPM.H Source/Hydro/Riemann.H Source/Hydro/Utilities.H Source/Hydro/Utilities.cpp Source/Hydro/sdc_hydro.cpp Source/Hydro/strang_hydro.cpp Source/Hydro/strang_hydro_fuse.cpp Source/Hydro/trace_ppm.cpp Source/Initialization/Nyx_initcosmo.cpp Source/SourceTerms/Make.package Source/Src_3d/Make.package Source/Tagging/Make.package Source/TimeStep/Make.package Source/TimeStep/Nyx_advance.cpp Source/TimeStep/Nyx_correct_gsrc.cpp Source/TimeStep/Nyx_sources.cpp Source/TimeStep/Nyx_time_center_sources.cpp Source/TimeStep/advance_particles.cpp Source/TimeStep/update_state_with_sources.cpp Source/compute_hydro_sources.cpp commit c07edab95e4f34a65821762b0f68f732e3aeed55 Author: Jean M. Sexton Date: Tue Nov 10 14:17:55 2020 -0800 Update Part2line tests and fix NO_HYDRO compile Exec/ParticleMeshTest/GNUmakefile Exec/ParticleMeshTest/Make.package Exec/ParticleMeshTest/Prob.H Exec/ParticleMeshTest/fixed_grids.mass Exec/ParticleMeshTest/inputs.2line Exec/ParticleMeshTest/inputs.2line.restarttest Exec/ParticleMeshTest/inputs.mass.nosub Exec/ParticleMeshTest/inputs.mass.sub Exec/ParticleMeshTest/particle_file.2line Exec/ParticleMeshTest/particle_file.mass Exec/ParticleOnlyTest/GNUmakefile Exec/ParticleOnlyTest/Make.package Exec/ParticleOnlyTest/Prob.H Exec/ParticleOnlyTest/fixed_grids.mass Exec/ParticleOnlyTest/inputs.2line Exec/ParticleOnlyTest/inputs.2line.restarttest Exec/ParticleOnlyTest/inputs.mass.nosub Exec/ParticleOnlyTest/inputs.mass.sub Exec/ParticleOnlyTest/particle_file.2line Exec/ParticleOnlyTest/particle_file.mass Source/HydroCpp/Make.package Source/Initialization/Nyx_setup.cpp Source/Nyx.H commit 33cc73cad1c21cdae7ec2ee73ade05a7cfa32d95 Merge: 3df9eeb4 4bd07945 Author: mic84 Date: Tue Nov 10 15:01:18 2020 -0800 Merge pull request #60 from mic84/mr/remove-nyx-error-f-h Remove Nyx_error_F.H commit 4bd07945d88d5eada6d07a5a9ada11b654c0fe1f Author: Michele Rosso Date: Tue Nov 10 15:07:41 2020 -0800 CMake: remove Nyx_error_F.H Source/Tagging/Make.package Source/Tagging/Nyx_error.cpp Source/Tagging/Nyx_error_F.H commit 3df9eeb457d9d1371bcb1c7adab60c4b26393df4 Author: Jean M. Sexton Date: Tue Nov 10 09:27:51 2020 -0800 Fix nested OMP, use ReduceOps in compute_rho_temp Source/Nyx.cpp commit 04e21c29b8739297997785716c7b44a3ef305c01 Author: Jean M. Sexton Date: Tue Nov 10 09:27:13 2020 -0800 Updated number of modes in forcing problems Source/Forcing/Forcing.cpp commit 65af552a9db5bc0862e0ea23738efe83cf16a761 Author: Jean M. Sexton Date: Fri Nov 6 13:07:14 2020 -0800 Fix box 0 vs 1 indexing in Forcing Source/Forcing/Forcing.cpp commit dc3d2bc68bc80b876cfacddc2ad2862d2460b130 Author: Jean M. Sexton Date: Thu Nov 5 08:11:17 2020 -0800 Fix spacing Exec/DrivenTurbulence/Nyx_sources.cpp Source/Forcing/Forcing.H Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp commit 5de85cd76d34dd5123bc6b30526f0e87649f8442 Merge: 54e97418 5267df7a Author: Jean M. Sexton Date: Thu Nov 5 07:45:14 2020 -0800 Merge branch 'forcing_update' into development commit 5267df7a81d156a2f1cb1befe40ea75597110653 Author: Jean M. Sexton Date: Wed Nov 4 12:05:30 2020 -0800 Index shift in mi mj mk in forcing Source/Forcing/Forcing.cpp commit 34cddb47b6dea444eee71a88ca09f8c68483cec9 Author: Jean M. Sexton Date: Wed Nov 4 11:57:22 2020 -0800 Fix modes number in Forcing Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp commit 1614ea5fd84b64b21f77d3daed32c2fd760927d7 Author: Jean M. Sexton Date: Wed Nov 4 08:55:37 2020 -0800 Compiles with all equations, nans Exec/DrivenTurbulence/Nyx_sources.cpp Source/Forcing/Forcing.H Source/Forcing/Forcing.cpp commit d98d34554d35d2693b21d289c7feff772799be8f Author: Jean M. Sexton Date: Tue Nov 3 09:03:25 2020 -0800 Add integrate_state_force to StochasticForcing class Exec/DrivenTurbulence/Nyx_sources.cpp Source/Forcing/Forcing.H Source/Forcing/Forcing.cpp commit 526a8b34eefa6004c84680dee0ebf2ef2e82f629 Author: Jean M. Sexton Date: Tue Nov 3 07:20:24 2020 -0800 Add forcing functions to Nyx class Exec/DrivenTurbulence/Nyx_sources.cpp Source/Nyx.H Source/SourceTerms/Nyx_sources.cpp commit 54e97418dce049dd24d666946539c56815df6127 Author: Ann Almgren Date: Mon Nov 2 19:08:37 2020 -0800 Update info about nightly tests Docs/sphinx_documentation/source/NightlyTests.rst commit 36716cc5545b99bc3c80a218ffc37e91c90e75b2 Author: Ann Almgren Date: Mon Nov 2 18:57:35 2020 -0800 fix typo that made table not show up Docs/sphinx_documentation/source/NightlyTests.rst commit 2f411eb670c70fece6fd2098ab1c699eaba7aa5a Author: Ann Almgren Date: Mon Nov 2 16:38:46 2020 -0800 Remove Network from Make.Nyx and clean up bc_fill* Exec/HydroTests/Make.Nyx Exec/Make.Nyx Source/Src_3d/bc_fill.H Source/Src_3d/bc_fill.cpp commit f2dbb4432b6dc4b3ee0ddc07bf09b35c5d92f251 Author: Ann Almgren Date: Mon Nov 2 16:18:26 2020 -0800 Remove unused Network directory Source/Network/Make.package commit aa4f4adc148c4aa8270ffb1894f49863772344ed Author: Ann Almgren Date: Mon Nov 2 16:17:33 2020 -0800 Remove any references to the master branch. Docs/sphinx_documentation/source/NightlyTests.rst Docs/sphinx_documentation/source/NyxGettingStarted.rst Docs/sphinx_documentation/source/NyxPreface.rst commit f5a0f5bce93cdb2533448f58c52606ad30e7b0af Author: Ann Almgren Date: Mon Nov 2 16:13:15 2020 -0800 fix error message to reflect the right routine Source/update_state_with_sources.cpp commit 379bddb85333c5b1fbcecae4fec0284ef011b301 Author: Ann Almgren Date: Mon Nov 2 15:38:25 2020 -0800 Remove unistd.h from files where it's not needed Source/AGN/AGN_halos.cpp Source/Initialization/read_plotfile.cpp Source/Nyx.cpp Source/Nyx_halos.cpp Source/nyx_main.cpp commit 20faf4ee66508fa9998e81ef95f9d09c7eb96667 Author: Ann Almgren Date: Mon Nov 2 15:33:21 2020 -0800 Remove test on WIN32 to include unistd.h Source/Initialization/read_plotfile.cpp Source/nyx_main.cpp commit c0b2458a58f5748e3f9a977c2f3c21514265a258 Author: Ann Almgren Date: Mon Nov 2 15:25:49 2020 -0800 Remove BL_ARR4_TO_FORTRAN Source/Nyx.H Source/Nyx.cpp commit 47e8abda8226c3104920f0d1c27f291a71d2bd9a Merge: 6fbae933 e447228b Author: Ann Almgren Date: Mon Nov 2 15:10:45 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 6fbae933df33e110f4f57535f8016c8a7b74ff8a Author: Ann Almgren Date: Mon Nov 2 15:10:27 2020 -0800 Remove Nyx_F.H and Gravity_F.H and all references to them. LyA still compiles. Exec/SantaBarbara/Nyx_error.cpp Source/AGN/AGN_halos.cpp Source/AGN/AGN_sources.cpp Source/EOS/eos_adiabatic.H Source/EOS/eos_hc.H Source/EOS/reset_internal_e.H Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Gravity/Gravity_F.H Source/Gravity/Make.package Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_box_3d_stubs.cpp Source/HeatCool/integrate_state_cell_3d.cpp Source/HeatCool/integrate_state_exact_3d.cpp Source/HeatCool/integrate_state_exact_3d_stubs.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp Source/IO/Nyx_output.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Make.package Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_advance.cpp Source/Nyx_halos.cpp Source/Particle/NyxParticles.cpp Source/SourceTerms/Nyx_sources.cpp Source/SourceTerms/Nyx_time_center_sources.cpp Source/advance_particles.cpp Source/comoving.cpp Source/compute_hydro_sources.cpp Source/sdc_hydro.cpp Source/sdc_reactions.cpp Source/strang_hydro.cpp Source/strang_hydro_fuse.cpp Source/strang_reactions.cpp Source/sum_integrated_quantities.cpp Source/sum_utils.cpp Source/update_state_with_sources.cpp commit b1895f61fdc329ad1e5694742e36345445acd088 Author: Jean M. Sexton Date: Mon Nov 2 14:39:50 2020 -0800 Add call to integrate_force_3d Exec/DrivenTurbulence/Nyx_sources.cpp commit 28fb8843ca57ccb8f7c915d69c747bd3d6f6984d Author: Jean M. Sexton Date: Mon Nov 2 13:33:28 2020 -0800 Update problem setup, add do_forcing checks Exec/DrivenTurbulence/Nyx_sources.cpp Exec/DrivenTurbulence/Prob.H Source/IO/Nyx_output.cpp Source/Nyx_advance.cpp Source/sum_integrated_quantities.cpp commit e6aa425af31410e01638ed798218dc145222f9c3 Author: Jean M. Sexton Date: Mon Nov 2 13:04:46 2020 -0800 Fix indexing bug Exec/DrivenTurbulence/Prob_3d.f90 Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp commit 277a2a31c3800e6d59bd06451d8e48af714431fb Author: Jean M. Sexton Date: Mon Nov 2 12:49:15 2020 -0800 DrivenTurbulence compiles Exec/DrivenTurbulence/Nyx_sources.cpp Exec/DrivenTurbulence/inputs Exec/DrivenTurbulence/inputs.regtest Exec/DrivenTurbulence/probin Source/Forcing/Forcing.H Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp Source/Forcing/Make.package Source/IO/Nyx_output.cpp commit e447228b629f109a3b4e2301df269ccd04c0d440 Merge: 63380626 049268af Author: mic84 Date: Mon Nov 2 11:33:14 2020 -0800 Merge pull request #59 from mic84/mr/submodules Add Git submodules for amrex and sundials commit 049268af19281f738d95ad99a5fbbef1dd5228c0 Author: Michele Rosso Date: Mon Nov 2 11:33:42 2020 -0800 Add Git submodules for amrex and sundials .gitmodules subprojects/amrex subprojects/sundials commit 633806266176f0e8ee0f527876a6de3392ccf2fe Merge: d497184e 2f9a857e Author: jmsexton03 Date: Mon Nov 2 14:10:16 2020 -0500 Merge pull request #58 from mclarsen/patch-1 update ascent ghost zone name commit 5437aebba70c07f9de98debbc47a18f4f4bee325 Author: Jean M. Sexton Date: Mon Nov 2 11:02:41 2020 -0800 Skeleton pass at forcing Exec/DrivenTurbulence/Nyx_error.cpp Exec/DrivenTurbulence/Nyx_sources.cpp Exec/DrivenTurbulence/Prob.H commit 2f9a857e74f4a9c955c67335e1fb99dbc30b4815 Author: Matt Larsen Date: Mon Nov 2 09:44:43 2020 -0800 update ascent ghost zone name The ghost zone name in amrex has been updated to the ascent default name. Source/IO/Nyx_output.cpp commit d497184e986298b7571e87a5b5840aebb619b5bb Merge: f2e56bb7 cc88d71a Author: Ann Almgren Date: Sun Nov 1 14:45:53 2020 -0800 Merge branch 'reduce_sum' into development commit f2e56bb78070b3e19bc68ad39f78e1f8e9ba9d4a Author: Ann Almgren Date: Sun Nov 1 14:45:18 2020 -0800 tweaks to README README.md commit cc88d71af6aa885187f870571baee2724c2c30f4 Author: Weiqun Zhang Date: Sun Nov 1 22:09:20 2020 +0000 reimplement reduce sum in Nyx::compute_gas_fractions Source/Nyx.cpp commit 33cacc46d3ec21b846a70323b45379ad917d96bc Author: Ann Almgren Date: Sun Nov 1 13:48:58 2020 -0800 Oops -- accidentally committed GNUmakefile with wrong settings Exec/LyA/GNUmakefile commit 78ef5b0463f7403ff0176b54f61e3f44797317e6 Author: Ann Almgren Date: Sun Nov 1 12:43:02 2020 -0800 Remove USE_CXX_PROB as option -- it is always true now. Exec/AMR-density/GNUmakefile Exec/AMR-density/GNUmakefile.cuda Exec/AMR-zoom/GNUmakefile Exec/GravityTests/zeldovich_dm/build/GNUmakefile Exec/Henson/amr-info/GNUmakefile Exec/Henson/extract-particles/GNUmakefile Exec/Henson/sample-analysis/GNUmakefile Exec/HydroTests/GNUmakefile Exec/HydroTests/Make.Nyx Exec/LyA/GNUmakefile Exec/LyA_Neutrinos/GNUmakefile Exec/Make.Nyx Exec/MiniSB/GNUmakefile Exec/RegressionTest/GNUmakefile Source/Initialization/Make.package Source/Initialization/Nyx_initdata.cpp Source/Nyx.cpp Source/Particle/NyxParticles.cpp Source/SourceTerms/Nyx_sources.cpp Source/Tagging/Make.package Source/Tagging/Nyx_error.cpp commit 7963f1d6f01d6d3a5190823a1e3173460addfae6 Author: Jean M. Sexton Date: Sun Nov 1 11:45:51 2020 -0800 Update orcid paper/paper.md commit 87052a97eb41112fd2585543e0905d00fa4350b6 Author: Ann Almgren Date: Sun Nov 1 10:39:23 2020 -0800 A better start on the JOSS paper paper/paper.bib paper/paper.md commit 5a25bda875478f1abb281f474ea9e65d90899d00 Author: Ann Almgren Date: Sun Nov 1 10:18:18 2020 -0800 Let the precision of the output in the runlog be controlled by a run-time parameter; the default behavior is unchanged but this makes regression testing easier Source/IO/write_info.cpp Source/Nyx.H Source/Nyx.cpp commit edcc6b5b390d77b4cd58afd87553317251d92b05 Author: Ann Almgren Date: Sun Nov 1 09:57:52 2020 -0800 Don't include magvel in the regression testing Exec/LyA/inputs.rt Exec/LyA/inputs.rt.garuda commit 6ec2e5c1c93abb27893ce0ab6ca82eba9a770a32 Author: Zarija Date: Fri Oct 30 17:12:26 2020 -0700 README update README.md commit 7b0898b5f90f3b3955a37d5cec4016ce28c1bd28 Author: Jean M. Sexton Date: Fri Oct 30 12:53:19 2020 -0700 Update HydroTests inputs to use gpu FillPatch Exec/HydroTests/inputs-sod-x Exec/HydroTests/inputs-sod-y Exec/HydroTests/inputs-sod-z Exec/HydroTests/inputs-test2-x Exec/HydroTests/inputs-test2-y Exec/HydroTests/inputs-test2-z Exec/HydroTests/inputs-test3-x Exec/HydroTests/inputs-test3-y Exec/HydroTests/inputs-test3-z Exec/HydroTests/inputs.regtest.sod Exec/HydroTests/inputs.regtest.test2 Exec/HydroTests/inputs.regtest.test3 Exec/HydroTests/inputs.restarttest.test2 commit d5da0d355870ccfcbbf75be9343f0c58ecd945ab Author: Zarija Date: Thu Oct 22 16:18:12 2020 -0700 Fix velocity units in converter Util/convert_all_fields/AmrDerive.cpp commit 1b384ec6de50d6ddc0612a9928b8c537ea7182c2 Author: Jean M. Sexton Date: Tue Oct 20 08:25:03 2020 -0700 Add BL_NO_FORT=TRUE for CXX_PROB=TRUE Exec/HydroTests/Make.Nyx Exec/Make.Nyx commit a5257c19f67f56da28f5c4ba672baf37e679b2a5 Author: Jean M. Sexton Date: Mon Oct 19 11:56:47 2020 -0700 Updated AMR-zoom Exec/AMR-density/GNUmakefile Exec/AMR-zoom/GNUmakefile Exec/AMR-zoom/Make.package Exec/AMR-zoom/Nyx_error.cpp Exec/AMR-zoom/Prob.H Exec/AMR-zoom/Prob_3d.f90 Exec/AMR-zoom/Tagging_3d.f90 Exec/AMR-zoom/inputs Exec/AMR-zoom/probdata.f90 Exec/AMR-zoom/probin Exec/AMR-zoom/rhsfn.f90 Source/DerivedQuantities/Derive.H Source/DerivedQuantities/Derive.cpp Source/Initialization/Nyx_setup.cpp commit 5d3d3df5b659138f9d518258959aebc11e5ebc89 Author: Jean M. Sexton Date: Fri Oct 16 09:16:45 2020 -0700 Move library link order Exec/LyA/GNUmakefile commit 34503fc9d7dfbfd0080077cc566976e35caac0b2 Author: Jean M. Sexton Date: Wed Oct 14 13:29:27 2020 -0700 Fix incorrect comment Exec/AMR-density/inputs.rt commit ad387941d3b937c7db5f80a5c3e12800b4a2a086 Author: Jean M. Sexton Date: Wed Oct 14 13:24:41 2020 -0700 Move USE_FUSED for HEATCOOL=FALSE in makefile Exec/AMR-density/GNUmakefile Exec/LyA/GNUmakefile Exec/LyA_Neutrinos/GNUmakefile commit 0d713d2896a81271ce5ae1bc50fc25c8d9357b05 Author: Jean M. Sexton Date: Wed Oct 14 11:18:44 2020 -0700 Update SUNDIALS_ROOT and inputs.rt in AMR-density Exec/AMR-density/GNUmakefile Exec/AMR-density/inputs.rt commit e5f151fabfd8469c6dfcf8bfe4f2af29b5814bf9 Author: Ann Almgren Date: Wed Oct 14 12:23:59 2020 -0700 remove unused variable Source/Gravity/Gravity.cpp commit e9869feb8bc557d40fcadd1c14c6ea2839be36f7 Author: Jean M. Sexton Date: Wed Oct 14 09:01:13 2020 -0700 Update LyA_Neutrinos and AMR-density makefile Exec/AMR-density/GNUmakefile Exec/LyA_Neutrinos/GNUmakefile commit 5ad126bc4c97571ac998ad660383b2a9d84a36e6 Author: Jean M. Sexton Date: Wed Oct 14 08:56:11 2020 -0700 Update OpenMP SDC vectors Source/HeatCool/integrate_state_with_source_3d.cpp commit a681827a7935475eff36718b32590a5f50620228 Author: Jean M. Sexton Date: Wed Oct 14 08:30:49 2020 -0700 Update sundials fused functions and LyA makefile Exec/LyA/GNUmakefile Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp commit 3f4f923b2aeb7bfb4919780be5f457348624e862 Author: Ann Almgren Date: Wed Oct 14 08:02:48 2020 -0700 Remove TurbForce -- it is superseded by DrivenTurbulence Exec/DrivenTurbulence/Make.package Exec/DrivenTurbulence/Prob.H Exec/TurbForce/Derive_forcing.cpp Exec/TurbForce/Derive_prob_3d.f90 Exec/TurbForce/GNUmakefile Exec/TurbForce/Make.package Exec/TurbForce/Nyx_error.cpp Exec/TurbForce/Prob_3d.f90 Exec/TurbForce/Tagging_3d.f90 Exec/TurbForce/ext_src_3d.f90 Exec/TurbForce/ext_src_force_3d.f90 Exec/TurbForce/inputs Exec/TurbForce/inputs.regtest Exec/TurbForce/integrate_state_force_3d.f90 Exec/TurbForce/probdata.f90 Exec/TurbForce/probin Exec/TurbForce/turbforce.f90 Exec/TurbForce/turbinit.f90 commit f3b0bfed193f8f692acb778dba76297e0a4e299d Author: Jean M. Sexton Date: Tue Oct 13 13:52:41 2020 -0700 Clean up LyA_Neutrinos GNUmakefile, switch inputs to sdc Exec/LyA_Neutrinos/GNUmakefile Exec/LyA_Neutrinos/inputs Exec/LyA_Neutrinos/inputs.rt commit e9e3897048ad9e6b106921f2d110575881c070fe Author: Jean M. Sexton Date: Tue Oct 13 13:49:54 2020 -0700 Clean up AMR-density GNUmakefile, switch inputs to sdc Exec/AMR-density/GNUmakefile Exec/AMR-density/inputs Exec/AMR-density/inputs.rt commit 99bb8b7634d918e210585b01c5ea14aabeb312a8 Author: Jean M. Sexton Date: Tue Oct 13 13:47:00 2020 -0700 Clean up LyA GNUmakefile, switch inputs to sdc Exec/LyA/GNUmakefile Exec/LyA/inputs Exec/LyA/inputs.cuda Exec/LyA/inputs.rt commit e64fe42fd400c25e7d3c440d0283e0da946a4c3a Author: Jean M. Sexton Date: Tue Oct 13 12:23:31 2020 -0700 Update zeldovich test Exec/GravityTests/zeldovich_dm/analysis/process_zeldovich.py Exec/GravityTests/zeldovich_dm/analysis/process_zeldovich_gas.py Exec/GravityTests/zeldovich_dm/build/Prob.H Exec/GravityTests/zeldovich_dm/run_hydro/inputs_hydro commit 85c0eee973d8f7999b031c57377f5d93a69c6004 Author: Jean M. Sexton Date: Tue Oct 13 11:15:15 2020 -0700 Remove zeldovich_dm problem files Exec/GravityTests/zeldovich_dm/build/GNUmakefile Exec/GravityTests/zeldovich_dm/build/Make.package Exec/GravityTests/zeldovich_dm/build/Nyx_error.cpp Exec/GravityTests/zeldovich_dm/build/Prob.H Exec/GravityTests/zeldovich_dm/build/Tagging_3d.f90 Exec/GravityTests/zeldovich_dm/build/probdata.f90 Exec/GravityTests/zeldovich_dm/run/inputs Exec/GravityTests/zeldovich_dm/run/inputs_hydro Exec/GravityTests/zeldovich_dm/run/inputs_wmap7 Exec/GravityTests/zeldovich_dm/run/probin Exec/GravityTests/zeldovich_dm/run_hydro/probin commit 6c19600288a15404510a850c14959012e78319f3 Author: Frederick Davies Date: Tue Feb 18 17:09:25 2020 -0800 modifying zeldovich test Exec/GravityTests/zeldovich_dm/build/GNUmakefile Exec/GravityTests/zeldovich_dm/ics/generate_zeldovich_ics.cpp commit 3b0b21b32f5a023dfed0d279e3c9bc465b8450f4 Author: Frederick Davies Date: Thu Jan 16 16:29:19 2020 -0800 messing with zeldovich Exec/GravityTests/zeldovich_dm/analysis/process_zeldovich.py Exec/GravityTests/zeldovich_dm/analysis/process_zeldovich_gas.py Exec/GravityTests/zeldovich_dm/build/Prob_3d.f90 Exec/GravityTests/zeldovich_dm/run/inputs Exec/GravityTests/zeldovich_dm/run_hydro/inputs_hydro Exec/GravityTests/zeldovich_dm/run_hydro/probin Exec/GravityTests/zeldovich_dm/run_hydro/runlog commit eb1fbcde4dbdbde61cea7d3de2b214ee7b380b02 Author: Jean M. Sexton Date: Tue Oct 13 10:52:34 2020 -0700 Update Scaling problem initialization to match LyA Exec/Scaling/Prob.H commit 1a01c8a0d366b3f51bdb2ec807d8d7180b18cbe4 Author: Jean M. Sexton Date: Tue Oct 13 10:51:01 2020 -0700 Update Scaling problem files Exec/Scaling/Make.package Exec/Scaling/Nyx_error.cpp Exec/Scaling/Prob.H Exec/Scaling/Tagging_3d.f90 Exec/Scaling/inputs Exec/Scaling/inputs.256.noreduceverb Exec/Scaling/inputs_short Exec/Scaling/probdata.f90 Exec/Scaling/probin commit cbdde4b9718f947b833a7230bcf7db13003a51e5 Author: Jean M. Sexton Date: Tue Oct 13 10:44:12 2020 -0700 Update LyA_* and Henson C++ problem setups Exec/Henson/amr-info/Prob.H Exec/Henson/extract-particles/Prob.H Exec/Henson/sample-analysis/Prob.H Exec/LyA_AGN/Prob.H Exec/LyA_Neutrinos/Prob.H commit 86402a0e65abbd85c400198dc39b5baf136bb357 Author: Jean M. Sexton Date: Tue Oct 13 10:41:53 2020 -0700 Update Henson to track LyA problem setup Exec/Henson/amr-info/GNUmakefile Exec/Henson/amr-info/Make.package Exec/Henson/amr-info/Prob.H Exec/Henson/amr-info/Tagging_3d.f90 Exec/Henson/amr-info/probdata.f90 Exec/Henson/extract-particles/GNUmakefile Exec/Henson/extract-particles/Make.package Exec/Henson/extract-particles/Prob.H Exec/Henson/extract-particles/Tagging_3d.f90 Exec/Henson/extract-particles/probdata.f90 Exec/Henson/sample-analysis/GNUmakefile Exec/Henson/sample-analysis/Make.package Exec/Henson/sample-analysis/Prob.H Exec/Henson/sample-analysis/Tagging_3d.f90 Exec/Henson/sample-analysis/probdata.f90 commit 987039c3372490767dcdea5e4e8d8a6710eb4a2a Author: Ann Almgren Date: Tue Oct 13 09:46:12 2020 -0700 Remove SanityCheck directory -- it is obsolete Exec/SanityCheck/GNUmakefile commit 1fe92a8805c6b3c875949ea386759f575440032f Author: Ann Almgren Date: Tue Oct 13 09:45:27 2020 -0700 Remove RayTracing-* directories -- these are out of date Exec/RayTracing-Expanding/GNUmakefile Exec/RayTracing-Expanding/Make.package Exec/RayTracing-Expanding/Nyx_error.cpp Exec/RayTracing-Expanding/Prob_3d.f90 Exec/RayTracing-Expanding/Tagging_3d.f90 Exec/RayTracing-Expanding/atomic_rates.f90 Exec/RayTracing-Expanding/inputs Exec/RayTracing-Expanding/probdata.f90 Exec/RayTracing-Expanding/probin Exec/RayTracing-Expanding/rhsfn.f90 Exec/RayTracing-NonComoving/GNUmakefile Exec/RayTracing-NonComoving/Make.package Exec/RayTracing-NonComoving/Nyx_error.cpp Exec/RayTracing-NonComoving/Prob_3d.f90 Exec/RayTracing-NonComoving/Tagging_3d.f90 Exec/RayTracing-NonComoving/bc_fill_3d.f90 Exec/RayTracing-NonComoving/inputs.3d.sph Exec/RayTracing-NonComoving/inputs.regtest Exec/RayTracing-NonComoving/probdata.f90 Exec/RayTracing-NonComoving/probin.3d.sph commit 477f9b08a6be9468c53e4609c365b79076fb562f Author: Ann Almgren Date: Tue Oct 13 09:44:51 2020 -0700 Remove HDF5_example directory -- it was out of date Exec/HDF5_example/64sssss_20mpc.nyx Exec/HDF5_example/GNUmakefile Exec/HDF5_example/Make.package Exec/HDF5_example/Nyx_error.cpp Exec/HDF5_example/Nyx_output.cpp Exec/HDF5_example/Prob_3d.f90 Exec/HDF5_example/TREECOOL_middle Exec/HDF5_example/Tagging_3d.f90 Exec/HDF5_example/inputs Exec/HDF5_example/knl.sl Exec/HDF5_example/probdata.f90 Exec/HDF5_example/probin Exec/HDF5_example/rhsfn.f90 commit 84e5bdf908f8eb30fcbf9048360f5d3f8418ead4 Author: Jean M. Sexton Date: Mon Oct 12 12:26:44 2020 -0700 Remove VODE, BLAS, Fortran heat-cool tests from Util Exec/HydroTests/Make.Nyx Exec/Make.Nyx Util/BLAS/GPackage.mak Util/BLAS/Make.package Util/BLAS/daxpy.f Util/BLAS/dcopy.f Util/BLAS/ddot.f Util/BLAS/dscal.f Util/BLAS/idamax.f Util/SUNDIALS3/GNUmakefile Util/SUNDIALS3/Make.package Util/SUNDIALS3/SetIC.f90 Util/SUNDIALS3/TREECOOL_middle Util/SUNDIALS3/atomic_rates.F90 Util/SUNDIALS3/comoving_nd.f90 Util/SUNDIALS3/comoving_params.f90 Util/SUNDIALS3/constants_cosmo.f90 Util/SUNDIALS3/constants_mod.f90 Util/SUNDIALS3/cvode_extras.F90 Util/SUNDIALS3/eos_hc.F90 Util/SUNDIALS3/eos_params.f90 Util/SUNDIALS3/f_rhs.F90 Util/SUNDIALS3/init_managed.F90 Util/SUNDIALS3/inputs Util/SUNDIALS3/inputs_atomic Util/SUNDIALS3/inputs_flags Util/SUNDIALS3/inputs_non_vectorized Util/SUNDIALS3/main.cpp Util/SUNDIALS3/meth_params.F90 Util/SUNDIALS3/misc_params.f90 Util/SUNDIALS3/myfunc_F.H Util/SUNDIALS3/ode_mod.f90 Util/SUNDIALS3/reion_aux_module.F90 Util/SUNDIALS3/summitdev.sh Util/SUNDIALS3/vode_aux.F90 Util/SUNDIALS_cuda_cpu_compute/GNUmakefile Util/SUNDIALS_cuda_cpu_compute/Make.package Util/SUNDIALS_cuda_cpu_compute/SetIC.f90 Util/SUNDIALS_cuda_cpu_compute/TREECOOL_middle Util/SUNDIALS_cuda_cpu_compute/atomic_rates.f90 Util/SUNDIALS_cuda_cpu_compute/comoving_nd.f90 Util/SUNDIALS_cuda_cpu_compute/comoving_params.f90 Util/SUNDIALS_cuda_cpu_compute/constants_cosmo.f90 Util/SUNDIALS_cuda_cpu_compute/constants_mod.f90 Util/SUNDIALS_cuda_cpu_compute/eos_hc.f90 Util/SUNDIALS_cuda_cpu_compute/eos_params.f90 Util/SUNDIALS_cuda_cpu_compute/f_rhs.f90 Util/SUNDIALS_cuda_cpu_compute/fcvode_extras.f90 Util/SUNDIALS_cuda_cpu_compute/init_managed.f90 Util/SUNDIALS_cuda_cpu_compute/inputs Util/SUNDIALS_cuda_cpu_compute/inputs_atomic Util/SUNDIALS_cuda_cpu_compute/main.cpp Util/SUNDIALS_cuda_cpu_compute/meth_params.f90 Util/SUNDIALS_cuda_cpu_compute/misc_params.f90 Util/SUNDIALS_cuda_cpu_compute/myfunc_F.H Util/SUNDIALS_cuda_cpu_compute/reion_aux_module.f90 Util/SUNDIALS_cuda_cpu_compute/summitdev.sh Util/SUNDIALS_cuda_cpu_compute/vode_aux.f90 Util/SUNDIALS_serial_test/GNUmakefile Util/SUNDIALS_serial_test/Make.package Util/SUNDIALS_serial_test/SetIC.f90 Util/SUNDIALS_serial_test/TREECOOL_middle Util/SUNDIALS_serial_test/atomic_rates.f90 Util/SUNDIALS_serial_test/comoving_nd.f90 Util/SUNDIALS_serial_test/comoving_params.f90 Util/SUNDIALS_serial_test/constants_cosmo.f90 Util/SUNDIALS_serial_test/constants_mod.f90 Util/SUNDIALS_serial_test/eos_hc.f90 Util/SUNDIALS_serial_test/eos_params.f90 Util/SUNDIALS_serial_test/f_rhs.f90 Util/SUNDIALS_serial_test/fcvode_extras.f90 Util/SUNDIALS_serial_test/init_managed.f90 Util/SUNDIALS_serial_test/inputs Util/SUNDIALS_serial_test/inputs_atomic Util/SUNDIALS_serial_test/main.cpp Util/SUNDIALS_serial_test/meth_params.f90 Util/SUNDIALS_serial_test/misc_params.f90 Util/SUNDIALS_serial_test/myfunc_F.H Util/SUNDIALS_serial_test/reion_aux_module.f90 Util/SUNDIALS_serial_test/summitdev.sh Util/SUNDIALS_serial_test/vode_aux.f90 Util/VODE/GPackage.mak Util/VODE/Make.package Util/VODE/dacopy.f Util/VODE/dewset.f Util/VODE/dgbfa.f Util/VODE/dgbsl.f Util/VODE/dgefa.f Util/VODE/dgesl.f Util/VODE/dumach.f Util/VODE/dvhin.f Util/VODE/dvindy.f Util/VODE/dvjac.f Util/VODE/dvjust.f Util/VODE/dvnlsd.f Util/VODE/dvnorm.f Util/VODE/dvode.f Util/VODE/dvset.f Util/VODE/dvsol.f Util/VODE/dvsrco.f Util/VODE/dvstep.f Util/VODE/iumach.f Util/VODE/ixsav.f Util/VODE/vode.H Util/VODE/xerrwd.f Util/VODE/xsetf.f Util/VODE/xsetun.f Util/VODE3_gpu/Makefile Util/VODE3_gpu/TREECOOL_middle Util/VODE3_gpu/arkode_interface.f90 Util/VODE3_gpu/atomic_rates.cuf Util/VODE3_gpu/atomic_rates.f90 Util/VODE3_gpu/comoving_nd.f90 Util/VODE3_gpu/comoving_params.f90 Util/VODE3_gpu/constants_cosmo.f90 Util/VODE3_gpu/constants_mod.f90 Util/VODE3_gpu/cvode_interface.f90 Util/VODE3_gpu/eos_hc.cuf Util/VODE3_gpu/eos_hc.f90 Util/VODE3_gpu/eos_params.f90 Util/VODE3_gpu/example_hc.out Util/VODE3_gpu/f_rhs.cuf Util/VODE3_gpu/f_rhs.f90 Util/VODE3_gpu/farkode.f90 Util/VODE3_gpu/fcvode.f90 Util/VODE3_gpu/fcvode_extras.f90 Util/VODE3_gpu/fmain.f90 Util/VODE3_gpu/fmain_gpu.cuf Util/VODE3_gpu/fmain_gpu_atomic.cuf Util/VODE3_gpu/fmain_vode.f90 Util/VODE3_gpu/fnvector_serial.f90 Util/VODE3_gpu/fnvector_serial_fprefix.f90 Util/VODE3_gpu/fsunlinsol_dense.f90 Util/VODE3_gpu/fsunmat_dense.f90 Util/VODE3_gpu/inputs_atomic Util/VODE3_gpu/inputs_hc Util/VODE3_gpu/inputs_hc_short Util/VODE3_gpu/integrate_state_vode_3d.cuf Util/VODE3_gpu/integrate_state_vode_3d.f90 Util/VODE3_gpu/meth_params.cuf Util/VODE3_gpu/meth_params.f90 Util/VODE3_gpu/misc_params.f90 Util/VODE3_gpu/reion_aux_module.f90 Util/VODE3_gpu/vode_aux.cuf Util/VODE3_gpu/vode_aux.f90 Util/VODE_test/Makefile Util/VODE_test/TREECOOL_middle Util/VODE_test/atomic_rates.f90 Util/VODE_test/comoving_nd.f90 Util/VODE_test/comoving_params.f90 Util/VODE_test/constants_cosmo.f90 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Util/sdc-test/inputs_flags Util/sdc-test/inputs_non_vectorized Util/sdc-test/main.cpp Util/sdc-test/meth_params.F90 Util/sdc-test/misc_params.f90 Util/sdc-test/myfunc_F.H Util/sdc-test/ode_mod.f90 Util/sdc-test/reion_aux_module.F90 Util/sdc-test/vode_aux.F90 Util/sdc-test/vode_system.H commit 24d366868dcaab13c849a1f0c2757de2e9ba6eb2 Author: Jean M. Sexton Date: Mon Oct 12 12:21:56 2020 -0700 Remove Fortran from Source Source/AGN/agn_3d.f90 Source/AGN/agn_params.f90 Source/Constants/constants_cgs.f90 Source/Constants/constants_cosmo.f90 Source/EOS/atomic_rates.F90 Source/EOS/eos_hc_nd.F90 Source/EOS/eos_stuff.F90 Source/EOS/reion_aux_module.F90 Source/Forcing/ext_src_force_3d.f90 Source/Forcing/forcing_spect.f90 Source/Forcing/integrate_state_force_3d.f90 Source/Gravity/Gravity_nd.f90 Source/Gravity/prescribe_grav_3d.f90 Source/Gravity/prescribe_grav_stub.f90 Source/HeatCool/cvode_extras.F90 Source/HeatCool/farkode_extras.f90 Source/HeatCool/fcvode_extras.f90 Source/HeatCool/fcvode_extras_src.f90 Source/HeatCool/heat_cool_stubs.f90 Source/HeatCool/integrate_state_3d.f90 Source/HeatCool/integrate_state_farkode_3d.f90 Source/HeatCool/integrate_state_farkode_3d_stubs.f90 Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_fcvode_3d_stubs.f90 Source/HeatCool/integrate_state_fcvode_vec_3d.f90 Source/HeatCool/integrate_state_fcvode_vec_3d_stubs.f90 Source/HeatCool/integrate_state_fcvode_with_source_3d.f90 Source/HeatCool/integrate_state_fcvode_with_source_3d_stubs.f90 Source/HeatCool/integrate_state_vode_3d.f90 Source/HeatCool/update.f90 Source/HeatCool/vode_aux.F90 Source/Initialization/cvode_simd.f90 Source/Initialization/init_managed.F90 Source/Network/network.f90 Source/Network/nyx_burner.f90 Source/Nyx_nd.f90 Source/Particle/particle_mod.f90 Source/SourceTerms/ext_src_3d.f90 Source/SourceTerms/ext_src_add_3d.f90 Source/Src_3d/bc_fill_3d.f90 Source/Src_3d/compute_temp_3d.F90 Source/Tagging/Tagging_3d.f90 Source/Tagging/Tagging_part_3d.f90 Source/comoving_nd.f90 Source/comoving_params.f90 Source/eos_params.f90 Source/meth_params.F90 Source/misc_params.f90 Source/uniform01.f90 commit c6fda76739eaa35a0ce9d2f7cdb441a9126c3f83 Author: Jean M. Sexton Date: Mon Oct 12 12:17:14 2020 -0700 Fix negative max_level error from Vector of values in AMRErrorTag Source/Tagging/Nyx_error.cpp commit d17bec1b83624bd33164baf259c27157db51ccca Merge: dc061a03 83840a6c Author: Jean M. Sexton Date: Wed Sep 30 13:59:29 2020 -0700 Merge branch 'development' into ppm commit dc061a0346c363e8f199a919b27d5e7f1bb1afc9 Author: Jean M. Sexton Date: Thu Sep 24 11:13:43 2020 -0400 Remove restrictions from SDC integral Source/HeatCool/integrate_state_with_source_3d.cpp commit af716fc9c7c0956967bc2d8eea710e32fde4a7dd Author: Jean M. Sexton Date: Thu Sep 24 09:44:34 2020 -0400 Add load_balance_start, try adding Default stream back in Source/HeatCool/integrate_state_with_source_3d.cpp Source/Nyx.H Source/Nyx.cpp commit d6b678bb531d6ce8db39fbabb32aa3809f236c9d Author: Jean M. Sexton Date: Thu Sep 24 07:56:56 2020 -0400 Add inhomo_reion temporary data, restore minimize_memory flag to mfiter, fix linking issue with limit_hydro Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/HydroCpp/Hydro.cpp Source/HydroCpp/Utilities.H Source/HydroCpp/Utilities.cpp commit e7fa8ed9aae721043178c6c32c9e0973091cc192 Author: Jean M. Sexton Date: Thu Sep 24 07:44:35 2020 -0400 Update makefile Exec/LyA/GNUmakefile commit ae80422414805867f521aab4e7e772af9642a8a2 Author: Jean M. Sexton Date: Fri Sep 18 16:36:43 2020 -0400 Make f_rhs_data a local variable Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp commit becb4dc4a42139b494281e9e6d31827bad681d37 Author: Ann Almgren Date: Wed Sep 23 13:02:18 2020 -0700 Fix formatting of print statement Source/Gravity/Gravity.cpp commit 7c805fac93cc5ddbb437e63599af83573ded8c25 Author: Jean M. Sexton Date: Fri Sep 18 14:10:13 2020 -0400 Use The_Arena instead of The_Managed_Arena, remove redundant code Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp commit f3495de302b01bf983feceaccf37f5bce4dc9b42 Author: Jean M. Sexton Date: Fri Sep 18 13:20:44 2020 -0400 Use f_rhs_data appropriately, fix sdc gpu statements Source/HeatCool/integrate_state_with_source_3d.cpp Source/sdc_hydro.cpp commit cd1f3010709b45882e8cf427c2f6510e288b60ef Author: Jean M. Sexton Date: Fri Sep 18 07:56:01 2020 -0700 Add AtomicRates dummy pointer for USE_HEATCOOL=FALSE Exec/HydroTests/Prob.H Source/EOS/eos_adiabatic.H Source/Nyx.cpp commit bc2028c76e6f2c3e522dafe3364be9356becfc52 Author: Jean M. Sexton Date: Thu Sep 17 14:55:18 2020 -0700 Fix MPI-only arguments Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp commit 6d7d5e41db2b394ec8dba8ad369c71636b7c533a Author: Jean M. Sexton Date: Thu Sep 17 10:47:19 2020 -0700 Make local copy and host init of f_rhs_data pointer Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp commit c1de171b23b2db05dd6de2f1639c5d899af8531e Author: Jean M. Sexton Date: Thu Sep 17 10:27:34 2020 -0700 Make local copy of atomic_rates pointer Source/EOS/atomic_rates.H Source/EOS/atomic_rates_data.H Source/EOS/atomic_rates_data.cpp Source/HeatCool/f_rhs.H Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp Source/Initialization/Nyx_initdata.cpp Source/Nyx.cpp Source/update_state_with_sources.cpp commit 7aa865a95abf1181bbfc1c00bae7ebdfd3413af3 Author: Jean M. Sexton Date: Thu Sep 17 10:02:48 2020 -0700 More device updates Source/EOS/atomic_rates.H Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp commit f8d673132401acdcb4d9d6d37fcdfddde31198d1 Author: Jean M. Sexton Date: Thu Sep 17 09:53:23 2020 -0700 Remove incorrect device pointers, add host copy Source/EOS/atomic_rates.H Source/EOS/atomic_rates_data.H Source/EOS/atomic_rates_data.cpp Source/HeatCool/f_rhs.H Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/Nyx.cpp commit b7cc7cfe0061615fe41006a41de626815716ccf3 Author: Jean M. Sexton Date: Thu Sep 17 09:25:56 2020 -0700 Compiles but has device vs host issues Source/EOS/atomic_rates.H Source/EOS/atomic_rates_data.H Source/EOS/atomic_rates_data.cpp Source/EOS/eos_hc.H Source/EOS/reset_internal_e.H Source/HeatCool/f_rhs.H Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_vec_3d.cpp Source/HeatCool/integrate_state_with_source_3d.cpp Source/Initialization/Nyx_initdata.cpp Source/Nyx.cpp Source/update_state_with_sources.cpp commit 83840a6c265a0e01c5d086eef842cbf3f216f01c Author: Jean M. Sexton Date: Thu Sep 17 07:43:37 2020 -0700 Add gravity header to sdc Source/sdc_hydro.cpp commit f3df29a37213ae0aae1ba7c4f412d0baa3fcfbde Author: Jean M. Sexton Date: Thu Sep 17 07:43:05 2020 -0700 Remove prints Source/HeatCool/f_rhs_struct.H commit 5e04671bf89159879476590d653d2a3243c5e633 Author: Jean M. Sexton Date: Thu Sep 17 06:59:03 2020 -0700 Fix scaling typo in e_src, change inputs.rt hctype Exec/LyA/inputs.rt Source/HeatCool/Make.package Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/sdc_hydro.cpp commit 88f2fd14539c03fde9244e48e793a45030857895 Author: Jean M. Sexton Date: Wed Sep 16 17:50:46 2020 -0700 Get ode_eos_finalize called and compiling Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/HeatCool/integrate_state_with_source_3d_stubs.cpp Source/sdc_hydro.cpp commit 77338f20077e0e73c24d296def0ca9048a5d2f9f Author: Jean M. Sexton Date: Wed Sep 16 14:27:12 2020 -0700 Create sdc f_rhs arrays and pass a_end through Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/Nyx.H Source/Nyx.cpp Source/sdc_reactions.cpp commit c0670234e36326e240435c42cbf5b745ae77838a Author: Jean M. Sexton Date: Wed Sep 16 10:39:43 2020 -0700 Move USE_FUSED in makefile Exec/LyA/GNUmakefile commit 0dd962c4098d764cfb075e34f49a9b837f570e8d Author: Jean M. Sexton Date: Wed Sep 16 09:25:37 2020 -0700 Fixes compile bugs Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/Nyx.H commit 56152449e2f28c32b4b1938dbdedf0881d75b698 Author: Jean M. Sexton Date: Wed Sep 16 08:41:29 2020 -0700 Update RhsData struct functions Source/HeatCool/Make.package Source/HeatCool/f_rhs_struct.H Source/HeatCool/integrate_state_with_source_3d.cpp Source/sdc_reactions.cpp commit 164e8d4d1a159016324d3c9a1d00f337ce166e32 Author: Jean M. Sexton Date: Wed Sep 16 08:41:03 2020 -0700 Move sdc integrate file Source/HeatCool/integrate_state_with_source_3d.cpp commit 67e88cad943299bf2ae666593e4183ef7e1a04a7 Author: Jean M. Sexton Date: Wed Sep 16 08:46:48 2020 -0700 Force no fortran sundials for USE_CUDA=TRUE Exec/LyA/GNUmakefile commit 974a0e8919437df57fa5e209a88e73d920967282 Author: Jean M. Sexton Date: Tue Sep 15 12:46:42 2020 -0700 Update fused make Exec/LyA/GNUmakefile commit 902cfdbd905c253c9467fa0ee0d51480428eab34 Author: Jean M. Sexton Date: Tue Sep 15 12:44:54 2020 -0700 Further updates for f_rhs Source/HeatCool/f_rhs_struct.H commit c8e7f6bf456d008a233f20af3bbaa68e809d3b6e Author: Jean M. Sexton Date: Tue Sep 15 08:43:08 2020 -0700 Delete extra functions Source/HeatCool/f_rhs_struct.H commit c9f027c5f6b082157390cea5ece21ebfd6da6ffb Author: Jean M. Sexton Date: Tue Sep 15 08:42:42 2020 -0700 Update sdc Source/HeatCool/f_rhs_struct.H Source/sdc_hydro.cpp Source/sdc_reactions.cpp commit c1d24107c94dfe98935acfe4596e00a2b8f19b2f Author: Ann Almgren Date: Mon Sep 14 09:55:02 2020 -0700 Modifications to align with changes in amrex Source/Particle/DarkMatterParticleContainer.cpp commit 5eb157c9989b79837fe6b92ad23688fc1a000cb9 Author: Ann Almgren Date: Mon Sep 14 17:15:54 2020 -0700 Get rid of all reference to BL_NOLINEVALUES Diagnostics/GNUmakefile Exec/HydroTests/Make.Nyx Exec/Make.Nyx Util/convert_all_fields/GNUmakefile Util/convert_amr/GNUmakefile Util/convert_lyaf/GNUmakefile Util/convert_nbody/GNUmakefile commit a53725fa55a8b71c72f896bd14116ce405c509ad Author: Ann Almgren Date: Mon Sep 14 17:08:07 2020 -0700 This is the right regression tests for hydro on but heatcool off. Exec/LyA/inputs.rt.garuda commit 18762f3149806832119565d1d88ce4b11911da68 Merge: 4a8ff07d 4cbace4a Author: Ann Almgren Date: Mon Sep 14 15:47:12 2020 -0700 Merge branch 'ppm' of https://github.com/AMReX-Astro/Nyx into ppm commit 4a8ff07d86102e69f54b3f76f4cbeef956e6183b Author: Ann Almgren Date: Mon Sep 14 15:46:49 2020 -0700 Don't include SUNDIALS if USE_SUNDIALS set to false on the command line Exec/LyA/GNUmakefile commit 4cbace4a31a88856ef3be7dc929b77868197eb71 Author: Jean M. Sexton Date: Mon Sep 14 13:44:04 2020 -0700 Make AtomicRates struct Source/EOS/atomic_rates.H Source/EOS/atomic_rates_data.H Source/EOS/atomic_rates_data.cpp Source/EOS/eos_hc.H Source/HeatCool/f_rhs.H Source/Nyx.cpp commit b3211d79e0b40924114b91a016bd98b069619182 Author: Ann Almgren Date: Mon Sep 14 14:03:13 2020 -0700 We should use ref_ratio rather than "2" when deciding how many ghost cells we need when depositing the effect of ghost particles on the fine grids. Source/Gravity/Gravity.cpp commit ba27d5b5170c5bdcef32fe3554624bc9d7da712b Author: Ann Almgren Date: Mon Sep 14 12:48:13 2020 -0700 Add inputs file to use on garuda for reg testing -- this has hydro but no heatcool Exec/LyA/inputs.rt.garuda commit 658e00dffa7da67198171c260cbda8c5ecd72fd2 Author: Ann Almgren Date: Mon Sep 14 12:36:30 2020 -0700 We no longer need probin in RegressionTest Exec/RegressionTest/probin commit 2c56478a33460eb56295916b9b57bc091c7ebbe7 Author: Ann Almgren Date: Mon Sep 14 12:30:05 2020 -0700 Remove probin file names from the inputs files. Exec/HydroTests/inputs-sod-z Exec/HydroTests/inputs-test2-x Exec/HydroTests/inputs-test2-y Exec/HydroTests/inputs-test2-z Exec/HydroTests/inputs.restarttest.test2 commit 8568e8c62550ad0a94c12703223c0edbd62ea927 Author: Ann Almgren Date: Mon Sep 14 09:55:02 2020 -0700 Modifications to align with changes in amrex Source/Particle/DarkMatterParticleContainer.cpp commit f50f11178eee2a0047ae795f031ea5f23220e946 Merge: fcb5d8a8 58f7f301 Author: Ann Almgren Date: Mon Sep 14 09:05:58 2020 -0700 Merge branch 'ppm' of https://github.com/AMReX-Astro/Nyx into ppm commit fcb5d8a8dca2a5a089fbe229fa55f45960926faf Author: Ann Almgren Date: Mon Sep 14 08:50:27 2020 -0700 Start to clean up the limit_hydro_fluxes routine Source/HydroCpp/Utilities.cpp commit 58f7f301aea61fbc9b28dda1b913b51d38360d6c Author: Jean M. Sexton Date: Mon Sep 14 09:38:28 2020 -0400 Define limit_hydro_fluxes_on_small_dens on ijk, not box Source/HydroCpp/Hydro.cpp Source/HydroCpp/Utilities.H Source/HydroCpp/Utilities.cpp commit 41c22bb7ea31b8308e26ef545052604d154b7200 Author: Jean M. Sexton Date: Mon Sep 14 06:08:58 2020 -0700 Move Sedov <=> sedov, add prob_type Exec/HydroTests/Prob.H Exec/HydroTests/Sedov/GNUmakefile Exec/HydroTests/Sedov/Make.package Exec/HydroTests/Sedov/Prob.H Exec/HydroTests/Sedov/bc_fill.cpp Exec/HydroTests/Sedov/probin.3d.sph Exec/HydroTests/inputs.3d.sph.sedov Exec/HydroTests/inputs.3d.sph.testsuite.sedov Exec/HydroTests/inputs.regtest.sedov commit 095ee1334e8a6c3bebbc09327e3e2431e4563d30 Author: Jean M. Sexton Date: Mon Sep 14 04:39:46 2020 -0700 Delete unused HydroTests files, move TurbForce Exec/HydroTests/DoubleRarefaction/GNUmakefile Exec/HydroTests/DoubleRarefaction/Make.package Exec/HydroTests/DoubleRarefaction/Nyx_error.cpp Exec/HydroTests/DoubleRarefaction/Prob_3d.f90 Exec/HydroTests/DoubleRarefaction/amrvis.defaults Exec/HydroTests/DoubleRarefaction/probdata.f90 Exec/HydroTests/DoubleRarefaction/probin-test2-x Exec/HydroTests/DoubleRarefaction/probin-test2-y Exec/HydroTests/DoubleRarefaction/probin-test2-z Exec/HydroTests/GNUmakefile Exec/HydroTests/StrongShockTube/GNUmakefile Exec/HydroTests/StrongShockTube/Make.package Exec/HydroTests/StrongShockTube/Nyx_error.cpp Exec/HydroTests/StrongShockTube/Prob_3d.f90 Exec/HydroTests/StrongShockTube/probdata.f90 Exec/HydroTests/StrongShockTube/probin-test3-x Exec/HydroTests/StrongShockTube/probin-test3-y Exec/HydroTests/StrongShockTube/probin-test3-z Exec/TurbForce/Derive_forcing.cpp Exec/TurbForce/Derive_prob_3d.f90 Exec/TurbForce/GNUmakefile Exec/TurbForce/Make.package Exec/TurbForce/Nyx_error.cpp Exec/TurbForce/Prob_3d.f90 Exec/TurbForce/Tagging_3d.f90 Exec/TurbForce/ext_src_3d.f90 Exec/TurbForce/ext_src_force_3d.f90 Exec/TurbForce/inputs Exec/TurbForce/inputs.regtest Exec/TurbForce/integrate_state_force_3d.f90 Exec/TurbForce/probdata.f90 Exec/TurbForce/probin Exec/TurbForce/turbforce.f90 Exec/TurbForce/turbinit.f90 commit 87b9e7e64dc0bf41407e7c1acb4974ff68ff288b Author: Jean M. Sexton Date: Mon Sep 14 04:34:22 2020 -0700 Move Sod, DoubleRarefaction, and StrongShockTube Sod <=> sod DoubleRarefaction <=> test2 StrongShockTube <=> test3 Exec/HydroTests/Figure-sod/density_x Exec/HydroTests/Figure-sod/density_y Exec/HydroTests/Figure-sod/density_z Exec/HydroTests/Figure-sod/eint_x Exec/HydroTests/Figure-sod/eint_y Exec/HydroTests/Figure-sod/eint_z Exec/HydroTests/Figure-sod/make_plots.gp Exec/HydroTests/Figure-sod/pressure_x Exec/HydroTests/Figure-sod/pressure_y Exec/HydroTests/Figure-sod/pressure_z Exec/HydroTests/Figure-sod/velocity_x Exec/HydroTests/Figure-sod/velocity_y Exec/HydroTests/Figure-sod/velocity_z Exec/HydroTests/Figure-test2/128/density_x Exec/HydroTests/Figure-test2/128/eint_x Exec/HydroTests/Figure-test2/128/pressure_x Exec/HydroTests/Figure-test2/128/velocity_x Exec/HydroTests/Figure-test2/512/density_x Exec/HydroTests/Figure-test2/512/eint_x Exec/HydroTests/Figure-test2/512/pressure_x Exec/HydroTests/Figure-test2/512/velocity_x Exec/HydroTests/Figure-test2/make_plots.gp Exec/HydroTests/Figure-test3/density_x Exec/HydroTests/Figure-test3/density_y Exec/HydroTests/Figure-test3/density_z Exec/HydroTests/Figure-test3/eint_x Exec/HydroTests/Figure-test3/eint_y Exec/HydroTests/Figure-test3/eint_z Exec/HydroTests/Figure-test3/make_plots.gp Exec/HydroTests/Figure-test3/pressure_x Exec/HydroTests/Figure-test3/pressure_y Exec/HydroTests/Figure-test3/pressure_z Exec/HydroTests/Figure-test3/velocity_x Exec/HydroTests/Figure-test3/velocity_y Exec/HydroTests/Figure-test3/velocity_z Exec/HydroTests/GNUmakefile Exec/HydroTests/Make.package Exec/HydroTests/Prob.H Exec/HydroTests/amrvis.defaults Exec/HydroTests/analytic/exact.ini.sod Exec/HydroTests/analytic/exact.ini.test2 Exec/HydroTests/analytic/exact.ini.test3 Exec/HydroTests/analytic/exact.out Exec/HydroTests/analytic/sod-exact.out Exec/HydroTests/analytic/test3-exact.out Exec/HydroTests/bc_fill.cpp Exec/HydroTests/inputs-sod-x Exec/HydroTests/inputs-sod-y Exec/HydroTests/inputs-sod-z Exec/HydroTests/inputs-test2-x Exec/HydroTests/inputs-test2-y Exec/HydroTests/inputs-test2-z Exec/HydroTests/inputs-test3-x Exec/HydroTests/inputs-test3-y Exec/HydroTests/inputs-test3-z Exec/HydroTests/inputs.regtest.sod Exec/HydroTests/inputs.regtest.test2 Exec/HydroTests/inputs.regtest.test3 Exec/HydroTests/inputs.restarttest.test2 commit e2f0e75028adcedd9051fdd95dd567798b4a3b46 Author: Jean M. Sexton Date: Mon Sep 14 04:06:48 2020 -0700 Use average_temp if no inputs small_pres set Source/Initialization/Nyx_initdata.cpp commit 3b99fc8f1a88cf8d2ae70cfef08479583b9bfa42 Author: Ann Almgren Date: Sun Sep 13 16:55:12 2020 -0700 Remove the flag normalize_species_fluxes -- the default for this is now 1. Source/Hydro/Nyx_advection_util.F90 Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/make_hydro_sources_3d.f90 Source/Initialization/Nyx_setup.cpp Source/Initialization/init_managed.F90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/meth_params.F90 commit 5f5b1363769648006d8ed354fc64d7b2ef5fde82 Author: Ann Almgren Date: Sun Sep 13 14:44:06 2020 -0700 1) Remove the flag "normalize_species_flux" 2) Add the code from Castro to limit fluxes to enforce minimum density -- this is still a WIP Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/Utilities.H Source/HydroCpp/Utilities.cpp Source/Initialization/init_managed.F90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/compute_hydro_sources.cpp Source/meth_params.F90 commit 5670aa64deca387eb41ec1152d929ca41821a72a Author: Jean M. Sexton Date: Sat Sep 12 19:26:39 2020 -0700 Add basic tagging and problem setups Exec/HydroTests/DoubleRarefaction/inputs.regtest commit ca6a19e1e775f881eebe3518487f5727728cdc2e Author: Jean M. Sexton Date: Sat Sep 12 14:49:14 2020 -0700 Update inputs to use prob and tagging flags Exec/HydroTests/StrongShockTube/inputs-x Exec/HydroTests/StrongShockTube/inputs-y Exec/HydroTests/StrongShockTube/inputs-z Exec/HydroTests/StrongShockTube/inputs.regtest commit 5fc0e44323548a12c1e2214a6268c20ae17b40d7 Author: Jean M. Sexton Date: Sat Sep 12 14:01:17 2020 -0700 Fix typo Exec/HydroTests/Sedov/Prob.H commit 784c1c93b095119f9f01e8ffcf5b8e4727a42447 Author: Jean M. Sexton Date: Sat Sep 12 13:59:15 2020 -0700 Use pass-by-reference Exec/AMR-density/Prob.H Exec/HydroTests/Sedov/Prob.H Exec/HydroTests/Sod/Prob.H Exec/LyA/Prob.H Exec/MiniSB/Prob.H Exec/RegressionTest/Prob.H commit d2e155318929630338c66149c6b7f6c7abfb3050 Author: Jean M. Sexton Date: Sat Sep 12 13:45:18 2020 -0700 Fix typo in problem dimension Exec/HydroTests/Sod/Prob.H commit 804f2238fefe92ebf0a694ca9f0b9dd5beda5902 Author: Jean M. Sexton Date: Sat Sep 12 13:41:57 2020 -0700 Add default problem tagging Exec/AMR-density/Prob.H Exec/HydroTests/Sedov/Prob.H Exec/HydroTests/Sod/Prob.H Exec/LyA/Prob.H Exec/LyA/inputs Exec/LyA/inputs.rt Exec/MiniSB/Prob.H Exec/RegressionTest/Prob.H Source/Tagging/Nyx_error.cpp commit 7c323079b106c10032eb6ecd6fc5d90035ef131b Author: Jean M. Sexton Date: Sat Sep 12 13:16:50 2020 -0700 Update probin and tagging defaults for Sod and Sedov Exec/HydroTests/Sedov/Prob.H Exec/HydroTests/Sod/Make.package Exec/HydroTests/Sod/Prob.H Exec/HydroTests/Sod/inputs-sod-x Exec/HydroTests/Sod/inputs-sod-x-short Exec/HydroTests/Sod/inputs-sod-y Exec/HydroTests/Sod/inputs-sod-z Exec/HydroTests/Sod/inputs.regtest Exec/HydroTests/Sod/probin-sod-x Exec/HydroTests/Sod/probin-sod-y Exec/HydroTests/Sod/probin-sod-z commit 449c312de7c8a080b26f329ea1051f814195ca55 Author: Jean M. Sexton Date: Sat Sep 12 12:37:53 2020 -0700 Update C++ bc and problem setup for Sod Exec/HydroTests/Sod/GNUmakefile Exec/HydroTests/Sod/Make.package Exec/HydroTests/Sod/Nyx_error.cpp Exec/HydroTests/Sod/Prob.H Exec/HydroTests/Sod/Prob_3d.f90 Exec/HydroTests/Sod/bc_fill.cpp Exec/HydroTests/Sod/probdata.f90 Source/IndexDefines.H commit 7a07eaf715a95208b07bca374fa836688a61c49c Author: Ann Almgren Date: Sat Sep 12 09:13:55 2020 -0700 1) Fix the deposition of ghost particles to be correct when the effect of the ghost particle spans more than one fine grid 2) Some clean-up including inclusion of cmath. Source/Gravity/Gravity.cpp Source/Initialization/read_plotfile.cpp Source/Particle/AGNParticleContainer.cpp Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NyxParticleContainer.H commit 731df595edfb03d84b0e973146e4234d23184ef9 Author: Ann Almgren Date: Sat Sep 12 09:12:18 2020 -0700 Remove all include cmath lines. Source/Gravity/Gravity.cpp Source/HydroCpp/Godunov.H Source/HydroCpp/PLM.H Source/HydroCpp/PPM.H commit 39b07bdf2d1a49450e5748f82692769c4052b749 Author: Ann Almgren Date: Sat Sep 12 09:04:23 2020 -0700 Remove unneeded includes Source/Gravity/Gravity.cpp commit 32abd11cef15159d767caf214a4ece8010667215 Author: Ann Almgren Date: Sat Sep 12 08:59:37 2020 -0700 Fix the deposition of ghost particles to be correct when the effect of the ghost particle spans more than one fine grid Source/Gravity/Gravity.cpp Source/Particle/DarkMatterParticleContainer.cpp commit a89d34dceecc44b8db9f560c6b0917d360701744 Author: Jean M. Sexton Date: Thu Sep 10 12:31:16 2020 -0700 Remove fortran heating-cooling calls Source/EOS/eos_hc.H Source/HeatCool/Make.package Source/HeatCool/f_rhs.H Source/HeatCool/integrate_state_vec_3d.cpp Source/comoving.cpp Source/strang_reactions.cpp commit 30a8975479d18e847af4f9cba358962ee6d94b13 Author: Jean M. Sexton Date: Thu Sep 10 11:31:57 2020 -0700 Remove print Exec/HydroTests/Sedov/Prob.H commit a029621b9575225f68a7df9d6e7835a398801100 Author: Jean M. Sexton Date: Thu Sep 10 11:20:53 2020 -0700 Update C++ bc and problem setup for Sedov Exec/HydroTests/Sedov/GNUmakefile Exec/HydroTests/Sedov/Make.package Exec/HydroTests/Sedov/Prob.H Exec/HydroTests/Sedov/bc_fill.cpp Source/Nyx.H Source/Src_3d/Make.package Source/Src_3d/bc_fill.H Source/Src_3d/bc_fill.cpp commit a2d37fc1a7c8eb8a5d58b29237c59c0568b661fc Author: Jean M. Sexton Date: Thu Sep 10 09:12:09 2020 -0700 Add Sedov C++ init for prob_type=33 Exec/HydroTests/Sedov/Prob.H Exec/HydroTests/Sedov/inputs.3d.sph Exec/HydroTests/Sedov/inputs.3d.sph.testsuite Exec/HydroTests/Sedov/inputs.regtest commit 2db9a7b560b06cc41733d5773eb3ef70586bfa70 Author: Jean M. Sexton Date: Thu Sep 10 08:19:43 2020 -0700 Add probin parameters for Sedov, update HydroTests Make Exec/HydroTests/Make.Nyx Exec/HydroTests/Sedov/GNUmakefile Exec/HydroTests/Sedov/Make.package Exec/HydroTests/Sedov/Prob.H Exec/HydroTests/Sedov/inputs.3d.sph Exec/HydroTests/Sedov/inputs.3d.sph.testsuite Exec/HydroTests/Sedov/inputs.regtest commit 0836b7b8294de4f72cda33983aea6967e1a89f72 Author: Jean M. Sexton Date: Thu Sep 10 07:53:00 2020 -0700 Update Prob.H to use GeometryData instead of dx Exec/AMR-density/Prob.H Exec/LyA/Prob.H Exec/LyA_AGN/Prob.H Exec/LyA_Neutrinos/Prob.H Exec/MiniSB/Prob.H Exec/RegressionTest/Prob.H Source/Initialization/Nyx_initdata.cpp Source/Particle/NyxParticles.cpp commit 98356d9866508bfc775f32b0213f2eb5cb46bec3 Author: Jean M. Sexton Date: Thu Sep 10 06:46:59 2020 -0700 Update GNUmakefile for LyA* and AMR-density to USE_CONST_SPECIES Exec/AMR-density/GNUmakefile Exec/AMR-density/inputs Exec/AMR-density/inputs.rt Exec/LyA_AGN/GNUmakefile Exec/LyA_Neutrinos/GNUmakefile commit c369bae6fa74b2cf79eebd8e9d545f26150b0644 Author: Jean M. Sexton Date: Thu Sep 10 06:31:05 2020 -0700 Update LyA_AGN problem files Exec/LyA_AGN/Make.package Exec/LyA_AGN/Nyx_error.cpp Exec/LyA_AGN/Prob.H Exec/LyA_AGN/Prob_3d.f90 Exec/LyA_AGN/Tagging_3d.f90 Exec/LyA_AGN/inputs Exec/LyA_AGN/inputs.rt Exec/LyA_AGN/probdata.f90 Exec/LyA_AGN/probin commit f44dcce7e93cbd29da3201781ea86030bbd27cfe Author: Jean M. Sexton Date: Thu Sep 10 06:27:48 2020 -0700 Update LyA_Neutrinos problem files Exec/LyA_Neutrinos/Make.package Exec/LyA_Neutrinos/Nyx_error.cpp Exec/LyA_Neutrinos/Prob.H Exec/LyA_Neutrinos/Prob_3d.F90 Exec/LyA_Neutrinos/Tagging_3d.f90 Exec/LyA_Neutrinos/inputs Exec/LyA_Neutrinos/inputs.no_hydro_64 Exec/LyA_Neutrinos/inputs.rt Exec/LyA_Neutrinos/inputs_gimlet_in_transit.dsc Exec/LyA_Neutrinos/probdata.f90 Exec/LyA_Neutrinos/probin Exec/LyA_Neutrinos/rhsfn.f90 commit 891061a4392979b30e397f1786abbebb961e0cc4 Author: Jean M. Sexton Date: Thu Sep 10 06:22:10 2020 -0700 Change problem-specific variables for LyA initdata Exec/LyA/Prob.H Source/IndexDefines.H Source/Initialization/Nyx_initdata.cpp Source/Particle/NyxParticles.cpp commit ebf47822c3a3c2fc8e74d1329bcaf355547d286b Author: Jean M. Sexton Date: Thu Sep 10 06:21:11 2020 -0700 Remove Sedov problem files Exec/HydroTests/Sedov/Nyx_error.cpp Exec/HydroTests/Sedov/Prob_3d.f90 Exec/HydroTests/Sedov/bc_fill_3d.f90 Exec/HydroTests/Sedov/probdata.f90 commit 2b070c403bf659ae6b0795024ffe62b96ad9f636 Author: Jean M. Sexton Date: Wed Sep 9 13:12:53 2020 -0400 Remove MiniSB problem files Exec/MiniSB/Make.package Exec/MiniSB/Nyx_error.cpp Exec/MiniSB/Tagging_3d.f90 Exec/MiniSB/probdata.f90 commit 3f6082fece584def5419cc05fa67b9fca12c534a Author: Jean M. Sexton Date: Wed Sep 9 13:11:03 2020 -0400 Remove RegressionTest problem files Exec/RegressionTest/Make.package Exec/RegressionTest/Nyx_error.cpp Exec/RegressionTest/Prob_3d.F90 Exec/RegressionTest/Tagging_3d.f90 Exec/RegressionTest/Tagging_part_3d.f90 Exec/RegressionTest/probdata.f90 commit 9c09c3c192f471fd92e7e31c7870e667b78cbc8a Author: Jean M. Sexton Date: Wed Sep 9 13:09:40 2020 -0400 Remove LyA problem files Exec/LyA/Make.package Exec/LyA/Nyx_error.cpp Exec/LyA/Tagging_3d.f90 Exec/LyA/probdata.f90 Exec/LyA/rhsfn.f90 commit 499c7a3efa3383b4d1d1085c935ddf337e4c95d3 Author: Jean M. Sexton Date: Wed Sep 9 13:05:11 2020 -0400 Move refinement input flags to error_setup, remove AMR-density error_setup file Exec/AMR-density/Nyx_error.cpp Source/Nyx.cpp Source/Tagging/Nyx_error.cpp commit 53be836cf62a299c8aedbe2f8512796fcb4008ef Author: Jean M. Sexton Date: Wed Sep 9 13:04:27 2020 -0400 Add denvol and overden to no_hydro_setup Source/Initialization/Nyx_setup.cpp commit 5ccaca6703f003f3bb48b8400d151e0c4edda6b5 Merge: 52282a01 37b9df5c Author: Ann Almgren Date: Wed Sep 9 09:39:08 2020 -0700 Merge branch 'ppm' of https://github.com/AMReX-Astro/Nyx into ppm commit 52282a014ea160b42ed52829ed06cfa85ce14251 Author: Ann Almgren Date: Wed Sep 9 09:36:40 2020 -0700 Make sure all include lines use angle brackets -- no change in functionality expected Source/AGN/AGN_halos.cpp Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/Derive_forcing.cpp Source/EOS/atomic_rates_data.H Source/EOS/eos_adiabatic.cpp Source/EOS/eos_hc.H Source/EOS/eos_hc.cpp Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp Source/Gravity/Gravity.cpp Source/HydroCpp/Godunov.H Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/PLM.H Source/HydroCpp/Riemann.H Source/HydroCpp/Utilities.H Source/HydroCpp/Utilities.cpp Source/IO/Nyx_output.cpp Source/IO/write_info.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/read_plotfile.cpp Source/Monitors/MemInfo.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxBld.cpp Source/Nyx_advance.cpp Source/Nyx_halos.cpp Source/Particle/AGNParticleContainer.H Source/Particle/AGNParticleContainer.cpp Source/Particle/DarkMatterParticleContainer.H Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NeutrinoParticleContainer.H Source/Particle/NeutrinoParticleContainer.cpp Source/Particle/NeutrinoParticles_K.H Source/Particle/NyxParticleContainer.H Source/advance_particles.cpp Source/comoving.cpp Source/compute_hydro_sources.cpp Source/nyx_main.cpp Source/sdc_hydro.cpp Source/sdc_reactions.cpp Source/strang_hydro.cpp Source/strang_hydro_fuse.cpp Source/strang_reactions.cpp Source/sum_integrated_quantities.cpp Source/update_state_with_sources.cpp commit 37b9df5cca90328f23cf2b7fb20aa4c9f941ca70 Author: Jean M. Sexton Date: Fri Sep 4 13:32:51 2020 -0700 Update RegressionTest inputs to use tagging, regtest_reduction, and remove probin Exec/RegressionTest/Make.package Exec/RegressionTest/Nyx_error.cpp Exec/RegressionTest/inputs.2line Exec/RegressionTest/inputs.2line.restarttest Exec/RegressionTest/inputs.mass.nosub Exec/RegressionTest/inputs.mass.sub commit aa067bc4d26ff96f013e121f73e43b4281dec972 Author: Jean M. Sexton Date: Fri Sep 4 14:12:13 2020 -0500 Add correct set_small_values Source/EOS/eos_adiabatic.H Source/EOS/eos_hc.H Source/Initialization/Nyx_initdata.cpp Source/Nyx.H Source/Nyx.cpp commit 1eb26ae564ade97d6deea0db75761a68c317ab0d Author: Jean M. Sexton Date: Fri Sep 4 12:38:06 2020 -0500 Fix AMR-density tagging Exec/AMR-density/inputs.rt Source/DerivedQuantities/Derive.cpp Source/Nyx.H Source/Nyx.cpp commit 0df2f514f78e6102e929ccd5891c4699b32fb6d5 Author: Jean M. Sexton Date: Fri Sep 4 10:20:30 2020 -0500 Add overden, hard-code species names Exec/AMR-density/Nyx_error.cpp Source/DerivedQuantities/Derive.H Source/DerivedQuantities/Derive.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/sum_integrated_quantities.cpp commit 8eae4c48d78aed9f8b8b08f10f51ed7d3e5ec470 Author: Jean M. Sexton Date: Fri Sep 4 08:32:33 2020 -0500 Update inputs files to use refinement criteria Exec/AMR-density/Make.package Exec/AMR-density/inputs Exec/AMR-density/inputs.cuda Exec/AMR-density/inputs.rt Exec/AMR-density/inputs_nohydro.rt Exec/LyA/Make.package Exec/LyA/inputs Exec/LyA/inputs-file-strong Exec/LyA/inputs-random-strong Exec/LyA/inputs-uniform-strong Exec/LyA/inputs.cuda Exec/LyA/inputs.rt Exec/LyA/inputs_nohydro.rt Exec/LyA/run128.summit Exec/LyA/run128.summit.mpi Exec/LyA/run128.summit.mpi.nocuda Exec/LyA/run128.summit.nocuda Source/Nyx.H commit a4d97b381d0a34ffe9ee564555b456fe339dcf68 Author: Jean M. Sexton Date: Fri Sep 4 07:39:56 2020 -0500 MiniSB compiles without fortran, added CXX_PROB ifs for AmrData fortran dependencies Exec/Make.Nyx Exec/MiniSB/Make.package Source/Initialization/Make.package Source/Initialization/Nyx_initdata.cpp Util/BLAS/Make.package commit e846e5ebf993c70c7e5d5ea70fec9d1927a76314 Author: Jean M. Sexton Date: Fri Sep 4 06:50:51 2020 -0500 Add cell volume * density tag Exec/MiniSB/inputs.32.ref Source/DerivedQuantities/Derive.H Source/DerivedQuantities/Derive.cpp Source/Initialization/Nyx_setup.cpp commit 8404540b11f8606a5fed277408289804ac8c0a4a Author: Jean M. Sexton Date: Thu Sep 3 20:41:15 2020 -0500 Add C++ tagging parsing Exec/MiniSB/Nyx_error.cpp Source/Nyx.H Source/Nyx.cpp Source/Tagging/Make.package commit 937af724afdc7ad48fea08d443f0e640b683d482 Author: Weiqun Zhang Date: Thu Sep 3 17:24:02 2020 -0700 fix typo Source/HydroCpp/Riemann.H commit 00911331bec7de9dec579d5315d471f0994f4c16 Author: Weiqun Zhang Date: Thu Sep 3 16:58:47 2020 -0700 changes for DPC++ Source/DerivedQuantities/Derive.cpp Source/EOS/eos_hc.H Source/HeatCool/f_rhs.H Source/HydroCpp/Godunov.H Source/HydroCpp/PPM.H Source/HydroCpp/Riemann.H Source/HydroCpp/Utilities.H Source/Nyx.cpp Source/Particle/AGNParticleContainer.cpp Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NyxParticleContainer.H commit ba95365ef59cebdce6616cfe70700a07fe243fa8 Author: Jean M. Sexton Date: Thu Sep 3 17:05:25 2020 -0500 Make bc_fill C++ Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Src_3d/Make.package Source/Src_3d/bc_fill.cpp commit 6293b117e6617dfd5fee15f0e9ae7664082eae97 Author: Jean M. Sexton Date: Thu Sep 3 09:55:20 2020 -0700 Make small inputs match Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref commit f33a453c850302ee424c1be7be2b91a2dfa134e3 Author: Jean M. Sexton Date: Thu Sep 3 11:28:06 2020 -0500 Update DeviceScalar ifdef to USE_GPU Source/Nyx.cpp commit 3adefb3998340b674496cc2d9ff55b5b9b5eea94 Author: Jean M. Sexton Date: Thu Sep 3 10:54:52 2020 -0500 Add compile guards for atomic_rates files, move more eos functions to headers Source/EOS/Make.package Source/EOS/eos_adiabatic.H Source/EOS/eos_hc.H Source/EOS/eos_hc.cpp Source/EOS/reset_internal_e.H Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp commit 62e5636a4ad8d2b2881d1d5a4b7b1e49062a2b70 Author: Jean M. Sexton Date: Thu Sep 3 05:02:44 2020 -0700 Move atomic_rates to compile only with USE_HEATCOOL=TRUE, fix index for zhi Source/EOS/Make.package Source/Initialization/Nyx_initdata.cpp commit 2265fcdc42de644e93030a35ff696beeab7e4625 Author: Jean M. Sexton Date: Wed Sep 2 18:53:21 2020 -0700 Add back in Tagging, bc_fill, fix small_pres Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp Source/Src_3d/Make.package Source/Src_3d/bc_fill_3d.f90 Source/Tagging/Make.package commit febf3d0130ac757732ba8e910bc7f8da24a45e1a Author: Jean M. Sexton Date: Wed Sep 2 18:20:25 2020 -0700 Remove Fortran from compile path Port init_zhi, integrate_comoving_a_to_z, add small_pres flag and inputs Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Source/AGN/Make.package Source/Constants/Make.package Source/Constants/constants_cosmo.H Source/EOS/Make.package Source/Forcing/Make.package Source/Gravity/Gravity.cpp Source/Gravity/Make.package Source/HeatCool/Make.package Source/IO/Nyx_output.cpp Source/Initialization/Make.package Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Make.package Source/Network/Make.package Source/Nyx.H Source/Nyx.cpp Source/Nyx_advance.cpp Source/Particle/Make.package Source/SourceTerms/Make.package Source/SourceTerms/Nyx_sources.cpp Source/Src_3d/Make.package Source/Tagging/Make.package Source/comoving.cpp Source/nyx_main.cpp Source/strang_reactions.cpp Source/update_state_with_sources.cpp Util/VODE/Make.package commit ab724d78cddb6200e977b82b347a514755ce1534 Author: Jean M. Sexton Date: Tue Sep 1 14:52:50 2020 -0700 Fix cuda ifdef Source/HeatCool/f_rhs.F90 commit f947c27473bd7d22e10f7e0ca0279ea6254e700e Author: Ann Almgren Date: Tue Sep 1 19:53:13 2020 -0700 Need Elixir in loop inside Gravity::get_crse_phi() Source/Gravity/Gravity.cpp commit c7287874bb8aa87ad5a93bba5fa2324c7810835c Author: Ann Almgren Date: Tue Sep 1 19:50:58 2020 -0700 Add Elixir in loop inside Gravity::get_crse_phi -- without this we were crashing for some runs on GPus Source/Gravity/Gravity.cpp commit 447384cdcbcb8d796348e01d98b235a57352c9cc Author: Ann Almgren Date: Tue Sep 1 16:11:04 2020 -0700 Remove small_vel from all calling sequences Source/HydroCpp/Godunov.H Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/Riemann.H Source/HydroCpp/trace_ppm.cpp commit 9e7f0af1d9ac3ca4908ab3a153f42fd217d45c72 Merge: 76e59794 6e94dbfb Author: Ann Almgren Date: Tue Sep 1 16:10:18 2020 -0700 Merge branch 'ppm' of https://github.com/AMReX-Astro/Nyx into ppm commit 76e59794702fbb0b987aab7e7d381f4bb1d0878c Author: Ann Almgren Date: Tue Sep 1 16:10:05 2020 -0700 Removing small_vel .. Source/Nyx.H Source/Nyx.cpp commit 6e94dbfbd6882c2d9c023adeddbe2fd8784035b6 Merge: f697fe8c 3f8a2010 Author: Jean M. Sexton Date: Tue Sep 1 12:33:53 2020 -0700 Merge branch 'eos_hc_cpp' into ppm commit 1c4918a6770668ef49dc26b07c1499af1b2c4730 Merge: a35c31f9 3f8a2010 Author: Ann Almgren Date: Tue Sep 1 11:40:19 2020 -0700 Merge branch 'eos_hc_cpp' into development commit a35c31f9cdb8e098cf20a65a98507a80e88af3ef Author: Jean M. Sexton Date: Mon Aug 31 06:10:36 2020 -0700 Make exponents double precision Source/EOS/atomic_rates.F90 commit 3f8a201064af1103eebfa1165a4bdea389e2339f Author: Jean M. Sexton Date: Mon Aug 31 10:19:56 2020 -0700 Make precision match Source/EOS/atomic_rates.F90 commit 2b72250c4cde3cd8712a50b305e9acdcbdb714c3 Author: Jean M. Sexton Date: Mon Aug 31 05:38:05 2020 -0700 Add pass by reference Source/EOS/eos_hc.H commit 59dc08f8cb53635e52db06d1003d3502213b3777 Author: Jean M. Sexton Date: Mon Aug 31 05:01:37 2020 -0700 Remove extra print Source/EOS/atomic_rates.H commit e93f92c47cd18b630f7e117593aa86005bd4ee5c Author: Jean M. Sexton Date: Thu Aug 27 16:00:00 2020 -0400 Make post_regrid use global redistribute Source/Particle/NyxParticles.cpp commit b17539eb1df55ad36d13402386e678f26c2d6fda Author: Jean M. Sexton Date: Tue Aug 25 16:40:14 2020 -0700 Update SUNDIALS flag Source/Nyx.cpp commit 86bd5b5011064a040c4ca251012f7e1995d43eba Author: Jean M. Sexton Date: Thu Aug 27 08:42:02 2020 -0700 Fix indexing typo for TREECOOL_middle use Source/EOS/atomic_rates_data.H commit 8b4bd3af9eb4be81765c82a6732b5a631c2de5ad Author: Jean M. Sexton Date: Wed Aug 26 10:31:36 2020 -0700 Fix z scaling in energy Source/HeatCool/f_rhs.H commit cf14220daa6f7a999514bc3b077b1822fb834cd1 Author: Jean M. Sexton Date: Tue Aug 25 16:32:46 2020 -0700 Replace fortran f_rhs with C++ f_rhs in integrate_state_vec Source/HeatCool/f_rhs.H Source/HeatCool/integrate_state_vec_3d.cpp Source/Nyx.cpp commit fbc8d150ea234ab290366ddadfaa206042990108 Author: Jean M. Sexton Date: Tue Aug 25 15:12:15 2020 -0700 Compiles f_rhs, hard-coded JH, JHe, gamma_minus_1, uvb_density Source/Constants/constants_cosmo.H Source/EOS/atomic_rates_data.H Source/EOS/atomic_rates_data.cpp Source/EOS/eos_hc.H Source/HeatCool/f_rhs.H Source/Nyx.cpp commit 49fba79be99d1101b394624a66e0fdeb2c806c3e Author: Jean M. Sexton Date: Tue Aug 25 13:44:42 2020 -0700 Update f_rhs Source/EOS/Make.package Source/EOS/eos_hc.H Source/EOS/eos_hc.cpp Source/HeatCool/f_rhs.H commit f697fe8c4323b1f10270ee23561688a8509bca76 Author: Ann Almgren Date: Tue Aug 25 08:59:08 2020 -0700 MiniSB runs don't use probin file any more Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Exec/MiniSB/inputs.analysis Exec/MiniSB/probin commit bdaff228f28497b64568909acd6e87829d4c7b71 Author: Jean M. Sexton Date: Tue Aug 25 08:11:55 2020 -0700 Add f_rhs.H with f_rhs_rpar Source/HeatCool/Make.package Source/HeatCool/f_rhs.H Source/HeatCool/integrate_state_vec_3d.cpp commit c3b31221f6eb9721a063eaeb08994ce2e7569324 Merge: 7f3149da 75ca315e Author: Jean M. Sexton Date: Tue Aug 25 07:13:13 2020 -0700 Merge branch 'development' into eos_hc_cpp commit e6267d9fb243a9000b3dc7a746153fc901f4046a Author: Jean M. Sexton Date: Tue Aug 25 09:38:05 2020 -0400 Remove redundant Nyx_sources.cpp Exec/HydroTests/TurbForce/Nyx_sources.cpp commit 75ca315e73dfad8caf3a85aa79e1c652bd7ca6a3 Author: Jean M. Sexton Date: Tue Aug 25 09:00:33 2020 -0400 Fix GPU compilation errors Source/Hydro/enforce_minimum_density.F90 Source/HydroFortran/Nyx_advection_3d.f90 commit 17462cfe1d6c20d3d4873401eee14d971ffe3ccb Author: Jean M. Sexton Date: Tue Aug 25 07:47:17 2020 -0400 Update fuse Source/Make.package Source/Nyx_advance.cpp Source/strang_hydro_fuse.cpp commit 84d769c496942c5ba7f13eee80dfaba6f272f845 Author: Jean M. Sexton Date: Tue Aug 25 07:15:18 2020 -0400 Make RegressionTest problem setup in C++ Exec/RegressionTest/GNUmakefile Exec/RegressionTest/Make.package Exec/RegressionTest/Prob.H commit ae2a6b43434f0a6cc54404d573ea68476a543a74 Author: Ann Almgren Date: Mon Aug 24 18:53:20 2020 -0700 1) Massive cleanup 2) convert use of nyx.use_const_species runtime input to USE_CONST_SPECIES compile-time input 3) convert Hydro tests to all use USE_CONST_SPECIES = TRUE Exec/DrivenTurbulence/GNUmakefile Exec/DrivenTurbulence/Prob_3d.f90 Exec/DrivenTurbulence/inputs Exec/DrivenTurbulence/inputs.regtest Exec/HydroTests/DoubleRarefaction/GNUmakefile Exec/HydroTests/DoubleRarefaction/Prob_3d.f90 Exec/HydroTests/DoubleRarefaction/inputs-test2-x Exec/HydroTests/DoubleRarefaction/inputs-test2-y Exec/HydroTests/DoubleRarefaction/inputs-test2-z Exec/HydroTests/DoubleRarefaction/inputs.regtest Exec/HydroTests/DoubleRarefaction/inputs.restarttest Exec/HydroTests/Make.Nyx Exec/HydroTests/Sedov/GNUmakefile Exec/HydroTests/Sedov/Prob_3d.f90 Exec/HydroTests/Sedov/inputs.3d.sph Exec/HydroTests/Sedov/inputs.3d.sph.testsuite Exec/HydroTests/Sedov/inputs.regtest Exec/HydroTests/Sod/GNUmakefile Exec/HydroTests/Sod/Prob_3d.f90 Exec/HydroTests/Sod/inputs-sod-x Exec/HydroTests/Sod/inputs-sod-x-short Exec/HydroTests/Sod/inputs-sod-y Exec/HydroTests/Sod/inputs-sod-z Exec/HydroTests/Sod/inputs.regtest Exec/HydroTests/StrongShockTube/GNUmakefile Exec/HydroTests/StrongShockTube/Prob_3d.f90 Exec/HydroTests/StrongShockTube/inputs-x Exec/HydroTests/StrongShockTube/inputs-y Exec/HydroTests/StrongShockTube/inputs-z Exec/HydroTests/StrongShockTube/inputs.regtest Exec/HydroTests/TurbForce/GNUmakefile Exec/HydroTests/TurbForce/Prob_3d.f90 Exec/HydroTests/TurbForce/inputs Exec/HydroTests/TurbForce/inputs.regtest Exec/LyA/GNUmakefile Exec/LyA/inputs.cuda Exec/LyA/inputs.rt Exec/Make.Nyx Exec/MiniSB/GNUmakefile Exec/MiniSB/Make.package Exec/MiniSB/Prob.H Exec/MiniSB/Prob_3d.f90 Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Source/HydroCpp/Hydro.cpp Source/IO/Nyx_output.cpp Source/IndexDefines.H Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/init_managed.F90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/Particle/NyxParticles.cpp Source/meth_params.F90 Source/sdc_hydro.cpp Source/strang_hydro.cpp Source/sum_integrated_quantities.cpp Source/update_state_with_sources.cpp commit e75216ba89fe20856e8960bd9ea5296493f2b94a Author: Ann Almgren Date: Sun Aug 23 17:12:55 2020 -0700 more cleanup .. using QVAR rather than nq Source/HydroCpp/Godunov.H Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.cpp commit c71d8ee04413bb6fd157917dc306e2ab82d88f53 Author: Ann Almgren Date: Sun Aug 23 16:36:07 2020 -0700 Fix oops from before -- NGDNV is 6 but nq is 8 ... we now use QVAR instead of nq Source/HydroCpp/Godunov.cpp Source/HydroCpp/trace_ppm.cpp Source/IndexDefines.H commit e8039e8e7e71f49b219750cd775dc138c1e6cc7a Author: Ann Almgren Date: Sun Aug 23 14:59:31 2020 -0700 remove prob_params ... Source/Initialization/Nyx_setup.cpp Source/Make.package Source/Nyx_nd.f90 Source/meth_params.F90 Source/prob_params.f90 commit 911b0b9a066e8c8b9252e91d43210cfe373dd533 Merge: f2f3e0a8 a4bd7316 Author: Ann Almgren Date: Sun Aug 23 12:12:48 2020 -0700 Merge branch 'ppm' into ppm_jbb commit 6d3f7f8fb587067e17023d1f9d0f73d8bc283807 Author: Ann Almgren Date: Sat Aug 22 15:02:22 2020 -0700 Fix typo Source/HydroFortran/trace_ppm_3d.f90 commit 79b8d66e27929b5aa0ca5ab94ea2cb657140f711 Author: Ann Almgren Date: Sat Aug 22 14:59:49 2020 -0700 Make sure rho_ref and p_ref are max'ed with the floors before constructing qp and qm from Im and Ip. Source/HydroFortran/trace_ppm_3d.f90 commit a4bd73164b6eb190012599cb544846d5067b80c9 Author: Jean M. Sexton Date: Sat Aug 22 13:17:17 2020 -0700 Update do_enforce_minimum_density to use small_temp reset, move to update_state file Source/HydroCpp/Hydro.H Source/update_state_with_sources.cpp commit ad4d4ec97fd8fa3f2137f30dfe9878710f517d77 Author: Jean M. Sexton Date: Sat Aug 22 13:16:22 2020 -0700 Update enforce_minimum_density to use small_temp reset Source/Hydro/Nyx_advection_util.F90 Source/Hydro/enforce_minimum_density.F90 Source/HydroFortran/Nyx_advection_3d.f90 commit 2bf26ed3ee5ddd6c53ccb478a17628a1e52dcb6b Author: Ann Almgren Date: Sat Aug 22 11:37:18 2020 -0700 1) add adot source terms to update_state_with_sources 2) Add UEDEN = UEINT to enforce_minimum_density 3) some formatting Source/HydroCpp/Hydro.H Source/HydroCpp/trace_ppm.cpp Source/update_state_with_sources.cpp commit d419bd62b8e3ab5b8dc75ccd230af920e6d84ab0 Author: Jean M. Sexton Date: Sat Aug 22 09:58:13 2020 -0700 Floor qint_gdpres with small_pres, not just the intermediate gdvn_state_p Source/HydroCpp/Riemann.H commit 7d25d94cc340d93a79fc926a3d01ad55c37db656 Author: Ann Almgren Date: Fri Aug 21 20:31:42 2020 -0700 More cleanup of unused variables Source/Initialization/Nyx_setup.cpp Source/Initialization/init_managed.F90 Source/Nyx_F.H Source/Nyx_nd.f90 Source/meth_params.F90 commit 2e65b06d8ff8caa50bc2cfd0cf4f1d1e6edcb9dd Author: Ann Almgren Date: Fri Aug 21 20:02:56 2020 -0700 More removal of unused variables Source/Initialization/init_managed.F90 Source/Nyx_nd.f90 Source/meth_params.F90 commit 8fb2d5d39d29a9ca566b3c993be993d9c7a095a1 Author: Ann Almgren Date: Fri Aug 21 19:53:23 2020 -0700 Getting rid of unused paremeters/variables Source/HydroCpp/Godunov.H Source/IndexDefines.H Source/Initialization/init_managed.F90 Source/Nyx_nd.f90 Source/meth_params.F90 commit 354a0d794db1c70f9c19accee661655cafc5fcf8 Author: Ann Almgren Date: Fri Aug 21 19:42:34 2020 -0700 Remove GD*, and things associated with npassive ... Source/Initialization/init_managed.F90 Source/Nyx_nd.f90 Source/meth_params.F90 commit f2f3e0a8b81e97fe8fffb8d7f740c1f287c055d9 Author: jbb Date: Fri Aug 21 19:21:50 2020 -0700 modest refactoring of Riemann solver Source/HydroCpp/Godunov.H Source/HydroCpp/Riemann.H commit 7c813158a3ce5178cb0e977aee354d211ab515c8 Merge: 1edc1b57 a7755643 Author: jbb Date: Fri Aug 21 18:34:24 2020 -0700 Merge branch 'ppm' of https://github.com/AMReX-Astro/Nyx into ppm commit a7755643e6842f35988fe5922a0c4578017bf4c1 Author: Ann Almgren Date: Fri Aug 21 18:22:36 2020 -0700 Fix sign error in trans* that only showed up when pressure < small_pres Source/HydroCpp/Godunov.H commit 21d6fc5468ff1d792bd99ad8c6af9d10ad6db72d Author: Ann Almgren Date: Fri Aug 21 17:16:12 2020 -0700 This version works; the previous commit of this file was wrong somehow Source/comoving.cpp commit 1edc1b570abb4792da9dee495fe7e6c30acfa1dc Author: jbb Date: Fri Aug 21 17:00:40 2020 -0700 cosmetic change to sound speed calculation Source/HydroCpp/Godunov.cpp commit ee4a1a7c529cb70e0d4d80150dd9b378e87bc993 Merge: d4b35526 e1fd6c7a Author: Ann Almgren Date: Fri Aug 21 16:01:52 2020 -0700 Merge branch 'ppm' of https://github.com/AMReX-Astro/Nyx into ppm Also clean up unused variables for fewer compiler warnings commit 9b7d9c19aaa29ef69508cafa215c774dba4496d7 Author: Jean M. Sexton Date: Fri Aug 21 15:03:13 2020 -0700 Change HydroFortran enforce_minimum_density floor algorithm Source/HydroFortran/Nyx_advection_3d.f90 commit e1fd6c7acc6749e76ba678093911b8b564ac9a5f Author: jbb Date: Fri Aug 21 12:11:53 2020 -0700 removed duplicate line Source/HydroCpp/Godunov.H commit a68d796638834d52591a2ca9a6bd2aa6d22631bc Merge: 871e3cbb 87f90086 Author: jbb Date: Fri Aug 21 11:22:18 2020 -0700 Merge branch 'ppm' of https://github.com/AMReX-Astro/Nyx into ppm commit 871e3cbbe752950b050e275da28976bdd9762e2e Merge: aa9b0260 d3280123 Author: jbb Date: Fri Aug 21 11:06:31 2020 -0700 Merge branch 'ppm' of https://github.com/AMReX-Astro/Nyx into ppm commit 87f90086e9581238b3d7dfc3ea375d3681debbd6 Author: Jean M. Sexton Date: Fri Aug 21 10:57:36 2020 -0700 Revert "Remove more unused variables" This reverts commit d32801238527bc5cf62c9d814a31e44bcb8335bb. Revert "Remove unused variables to quiet compiler warnings" This reverts commit 0fdaf2a8eba0401d90664c78ca81b291df69ca0f. Source/HydroCpp/Godunov.H Source/HydroCpp/Riemann.H commit 7f3149da451172217a331a1b6e15c322e4a7be0e Author: Jean M. Sexton Date: Fri Aug 21 08:23:25 2020 -0700 Fix include statement Source/EOS/eos_adiabatic.cpp commit 73445772207963fb9c920e2899f7f5de093673c3 Merge: fc7fea7b 96561733 Author: Jean M. Sexton Date: Fri Aug 21 10:05:45 2020 -0700 Merge branch 'development' into eos_hc_cpp commit d4b355263d6c801a90be397cf4fbfb51cd9f4bce Author: Ann Almgren Date: Fri Aug 21 10:02:55 2020 -0700 Revert "Remove more unused variables" This reverts commit d32801238527bc5cf62c9d814a31e44bcb8335bb. Source/HydroCpp/Godunov.H commit c7500525a40dd8d26183c51562b363c71c64f881 Author: Jean M. Sexton Date: Fri Aug 21 10:01:06 2020 -0700 Update SUNDIALS_ROOT and USE_SUNDIALS flags Exec/AMR-density/GNUmakefile Exec/AMR-density/GNUmakefile.cuda Exec/LyA/GNUmakefile commit aa9b0260f75de80a14d42ee91b58e4fe3e490597 Author: jbb Date: Fri Aug 21 09:49:40 2020 -0700 added changes to enforce small press in trans Source/HydroCpp/Godunov.H commit 9656173330ada3fe6b0bfcb76bf95b114568b8d5 Merge: 1da18638 60a6e2c8 Author: Jean M. Sexton Date: Fri Aug 21 09:42:25 2020 -0700 Merge branch 'dev_match' into development commit d32801238527bc5cf62c9d814a31e44bcb8335bb Author: Ann Almgren Date: Fri Aug 21 08:42:20 2020 -0700 Remove more unused variables Source/HydroCpp/Godunov.H commit 0fdaf2a8eba0401d90664c78ca81b291df69ca0f Author: Ann Almgren Date: Fri Aug 21 08:35:25 2020 -0700 Remove unused variables to quiet compiler warnings Source/HydroCpp/Godunov.H Source/HydroCpp/Riemann.H commit 019bfdd7d2123a043b2e1b574ff8c589b24eb0d4 Merge: def8146c f32adab6 Author: Ann Almgren Date: Fri Aug 21 08:21:41 2020 -0700 Merge branch 'ppm' of https://github.com/AMReX-Astro/Nyx into ppm commit def8146c2412e4d0babe9648f3b0f1a672ba626e Author: Ann Almgren Date: Fri Aug 21 08:21:21 2020 -0700 Update to compile on GPUs, courtesy of PeleC folks Source/HydroCpp/trace_ppm.cpp commit f32adab6cdaff7526b51247208a37c822d08a891 Author: Ann Almgren Date: Fri Aug 21 07:55:28 2020 -0700 amrex::Math::sqrt --> std::sqrt Source/Particle/NeutrinoParticles_K.H commit 1b69312d897dd40d4ec92a4c42fcbb69e485b812 Author: Jean M. Sexton Date: Fri Aug 21 08:12:34 2020 -0700 Update inputs files to not use probin Exec/AMR-density/inputs Exec/AMR-density/inputs.cuda Exec/AMR-density/inputs.rt Exec/AMR-density/inputs_nohydro.rt Exec/AMR-density/probin Exec/LyA/inputs Exec/LyA/inputs.256.noreduceverb Exec/LyA/inputs.cuda Exec/LyA/inputs.rt Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA/inputs_hydro1.rt Exec/LyA/inputs_nohydro.rt commit 1da18638ef382bab9f5efb092b6ece7cdc036005 Author: Ann Almgren Date: Fri Aug 21 07:55:28 2020 -0700 amrex::Math::sqrt --> std::sqrt Source/Particle/NeutrinoParticles_K.H commit 60a6e2c8a1ea101a8674e08cd617c1a6f346c696 Author: Jean M. Sexton Date: Thu Aug 20 18:11:00 2020 -0700 Add ONE to csmall max Source/HydroFortran/Nyx_advection_3d.f90 commit 84d85c4f491b6be94fcabe8f6c773f3d4b1c22a6 Author: Jean M. Sexton Date: Thu Aug 20 18:10:11 2020 -0700 Update csmall, small Source/HydroCpp/Godunov.H Source/HydroCpp/Riemann.H Source/Nyx.cpp commit 5fe53f2ac41e9fafa8e6b32ca84d8ff055c69cfe Author: Ann Almgren Date: Thu Aug 20 17:49:14 2020 -0700 changed what we use for csmall Source/HydroFortran/Nyx_advection_3d.f90 commit 81a9aa22987e3013ce7cfaa9268503a9573ba181 Author: Ann Almgren Date: Thu Aug 20 17:40:04 2020 -0700 changed enforcement of small_pres in transverse terms Source/HydroFortran/trans_3d.f90 commit 1d20a2aaad3dfda74fdf14febeb3d7162417d870 Author: Jean M. Sexton Date: Thu Aug 20 17:17:28 2020 -0700 Add QREINT based on gamma-law Source/HydroFortran/trans_3d.f90 commit 6d33135922cd954e28eb584d15bc1ce1adc7e9c8 Author: Jean M. Sexton Date: Thu Aug 20 14:29:45 2020 -0700 Add QREINT based on gamma-law Source/HydroCpp/Godunov.H commit 0285df52a40b3baf80b439ffa1f559c38953d598 Author: Jean M. Sexton Date: Thu Aug 20 10:23:58 2020 -0700 Pass small_pres to flattening Source/HydroCpp/Godunov.H Source/HydroCpp/Godunov.cpp Source/HydroCpp/PLM.H Source/HydroCpp/trace_ppm.cpp commit 71d8cfc02c36d9e830be65d7626db9fa30b04ae9 Author: Ann Almgren Date: Thu Aug 20 09:59:41 2020 -0700 amrex::Math::sqrt --> std::sqrt Source/HydroCpp/Riemann.H commit bb1aeeb658946309155f0cdd8a18775da0ee2299 Author: Jean M. Sexton Date: Thu Aug 20 09:02:54 2020 -0700 Add valid temperature floor for problem setup Source/Initialization/Nyx_initdata.cpp commit 2d5924d7c9769d6e17daab23ea5b7867f9758bcd Author: Jean M. Sexton Date: Thu Aug 20 09:00:49 2020 -0700 Add valid temperature floor for problem setup Source/Initialization/Nyx_initdata.cpp commit 8e158518cbd902f941f7ad24e961ce0604388a52 Author: Jean M. Sexton Date: Thu Aug 20 09:01:51 2020 -0700 Remove prints Source/HydroCpp/Godunov.H Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.H Source/HydroCpp/Riemann.H commit 52a7274df0c38c3f55f5cec58253f4854cbe6dbf Author: Jean M. Sexton Date: Thu Aug 20 08:42:03 2020 -0700 Remove prints Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/trans_3d.f90 commit 4589ea82635e5697d801c8803a46df73a69c2112 Author: Jean M. Sexton Date: Thu Aug 20 07:40:10 2020 -0700 Prints Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/trans_3d.f90 commit 1dacd2bccb61e35e8ee796017557bc58cd0e51b7 Author: Jean M. Sexton Date: Thu Aug 20 07:39:49 2020 -0700 Add forgotten rrnewr<0 reset Source/HydroCpp/Godunov.H Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.H Source/HydroCpp/Riemann.H commit 6d656ea11ff7a54a77ee6037274577baabb76096 Author: Jean M. Sexton Date: Thu Aug 20 07:13:39 2020 -0700 Prints Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.H Source/HydroCpp/Riemann.H Source/HydroCpp/trace_ppm.cpp commit 38b875973fd946aa7e687f427880a7134c4bafec Author: Jean M. Sexton Date: Thu Aug 20 07:13:20 2020 -0700 Prints+ qxpo->qxmo typo fix Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/trans_3d.f90 commit 28ff2b2168511b2df9bcc723617276b64f673c07 Author: Jean M. Sexton Date: Thu Aug 20 07:12:04 2020 -0700 Add reset for rrnewr<0 Source/HydroCpp/Godunov.H commit e46b8c946889b7eb3f1bffd7f0ae07a4d32f15cd Merge: c95b1d55 434a4fa9 Author: Jean M. Sexton Date: Wed Aug 19 14:10:21 2020 -0700 Merge branch 'ppm' into try_match_rel commit 434a4fa92d3509f9a3306bab44c3d3c2ce3b4d7c Author: Jean M. Sexton Date: Wed Aug 19 13:01:33 2020 -0700 Increase valid box size bx->bxg2 Source/HydroCpp/Godunov.cpp commit 94ab55eb0c357ce690324f0b3e2f9e7af357c9f8 Author: Jean M. Sexton Date: Wed Aug 19 11:56:02 2020 -0700 Try matching with just max on small_pres Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/analriem.f90 Source/HydroFortran/trans_3d.f90 commit c95b1d55e038695bd543f62ee5f5a36c28422cf5 Author: Jean M. Sexton Date: Wed Aug 19 11:55:09 2020 -0700 Try matching Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.H Source/HydroCpp/Riemann.H commit 295e85e1ef314fec575e5b1c864c343053699244 Author: Jean M. Sexton Date: Wed Aug 19 09:49:10 2020 -0700 Comment erroneous line Source/HydroFortran/trace_3d.f90 commit 3f4b52acf905427c57b55122f27a8e6f360538a4 Author: Jean M. Sexton Date: Wed Aug 19 08:44:00 2020 -0700 Remove print Source/HydroCpp/PLM.H commit 3c6c0c371255ae5c0b83043858e71810255f9c51 Author: Jean M. Sexton Date: Wed Aug 19 08:41:18 2020 -0700 Remove out of bounds error by increasing box size bxg1 -> bxg2, flatten has contains to test for validity Source/HydroCpp/Godunov.H Source/HydroCpp/Godunov.cpp commit 722a140e2ff614036aa1dec64f7ce9524deef8df Author: Jean M. Sexton Date: Wed Aug 19 08:05:31 2020 -0700 Add small_pres limiters in riemann Source/HydroCpp/Riemann.H commit 413f3db000869f18d47d6320893809e7bc790173 Author: Jean M. Sexton Date: Wed Aug 19 07:54:57 2020 -0700 Remove prints Source/HydroCpp/Hydro.H Source/HydroCpp/Riemann.H commit 080462eb176192a27dc65cf62161e4afa61bdcf5 Author: Jean M. Sexton Date: Wed Aug 19 07:51:06 2020 -0700 Remove ijk print, make default srcQ non-zero Source/HydroCpp/Hydro.H Source/HydroCpp/Riemann.H commit 27bbb554ca0d851a45345d5ee66cf2a905455fdd Author: Jean M. Sexton Date: Wed Aug 19 06:44:09 2020 -0700 Use HydroFortran style csmall, not Castro style csmall Source/HydroCpp/Godunov.H commit 6d678a88411d63ce12715d3384ba3f41c1ee7601 Author: Jean M. Sexton Date: Wed Aug 19 05:26:45 2020 -0700 Fix typo Source/HydroCpp/PLM.H commit 8cc56126bcbeae15c9a489f685009e3b373a07d2 Author: Ann Almgren Date: Tue Aug 18 20:39:07 2020 -0700 This version has the changes we think we need to match the Fortran, but the z-mom blows up in 1 step for MiniSB so something still needs fixing. Source/HydroCpp/Constants.H Source/HydroCpp/Godunov.H Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.H Source/HydroCpp/Make.package Source/HydroCpp/PLM.H Source/HydroCpp/Riemann.H Source/HydroCpp/Utilities.H commit 27ee183b205213a7b66d2d790082b2e62a16bada Author: Ann Almgren Date: Tue Aug 18 20:29:17 2020 -0700 Change how we floor the density and pressure in both PLM and PPM tracing. Source/HydroFortran/trace_3d.f90 Source/HydroFortran/trace_ppm_3d.f90 commit cf380559ca651e8e60c33629aa62c4e67f353f12 Author: Jean M. Sexton Date: Tue Aug 18 10:07:21 2020 -0700 Simplify small_pres limiter in PPM to match Castro Source/HydroFortran/trace_ppm_3d.f90 commit 69c71756ef1fb425aaefc7adaf51d4268ed72ea4 Author: Jean M. Sexton Date: Tue Aug 18 08:18:31 2020 -0700 Fix hdt typo Source/HydroCpp/Godunov.H commit 43d362cfda55c199a787d17d69e08fb1d0281673 Author: Jean M. Sexton Date: Mon Aug 17 14:11:51 2020 -0700 Update limiter for csmall Source/HydroCpp/Godunov.H Source/HydroCpp/Riemann.H commit ac3c721ca0fd0fa4c6eb5557441a596012da647d Author: Ann Almgren Date: Sun Aug 16 15:42:18 2020 -0700 Read in nyx.fix_random_seed flag and if set to 1, call amrex::InitRandomSeed so we can use the same seed across all MPI processes. Source/Initialization/Nyx_initdata.cpp commit 5da8bfff4d0236a9cc08d93a519e90b64aacdafb Author: Ann Almgren Date: Sun Aug 16 15:38:12 2020 -0700 Update the TurbForce regression test so that we use the same seed across MPI ranks because nyx.fix_random_seed = 1 in the inputs.regtest (and we now read it in Nyx_initdata.cpp) Exec/HydroTests/TurbForce/inputs.regtest Exec/HydroTests/TurbForce/integrate_state_force_3d.f90 Exec/HydroTests/TurbForce/turbinit.f90 Source/Initialization/Nyx_initdata.cpp commit 5b8abcc18bad5cd9cf57d54ef3e795245815a790 Author: Ann Almgren Date: Sun Aug 16 15:37:03 2020 -0700 Update the TurbForce regression test so that we use the same seed across MPI ranks because nyx.fix_random_seed = 1 in the inputs.regtest (and we now read it in Nyx_initdata.cpp) Exec/HydroTests/TurbForce/inputs.regtest Exec/HydroTests/TurbForce/integrate_state_force_3d.f90 Exec/HydroTests/TurbForce/turbinit.f90 commit 72ee4778c75dac0cf132b1aae14f5f8ba6776c9d Author: Ann Almgren Date: Sat Aug 15 18:53:15 2020 -0700 more cleanup ... Source/sum_integrated_quantities.cpp Source/update_state_with_sources.cpp commit f2baa38f3ee5bd3c4b1e1b1015a505f99b838bbf Author: Ann Almgren Date: Sat Aug 15 18:24:46 2020 -0700 Some cleanup ... no change on solution Source/HydroCpp/Hydro.cpp Source/sum_integrated_quantities.cpp commit c3b93ceb431da4a4687994958a16650258ab7af6 Author: Ann Almgren Date: Thu Aug 13 17:53:16 2020 -0700 This version sets qp(i,j,k,QREINT) = qp(i,j,k,QPRES) / (gamma - 1) and qm(i,j,k,QREINT) = qm(i,j,k,QPRES) / (gamma - 1) and in the PPM tracing. Castro does not do this (since Castro does not assume a gamma law gas) but the PPM tracing in HydroFortran does. Source/HydroCpp/Hydro.H Source/HydroCpp/trace_ppm.cpp commit 8a2c1b968761f954c15307b976f24feedfc60cbe Author: Ann Almgren Date: Thu Aug 13 17:46:00 2020 -0700 fixed source terms in ppm Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/trace_ppm_3d.f90 commit cb43611adf1bdd08eaf19315d8d7b92e65d3d323 Author: Ann Almgren Date: Thu Aug 13 15:41:59 2020 -0700 fixed indexing bug in plm source terms Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/trace_3d.f90 Source/HydroFortran/trans_3d.f90 commit fc7fea7b195db82d37b3fc5358ab37c033b74a12 Author: Jean M. Sexton Date: Thu Aug 13 12:29:27 2020 -0700 Move constants into seperate header, port iterate_ne to C++ Source/Constants/Make.package Source/Constants/constants_cosmo.H Source/EOS/atomic_rates_data.H Source/EOS/eos_adiabatic.cpp Source/EOS/eos_hc.cpp Source/Nyx.H Source/comoving.cpp commit 9ed59284ecc9ed1dd9a5b2eb0f35b31f7ddb7715 Author: Jean M. Sexton Date: Thu Aug 13 09:15:18 2020 -0700 Rename eos files Source/EOS/Make.package Source/EOS/eos_adiabatic.cpp Source/EOS/eos_hc.cpp Source/EOS/eos_hc_nd.F90 commit 2ab258a778a74fa35e7d1fe92fe7f02dc0e132c4 Author: Jean M. Sexton Date: Thu Aug 13 08:48:08 2020 -0700 Read in rates table Source/EOS/Make.package Source/EOS/atomic_rates.H Source/EOS/atomic_rates_data.H Source/EOS/atomic_rates_data.cpp Source/Initialization/Nyx_setup.cpp commit db058fb993ab4228faf85ac7a6b62326b2b74a39 Author: Ann Almgren Date: Wed Aug 12 15:23:06 2020 -0700 We now incorporate sources *only* in the tracing for both PLM and PPM; there are no longer any contributions from source terms in the "trans" routines. Source/HydroCpp/Godunov.H Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.cpp Source/HydroCpp/PLM.H commit 12986bc163a0c3aa0d8339c774b39a69c5c21623 Author: Jean M. Sexton Date: Sat Jul 18 08:38:19 2020 -0700 Update eos_given_RT Source/EOS/eos_interface.cpp Source/Nyx.H commit d36397d0a05f0a8e95d835bff5e3e0d1d5114bac Author: Jean M. Sexton Date: Mon Jul 6 15:29:55 2020 -0700 Add managed atomic rates data Source/EOS/Make.package Source/EOS/atomic_rates_data.H Source/EOS/atomic_rates_data.cpp commit 37f14b01c9b6efd6577f1a19ded7a1509c2e20ac Author: Ann Almgren Date: Mon Aug 10 18:07:17 2020 -0700 fix typo Source/HydroCpp/trace_ppm.cpp commit 08c0cb77c46829ff32a0bc08749c021f38a486c4 Author: Ann Almgren Date: Mon Aug 10 17:18:18 2020 -0700 fixed dtdxovera in profile integration Source/HydroCpp/trace_ppm.cpp commit e1ceb2ed2efe688635d61674107e48f5ee6f18f4 Author: Ann Almgren Date: Mon Aug 10 15:45:16 2020 -0700 updated ppm Source/HydroFortran/ppm_3d.f90 Source/HydroFortran/trace_ppm_3d.f90 commit 6605fa2e79472d456553a21929331702d62dc657 Author: Ann Almgren Date: Mon Aug 10 15:12:36 2020 -0700 Remove unused variables (commented out) Source/HydroCpp/Riemann.H commit a16033393bf54776e372e94a8fd5fc5751c0ac74 Merge: 6a9e5814 16eb5f8b Author: jbb Date: Mon Aug 10 10:59:41 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 6a9e58148f363c89a3122065cde4319e1ddb72f5 Author: jbb Date: Mon Aug 10 10:57:44 2020 -0700 minor tweak Source/HydroFortran/trace_ppm_3d.f90 commit 16eb5f8b7531f9ea719fc7f64fbc0f589fb929f5 Author: Ann Almgren Date: Sun Aug 9 20:10:33 2020 -0700 1) Fix trans_3d so that ppm_type = 0 (aka PLM) will correctly add the sources in the trans routines -- we used to test on (version_2 == 0) but now we test on (ppm_type == 0 ) 2) Eliminate the run-time parameters: ppm_reference, ppm_reference_eignevectors, ppm_flatten_before_integrals. The new behavior is that of ppm_reference = 1 (same as previous default) and ppm_flatten_before_integrals = 1 (previous default was 0). This should make the PPM regression tests fail. Exec/AMR-density/inputs Exec/AMR-density/inputs.rt Exec/AMR-density/inputs_nohydro.rt Exec/AMR-zoom/inputs Exec/GravityTests/zeldovich_dm/run/inputs Exec/GravityTests/zeldovich_dm/run/inputs_hydro Exec/HDF5_example/inputs Exec/LyA/inputs Exec/LyA/inputs.256.noreduceverb Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA_AGN/inputs Exec/LyA_Neutrinos/inputs Exec/LyA_Neutrinos/inputs.no_hydro_64 Exec/LyA_Neutrinos/inputs_gimlet_in_transit.dsc Exec/RayTracing-Expanding/inputs Exec/Scaling/inputs Exec/Scaling/inputs.256.noreduceverb Exec/Scaling/inputs_short Source/Hydro/ppm_nd.F90 Source/Hydro/trace_ppm.F90 Source/HydroFortran/ppm_3d.f90 Source/HydroFortran/trace_ppm_3d.f90 Source/HydroFortran/trans_3d.f90 Source/Initialization/Nyx_setup.cpp Source/Initialization/init_managed.F90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/meth_params.F90 Util/SUNDIALS3/init_managed.F90 Util/SUNDIALS3/meth_params.F90 Util/SUNDIALS_cuda_cpu_compute/meth_params.f90 Util/SUNDIALS_serial_test/meth_params.f90 Util/VODE3_gpu/meth_params.cuf Util/VODE3_gpu/meth_params.f90 Util/VODE_test/meth_params.f90 Util/sdc-test/init_managed.F90 Util/sdc-test/meth_params.F90 commit d2eb1ef44140e0d6b8cf176c24a1cd66fbec8744 Merge: f811a1fd 5d8b2dec Author: jbb Date: Sun Aug 9 19:09:39 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit f811a1fd590ea00396e633b717232eca184a055c Author: jbb Date: Sun Aug 9 19:09:16 2020 -0700 fixing trace to use ref states as done in castro Source/HydroFortran/trace_ppm_3d.f90 commit 5d8b2dec1d90f600338740d83e67d3eaa2a6762e Author: Ann Almgren Date: Sun Aug 9 19:07:16 2020 -0700 Remove version_2 option -- the code now implements what was previously labeled version_2 = 2. Note this only affects ppm hydro. Exec/Scaling/inputs Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/trace_ppm_3d.f90 Source/HydroFortran/trans_3d.f90 Source/Initialization/Nyx_setup.cpp Source/Initialization/init_managed.F90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/meth_params.F90 Util/SUNDIALS3/init_managed.F90 Util/SUNDIALS3/meth_params.F90 Util/SUNDIALS_cuda_cpu_compute/meth_params.f90 Util/SUNDIALS_serial_test/meth_params.f90 Util/VODE3_gpu/meth_params.cuf Util/VODE3_gpu/meth_params.f90 Util/VODE_test/meth_params.f90 Util/sdc-test/init_managed.F90 Util/sdc-test/meth_params.F90 commit f8d6a48e3f32273a19deb0ba5a395c259a773685 Author: Jean M. Sexton Date: Sun Aug 9 15:48:39 2020 -0700 Remove namespace-dependent macro Source/HydroCpp/Hydro.H commit 2e80740463bcfea4d13a168293390cb68d493aa6 Author: Jean M. Sexton Date: Sun Aug 9 15:46:21 2020 -0700 Add cell-wise enforce_minimum_density Source/HydroCpp/Hydro.H Source/Nyx.cpp Source/update_state_with_sources.cpp commit e56051e29943b87f6db40420cf91f676a0b6fca4 Author: Jean M. Sexton Date: Sun Aug 9 15:20:27 2020 -0700 Add a scaling for flux registers Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp commit 6c10bf3040be2d090073b78380a633e669d19cd2 Author: Jean M. Sexton Date: Sun Aug 9 15:18:46 2020 -0700 Make version_2=0 default for plm Source/Nyx.cpp commit dfc2801bc1410d6ea7a3d9f9de736a82f58c3d63 Author: Ann Almgren Date: Sun Aug 9 08:19:20 2020 -0700 Set default version_2 = 2 in Nyx.cpp -- the previous default was 0. (This is only relevant when ppm_type > 0) Source/Nyx.cpp commit a3be5f68a0db6711735b646ed39a018a75dc4137 Author: Ann Almgren Date: Sat Aug 8 17:39:38 2020 -0700 Move definition of indices into IndexDefines.H (out of Nyx.H) Source/Gravity/Gravity.cpp Source/HydroCpp/Hydro.cpp Source/IndexDefines.H Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 commit 8f26cfaf5922fb15f5940e69ed5ed1e4ae2f06b9 Author: Ann Almgren Date: Sat Aug 8 17:07:35 2020 -0700 ppm_type = 2 --> ppm_type = 1 (since we will no longer support ppm_type = 2) Exec/DrivenTurbulence/inputs Exec/DrivenTurbulence/inputs.regtest Exec/HydroTests/StrongShockTube/inputs.regtest Exec/HydroTests/TurbForce/inputs Exec/HydroTests/TurbForce/inputs.regtest commit 1970b10922f0725bd1129c09233ad835a7bddcea Author: Ann Almgren Date: Sat Aug 8 16:56:27 2020 -0700 Change all inputs files with ppm_type = 2 to have ppm_type = 1 Exec/DrivenTurbulence/inputs Exec/DrivenTurbulence/inputs.regtest Exec/HydroTests/StrongShockTube/inputs.regtest Exec/HydroTests/TurbForce/inputs Exec/HydroTests/TurbForce/inputs.regtest commit 24c904086f06ba227dda1ecc55e2218d942d0aa9 Author: Ann Almgren Date: Sat Aug 8 16:49:00 2020 -0700 Update to flux registers needs to be outside OMP parallel region Source/HydroCpp/Hydro.cpp commit 37b42c68ff18c5595663258429ffc1c38cc8a138 Author: Jean M. Sexton Date: Sat Aug 8 14:33:31 2020 -0700 Update Make.package Source/HydroCpp/Make.package Source/Src_3d/Make.package commit ea3d4c00d3f46b2ff3340cc10b524a482b9bab98 Author: Jean M. Sexton Date: Sat Aug 8 14:17:53 2020 -0700 Remove redundant enfore_nonnegative_species files Source/HydroCpp/enforce_nonnegative_species.F90 Source/Src_3d/enforce_nonnegative_species_3d.f90 commit 7398d4200a046cb24140139c941e1b9810a1912d Author: Ann Almgren Date: Fri Aug 7 22:01:59 2020 -0700 Pass a_old to trace_ppm and divide the source terms by a_old in the ppm tracing Source/HydroCpp/Godunov.cpp Source/HydroCpp/PLM.H Source/HydroCpp/trace_ppm.cpp commit b3d5321d0e75b4a18d7a2bcfb9ff93d8dca4d2b6 Author: Ann Almgren Date: Fri Aug 7 21:43:31 2020 -0700 Remove tabs Source/HydroCpp/Godunov.H Source/HydroCpp/Hydro.H Source/HydroCpp/PLM.H Source/Make.package Source/Nyx.H Source/Nyx.cpp Source/update_state_with_sources.cpp commit 21db28540e463764384293352486380545addd9f Author: Ann Almgren Date: Fri Aug 7 21:42:09 2020 -0700 Remove hydro_convert from inputs files since this branch only has HydroCpp ... Exec/AMR-density/inputs Exec/AMR-density/inputs.cuda Exec/HydroTests/Sedov/inputs.3d.sph.testsuite Exec/HydroTests/Sod/inputs-sod-x-short Exec/LyA/inputs-file-strong Exec/LyA/inputs-random-strong Exec/LyA/inputs-uniform-strong Exec/LyA/inputs.256.noreduceverb Exec/LyA/inputs.cuda Exec/LyA/inputs.rt Exec/LyA/inputs_hydro1.rt Exec/LyA/inputs_nohydro.rt Exec/LyA/test.sh Exec/Scaling/inputs.256.noreduceverb Exec/Scaling/test.sh Source/Nyx.H Source/Nyx.cpp Source/strang_hydro_fuse.cpp commit 33006ce18b1f945053c05a7cade0f4aba63378b5 Author: Ann Almgren Date: Fri Aug 7 21:29:46 2020 -0700 No more C_CellMG in amrex Exec/HydroTests/Make.Nyx Exec/Make.Nyx Source/Gravity/Gravity.cpp commit 149adfcff9ddf9a9a692617f39f323324cd84436 Author: Ann Almgren Date: Fri Aug 7 21:22:28 2020 -0700 There is no longer a Cell_MG directory in amrex Exec/HydroTests/Make.Nyx Exec/Make.Nyx Source/Gravity/Gravity.cpp commit 2dafd56e5a54241ceb2574502614455a799cb60a Author: Ann Almgren Date: Fri Aug 7 21:15:30 2020 -0700 Remove hydro parameters that aren't used by ppm from Castro Source/Initialization/Nyx_setup.cpp Source/Initialization/init_managed.F90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/meth_params.F90 commit 93773f8efbd1c9d325788805a58587ad01ac2d2b Author: Ann Almgren Date: Fri Aug 7 20:50:49 2020 -0700 Get rid of Hydro, HydroFortran , and some flags we don't use anymore in HydroCpp Source/Hydro/Make.package Source/Hydro/Nyx_advection_util.F90 Source/Hydro/Nyx_ctu_fuse.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/Nyx_ctu_nd.F90 Source/Hydro/Nyx_hydro.cpp Source/Hydro/check_for_nan.f90 Source/Hydro/enforce_minimum_density.F90 Source/Hydro/enforce_nonnegative_species.F90 Source/Hydro/flatten_nd.F90 Source/Hydro/ppm_nd.F90 Source/Hydro/riemann_nd.F90 Source/Hydro/riemann_util.F90 Source/Hydro/slope_nd.F90 Source/Hydro/trace_plm.F90 Source/Hydro/trace_ppm.F90 Source/Hydro/trans.F90 Source/HydroFortran/Make.package Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/add_grav_source_3d.f90 Source/HydroFortran/analriem.f90 Source/HydroFortran/enforce_minimum_density_3d.f90 Source/HydroFortran/flatten_3d.f90 Source/HydroFortran/make_hydro_sources_3d.f90 Source/HydroFortran/normalize_species_3d.f90 Source/HydroFortran/ppm_3d.f90 Source/HydroFortran/slope_3d.f90 Source/HydroFortran/trace_3d.f90 Source/HydroFortran/trace_ppm_3d.f90 Source/HydroFortran/trace_src_3d.f90 Source/HydroFortran/trans_3d.f90 Source/Initialization/Nyx_setup.cpp Source/Initialization/init_managed.F90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/meth_params.F90 commit d53e95a12dbcf8a8196d28571d049b7939b6afae Author: Ann Almgren Date: Fri Aug 7 20:10:53 2020 -0700 This version compiles and runs in DEBUG mode. Source/HydroCpp/Godunov.H Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.cpp Source/HydroCpp/PLM.H commit 02c778b20c6bda2dea5acd7ec58e616a99c4be79 Author: Ann Almgren Date: Fri Aug 7 19:52:27 2020 -0700 This compiles and has no dependencies on Nyx.H in HydroCpp/* Source/HydroCpp/Godunov.H Source/HydroCpp/Hydro.H Source/HydroCpp/Make.package Source/HydroCpp/PLM.H Source/HydroCpp/Riemann.H Source/HydroCpp/trace_ppm.cpp Source/IndexDefines.H Source/Make.package Source/Nyx.cpp commit e46b941cf2e26c29a7af00ac03d6dabd1bb625dc Author: Ann Almgren Date: Fri Aug 7 17:33:11 2020 -0700 pass more to trace_ppm Source/HydroCpp/Godunov.cpp Source/HydroCpp/trace_ppm.cpp commit 54ad720f36c8d80494e0e6c54cf86daf051eb7e3 Author: Ann Almgren Date: Fri Aug 7 17:27:28 2020 -0700 pass more to trace_ppm Source/HydroCpp/Godunov.cpp Source/HydroCpp/trace_ppm.cpp commit 99493af39a2b2560f12cc43f8af6a34e911cb7b5 Merge: b11396e5 19dff8a1 Author: Ann Almgren Date: Fri Aug 7 17:20:55 2020 -0700 Merge branch 'ppm' of https://github.com/AMReX-Astro/Nyx into ppm commit b11396e544241d8e137e9233f83f9130d6faa5f3 Author: Ann Almgren Date: Fri Aug 7 17:20:51 2020 -0700 Pass nq Source/HydroCpp/Godunov.cpp commit 19dff8a1ed9667726040836b6025962e61169fc8 Author: jbb Date: Fri Aug 7 17:12:58 2020 -0700 fix typo Source/HydroCpp/Godunov.cpp commit 33244c6bcdca8d785c415b50b97bcdc61c7dd648 Author: Ann Almgren Date: Fri Aug 7 17:10:38 2020 -0700 pass more through to trace_ppm Source/HydroCpp/Godunov.cpp Source/HydroCpp/trace_ppm.cpp commit e12228ba0d2f61b6e172e1490a4267e0bee54d8b Author: Ann Almgren Date: Fri Aug 7 16:58:16 2020 -0700 add to .H file again Source/HydroCpp/Godunov.H commit 27f568184f66f1d7da6b95ceb68f0d9a23b4b452 Author: Ann Almgren Date: Fri Aug 7 16:57:26 2020 -0700 add to .H file Source/HydroCpp/Hydro.H commit b44b5ef606c58762a20f4f1af0dbbc0e56a27c01 Author: Ann Almgren Date: Fri Aug 7 16:55:53 2020 -0700 pass ppm_type through to pc_umdrv Source/HydroCpp/Hydro.cpp commit e1356f684b4a483159998d5e896b1eb7cc1d6a6f Author: jbb Date: Fri Aug 7 16:52:30 2020 -0700 fixed Source/HydroCpp/Godunov.cpp commit 6110edfd70203fe20a3c8584f2f1a7da93d69101 Merge: 6286196a 787eeb47 Author: jbb Date: Fri Aug 7 16:40:35 2020 -0700 Merge branch 'ppm' of https://github.com/AMReX-Astro/Nyx into ppm commit 6286196a2238244d064c88b1da7142bca44b2c5d Author: jbb Date: Fri Aug 7 16:39:01 2020 -0700 starting to link in ppm Exec/HydroTests/Sedov/GNUmakefile Source/HydroCpp/Godunov.cpp Source/HydroCpp/PLM.H Source/HydroCpp/trace_ppm.cpp commit 787eeb477092de7bd2988092717b14344b96e0ed Merge: 91744780 ba5a672a Author: Ann Almgren Date: Fri Aug 7 16:38:10 2020 -0700 Merge branch 'hydro_cpp' into ppm commit ba5a672a2040c75a8674481312b18ecf8ce7ad5a Author: Ann Almgren Date: Fri Aug 7 16:34:44 2020 -0700 We can use bxg1 instead of bxg2 for the Godunov tracing. Source/HydroCpp/Godunov.cpp commit 91744780ef96052064d5283528a98e1612b8fedc Author: Ann Almgren Date: Fri Aug 7 15:31:56 2020 -0700 more tweaks towards compiling Source/HydroCpp/Godunov.cpp Source/HydroCpp/PPM.H Source/HydroCpp/trace_ppm.cpp commit 22cb948d5becee58252249dd2b9d5e1529aa5a00 Author: jbb Date: Fri Aug 7 15:23:34 2020 -0700 added ppm header Source/HydroCpp/Godunov.cpp commit 0d1de1906407887129b84625357ad820ba4d0d33 Merge: 82578c55 7c459af4 Author: jbb Date: Fri Aug 7 15:21:10 2020 -0700 Merge branch 'hydro_cpp' into ppm commit 82578c5555cb7a5fad7ce3c6e9c9e81478d3a405 Merge: 44f83b4b ed259abc Author: jbb Date: Fri Aug 7 15:19:33 2020 -0700 Merge branch 'hydro_cpp' into ppm commit 7c459af46b0b21a8305401384ad41968aaf98ab7 Author: Ann Almgren Date: Fri Aug 7 15:12:21 2020 -0700 Separate out PLM.H from Godunov.H Source/HydroCpp/Godunov.H Source/HydroCpp/Godunov.cpp Source/HydroCpp/Make.package Source/HydroCpp/PLM.H commit ed259abc48c4ee4776bdbff00ea0014ddfc1979d Author: Ann Almgren Date: Fri Aug 7 15:02:05 2020 -0700 Move PLM.* --> Godunov.* since we will have both PLM and PLM options Source/HydroCpp/Godunov.H Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.H Source/HydroCpp/Make.package commit 44f83b4b7c4e7b208c402e69a3fd75475884450a Author: Ann Almgren Date: Fri Aug 7 14:48:24 2020 -0700 Pass the use_flattening flag through Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.cpp commit 20275e8da61ae3fc8502aad856d34e14e61675fd Author: jbb Date: Thu Aug 6 13:54:29 2020 -0700 initial tweaks at adding ppm Source/HydroCpp/Godunov.cpp Source/HydroCpp/trace_ppm.cpp commit 30d620ce6986d19a8fda796aa3ab94d540678f7d Author: Ann Almgren Date: Thu Aug 6 10:24:09 2020 -0700 We can assume that PRIM_SPECIES_HAVE_SOURCES is false Source/HydroCpp/trace_ppm.cpp commit d5a7f399a4bd55b17fbf4d558f4a7ac80f439eee Author: Ann Almgren Date: Thu Aug 6 10:22:16 2020 -0700 1) get rid of AMREX_D_DECL 2) BL_SPACEDIM --> AMREX_SPACEDIM 3) get rid of anything for AMREX_SPACEDIM < 3 Source/HydroCpp/Godunov.cpp Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/PLM.H Source/HydroCpp/trace_plm.cpp Source/HydroCpp/trace_ppm.cpp commit 01b6b20051ab202045a0d3ecf860094780a26266 Author: Ann Almgren Date: Thu Aug 6 10:16:08 2020 -0700 get rid of any mention of radiation Source/HydroCpp/Hydro.cpp Source/HydroCpp/trace_ppm.cpp commit 19875fcb10af166c719a072bf2d84b0644ae36b4 Author: Ann Almgren Date: Thu Aug 6 10:10:56 2020 -0700 more migration Source/HydroCpp/Make.package Source/HydroCpp/PPM.H commit b1b106102368b1d5e5091abe6ad1c49216166a41 Author: Ann Almgren Date: Thu Aug 6 10:10:05 2020 -0700 split PLM.cpp into two separate files Source/HydroCpp/Godunov.cpp Source/HydroCpp/trace_plm.cpp commit a6a303a34cfcc262934a798a918f57c298d7b980 Author: Ann Almgren Date: Thu Aug 6 10:07:48 2020 -0700 Add ppm files borrowed from Castro Source/HydroCpp/ppm.H Source/HydroCpp/trace_ppm.cpp commit 9117d9eba5503c0b937926a4d34b8cc8dd320314 Author: Jean M. Sexton Date: Wed Aug 5 11:49:00 2020 -0700 Add flattening in-place with input flag Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp commit c258fc0bb219fc0f78306e304d8e1d1060498aed Author: Jean M. Sexton Date: Tue Aug 4 14:08:02 2020 -0700 Put add_grav_source in update_state Source/update_state_with_sources.cpp commit c26e2b312856ec8109cce3b2c9d56aad55d55a5f Author: Jean M. Sexton Date: Tue Aug 4 13:27:27 2020 -0700 Add enforce_nonnegative_species to update_state Source/Nyx.cpp Source/update_state_with_sources.cpp commit 300a2672655651feabaf3f81fde111577849c055 Author: Jean M. Sexton Date: Tue Aug 4 13:14:34 2020 -0700 Add example input files Exec/LyA/inputs-file-strong Exec/LyA/inputs-random-strong Exec/LyA/inputs-uniform-strong commit 7a8cc5c033fff23cb42a4cdc0fe7b87b39346f27 Author: Jean M. Sexton Date: Tue Aug 4 12:41:53 2020 -0700 Make USE_CXX_PROB flag Exec/AMR-density/GNUmakefile Exec/AMR-density/GNUmakefile.cuda Exec/LyA/GNUmakefile Exec/LyA/probin Source/Initialization/Nyx_initdata.cpp Source/Nyx.H Source/Nyx.cpp Source/Particle/NyxParticles.cpp commit ba2946377a8712b6e553d9be844121a39a86cc88 Merge: 9be5037f b609035e Author: Jean M. Sexton Date: Tue Aug 4 11:41:46 2020 -0700 Merge branch 'test_cuda11' into hydro_cpp commit 9be5037ff775f00e6ba191d0beb1165e9591216a Author: Jean M. Sexton Date: Tue Aug 4 11:37:07 2020 -0700 Remove prints Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp Source/update_state_with_sources.cpp commit 09aeb5d8794b56367e16729a9ce1c3f7a8974546 Author: Jean M. Sexton Date: Tue Aug 4 09:29:32 2020 -0700 Add back in pdivu Source/HydroCpp/Hydro.H commit e439adf0ea6e0b18c6420775a420bd058e3d11d9 Author: Jean M. Sexton Date: Tue Aug 4 07:28:56 2020 -0700 Update srctoprim, hdt a_old factor (srcrho*rhoinv assumption) Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp Source/update_state_with_sources.cpp commit 82d126b82cc5286ab406de0845022b00fdf26ad4 Author: Jean M. Sexton Date: Mon Aug 3 18:27:50 2020 -0700 Add non-zero a to consup, srctoprim, update, plm Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp Source/update_state_with_sources.cpp commit 2ae3aa0f5a87acd2d6bcc0d1be41599c14856255 Author: Jean M. Sexton Date: Mon Aug 3 11:22:15 2020 -0700 Add grav_vector, fix plm a_old factors Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp Source/Nyx.H Source/compute_hydro_sources.cpp commit 95c10ae8d00e5c54709b9082f0814ee9261a31c0 Author: Jean M. Sexton Date: Fri Jul 31 09:09:25 2020 -0700 Fix typo in transz1 Source/HydroCpp/PLM.H commit ab7b9e55c871051c1a964c3e637fce205c98c86f Author: Jean M. Sexton Date: Thu Jul 30 12:34:44 2020 -0700 Remove prints Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp Source/HydroCpp/Utilities.H commit a516aebc14a204c3f01f00a368203954b807d343 Author: Jean M. Sexton Date: Thu Jul 30 12:21:43 2020 -0700 Match plm_z Source/HydroCpp/PLM.H commit a37cfd0296792f2bccf883d6a1083a3cf9ae9e36 Author: Jean M. Sexton Date: Thu Jul 30 12:15:04 2020 -0700 Match plm_y Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp Source/HydroCpp/Utilities.H commit b59019264d12ef6819665964e3419bdeed4f37e0 Author: Jean M. Sexton Date: Mon Jul 27 15:06:03 2020 -0700 Remove prints Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp Source/HydroCpp/Riemann.H commit a965446627f9641aa3695d716284e8921fc879f0 Author: Jean M. Sexton Date: Mon Jul 27 14:56:41 2020 -0700 Fix c scaling Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp Source/HydroCpp/Riemann.H commit 3c04eada7fe45189f2ad6d494df643295ee4352f Author: Jean M. Sexton Date: Mon Jul 27 10:48:30 2020 -0700 Fix rho scaling in c, plm trace Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp commit 58b168e9756fe3da285a8474e01598de74daa632 Author: Jean M. Sexton Date: Mon Jul 27 08:49:37 2020 -0700 Remove incorrect limiter Source/HydroCpp/PLM.H commit 3a1b39671b315515cf46e19c16f88a4c7ccdc17a Merge: 617cc766 59ab06d2 Author: Jean M. Sexton Date: Mon Jul 27 08:25:21 2020 -0700 Merge branch 'development' into hydro_cpp commit 617cc766568308c21011a7f0786613c1e1386743 Author: Jean M. Sexton Date: Fri Jul 24 17:20:10 2020 -0700 Fix *_ref in plm trace x, change x slopes Source/HydroCpp/PLM.H commit 59ab06d22714cdc382847b72f9c5e2fc50162ac6 Author: Andrew Myers Date: Fri Jul 24 12:08:38 2020 -0700 remove direct access of id and cpu, which will be removed from amrex Exec/Henson/extract-particles/main.cpp Source/Particle/DarkMatterParticleContainer.cpp commit b609035e522f3163aac700b440e4a1f1388b5056 Author: Jean M. Sexton Date: Thu Jul 23 14:03:27 2020 -0400 Move AMR-density and LyA to cpp problem init Exec/AMR-density/Make.package Exec/AMR-density/Prob.H Exec/AMR-density/Prob_3d.F90 Exec/LyA/Make.package Exec/LyA/Prob.H Exec/LyA/Prob_3d.F90 Source/Initialization/Nyx_initdata.cpp Source/Nyx.H Source/Particle/NyxParticles.cpp commit ff615dde04d98c586422a73ff6fec6246e1801cc Author: Jean M. Sexton Date: Thu Jul 23 13:53:30 2020 -0400 Make eos cpp functions not member functions Source/EOS/eos_interface.cpp Source/Nyx.H commit ce3ab4a9bfc9f9fd4f250510689ebb17b467f57c Author: Jean M. Sexton Date: Thu Jul 23 11:12:00 2020 -0400 Port enforce_nonnegative_density to C++ Source/Nyx.cpp commit ae24cccadde4527e8ff001fcea59f42f01169a45 Author: Jean M. Sexton Date: Thu Jul 23 10:35:06 2020 -0400 Fix "error: Implicit capture of 'this' in extended lambda expression" Source/Particle/DarkMatterParticleContainer.H Source/Particle/DarkMatterParticleContainer.cpp commit 893df10b8caeaff9d249b5ec87aeaab3290d7c49 Author: Jean M. Sexton Date: Thu Jul 23 10:10:37 2020 -0400 Fix NOHYDRO sundials compile error Exec/LyA/GNUmakefile commit 694daae7824f51228e0c2bc97239f964886450e0 Author: Jean M. Sexton Date: Wed Jul 22 10:19:05 2020 -0400 Add particle derived fields to blueprint for NO_HYDRO * particle_mass_density, particle_count, particle_x_velocity, particle_y_velocity, particle_z_velocity * Fix inputs plot_int Exec/LyA/ascent_actions_nohydro.yaml Exec/LyA/inputs Source/IO/Nyx_output.cpp commit 1c7c9e0f37fa63cef8a3837743e8902d0e74e1a7 Author: Jean M. Sexton Date: Tue Jul 21 13:12:34 2020 -0700 Fix cuda compile Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp Source/Nyx.cpp commit c3f0662081b9b7fb42ad1036138514fd82d77094 Author: Jean M. Sexton Date: Tue Jul 21 11:40:02 2020 -0700 Change location of dt factor to fix flux registers Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/update_state_with_sources.cpp commit 17535d81529ddbc7057db068cb44399ea63bb315 Author: Jean M. Sexton Date: Tue Jul 21 11:22:47 2020 -0700 Update index ordering for consistency Source/Nyx.H commit f12b0f4daf3efd3487118d57b003b7f9c53b9b3a Author: Jean M. Sexton Date: Tue Jul 21 09:32:59 2020 -0700 Use p=e*(gamma_minus_1) Source/HydroCpp/PLM.H commit 92297a70f9e8bdd8a78086939d17a0600ba3f519 Author: Jean M. Sexton Date: Mon Jul 20 16:06:16 2020 -0700 Make AMR-density regression format consistent with LyA format Exec/AMR-density/inputs.rt commit 57cbf5f2ebe5e88d4dba0ed79c7b480e530b0b81 Author: Jean M. Sexton Date: Thu Jun 25 17:11:42 2020 -0400 Test outputs Exec/LyA/GNUmakefile Exec/LyA_Neutrinos/GNUmakefile Exec/LyA_Neutrinos/GNUmakefile.cuda Exec/LyA_Neutrinos/ascent_actions.yaml Exec/LyA_Neutrinos/inputs.rt Source/IO/Nyx_output.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp commit 31010a938f83f25f7e89e40d745cbc7e4cfaf16f Author: zarija Date: Mon Jul 20 14:45:00 2020 -0700 Remove particle count, fix hdf5 field names in converter Util/convert_all_fields/AmrDerive.cpp commit 8599608caa3b73288b441aa5207b739599bc9efc Author: Jean M. Sexton Date: Mon Jul 20 10:34:50 2020 -0700 Fix scope in Riemann Source/HydroCpp/Riemann.H commit 92f155d845aafa9d67b48cdf5d4f7c96c9c99352 Author: Jean M. Sexton Date: Sun Jul 19 14:30:28 2020 -0700 Hack out species defines, add small inputs Exec/HydroTests/Sod/inputs-sod-x-short Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/IndexDefines.H Source/Initialization/Nyx_setup.cpp commit a66145f47e212c881ea2b053af76264c61c54d55 Author: Jean M. Sexton Date: Sat Jul 18 18:22:30 2020 -0700 Add uin and gamma factor to pdivu Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp commit 311ad535451d5303ba08b4ab50c91a5502f3c4be Author: Jean M. Sexton Date: Sat Jul 18 18:19:20 2020 -0700 Fix a_old, a_new, dt order Source/compute_hydro_sources.cpp commit 448909547c6be6a658927eb6771988d9b69d3be4 Author: Andrew Myers Date: Fri Jul 17 15:47:01 2020 -0700 Reimplement sumParticleMass using general, GPU-capable reductions (#55) * reimplement sumParticleMass using general, GPU-capable reductions * add particle validity check Source/Particle/NyxParticleContainer.H commit 067caa1da9094da2b38b8cafcfa9dfb62a1fad71 Author: Andrew Myers Date: Fri Jul 17 15:47:01 2020 -0700 Reimplement sumParticleMass using general, GPU-capable reductions (#55) * reimplement sumParticleMass using general, GPU-capable reductions * add particle validity check Source/Particle/NyxParticleContainer.H commit d4dc1eb76de593bc8f5b5c0365154cf16678b524 Author: Jean M. Sexton Date: Fri Jul 17 13:22:03 2020 -0700 Fix pdivu Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp commit be9236c5df8746346dbfeee328927df25f375fdc Author: Ann Almgren Date: Thu Jul 16 15:28:50 2020 -0700 remove remaining write statement "LEAVING ROUTINE" Source/HydroCpp/Riemann.H commit cd27f0f75e3ec78c6c54ba54d5a29866f43b3e57 Author: Jean M. Sexton Date: Thu Jul 16 15:17:26 2020 -0700 Fix abs Source/HydroCpp/PLM.cpp Source/HydroCpp/Riemann.H commit 5e986d4bce84496d7ef9b491b95216a5d4f98f80 Author: Jean M. Sexton Date: Thu Jul 16 14:50:08 2020 -0700 Move reset_internal_e to C++ Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Src_3d/Make.package Source/Src_3d/reset_internal_energy_3d.F90 commit 7452458fcfec094ca94d86728270c38886bb0986 Author: Ann Almgren Date: Thu Jul 16 14:13:27 2020 -0700 get rid of all (of Ann's) print statements Source/HydroCpp/PLM.H commit 83f4f4820d804990d123bdcef0836908b7cb4734 Author: Jean M. Sexton Date: Thu Jul 16 14:05:45 2020 -0700 Use QREINT for c Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp commit 8853be9da6dbd2fcb473bd42c89276b24806672b Author: Jean M. Sexton Date: Thu Jul 16 13:24:34 2020 -0700 Fix cavg Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp commit 7c170c78062f95ec5de53d6703323e5a08eafefe Author: Jean M. Sexton Date: Thu Jul 16 12:18:17 2020 -0700 Add small_dens limiter for rl, rr Source/HydroCpp/Riemann.H commit a7604f326c758b9c82424e859e72094ba7d5d452 Author: Jean M. Sexton Date: Thu Jul 16 12:17:49 2020 -0700 Remove indxmap Source/HydroCpp/IndexDefines.H Source/HydroCpp/IndexDefines.cpp Source/HydroCpp/Make.package Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp commit 6796638a283e38b79ab02ce84c212837cfe2c058 Author: Ann Almgren Date: Thu Jul 16 11:57:37 2020 -0700 No more "QC" and mostly got rid of "qaux" Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/IndexDefines.H Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp Source/HydroCpp/Utilities.H commit 989cbeda02b933e18462ce22006f208d96f4564e Merge: 5f62c6ad 7fb093f4 Author: Ann Almgren Date: Thu Jul 16 11:42:05 2020 -0700 Merge branch 'hydro_cpp' of https://github.com/AMReX-Astro/Nyx into hydro_cpp commit 5f62c6ade8d8a648dad0d33311961aa4745315d1 Author: Ann Almgren Date: Thu Jul 16 11:35:32 2020 -0700 No more GAMC in PLM.H (now we pass gamma_minus_1 instead) Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/IndexDefines.H Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp commit 7fb093f48e2c5f84c38a5cc595a86d633f420687 Author: Jean M. Sexton Date: Thu Jul 16 11:21:13 2020 -0700 Pass NumSpec and gamma Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp commit 5e86d87f4566385560da738bcf2c33c15dc7eee6 Author: Ann Almgren Date: Thu Jul 16 09:42:55 2020 -0700 Add analytic Riemann solver Source/HydroCpp/Riemann.H commit 193f88ddca0adfee8dd2c1218f32c5ef0f13e917 Author: Jean M. Sexton Date: Thu Jul 16 12:26:54 2020 -0400 Fix compile Source/HydroCpp/Riemann.H commit 0fdde61031353591909baaee3dff24354a7e43e1 Author: Jean M. Sexton Date: Thu Jul 16 12:19:55 2020 -0400 Remove old comments, add variables Source/HydroCpp/Riemann.H commit 2127da265fce38578fbbbd3aaafa987bd198aa13 Author: Jean M. Sexton Date: Thu Jul 16 11:15:50 2020 -0400 Start matching Riemann eos variables Source/HydroCpp/PLM.H Source/HydroCpp/Riemann.H commit f26091482385b2add75fe024434c14597c526749 Author: Ann Almgren Date: Wed Jul 15 18:29:58 2020 -0700 Getting close to running without crashing ... Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/IndexDefines.H Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp Source/HydroCpp/Riemann.H Source/HydroCpp/Utilities.H Source/HydroCpp/Utilities.cpp Source/Initialization/Nyx_initdata.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_nd.f90 commit 85bee211d5ce0e4a0fce6d41449c9f895f6f4812 Author: Ann Almgren Date: Wed Jul 15 14:20:09 2020 -0700 Remove "exit" and print statement Source/HydroCpp/Hydro.cpp Source/HydroCpp/PLM.cpp commit 01ec15a20bcdc064e5b18eb83fad9da7359f1f50 Author: Ann Almgren Date: Wed Jul 15 14:17:42 2020 -0700 1) define gamma_minus_1 as Real not int 2) define nq = q.nComp() and use nq instead of QVAR for loops 3) pass nq in to pc_umeth_3D 4) get rid of 1D and 2D versions Source/HydroCpp/Hydro.cpp Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp commit b3ce1abdd1bea8c2b261f019ef3162e79d1f963b Author: Jean M. Sexton Date: Fri Jul 10 11:24:49 2020 -0700 Partially update srctoprim Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/Riemann.H Source/HydroCpp/Utilities.H Source/Nyx.H Source/compute_hydro_sources.cpp commit 9c4436b8bfb2b66cd3970bb4efeb1037802843b2 Author: Jean M. Sexton Date: Thu Jul 9 11:50:24 2020 -0700 Update ctoprim Source/HydroCpp/Hydro.cpp Source/HydroCpp/IndexDefines.H Source/HydroCpp/Utilities.H Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp commit d19a40d0414d4a3018ae374c8bf75eea6d925cf8 Author: Jean M. Sexton Date: Wed Jul 8 10:28:56 2020 -0700 Fix indentation Source/HydroCpp/Hydro.cpp Source/IO/Nyx_output.cpp Source/compute_hydro_sources.cpp Source/update_state_with_sources.cpp commit c5d5cd46a9d83c66d427ac299e155c813988c9db Author: Jean M. Sexton Date: Wed Jul 8 10:19:58 2020 -0700 Remove NVAR and UTEMP to fix indexing segfault Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/IndexDefines.H Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp Source/HydroCpp/Utilities.H Source/Nyx.cpp commit db6595a89cfaf03c40a97e2c6160cc9c583dbba7 Author: Ann Almgren Date: Wed Jul 8 10:50:26 2020 -0700 Get this to compile in debug mode Source/HydroCpp/Hydro.cpp Source/HydroCpp/Make.package Source/HydroCpp/enforce_nonnegative_species.F90 commit 7e6b6b85bfe75d6194b6bcd503a1dad92c20ddc3 Author: Jean M. Sexton Date: Wed Jul 8 08:45:03 2020 -0700 Call update hydro, compiles Sedov Source/strang_hydro.cpp Source/update_state_with_sources.cpp commit 9becc439c3bcef33f53d6b9ee32878811c30756f Author: Jean M. Sexton Date: Wed Jul 8 05:35:08 2020 -0700 Call compute/construct hydro Source/HydroCpp/Hydro.cpp Source/HydroCpp/Make.package Source/HydroCpp/PLM.H Source/Nyx.H Source/compute_hydro_sources.cpp Source/strang_hydro.cpp commit fe0669a307901e92b75937b7e719fb1fe29d2671 Author: Jean M. Sexton Date: Wed Jul 8 04:42:31 2020 -0700 Use Multifab fluxes w/ FluxRegister Source/HydroCpp/Hydro.cpp Source/Nyx.H commit 1383cb0ac7ccec05f40b9e84d62c7948b4e59a7d Author: Jean M. Sexton Date: Tue Jul 7 18:36:22 2020 -0700 Add redundant area/volume Source/HydroCpp/Hydro.cpp Source/Nyx.H commit ecced5d584c0388881406f452505436775eb0491 Author: Ann Almgren Date: Tue Jul 7 18:07:25 2020 -0700 a little closer to compiling ... Source/HydroCpp/Hydro.cpp Source/Nyx.H commit d232ef9322954928a8c358a7c1df0ec79fd74681 Author: Jean M. Sexton Date: Tue Jul 7 15:07:51 2020 -0700 Comment EOS, add prototype Source/HydroCpp/Riemann.H Source/HydroCpp/Utilities.H Source/HydroCpp/Utilities.cpp Source/Nyx.H commit 502e366d3e58ae382584047cbd030b81137bd435 Author: Ann Almgren Date: Tue Jul 7 13:54:04 2020 -0700 hard-wire NUM_SPECIES to 2 Source/HydroCpp/IndexDefines.H commit 7b96e9c71566c2c24fc4f6589a053ce9d69f4a71 Author: Ann Almgren Date: Tue Jul 7 13:51:41 2020 -0700 update more files Exec/HydroTests/Make.Nyx Exec/Make.Nyx Source/HydroCpp/Constants.H Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/IndexDefines.H Source/HydroCpp/PLM.H Source/HydroCpp/Riemann.H Source/HydroCpp/Utilities.H Source/HydroCpp/Utilities.cpp commit 1d4c2064c6ead4409af48a737680e02d94484623 Author: Ann Almgren Date: Tue Jul 7 13:46:03 2020 -0700 more files Source/HydroCpp/Make.package Source/HydroCpp/PLM.H Source/HydroCpp/PLM.cpp commit 4c1903301d4c6b6fe8f46ca58e39a4c0421f7ad6 Author: Ann Almgren Date: Tue Jul 7 13:41:39 2020 -0700 Start new directory for cpp hydro Source/HydroCpp/Hydro.H Source/HydroCpp/Hydro.cpp Source/HydroCpp/IndexDefines.H Source/HydroCpp/IndexDefines.cpp Source/HydroCpp/Make.package Source/HydroCpp/PLM.H Source/HydroCpp/Riemann.H commit 5d76c79a83b4c7bcabcef839cdb127eb046126ba Author: Jean M. Sexton Date: Thu Jun 18 18:56:54 2020 -0400 First pass hdf5 plotfile Exec/LyA/GNUmakefile Exec/LyA/inputs.cuda Source/IO/Nyx_output.cpp Source/Nyx.H Source/Nyx.cpp commit f80923dfddf16e838296ac5cbf570d00adf552f2 Author: Jean M. Sexton Date: Wed Jun 17 17:52:25 2020 -0400 Fix typo Exec/LyA/GNUmakefile commit 54699dd3c511c45a777d0da314b4ea978120247e Author: Jean M. Sexton Date: Tue Jun 16 19:22:07 2020 -0400 Update hacked paths Exec/LyA/GNUmakefile commit 26cb4a9a7889e0452d8259e38283c8e9d74281e3 Author: Jean M. Sexton Date: Tue Jun 16 15:25:04 2020 -0400 First pass: Reeber halo print Exec/LyA/GNUmakefile Source/IO/Nyx_output.cpp Source/Nyx.H Source/Nyx_halos.cpp commit 69a9df04e47e38b97f4b20e0e1e5e31cf8d7267b Author: Jean M. Sexton Date: Mon Jun 15 19:52:28 2020 -0700 Update tabs Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_halos.cpp commit a4918a5a8f0e7864141141bdd642919ba6ccb669 Author: Jean M. Sexton Date: Mon Jun 15 19:39:24 2020 -0700 Fix derive Source/Nyx.cpp commit e84117d8caa88976f591373cbd360ee53cefb202 Author: Jean M. Sexton Date: Mon Jun 15 20:32:02 2020 -0400 Make particle-only blueprint for NO_HYDRO Source/IO/Nyx_output.cpp commit 8d3d97b0725c70d062d15abdaf1981fd8625f0af Author: Jean M. Sexton Date: Mon Jun 15 19:08:48 2020 -0400 Hack Source/Particle/NyxParticles.cpp commit 24632bb7ce376af699539cab83e73db56819b456 Author: Jean M. Sexton Date: Mon Jun 15 18:07:49 2020 -0400 Use AmrLevel write Source/IO/Nyx_output.cpp commit fb5aea772e49ed7a2318bd0a40a595a34ad9ec96 Author: Jean M. Sexton Date: Mon Jun 15 18:02:23 2020 -0400 Update make Exec/LyA/GNUmakefile Exec/LyA/GNUmakefile.cuda commit e35ed93c7c745b81469ec0f313eb6d095802b100 Author: Jean M. Sexton Date: Mon Jun 15 16:30:14 2020 -0400 Update path Exec/LyA/GNUmakefile commit 2332f1f82345b85dcd07bc4584ec11c4354792fc Author: Jean M. Sexton Date: Mon Jun 15 13:35:44 2020 -0700 Add flags to input files Exec/LyA/inputs Exec/LyA/inputs.cuda commit 4f60d214e5b5dfb744068f073809f671dd4f5395 Author: Jean M. Sexton Date: Mon Jun 15 12:58:22 2020 -0700 Update compiler flag verbosity Exec/LyA/GNUmakefile commit fb3069bc95ac5d1116b46cfb57b0aacea0052752 Author: Jean M. Sexton Date: Mon Jun 15 12:29:30 2020 -0700 Add verbosity guards Source/IO/Nyx_output.cpp Source/Nyx_halos.cpp commit ef57a24062953b584eb99d5af5adf00fca8d18b8 Author: Jean M. Sexton Date: Mon Jun 15 12:19:10 2020 -0700 Add insitu flags Source/Nyx.H Source/Nyx.cpp commit b6b1d6ddd2340b0d281b70d3d6c8dfae14becc02 Author: Jean M. Sexton Date: Mon Jun 15 12:10:45 2020 -0700 Move halo_find to insitu Source/IO/Nyx_output.cpp Source/Nyx.cpp commit efc9af63a89dcf4ecd4b2e0c5c10aff8fdc1f6c7 Author: Jean M. Sexton Date: Mon Jun 15 12:05:07 2020 -0700 Seperate blueprint call from write_info Exec/LyA/inputs Source/IO/Nyx_output.cpp Source/IO/write_info.cpp Source/Nyx.H Source/Nyx.cpp commit a6233db59fb0bd8bb9cfa33875d88273d180b64e Merge: 32c837df bd7fe8a9 Author: Jean M. Sexton Date: Mon Jun 15 08:39:13 2020 -0700 Merge branch 'ascent' into development commit 32c837dfb5ec4abc875fc57d2743d1fb46e49a41 Author: Jean M. Sexton Date: Thu Jun 11 10:43:01 2020 -0700 Move agn-related functions to AGN folder Exec/Make.Nyx Source/AGN/AGN_halos.cpp Source/AGN/Make.package Source/Make.package Source/Nyx.H Source/Nyx.cpp Source/Nyx_halos.cpp commit a3cd891b74b284e59dc9ba20b2ccfdc1d749ef2a Author: Jean M. Sexton Date: Tue Jun 9 10:51:17 2020 -0700 Update ifdef for particle vels Source/Initialization/Nyx_setup.cpp commit 53001aaede54edbd0efe101fed9e1db1213700dc Author: zarija Date: Mon Jun 8 16:58:11 2020 -0700 Mac .gitignore commit 73efa288bdb8e6bcb6a8a9c3e71001f6b2b0cce5 Author: zarija Date: Mon Jun 8 16:53:52 2020 -0700 Missing NO_HYDRO flags Source/Nyx.cpp commit e58b2b7b6bafcad0552d809933162e06d31b1285 Author: Jean M. Sexton Date: Mon Jun 8 19:02:38 2020 -0400 Remove cgs constant Source/Nyx.H commit ced10081abede7ea246b07b8fe6ff6f1081ce563 Author: Jean M. Sexton Date: Mon Jun 8 19:01:39 2020 -0400 Remove if guards on particle velocities Source/Initialization/Nyx_setup.cpp commit 74b981271acbbb481572c27cd1d939571e8abdf7 Author: Jean M. Sexton Date: Mon Jun 8 19:00:52 2020 -0400 Fix ifndef NO_HYDRO Source/Initialization/Nyx_initdata.cpp Source/Nyx_advance.cpp commit 3d75e4f49eb3c045b1ffee60b6530c6259255de9 Author: Ann Almgren Date: Mon Jun 8 12:48:48 2020 -0700 This is the current version being used on battra Util/regression_testing/Nyx-tests.ini commit da9d640b002b33bfb965e2fe3c35c78a12171e02 Author: Ann Almgren Date: Mon Jun 8 12:33:06 2020 -0700 don't need extra inputs.rt file Exec/LyA_Neutrinos/inputs.rt.battra commit dd700253bb6cf846cedf6fac8ef20b7bbdb53b7c Author: Ann Almgren Date: Mon Jun 8 12:14:45 2020 -0700 Add inputs file specifcially for regression testing on battra -- note that with this inputs, gpu_dev and development branches match to 1e-15 relative tolerance Exec/LyA_Neutrinos/inputs.rt.battra commit 3d9251cb1c7a2318b95b48239650378dcaeee3b2 Author: Jean M. Sexton Date: Mon Jun 8 12:02:36 2020 -0700 Update neutrinos inputs.rt Exec/LyA_Neutrinos/inputs.rt commit 6f88b7152958b724ce0f3883bf59a5609323af5d Author: Jean M. Sexton Date: Sat Jun 6 16:35:43 2020 -0700 Move some comoving functions to C++ Exec/RegressionTest/inputs.2line Exec/RegressionTest/inputs.2line.restarttest Exec/RegressionTest/inputs.mass.nosub Exec/RegressionTest/inputs.mass.sub Source/Nyx.H Source/Nyx_F.H Source/comoving.cpp Source/comoving_nd.f90 commit a64d082f5515653baa1183d143c56844946b1c85 Author: Jean M. Sexton Date: Sat Jun 6 14:16:50 2020 -0700 Make C++ version of fort_integrate_comoving_a Source/Nyx.H Source/Nyx.cpp Source/comoving.cpp Source/comoving_nd.f90 commit 19471dd846701a0fe8bbe68c0b46f7fc50a76b2c Author: Jean M. Sexton Date: Sat Jun 6 12:50:41 2020 -0700 Move fort_integrate_time_given_a Source/Nyx.H Source/comoving.cpp Source/comoving_nd.f90 commit 749103012ebfb93e92173c193f49718e7d31f7ba Merge: 9e1b8e60 d7e0169b Author: jmsexton03 Date: Mon Jun 8 11:59:03 2020 -0700 Merge pull request #54 from AMReX-Astro/remove_dm_particle_t remove unused dm_particle_t commit 9e1b8e608eee92218832d24e3fe77bfad3a37074 Merge: 0a70093b 7d6127c7 Author: jmsexton03 Date: Mon Jun 8 11:58:36 2020 -0700 Merge pull request #53 from AMReX-Astro/port_neutrino_particles Port neutrino particles to C++ commit 0a70093bdac721c61c181d98dfa91c13187284f1 Author: Andrew Myers Date: Sun Jun 7 10:44:42 2020 -0700 port update_agn_particles to C++ Source/AGN/agn_F.H Source/Particle/AGNParticleContainer.H Source/Particle/AGNParticleContainer.cpp Source/Particle/Make.package Source/Particle/update_particles_3d.f90 commit d7e0169bea8be8c700de321888fba6121470d7d1 Author: Andrew Myers Date: Sun Jun 7 11:30:11 2020 -0700 remove unused dm_particle_t Source/Particle/particle_mod.f90 commit 7d6127c742c4376142c11ba30ef34661c638d801 Author: Andrew Myers Date: Sun Jun 7 11:26:46 2020 -0700 add new file Source/Particle/NeutrinoParticles_K.H commit 72b8de7d4cc00098b94e1c3d728cb8fb25cffe40 Author: Andrew Myers Date: Sun Jun 7 11:24:11 2020 -0700 port neutrino deposit stuff to C++ Source/Particle/Make.package Source/Particle/NeutrinoParticleContainer.cpp Source/Particle/NeutrinoParticles_F.H Source/Particle/Neutrino_Particle_mod_3d.F90 commit bb85723db24dd30f856930be045ef2d13c341a8e Author: Jean M. Sexton Date: Thu Jun 4 13:37:14 2020 -0700 Move enforce for permissions Source/Nyx.H commit 6d73e4f4da073c99992026f78c41cc0c7769aece Author: Jean M. Sexton Date: Thu Jun 4 13:11:53 2020 -0700 Move if statement so small values are properly tracked Source/Hydro/riemann_nd.F90 commit f92850c24f257a1ed1612b8f06f4dd635f2fd97a Author: Ann Almgren Date: Thu Jun 4 11:59:53 2020 -0700 Fix C++ version of nyx_eos_given_RT Source/EOS/eos_interface.cpp commit 3af6c2b4d842a764c33a230fe90e18385af49393 Author: Ann Almgren Date: Thu Jun 4 11:06:29 2020 -0700 Make sure to use CellSizeArray rather than CellSize Source/sum_utils.cpp commit 4b0385776d4ff20916f880d1b360e885cf51bf77 Author: Ann Almgren Date: Thu Jun 4 08:24:31 2020 -0700 Add the shell script to remove tabs. tab_exterminator.sh commit b31f7944e840c41d8036870aa032f092029ab471 Author: Jean M. Sexton Date: Thu Jun 4 07:49:42 2020 -0700 Remove incorrect pointer-based assertion Source/sum_utils.cpp commit 10a892c08011d894c110878688a1525a2dd21a33 Author: Ann Almgren Date: Wed Jun 3 19:32:33 2020 -0700 Ran the tab_exterminator script -- converted all tabs to spaces. Source/AGN/agn_3d.f90 Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/ParticleDerive.cpp Source/EOS/atomic_rates.F90 Source/EOS/eos_hc.F90 Source/Forcing/Forcing.H Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp Source/Forcing/MersenneTwister.cpp Source/Forcing/forcing_spect.f90 Source/Forcing/integrate_state_force_3d.f90 Source/Gravity/Gravity.cpp Source/HeatCool/Make.package Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_cell_3d.cpp Source/HeatCool/integrate_state_exact_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/Nyx_ctu_fuse.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/Nyx_hydro.cpp Source/HydroFortran/trace_ppm_3d.f90 Source/IO/Nyx_output.cpp Source/IO/write_info.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Monitors/test/Makefile Source/Nyx.H Source/Nyx.cpp Source/NyxBld.cpp Source/Nyx_F.H Source/Nyx_advance.cpp Source/Nyx_halos.cpp Source/Particle/AGNParticleContainer.cpp Source/Particle/DarkMatterParticleContainer.H Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NeutrinoParticleContainer.cpp Source/Particle/NyxParticleContainer.H Source/Particle/NyxParticles.cpp Source/SourceTerms/Nyx_sources.cpp Source/comoving.cpp Source/compute_hydro_sources.cpp Source/sdc_hydro.cpp Source/sdc_reactions.cpp Source/strang_hydro.cpp Source/strang_hydro_fuse.cpp Source/strang_reactions.cpp Source/sum_integrated_quantities.cpp Source/update_state_with_sources.cpp commit ccb8db8cdd6403ce7d5b878a1402a9302e78feab Author: Ann Almgren Date: Wed Jun 3 19:29:43 2020 -0700 1) move some files from Source to Source/IO 2) remove Nyx_sums_3d.f90 -- those now written in C++ in sum_utils.cpp Exec/HydroTests/Make.Nyx Exec/Make.Nyx Source/IO/Make.package Source/IO/Nyx_output.H Source/IO/Nyx_output.cpp Source/IO/write_info.cpp Source/Initialization/Nyx_initdata.cpp Source/Make.package Source/Nyx.H Source/Nyx_F.H Source/Src_3d/Make.package Source/Src_3d/Nyx_sums_3d.f90 Source/Src_3d/ang_mom_sums_3d.f90 Source/sum_utils.cpp commit 2c42635e7c9e4a93db6d573458be50c0bb65d5c8 Author: Jean M. Sexton Date: Wed Jun 3 14:58:53 2020 -0700 Update eos call Source/Initialization/Nyx_initdata.cpp commit 6f99013b4e03b89c86d3cbf269680a60e4dd6886 Author: Ann Almgren Date: Wed Jun 3 14:55:09 2020 -0700 Move enforce_consistent_e from Fortran to C++ Source/Initialization/Nyx_initdata.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Particle/Make.package Source/Particle/update_particles_3d.f90 Source/Src_3d/Make.package Source/Src_3d/enforce_consistent_e_3d.f90 commit fe73ec4cf3e4d09ad794d81967f61c1426634565 Author: Ann Almgren Date: Wed Jun 3 14:31:53 2020 -0700 Remove more fortran from Source/Initialization Source/Initialization/Make.package Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/init_e_from_rhoe_3d.f90 Source/Initialization/init_e_from_t_3d.F90 Source/Nyx.H Source/Nyx_F.H Source/Particle/NyxParticles.cpp commit 022f624cc22da0963498ce65cbd413c003ffd3e6 Author: Ann Almgren Date: Wed Jun 3 12:48:31 2020 -0700 Remove interpolate.f90 -- no one was using it Source/Initialization/Make.package Source/Initialization/interpolate.f90 commit 3b3614a006032ef7fd5e95b122c97409c37e396e Author: Ann Almgren Date: Wed Jun 3 12:32:05 2020 -0700 Fix new C++ version of check_initial_species Source/Initialization/Nyx_initdata.cpp commit 5fce8b82275e4ebe664fd11bfed09e14261798c9 Author: Jean M. Sexton Date: Wed Jun 3 04:56:35 2020 -0700 Add missing file Source/Particle/Make.package commit c69672527c07c3d2d93ff8b2fa6a208eed853b20 Author: Jean M. Sexton Date: Tue Jun 2 18:29:06 2020 -0700 Move Particle files into sub-directory Exec/HydroTests/Make.Nyx Exec/Make.Nyx Source/AGN/Make.package Source/AGN/agn_params.f90 Source/Make.package Source/Particle/AGNParticleContainer.H Source/Particle/AGNParticleContainer.cpp Source/Particle/DarkMatterParticleContainer.H Source/Particle/DarkMatterParticleContainer.cpp Source/Particle/NeutrinoParticleContainer.H Source/Particle/NeutrinoParticleContainer.cpp Source/Particle/NeutrinoParticles_F.H Source/Particle/Neutrino_Particle_mod_3d.F90 Source/Particle/NyxParticleContainer.H Source/Particle/NyxParticles.cpp Source/Particle/particle_mod.f90 commit 2da2e86b010f32229ccc68a484d171fa7f41e62a Merge: 54ee0883 760971af Author: Jean M. Sexton Date: Tue Jun 2 19:31:27 2020 -0400 Merge branch 'reeber' into development commit 54ee0883c74bdc081039e58eea6ce865528bd7c3 Author: Jean M. Sexton Date: Tue Jun 2 19:31:19 2020 -0400 Use NumSpec and FirstSpec Source/Initialization/Nyx_initdata.cpp commit 760971af0a033a0320ad20f38d868ecf04dad220 Author: Jean M. Sexton Date: Tue Jun 2 18:49:51 2020 -0400 Make GNUmakefile consistent Exec/LyA/GNUmakefile commit 1dc5340f76479d13eeccca7d5b9aabf13e2faf83 Merge: 08bdcd38 e23cd1ef Author: Ann Almgren Date: Tue Jun 2 15:14:39 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 08bdcd38371861b9a4e528eb950028246e2079ba Author: Ann Almgren Date: Tue Jun 2 15:12:48 2020 -0700 move check_initial_data from Fortran to C++ Source/Initialization/Make.package Source/Initialization/Nyx_initdata.cpp Source/Initialization/check_initial_species_3d.f90 Source/Nyx.H Source/Nyx_F.H commit e23cd1ef8eb4bac05fe09014159f8addfa192793 Author: Jean M. Sexton Date: Tue Jun 2 17:14:01 2020 -0400 Neglect small_dens cells from dt estimation using flags, use enforce_minimum_density for conservation Source/Hydro/Nyx_advection_util.F90 Source/Nyx.cpp commit 8b057fea7d2ad87fee4cf752050140aeb5c7e8f6 Author: Ann Almgren Date: Tue Jun 2 13:36:08 2020 -0700 Quiet compiler warning by adding additional parentheses Source/EOS/atomic_rates.F90 commit ec74e4eba33074443d365214ca13daafc774a968 Merge: aec6457b 71a9302e Author: Ann Almgren Date: Tue Jun 2 12:25:47 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 71a9302ea55a0c90059b0c85308736d50c5f0883 Author: Andrew Myers Date: Tue Jun 2 11:22:15 2020 -0700 remove the coarsened ascii option Source/Nyx.H Source/NyxParticles.cpp commit aec6457bc9cf34c7e323f3b0769676d68c04ed52 Author: Ann Almgren Date: Tue Jun 2 09:11:43 2020 -0700 Make sure forcex/y/z a returned as 0 not undefined Exec/HydroTests/TurbForce/Derive_forcing.cpp commit 93186111383486db8f40072efcd63421e338c792 Author: Jean M. Sexton Date: Mon Jun 1 23:55:16 2020 -0400 Add launch and comment out invalid RunOn debug statements Source/Nyx_advance.cpp Source/strang_hydro.cpp Source/strang_hydro_fuse.cpp Source/strang_reactions.cpp commit dc2d3af1dd00972862d5bc0be810783aab2fcd42 Author: Ann Almgren Date: Mon Jun 1 18:00:47 2020 -0700 slight update to forcing Exec/HydroTests/TurbForce/Derive_forcing.cpp commit a63bd847d847c5da263a55835c84436895637072 Author: Ann Almgren Date: Mon Jun 1 17:59:54 2020 -0700 Replace amr.derive_plot_vars = ALL by amr.derive_plot_vars = pressure since the list of potentially derived quantities is too long Exec/HydroTests/Sedov/inputs.3d.sph Exec/HydroTests/Sedov/inputs.3d.sph.testsuite Exec/RayTracing-NonComoving/inputs.3d.sph commit 735182b57d5c2e62fea2146e37312617dc0a80e0 Author: Ann Almgren Date: Mon Jun 1 17:51:39 2020 -0700 1) move the last of the derive functions to C++ 2) Move the TurbForce derforce* routines to C++ Exec/HydroTests/TurbForce/Derive_forcing.cpp Exec/HydroTests/TurbForce/Make.package Source/DerivedQuantities/Derive.H Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/Derive_3d.f90 Source/DerivedQuantities/Derive_F.H Source/DerivedQuantities/Derive_forcing.cpp Source/DerivedQuantities/Make.package Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp Source/Nyx_halos.cpp commit 806d9973659c0ebfb65ba1ab2fca81dbeaa9f816 Author: Ann Almgren Date: Mon Jun 1 15:50:55 2020 -0700 Add derforce* to Derive.H Source/DerivedQuantities/Derive.H commit 94879bdb7197f6fa641ac851d5dce084a508600f Author: Ann Almgren Date: Mon Jun 1 15:46:09 2020 -0700 Remove use_colglaz parameter (it was defaulted to 0 and almost always used that way) Exec/AMR-density/inputs Exec/AMR-density/inputs.rt Exec/AMR-density/inputs_nohydro.rt Exec/AMR-zoom/inputs Exec/GravityTests/zeldovich_dm/run/inputs Exec/GravityTests/zeldovich_dm/run/inputs_hydro Exec/HDF5_example/inputs Exec/HydroTests/DoubleRarefaction/inputs-test2-x Exec/HydroTests/DoubleRarefaction/inputs.regtest Exec/HydroTests/DoubleRarefaction/inputs.restarttest Exec/HydroTests/Sod/inputs-sod-x Exec/HydroTests/Sod/inputs-sod-y Exec/HydroTests/Sod/inputs-sod-z Exec/HydroTests/Sod/inputs.regtest Exec/HydroTests/StrongShockTube/inputs-x Exec/HydroTests/StrongShockTube/inputs.regtest Exec/LyA/inputs Exec/LyA/inputs.256.noreduceverb Exec/LyA/inputs.small.dsc Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA_AGN/inputs Exec/LyA_Neutrinos/inputs Exec/LyA_Neutrinos/inputs.no_hydro_64 Exec/LyA_Neutrinos/inputs.small.dsc Exec/LyA_Neutrinos/inputs_gimlet_in_transit.dsc Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Exec/MiniSB/inputs.analysis Exec/RayTracing-Expanding/inputs Exec/SantaBarbara/inputs Exec/Scaling/inputs Exec/Scaling/inputs.256.noreduceverb Exec/Scaling/inputs_short Source/HydroFortran/Make.package Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/trace_colglaz_3d.f90 Source/Initialization/Nyx_setup.cpp Source/Initialization/init_managed.F90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/meth_params.F90 Util/SUNDIALS3/init_managed.F90 Util/SUNDIALS3/meth_params.F90 Util/SUNDIALS_cuda_cpu_compute/meth_params.f90 Util/SUNDIALS_serial_test/meth_params.f90 Util/VODE3_gpu/meth_params.cuf Util/VODE3_gpu/meth_params.f90 Util/VODE_test/meth_params.f90 Util/sdc-test/init_managed.F90 Util/sdc-test/meth_params.F90 commit c74ecd1146e5cb0e3516309dfc678a4be80cb9bd Author: Ann Almgren Date: Mon Jun 1 15:14:44 2020 -0700 Remove corner_coupling flag since it is always 1 Exec/AMR-density/inputs Exec/AMR-density/inputs.rt Exec/AMR-density/inputs_nohydro.rt Exec/AMR-zoom/inputs Exec/GravityTests/zeldovich_dm/run/inputs Exec/GravityTests/zeldovich_dm/run/inputs_hydro Exec/HDF5_example/inputs Exec/LyA/inputs Exec/LyA/inputs.256.noreduceverb Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA_AGN/inputs Exec/LyA_Neutrinos/inputs Exec/LyA_Neutrinos/inputs.no_hydro_64 Exec/LyA_Neutrinos/inputs_gimlet_in_transit.dsc Exec/RayTracing-Expanding/inputs Exec/Scaling/inputs Exec/Scaling/inputs.256.noreduceverb Exec/Scaling/inputs_short Source/HydroFortran/Nyx_advection_3d.f90 Source/Nyx.H Source/meth_params.F90 Util/SUNDIALS_cuda_cpu_compute/meth_params.f90 Util/SUNDIALS_serial_test/meth_params.f90 Util/VODE3_gpu/meth_params.cuf Util/VODE3_gpu/meth_params.f90 Util/VODE_test/meth_params.f90 commit d339500ddbe3040477c8abf38c254bb4258d0dfe Merge: ad2db09d d9135a97 Author: Ann Almgren Date: Mon Jun 1 11:39:23 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit ad2db09dd452d468d2c5a591670cf7b660eb03c1 Author: Ann Almgren Date: Mon Jun 1 11:38:51 2020 -0700 More clean-up ... Source/DarkMatterParticleContainer.cpp Source/DerivedQuantities/Derive.cpp Source/Initialization/Nyx_setup.cpp Source/Make.package Source/NeutrinoParticleContainer.cpp Source/dm_F.H commit d9135a979bc5831330875ee53c6470945cb84f81 Author: Jean M. Sexton Date: Sun May 31 18:41:38 2020 -0700 Fixed logden to use log10 instead of log, remove magvort scaling by density, fix indices for divu density scaling Source/DerivedQuantities/Derive.cpp commit 93613754409bb345b54bdec06539e5e717d67e56 Author: Ann Almgren Date: Sun May 31 17:45:54 2020 -0700 Don't use USE_FORCING=TRUE here Exec/HydroTests/TurbForce/GNUmakefile commit 8043b6bdec37ab9decbb56f59a1cba139b197be5 Author: Jean M. Sexton Date: Sun May 31 15:06:49 2020 -0700 Update dersoundspeed and dermachnumber Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/Derive_3d.f90 commit f00ce38634ddcb1488f35fc525163f832d84a2f8 Author: Ann Almgren Date: Sun May 31 14:15:25 2020 -0700 All the directories should compile now and we now have C++ versions of more of the derived quantities Exec/DrivenTurbulence/Derive_3d.f90 Exec/DrivenTurbulence/Derive_prob_3d.f90 Exec/DrivenTurbulence/Make.package Exec/DrivenTurbulence/probdata.f90 Exec/HydroTests/Sod/probdata.f90 Exec/HydroTests/TurbForce/Derive_3d.f90 Exec/HydroTests/TurbForce/Derive_prob_3d.f90 Exec/HydroTests/TurbForce/GNUmakefile Exec/HydroTests/TurbForce/Make.package Exec/HydroTests/TurbForce/Nyx_setup.cpp Exec/RegressionTest/Tagging_3d.f90 Exec/RegressionTest/Tagging_part_3d.f90 Source/DerivedQuantities/Derive.H Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/Derive_F.H Source/DerivedQuantities/Make.package Source/Initialization/Nyx_setup.cpp commit ab017d903047575155fc99783d3d21ae63a02838 Author: Jean M. Sexton Date: Sat May 30 15:31:38 2020 -0700 Need to use Eint and Eden instead of UEDEN and UEINT Source/DerivedQuantities/Derive.cpp commit 9bdef76a0ed5a1cce54aeafb0399a6f29077031a Author: Jean M. Sexton Date: Sat May 30 14:25:44 2020 -0700 Revert "Revert "Update some derive functions to C++"" This reverts commit 8ea6a264d363bf9121a1ec5757d753167ba387f2. Revert "Revert "Revert initial derpres conversion"" This reverts commit 89b03f02f0ac294374bfb8057cb7ea965eae5fac. Revert "Revert initial derpres conversion" This reverts commit 43606750369f3799511df34e97466993240937e8. Source/DerivedQuantities/Derive.H Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/Derive_3d.f90 Source/DerivedQuantities/Derive_F.H Source/DerivedQuantities/Make.package Source/Initialization/Nyx_setup.cpp Source/Nyx.H commit c77c13d64a3ccc4818f2db04cbf64bac13229d18 Author: Jean M. Sexton Date: Sat May 30 16:54:47 2020 -0700 Added max_*_lev fields to probdata for expanded Tagging Exec/HydroTests/Sedov/probdata.f90 Exec/HydroTests/Sod/probdata.f90 Exec/HydroTests/StrongShockTube/probdata.f90 commit 8ea421c5c44240a89c4467e9cb5f68598870994f Author: Jean M. Sexton Date: Sat May 30 19:30:15 2020 -0400 Include module for rt(real) Source/Tagging/Tagging_part_3d.f90 commit b7f9668bf338a7efcb40bbce808db4d70a29ea05 Author: Ann Almgren Date: Sat May 30 15:08:30 2020 -0700 Update the hydro tests to use a Make.Nyx that sets USE_PARTICLES = FALSE Exec/HydroTests/DoubleRarefaction/GNUmakefile Exec/HydroTests/Make.Nyx Exec/HydroTests/Sedov/GNUmakefile Exec/HydroTests/Sod/GNUmakefile Exec/HydroTests/StrongShockTube/GNUmakefile Exec/HydroTests/TurbForce/GNUmakefile commit 541dbddb1f74372650b5a453b444b907a3b8471a Author: Ann Almgren Date: Sat May 30 14:55:19 2020 -0700 Separate out the tagging routines that assume we have particles. Source/Tagging/Make.package Source/Tagging/Tagging_3d.f90 Source/Tagging/Tagging_part_3d.f90 commit 713d5f26f4886cb57eac0abccf8dcad4db3a5bf0 Merge: 3df17fd1 123712b8 Author: Ann Almgren Date: Sat May 30 14:22:35 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 3df17fd12462c813c5d176ff5b98201fbb5bf766 Author: Ann Almgren Date: Sat May 30 14:22:23 2020 -0700 More clean-up and replacing Fortran by C++ Exec/HydroTests/DoubleRarefaction/Tagging_3d.f90 Exec/HydroTests/Sedov/Tagging_3d.f90 Exec/HydroTests/Sod/Tagging_3d.f90 Exec/HydroTests/StrongShockTube/Tagging_3d.f90 Exec/HydroTests/TurbForce/Nyx_sources.cpp Source/AGN/AGN_sources.cpp Source/Nyx.H Source/Nyx_F.H Source/Nyx_advance.cpp Source/Nyx_nd.f90 Source/SourceTerms/Make.package Source/SourceTerms/Nyx_grav_sources_3d.F90 Source/SourceTerms/Nyx_sources.cpp Source/SourceTerms/Nyx_sources_3d.f90 Source/SourceTerms/Nyx_time_center_sources.cpp commit 123712b8d98585e39f79cbdd6c6c7b4c55a915e4 Author: Jean M. Sexton Date: Sat May 30 11:51:25 2020 -0700 Make default values of species in C++ consistent Source/Nyx.cpp commit a68d81c6b8dd7f660ff8b98f0af8b8c5fa47d256 Author: Jean M. Sexton Date: Sat May 30 10:21:50 2020 -0700 Revert "Put eos_interface.cpp back in, but only use it for USE_HEATCOOL=TRUE" This reverts commit aedb9443fada84408b4569fbebecc7c6076fb112. Revert "Revert "Add C++ version of eos_stuff.f90 and interface for converting eos_hc.F90"" This reverts commit e775a169b4f84c44b561cf5bdc851d4970a5d7dc. Source/Nyx.cpp commit a7fcb778e69a79cad61ce2d3153fe659879a2620 Author: Ann Almgren Date: Sat May 30 11:21:33 2020 -0700 Replace UMX since that is implicitly the Fortran numbering Source/Nyx.cpp commit 2911178439b3b904886eae1474337f559ad61673 Author: Ann Almgren Date: Sat May 30 11:07:51 2020 -0700 Remove some un-used Fortran and replace some other Fortran by C++ Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Gravity/Gravity_3d.f90 Source/Gravity/Gravity_F.H Source/Gravity/Make.package Source/Gravity/set_dirichlet_bcs_3d.f90 Source/Nyx.cpp Source/Nyx_F.H Source/SourceTerms/Nyx_grav_sources_3d.F90 Source/Src_3d/update_particles_3d.f90 commit 2cc1119ae3f59998ff702c4255f93e49152b8eda Author: Jean M. Sexton Date: Sat May 30 09:15:43 2020 -0700 Fix typo in comp/grow arg in NyxParticles.cpp Source/NyxParticles.cpp commit 75e42e06f8d219dd4b89be16d86e89554f8448e4 Author: Jean M. Sexton Date: Fri May 29 12:23:16 2020 -0400 large_temp CUDA fixes Exec/LyA/GNUmakefile.cuda Source/Nyx.cpp commit 90adaf405de546bcb9d09b2aee9b6e5ff37a9ed8 Author: Jean M. Sexton Date: Thu May 28 20:18:14 2020 -0700 Fix pp Source/Nyx.cpp commit aedb9443fada84408b4569fbebecc7c6076fb112 Author: Jean M. Sexton Date: Thu May 28 20:13:01 2020 -0700 Put eos_interface.cpp back in, but only use it for USE_HEATCOOL=TRUE Source/EOS/Make.package Source/EOS/eos_hc.F90 Source/EOS/eos_interface.cpp Source/EOS/eos_stuff.F90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H commit e775a169b4f84c44b561cf5bdc851d4970a5d7dc Author: Jean M. Sexton Date: Thu May 28 19:55:48 2020 -0700 Revert "Add C++ version of eos_stuff.f90 and interface for converting eos_hc.F90" This reverts commit 4ed277b0828aacb9d7b0960294d8c2ab2b65a411. Source/EOS/Make.package Source/EOS/eos_hc.F90 Source/EOS/eos_interface.cpp Source/EOS/eos_stuff.F90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H commit 2930156d5ce9b9f05a1770b466d4799dd60862ad Author: Jean M. Sexton Date: Thu May 28 18:17:39 2020 -0700 Move working Nyx_setup.cpp back into TurbForce Exec/HydroTests/TurbForce/Nyx_setup.cpp Source/Initialization/Nyx_setup.cpp commit 8ea6a264d363bf9121a1ec5757d753167ba387f2 Author: Jean M. Sexton Date: Thu May 28 18:17:39 2020 -0700 Revert "Update some derive functions to C++" This reverts commit fbdddb4ad06c36e5aa16758d9983bb2d7f965517. Source/DerivedQuantities/Derive.H Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/Derive_3d.f90 Source/DerivedQuantities/Derive_F.H Source/DerivedQuantities/Make.package Source/Initialization/Nyx_setup.cpp Source/Nyx.H commit 89b03f02f0ac294374bfb8057cb7ea965eae5fac Author: Jean M. Sexton Date: Thu May 28 18:16:33 2020 -0700 Revert "Revert initial derpres conversion" This reverts commit 43606750369f3799511df34e97466993240937e8. Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/Derive_3d.f90 Source/Initialization/Nyx_setup.cpp commit 06e37393fbb33dd97bb425b35410813b76e2ba18 Author: Jean M. Sexton Date: Thu May 28 18:16:05 2020 -0700 Remove ifdef FORCING from descriptor list Source/Initialization/Nyx_setup.cpp commit 60419a80e3db8fc3ab0c1c55c9a4c9affcb8bd94 Author: Jean M. Sexton Date: Thu May 28 17:49:15 2020 -0700 Maximum temperature in compute_new_temp input flag Source/Nyx.H Source/Nyx.cpp commit ffb4cc58a56b04898e3d31ef308e425660e57591 Author: Jean M. Sexton Date: Thu May 28 16:49:51 2020 -0700 Remove redundant file from HydroTests Exec/HydroTests/TurbForce/Nyx_setup.cpp commit a4dd4b142e94192c7d51153f217fa54d0f6921c3 Author: Jean M. Sexton Date: Thu May 28 19:08:18 2020 -0400 Update CUDA initialization for RegressionTest Exec/RegressionTest/Make.package Exec/RegressionTest/Prob_3d.F90 commit 7a0d510230a08d1e3128b3d93c5bc4bf3cf6443d Author: Jean M. Sexton Date: Thu May 28 18:43:19 2020 -0400 Split off shrink_to_fit flag Source/Nyx.H Source/Nyx.cpp commit 32d1e855051f0e280f09b8f204777d05d15e12d6 Merge: 639f8d62 3f944ae5 Author: asalmgren Date: Thu May 28 15:08:14 2020 -0700 Merge pull request #51 from AMReX-Astro/gpu_dev Merge gpu_dev branch into development commit 3f944ae56913c7a87df195eb8efc22988be70657 Merge: e2e43dbe 639f8d62 Author: Jean M. Sexton Date: Thu May 28 17:59:00 2020 -0400 Merge branch 'development' into gpu_dev commit e2e43dbe8447de2c148c206b8e76a4b786deb902 Author: Jean M. Sexton Date: Thu May 28 12:10:31 2020 -0400 Use fused vector operations for sundials>=5.3.0 Exec/LyA/GNUmakefile.cuda Source/HeatCool/integrate_state_vec_3d.cpp Source/Nyx.H Source/Nyx.cpp commit 639f8d623065042403b7c006b8753060bdb9a6f8 Author: Ann Almgren Date: Wed May 27 19:03:32 2020 -0700 Replace "BoxLib" by AMReX in all comments Diagnostics/GNUmakefile Exec/DrivenTurbulence/GNUmakefile Exec/GravityTests/MacLaurin/GNUmakefile Exec/GravityTests/zeldovich_dm/build/GNUmakefile Exec/HydroTests/DoubleRarefaction/GNUmakefile Exec/HydroTests/Sedov/GNUmakefile Exec/HydroTests/Sod/GNUmakefile Exec/HydroTests/StrongShockTube/GNUmakefile Exec/HydroTests/TurbForce/GNUmakefile Exec/MiniSB/GNUmakefile Exec/RayTracing-NonComoving/GNUmakefile Exec/RegressionTest/GNUmakefile Exec/SantaBarbara/GNUmakefile README.md Util/regression_testing/Nyx-tests.ini commit 6fef882c95d54bc7371fe8c573d62858b05026ee Author: Jean M. Sexton Date: Wed May 27 17:28:01 2020 -0400 Add rhoe ceiling to compute_new_temp Source/EOS/eos_hc.F90 Source/Hydro/enforce_minimum_density.F90 Source/Nyx.cpp commit 47857c613819d5cc62f11bd13c17981269dfd982 Author: Jean M. Sexton Date: Tue May 26 17:30:01 2020 -0400 Remove unneeded copy Source/Hydro/Nyx_advection_util.F90 commit 43606750369f3799511df34e97466993240937e8 Author: Jean M. Sexton Date: Tue May 26 13:03:51 2020 -0700 Revert initial derpres conversion Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/Derive_3d.f90 Source/Initialization/Nyx_setup.cpp commit fbdddb4ad06c36e5aa16758d9983bb2d7f965517 Author: Jean M. Sexton Date: Wed May 13 14:38:41 2020 -0700 Update some derive functions to C++ Source/DerivedQuantities/Derive.H Source/DerivedQuantities/Derive.cpp Source/DerivedQuantities/Derive_3d.f90 Source/DerivedQuantities/Derive_F.H Source/DerivedQuantities/Make.package Source/Initialization/Nyx_setup.cpp Source/Nyx.H commit b45133473d0ea0bbf8dfb2cd5fa38417788a3e95 Author: Jean M. Sexton Date: Tue May 26 11:53:49 2020 -0700 Short fix for enforce_minimum_density Source/Hydro/Nyx_advection_util.F90 Source/Hydro/enforce_minimum_density.F90 commit faf32b88c4b3a34d36bd72c48f032216527ef1c3 Author: Jean M. Sexton Date: Tue May 26 12:48:32 2020 -0400 Update namespace for abs calls from sub-function of moveKick and moveKickDrift Source/DarkMatterParticleContainer.cpp commit c536357b981b076e46e8f49d564d4724f96ab266 Author: Jean M. Sexton Date: Wed May 13 11:52:12 2020 -0700 Update virtual and ghost particle launches, fix a type in launching restart, change RunOn for crse_phi Source/DarkMatterParticleContainer.cpp Source/Gravity/Gravity.cpp Source/NyxParticles.cpp commit cd64951d2ee1bb64937df99429d9e5c45770fd9f Merge: 5496d3ef 47647347 Author: Arnur Nigmetov Date: Wed May 13 18:55:51 2020 +0200 Merge. commit 5496d3ef203f933fae12b60ba7326cff7fd7889d Merge: b9db3fd3 f8e5f83d Author: Arnur Nigmetov Date: Wed May 13 18:50:30 2020 +0200 Fix Reeber code (DIY DiscreteBounds ctor). commit f8e5f83d288704e301d3a87895048e4c5447592f Author: Jean M. Sexton Date: Wed May 13 12:08:24 2020 -0400 Update paths for Reeber2 Exec/LyA_AGN/GNUmakefile Exec/Make.Nyx Util/reeber/Make.package commit 68c67a57e60bde5450eb92f573f32973191a0b8b Author: Jean M. Sexton Date: Mon Apr 27 17:19:00 2020 -0400 Update gpu compile for NeutrinoParticleContainer Exec/LyA_Neutrinos/GNUmakefile.cuda Exec/LyA_Neutrinos/Make.package Exec/LyA_Neutrinos/Prob_3d.F90 Source/NeutrinoParticleContainer.H Source/NeutrinoParticleContainer.cpp commit d1fe9e9a99680c696e73ac4937cf80c8242bdd42 Author: Jean M. Sexton Date: Mon Mar 23 20:02:47 2020 -0700 Use makeFineMask and preserve previous Host behavior Source/Gravity/Gravity.cpp Source/Nyx.cpp Source/NyxParticles.cpp Source/compute_hydro_sources.cpp Source/strang_reactions.cpp Source/sum_utils.cpp commit e844df208714ab95d32eac421b0d36616d363aba Author: Jean M. Sexton Date: Mon Mar 23 19:45:29 2020 -0700 Fixed compilation bugs Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_box_3d.cpp Source/Nyx.cpp Source/NyxParticles.cpp Source/SourceTerms/Nyx_sources.cpp Source/compute_hydro_sources.cpp Source/strang_reactions.cpp Source/sum_utils.cpp commit f89e7d658e65ce3b0a6e4aef05d064018065698d Merge: c19ba021 ad687d90 Author: Jean M. Sexton Date: Fri Mar 13 16:50:44 2020 -0700 Merge branch 'development' into gpu_dev commit ad687d90182c2f4bc8352751058768e8e93d4084 Author: Jean Sexton Date: Tue Mar 10 09:53:25 2020 -0700 Add curly braces after Initialize and before Finalize to put main body of converter in local scope Util/convert_lyaf/AmrDerive.cpp Util/convert_nbody/AmrDerive.cpp commit c19ba021422a773aca179ec08a7fa017eb145832 Merge: 985ec09d 4a0c12b1 Author: Jean M. Sexton Date: Thu Mar 5 17:17:06 2020 -0800 Merge branch 'development' into gpu_dev commit 4a0c12b1fc74acc438fb3d00eeabffae2551a120 Author: Jean M. Sexton Date: Thu Mar 5 17:16:36 2020 -0800 Remove duplicate writeJobInfo Source/Nyx_output.cpp commit ca35cdbdd53e418486d7ff1db1348198a45e7aaf Author: Ann Almgren Date: Fri Apr 5 16:40:54 2019 -0700 Add factor of a_half_inv to update for (rho q) Source/HydroFortran/Nyx_advection_3d.f90 commit 985ec09d230feb8816c1afe4249253baf4151b2e Merge: f804cf5b 61554111 Author: Jean M. Sexton Date: Wed Mar 4 17:30:06 2020 -0800 Merge branch 'development' into gpu_dev commit 61554111d7111edc88e4b683d9d2da0825256830 Author: Jean M. Sexton Date: Wed Mar 4 17:28:46 2020 -0800 Only call writeJobInfo in checkPoint for level 0 and IOProc Source/Nyx_output.cpp commit f804cf5b4a994ed89b7a5ae840fe1a8fc072f3c3 Author: Jean M. Sexton Date: Tue Mar 3 11:06:01 2020 -0500 Add round robin Source/Nyx.cpp commit 1448d2806af9c976eda1bc40e549185dad7f7777 Author: Jean M. Sexton Date: Tue Mar 3 01:54:25 2020 -0500 Add ShrinkToFit after Regrid Source/Nyx.cpp commit 48d5a4e91eee44495d4264137ea5975b12aaa41c Author: Jean M. Sexton Date: Tue Mar 3 01:15:22 2020 -0500 Launch Copy Source/advance_particles.cpp commit c5120951aa5be861bae3565d1949e3dc10dafff0 Author: Jean M. Sexton Date: Mon Mar 2 20:06:31 2020 -0500 Use balancing strategy from nyx inputs flag Source/Nyx.cpp commit 5d8e60ff3056ee8c831957dc2988c104de272993 Author: Jean M. Sexton Date: Mon Mar 2 19:53:36 2020 -0500 Set load_balance_strategy seperately from general dmap Source/Nyx.H Source/Nyx.cpp commit 599c1f9428f8c39ec39bdd21952f0b97de14aafc Author: jmsexton03 Date: Mon Mar 2 13:28:11 2020 -0800 Reeber (#50) * First version with actual Reeber code compiles. * interim, to save code * Interim, compiles. TODO: positions in true AMR * fix assertion error * Fixed component names for AGN particle plotfile, added profile timers for halo functions and make guards for REEBER=FALSE case * Use unique_ptr for copies; discard ghost data. * Fill more halos info, disable debug output Also clean up GNUmakefile-s. * Change default REEBER_EXT_HOME. Reeber repo is called reeber2-git, not reeber. Exec/LyA/GNUmakefile Exec/LyA_AGN/GNUmakefile Exec/Make.Nyx Source/AGNParticleContainer.H Source/Nyx.H Source/Nyx_halos.cpp Util/reeber/Make.package Util/reeber/include/reeber.H Util/reeber/src/reeber.cpp commit bd7fe8a9f553b9588ea1f90b37705add05d9fec2 Author: Cyrus Harrison Date: Mon Mar 2 13:26:58 2020 -0800 working on ascent updates with jean (#49) * tweaks to Lya makefile for ascent support * tweaks to ascent integration in Nyx_output.cpp * add guarded mpi init of ascent, add pass of cycle * move to use yaml files to override builtin actions * add example actions yaml files * use single publish with both particles and mesh * cleanup and simplify ascent integration * remove old file * skip dumping mesh to hdf5 Exec/LyA/GNUmakefile Exec/LyA/ascent_actions.yaml Source/Nyx_output.cpp Source/write_info.cpp commit b0d2089e7d5e18692c840721f6d583c9c0f1960b Author: Jean M. Sexton Date: Wed Feb 26 23:53:06 2020 -0500 Add nmax and use amrex strategy flags Source/Nyx.H Source/Nyx.cpp commit 15511742b930417b5bf29afbee7a53f4fb48d37f Author: Jean M. Sexton Date: Wed Feb 26 18:00:06 2020 -0500 Cleanup prints Source/DarkMatterParticleContainer.cpp commit 9dc7c059549d23d4f18fb2d09893ed47260d04c0 Merge: 77f14766 d4a1446b Author: Jean M. Sexton Date: Wed Feb 26 17:56:39 2020 -0500 Merge branch 'gpu_dm' into gpu_dev commit d4a1446beee0f3764970f0ac9c7651fe1b0acfa2 Author: Jean M. Sexton Date: Wed Feb 26 17:51:24 2020 -0500 Remove remake_level and grid resize from postCoarseTimeStep and Gravity Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Nyx.H Source/Nyx.cpp commit 77f147666c566a9456be6746f8644f6f8bd483d8 Merge: b600167c 241f7b51 Author: Jean M. Sexton Date: Tue Feb 25 10:09:14 2020 -0800 Merge branch 'development' into gpu_dev commit 241f7b5182b872840ffbb7313960da18d9d285e2 Author: Zarija Date: Tue Feb 25 00:29:20 2020 -0500 Added radiation component Exec/LyA/inputs Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/comoving_nd.f90 Source/comoving_params.f90 commit b600167cd7f283a54e8510cb1b27b295cecfd3ad Author: Jean M. Sexton Date: Mon Feb 24 19:44:21 2020 -0500 Add minimize_memory input flag for using synchronize in hydro and ShrinkToFit in post_timestep Source/Hydro/Nyx_ctu_hydro.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticleContainer.H commit 12dc2c5ab04d5cbbcb4b7a7e87ad54dc98deb5b0 Author: Jean M. Sexton Date: Mon Feb 24 17:33:28 2020 -0500 Add timer to strang_*_step Source/strang_reactions.cpp commit f82ab829bec74b23b8ac23f013ac756e3c6a5a80 Author: Jean M. Sexton Date: Mon Feb 24 17:24:30 2020 -0500 Added RegionTag memory tracking Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/Nyx.cpp Source/Nyx_advance.cpp Source/update_state_with_sources.cpp commit 3878988bb1cfe0fba2d0c4e06d2220ca67eeafb8 Author: Jean M. Sexton Date: Sun Feb 23 19:44:24 2020 -0500 ifndef -> ifdef Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_cell_3d.cpp Source/strang_hydro.cpp Source/strang_hydro_fuse.cpp Util/sdc-test/main.cpp commit 631d31690d09e16495a0cd9273bd4f8cacf4180c Merge: 7aa56e3d 27d6dc78 Author: Jean M. Sexton Date: Sun Feb 23 19:42:59 2020 -0500 Merge branch 'development' into gpu_dev commit 27d6dc78d2e801ca11747238383685d99ab1532d Author: Jean M. Sexton Date: Sun Feb 23 19:40:39 2020 -0500 ifndef -> ifdef Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_exact_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/strang_hydro.cpp Source/strang_reactions.cpp Util/SUNDIALS3/main.cpp commit 7aa56e3d9ea10eb7af60500198a93ed9481893cb Author: Jean M. Sexton Date: Sun Feb 23 19:30:26 2020 -0500 NDEBUG -> AMREX_DEBUG Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_cell_3d.cpp Source/strang_hydro.cpp Source/strang_hydro_fuse.cpp Util/sdc-test/main.cpp commit e28099bae3a42206f2d07462f589f1ee342499e8 Merge: a9bb5d6c 0fa2149c Author: Jean M. Sexton Date: Sun Feb 23 19:29:19 2020 -0500 Merge branch 'development' into gpu_dev commit 0fa2149cb337c9b9cbad3dfd60cda894e7f2f071 Author: Jean M. Sexton Date: Sun Feb 23 19:17:17 2020 -0500 NDEBUG -> AMREX_DEBUG Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_exact_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/strang_hydro.cpp Source/strang_reactions.cpp Util/SUNDIALS3/main.cpp Util/VODE3_gpu/Makefile commit a9bb5d6c24dd34215d0d7b629a37410a41958580 Merge: e2c7ae38 54605b99 Author: zarija Date: Fri Feb 21 11:56:03 2020 -0800 Merge branch 'gpu_dev' of https://github.com/AMReX-Astro/Nyx into gpu_dev commit e2c7ae3831ad2641c2085a900750eab28cd2b2ff Author: Jean M. Sexton Date: Mon Feb 17 12:40:26 2020 -0800 Uncomment build lines to build doxygen build_and_deploy.sh commit 5ce2dade401028be463ed13d81580fb22ea2fb0f Author: Jean M. Sexton Date: Mon Feb 17 12:30:23 2020 -0800 Fix doxygen source location Docs/sphinx_documentation/Doxyfile Docs/sphinx_documentation/source/conf.py commit 12ec0324d574dcc06980f5fecf972fe6fcf803c9 Author: Jean M. Sexton Date: Mon Feb 17 12:09:23 2020 -0800 Update particle documentation Docs/sphinx_documentation/source/NyxPreface.rst Docs/sphinx_documentation/source/Particles.rst commit ad49aa6e2c0c73c0dcd416d7d12bf38ae7f086bc Author: Jean M. Sexton Date: Mon Feb 17 12:08:50 2020 -0800 Only allow -DHEATCOOL if NO_HYDRO=FALSE Exec/Make.Nyx commit 54605b997753e5f550c1af0a57a11c2962dcb3e6 Author: Jean M. Sexton Date: Fri Feb 14 21:11:16 2020 -0500 Add do_hydro guard statement for Amr init Source/Nyx.cpp commit 4376463396601a5daf8a814510656c0552bfb67c Author: Jean M. Sexton Date: Fri Feb 14 18:47:34 2020 -0500 Add template inputs file for cuda setup using 64^3 Exec/AMR-density/GNUmakefile.cuda Exec/AMR-density/inputs.cuda Exec/LyA/inputs.cuda commit 9b9df8dc325b2224a27fcb5cf6209e51fb44ab8f Author: Jean M. Sexton Date: Fri Feb 14 15:17:31 2020 -0500 Make particle_redistribute use ActiveParticles and match post_timestep Source/NyxParticles.cpp commit 6fae1d8b8d34c3e7ba873235c244a9bb6bfcb00a Author: Jean M. Sexton Date: Fri Feb 14 15:16:52 2020 -0500 Use baryonic density as default work estimate Source/Nyx.H commit 8d1780d2ac192a199f5cc1563831aefe8be9c144 Author: Hannah Ross Date: Wed Feb 12 16:13:19 2020 -0800 Temperature now only read in hydro runs for convert_all_fields Util/convert_all_fields/AmrDerive.cpp commit 73437ca64f9de2f9e4e3e3ed7253e215891974a7 Merge: 99c08273 62639ef6 Author: Hannah Ross Date: Wed Feb 12 16:06:31 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 99c0827340afe1454ec0cd2a8fbedbbafa5ff4fa Author: Hannah Ross Date: Wed Feb 12 15:49:08 2020 -0800 Now reads particle count Util/convert_all_fields/AmrDerive.cpp commit 647bd87b0135597f1074d2ad14bbb673bf4fb527 Merge: 6ced5dd5 62639ef6 Author: Jean M. Sexton Date: Tue Feb 4 10:06:45 2020 -0500 Merge branch 'development' into gpu_dev commit 62639ef6ba54bd33371423cbc4acd8adb4695dfa Author: Jean M. Sexton Date: Tue Feb 4 09:57:37 2020 -0500 Update sundials flags, remove spurious print Source/HeatCool/cvode_extras.f90 Source/HeatCool/integrate_state_vec_3d.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_output.cpp Source/strang_reactions.cpp commit 9245e85dd6622c3c2e39d123fd750dc8add4299f Author: Jean M. Sexton Date: Tue Jan 28 23:47:19 2020 -0500 Add run flags and clean up load balancing options Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Nyx.H Source/Nyx.cpp commit 363aa24e4c1805d0b9c957947c3d52c12708bd8d Merge: 9b18d70e 6ced5dd5 Author: Jean M. Sexton Date: Wed Jan 29 09:08:47 2020 -0500 Merge branch 'gpu_dev' into gpu_dm commit 9b18d70ed1999c4a964edc027834d7b43fa99722 Merge: 668a0392 aeb0f7b8 Author: Jean M. Sexton Date: Tue Jan 28 20:03:25 2020 -0500 Merge branch 'gpu_dev' into gpu_dm commit 6ced5dd5c1ca4fbb20954be0422b9043dbc40348 Author: Jean M. Sexton Date: Wed Jan 29 08:59:15 2020 -0500 Fix if statement for heating-cooling flag Source/HeatCool/integrate_state_vec_3d.cpp commit aeb0f7b8e26e9f4e3f0fdb8c449c6bf5ae0cd51d Author: Jean M. Sexton Date: Fri Jan 24 20:36:48 2020 -0500 Add MPI+CUDA using Sundials makefile Exec/LyA/GNUmakefile.cuda commit 0680099db128aa40c68032e9bf1cae8f7a8e8770 Author: Jean M. Sexton Date: Tue Jan 21 19:36:06 2020 -0800 Store maximum step numbers for work estimate Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/Nyx_ctu_fuse.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_output.cpp Source/strang_reactions.cpp commit d186e6ec5ae3c022fa04b78c72dbfaa01d005124 Author: Jean M. Sexton Date: Tue Jan 21 12:32:23 2020 -0800 Remove default for global redistribute based on timestep Source/Nyx.cpp commit 5250d00fa8a78efa6e47a32518162cce96ee83f7 Author: Jean M. Sexton Date: Tue Jan 21 12:31:25 2020 -0800 Add input flag for heating-cooling memory management strategy Source/HeatCool/integrate_state_vec_3d.cpp Source/Nyx.cpp commit 79a7ce3c609ed1dfbaab4136765e89635f361e76 Merge: 6ed8e500 2651da94 Author: Jean M. Sexton Date: Mon Jan 20 15:36:00 2020 -0800 Merge branch 'development' into gpu_dev commit 2651da94affcdb840cc6e980ea109d79d9e804e1 Author: Jean M. Sexton Date: Wed Jan 15 13:22:08 2020 -0500 Add default false for extra ascii, rank, and species plotting Source/Nyx_output.cpp commit 6ed8e50068a8f27a22d255113b6f3a98fac292e6 Author: Jean M. Sexton Date: Mon Jan 13 16:57:36 2020 -0500 Add redundant launch safe guards, fix multi-level print statement Source/Initialization/Nyx_initdata.cpp Source/Nyx_advance.cpp Source/Nyx_output.cpp Source/sum_integrated_quantities.cpp commit 47647347e291d97581f9694476be81e073d5941e Author: Arnur Nigmetov Date: Sat Jan 11 17:32:18 2020 +0100 Change default REEBER_EXT_HOME. Reeber repo is called reeber2-git, not reeber. Util/reeber/Make.package commit b9db3fd36355208c1f6b0e470eca8544937c4516 Author: Arnur Nigmetov Date: Wed Dec 18 20:46:19 2019 +0100 Fill more halos info, disable debug output Also clean up GNUmakefile-s. Exec/LyA/GNUmakefile Exec/LyA_AGN/GNUmakefile Source/Nyx_halos.cpp Util/reeber/Make.package Util/reeber/include/reeber.H Util/reeber/src/reeber.cpp commit dc60279c8fbd3ca319c19fa261f316c6b56892cf Author: Jean M. Sexton Date: Wed Dec 18 01:04:32 2019 -0500 Add OnePerCell initialization option, update integrate_state_vec Source/HeatCool/integrate_state_vec_3d.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticles.cpp commit 668a03925df580c994f114fbbc791e008735886e Author: Jean M. Sexton Date: Wed Dec 18 00:03:37 2019 -0500 Return to one box size strategy Source/Nyx.cpp commit c1282531007832ea95b2318d46566d0b4d6fba69 Author: Jean M. Sexton Date: Tue Dec 17 23:30:44 2019 -0500 Test using different size boxes for DMPC and MultiFab Source/Nyx.cpp commit a2c30733458e7a5ac19ec7ca65a50e8dd23a112b Author: Jean M. Sexton Date: Tue Dec 17 16:08:50 2019 -0500 Remove particle velocities with do_hydro=0 due to assertion fail Source/Initialization/Nyx_setup.cpp Source/sum_integrated_quantities.cpp commit f66edc59f208e1ebeebacb36b3f2dbf20a80f0e5 Merge: 02623c05 fdc9a87b Author: Jean M. Sexton Date: Mon Dec 16 19:08:26 2019 -0500 Merge branch 'gpu_dev' into gpu_dm Conflicts: Source/NyxParticleContainer.H commit daaf2ab70dc48972f3028f7cd542eb1f91e10583 Author: Jean M. Sexton Date: Tue Dec 10 17:13:07 2019 -0800 Update zeldovich tests Exec/GravityTests/zeldovich_dm/analysis/process_zeldovich.py Exec/GravityTests/zeldovich_dm/build/Prob_3d.f90 Exec/GravityTests/zeldovich_dm/run/inputs Exec/GravityTests/zeldovich_dm/run/inputs_hydro Exec/GravityTests/zeldovich_dm/run/probin Source/Nyx_output.cpp commit fdc9a87b8bc2cd1350d32e29334b1b6660da3d0d Author: Jean M. Sexton Date: Mon Dec 9 20:03:03 2019 -0500 Fix launch regions for n-body case, remove non-launched number of valid particle check from estTimeStep Source/NyxParticleContainer.H Source/advance_particles.cpp commit 02623c05e4881dfb71a779f3c3088f90aa4132dd Author: Jean M. Sexton Date: Tue Dec 3 13:36:36 2019 -0500 Remove diagnostic print and serial test for validity, added extra logic to when to regrid, removed extra Redistribute Source/Nyx.cpp Source/NyxParticleContainer.H Source/advance_particles.cpp commit c5b88ea3951dd4deae0868ea0ad7079d327c10c3 Author: Jean M. Sexton Date: Mon Dec 2 18:47:55 2019 -0500 Added particle regrid to post-timestep, fixed corresponding redistribute for moveKick and moveKickDrift Source/DarkMatterParticleContainer.cpp Source/Nyx.cpp Source/NyxParticleContainer.H Source/advance_particles.cpp commit be919b03c38f1a89283312d8d8ad4de29a07c562 Author: Jean M. Sexton Date: Mon Dec 2 18:53:21 2019 -0500 Revert "DistributionMaps match, checking correctness of pointer copy/swap" This reverts commit 7ac833a6b54171701db603596979f9e4f8c2bb51. Revert "Copying gravity matches to round-off" This reverts commit 6d745711b62e8df812983000a8bd4125d7feac07. Revert "Test with deleting and adding again changes to 1e-12" This reverts commit bbffb5d7cc732b36b706ee49e8a87ab616ae29ea. Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticleContainer.H commit 7ac833a6b54171701db603596979f9e4f8c2bb51 Author: Jean M. Sexton Date: Sat Nov 30 00:34:39 2019 -0500 DistributionMaps match, checking correctness of pointer copy/swap Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticleContainer.H commit 6d745711b62e8df812983000a8bd4125d7feac07 Author: Jean M. Sexton Date: Fri Nov 29 12:30:31 2019 -0500 Copying gravity matches to round-off Source/Gravity/Gravity.cpp Source/Nyx.cpp commit bbffb5d7cc732b36b706ee49e8a87ab616ae29ea Author: Jean M. Sexton Date: Fri Nov 29 12:22:49 2019 -0500 Test with deleting and adding again changes to 1e-12 Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Nyx.H Source/Nyx.cpp commit 1ce1e72055bdd5efa8702b54771b0b41fc695279 Author: Jean M. Sexton Date: Mon Nov 25 14:19:20 2019 -0800 Fix interp parameter in reset after merge Source/Src_3d/reset_internal_energy_3d.F90 commit d0744dbf46ccfeb532ea4e12bc2834736916c63f Merge: 12702d63 ddcea07f Author: Jean M. Sexton Date: Mon Nov 25 08:51:09 2019 -0800 Merge branch 'development' into gpu_dev commit ddcea07f2cc16e78e8dbb5c958d57f6745882c3f Author: Frederick Davies Date: Sat Nov 16 17:33:41 2019 -0800 sdc fix? Source/sdc_hydro.cpp commit 12702d63037f421de2c0e9566d51ca70666bc7b1 Merge: defd44d4 23695023 Author: Jean M. Sexton Date: Mon Nov 25 08:44:12 2019 -0800 Merge branch 'development' into gpu_dev commit 236950235cae5ad0f15c7c5234f75be9b99e3a06 Author: Jean M. Sexton Date: Wed Nov 13 16:33:50 2019 -0800 Remove print statements Source/Nyx.cpp commit bfe3a799f6ce696f5fd9bf91948603615c254ccf Author: Jean M. Sexton Date: Wed Nov 13 16:32:10 2019 -0800 Add interpolating-specific reset to init() and init(AmrLevel &old) Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Src_3d/reset_internal_energy_3d.f90 commit 188bdd7dc6dd817f28797a1386ae44ad9b5cd141 Author: Jean M. Sexton Date: Mon Nov 11 10:48:42 2019 -0500 Move loop exit outside OMP critical region Source/EOS/eos_hc.f90 commit 0fcd3b21f07dd4fc1e797a1cb174a7557b410236 Author: Jean M. Sexton Date: Fri Nov 8 20:13:41 2019 -0500 Remove forced abort for high iteration count in Newton-Raphson in iterate_ne Source/EOS/eos_hc.f90 commit d722a86b77d2f5314bffeb93d2691ed72e04f0eb Author: Hannah Ross Date: Thu Nov 7 12:16:14 2019 -0800 Temperature now written correctly Util/convert_all_fields/AmrDerive.cpp commit a55cabfe7239a116eac6506153b1ef9ac20c307c Author: Hannah Ross Date: Tue Nov 5 15:30:29 2019 -0800 Converter now has correct units Util/convert_all_fields/AmrDerive.cpp commit 9f73c26b666d22ba987ce089ca9c405ec68a76c9 Merge: 64b5df75 13919ce4 Author: Hannah Ross Date: Tue Nov 5 10:58:37 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development Nyx changed while I was updating converter commit 64b5df75787ce18e22d7d8bd1d8f7d11aa794e67 Author: Hannah Ross Date: Tue Nov 5 10:57:33 2019 -0800 Particle velocities added to converter Util/convert_all_fields/AmrDerive.cpp commit defd44d4586ececef2f7b7fe5395768a72c54a1e Author: Jean M. Sexton Date: Tue Nov 5 12:19:01 2019 -0500 Add extra diagnostic particle print statements, add input files to test nbody case Exec/AMR-density/inputs_nohydro.rt Exec/LyA/inputs_nohydro.rt Source/Initialization/Nyx_initdata.cpp Source/Nyx.H Source/NyxParticleContainer.H Source/NyxParticles.cpp commit 6f636d2b6443cf12cd6d61a60eb2d3c8f851e535 Merge: 8ab2c977 13919ce4 Author: Jean M. Sexton Date: Mon Nov 4 18:16:19 2019 -0500 Merge branch 'development' into gpu_dev commit 13919ce45f6c0345fc6833a324f1708a92fdd8f1 Author: Jean M. Sexton Date: Mon Nov 4 15:05:52 2019 -0500 Restore deleted file Util/convert_amr/AmrElements.cpp commit 409e89048e6319d8d9089e283a060067d8585d92 Merge: a41fb541 11fbbc5f Author: Jean M. Sexton Date: Mon Nov 4 15:16:48 2019 -0500 Merge branch 'master' into development commit a41fb5410347244b90fbc22deb6c66933d0de0d1 Author: Jean M. Sexton Date: Thu Oct 31 17:53:11 2019 -0400 Add line to output plotfile info, fixed SDC fortran modules Source/HeatCool/integrate_state_with_source_3d.f90 Source/Nyx_output.cpp commit 66d4f5752d8597edf53ac034df29bbf2e6111f0f Author: Jean M. Sexton Date: Thu Oct 31 15:34:53 2019 -0400 Added {} to ensure all amrex objects are out of scope before amrex::Finalize() Util/convert_all_fields/AmrDerive.cpp commit 262ee9bb6ba56971f9cca1b4c336c309cb749180 Merge: d393561f bc55b7de Author: Hannah Ross Date: Thu Oct 31 12:18:10 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development "Made changes to the converter without pulling Nyx first" commit d393561fdd31027101717acd370348c0d1af37c2 Author: Hannah Ross Date: Thu Oct 31 12:16:46 2019 -0700 Added converter for all fields with correct variable names for gimlet Util/convert_all_fields/AmrDerive.cpp commit 8ab2c977436aa22feec823e7509b87408fed8a24 Author: Jean M. Sexton Date: Wed Oct 23 18:20:09 2019 -0400 Update BinaryFile and BinaryMetaFile particle read types to be in a launch region, fix return for estTimeStep Source/NyxParticleContainer.H Source/NyxParticles.cpp commit 895f04bf3a1d699c202009042ed0f0f5520ec085 Author: Jean M. Sexton Date: Mon Oct 21 17:50:27 2019 -0400 Fix index bug in My_Rank derive Source/Nyx.cpp commit 1f640157a3748f6d3063358927d00333fb5a0c6b Author: Jean M. Sexton Date: Sat Oct 19 20:27:26 2019 -0400 Test particle est time step changes Source/Nyx.cpp Source/NyxParticleContainer.H commit 3ef1edd91f37606de7ca860fdd4e0f9ce5bec04d Author: Jean M. Sexton Date: Thu Oct 17 14:51:46 2019 -0700 Update NO_HYDRO flags for new hydro and update ifdef USE_CUDA -> ifdef USE_CUDA_FORTRAN for attribute statements Source/EOS/atomic_rates.F90 Source/EOS/eos_hc.F90 Source/EOS/reion_aux_module.F90 Source/HeatCool/vode_aux.F90 Source/Hydro/Make.package Source/Initialization/Nyx_initdata.cpp Source/Make.package Source/meth_params.F90 commit e2c5761649304baecb3e660c164faf7d712adda7 Merge: 36dc605c bc55b7de Author: Jean M. Sexton Date: Thu Oct 17 13:39:39 2019 -0700 Merge branch 'development' into gpu_dev commit bc55b7dea5259f9be7be2d8a445a120f2ee72557 Author: Jean M. Sexton Date: Thu Oct 17 13:37:13 2019 -0700 Update NO_HYDRO flags Source/DerivedQuantities/ParticleDerive.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Make.package Source/Nyx.cpp commit 938cc9394d0b1e3985ff82a73d2bdfe638902f79 Author: Jean M. Sexton Date: Tue Oct 15 16:57:06 2019 -0700 Add Nyx git hash to stdout print Source/Initialization/Nyx_setup.cpp commit 5896271dac25e209b20a86bbb91d4d1d8c8608d4 Author: hr203 Date: Wed Oct 16 11:03:45 2019 -0700 Hannah dev (#48) * Updates to amr to binary converter * Converter for new fields Util/convert_all_fields/AmrDerive.cpp Util/convert_all_fields/GNUmakefile Util/convert_all_fields/Make.package Util/convert_amr/AmrElements.cpp commit 36dc605cc8340433f2c7d08c08dfefb665c27bef Author: Jean M. Sexton Date: Tue Oct 15 14:31:41 2019 -0400 Make global redistribute potentially launched Source/NyxParticleContainer.H commit bccb1d1ee21350a2ad3460459e72df5855174543 Author: Jean M. Sexton Date: Fri Oct 11 15:50:19 2019 -0400 Force binary particle init and global redistribute to synchronize and run CPU version Source/NyxParticleContainer.H Source/NyxParticles.cpp commit 1252ceacf27fc5769c5b41a555a71eb44449fe01 Author: Jean M. Sexton Date: Fri Sep 27 09:49:19 2019 -0400 Fixed ifdef flag, use global Redistribute for the first 3 steps for sanity Source/Nyx.cpp Source/Nyx_advance.cpp commit 8a0fbcbae007fdfe95883341ab171ba8702437c8 Author: Jean M. Sexton Date: Tue Sep 24 20:15:50 2019 -0400 Test integrators for hackathon Util/sdc-test/GNUmakefile Util/sdc-test/Make.package Util/sdc-test/SetIC.f90 Util/sdc-test/SparseGaussJordan.H Util/sdc-test/TREECOOL_middle Util/sdc-test/atomic_rates.F90 Util/sdc-test/comoving_nd.f90 Util/sdc-test/comoving_params.f90 Util/sdc-test/constants_cosmo.f90 Util/sdc-test/constants_mod.f90 Util/sdc-test/cvode_extras.F90 Util/sdc-test/eos_hc.F90 Util/sdc-test/eos_params.f90 Util/sdc-test/f_rhs.F90 Util/sdc-test/init_managed.F90 Util/sdc-test/inputs Util/sdc-test/inputs_atomic Util/sdc-test/inputs_flags Util/sdc-test/inputs_non_vectorized Util/sdc-test/main.cpp Util/sdc-test/meth_params.F90 Util/sdc-test/misc_params.f90 Util/sdc-test/myfunc_F.H Util/sdc-test/ode_mod.f90 Util/sdc-test/reion_aux_module.F90 Util/sdc-test/vode_aux.F90 Util/sdc-test/vode_system.H commit 4ed277b0828aacb9d7b0960294d8c2ab2b65a411 Author: Jean M. Sexton Date: Tue Sep 24 17:33:15 2019 -0400 Add C++ version of eos_stuff.f90 and interface for converting eos_hc.F90 Source/EOS/Make.package Source/EOS/eos_hc.F90 Source/EOS/eos_interface.cpp Source/EOS/eos_stuff.F90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H commit 966d5a5d87b4d7205e5d1814ecf92dfe4e6927a4 Author: Jean M. Sexton Date: Sat Sep 21 18:44:02 2019 -0400 Add more ODE solver options to test problem Util/SUNDIALS3/GNUmakefile Util/SUNDIALS3/inputs_flags Util/SUNDIALS3/main.cpp commit 11fbbc5fa4e516b76c3e3103ba689e6e597e9279 Author: Ann Almgren Date: Fri Sep 20 09:25:11 2019 -0700 Add "Powered by AMReX" README.md commit b61626145a8ac9d34a05456440794a76198e4f67 Author: Ann Almgren Date: Fri Sep 20 09:25:11 2019 -0700 Add "Powered by AMReX" README.md commit 8e7873169537cfcdc08c16dc7fedd457fb1dc64d Author: Jean M. Sexton Date: Wed Sep 18 19:10:03 2019 -0400 Add input flag to control negative energy constraint, added profile regions for tiny profiling, tweaked convergence test for iterate_ne to include maximum iteration check Source/EOS/eos_hc.F90 Source/HeatCool/integrate_state_vec_3d.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_advance.cpp Source/nyx_main.cpp commit de448afcb966ef3b8e9302f1a2f6d2c78f727ecd Author: Jean M. Sexton Date: Wed Sep 18 16:03:16 2019 -0400 Remove extra testing statements Source/HeatCool/integrate_state_vec_3d.cpp commit e348de2a0b344f996c7947b7cc8f42e87a45f8a4 Author: Jean M. Sexton Date: Wed Sep 18 10:50:33 2019 -0400 Update Util test to current use case, cleaned up print statements Source/HeatCool/integrate_state_vec_3d.cpp Util/SUNDIALS3/cvode_extras.F90 Util/SUNDIALS3/init_managed.F90 Util/SUNDIALS3/inputs_non_vectorized Util/SUNDIALS3/main.cpp commit dbc44ea61c5db5b46d27f8a2db12413908e15b62 Author: Jean M. Sexton Date: Wed Sep 18 10:42:34 2019 -0400 Updated syntax to match new sundials version Source/HeatCool/integrate_state_vec_3d.cpp commit 6b068aa6dfc9973b4f50a34ecd797c9a68287069 Author: Jean M. Sexton Date: Tue Sep 17 09:03:32 2019 -0400 Make verbose maximum temperature calculation use GPU Source/Nyx.cpp commit 92905449b26d877b14dc8645e0b14f84337aff59 Merge: a6ee51ea 47b18e8d Author: Jean M. Sexton Date: Wed Sep 11 19:42:06 2019 -0400 Merge remote-tracking branch 'origin/development' into gpu_dev commit 47b18e8d8155f7079ced93ebcb41ed412af659b5 Author: Jean M. Sexton Date: Wed Sep 4 16:34:04 2019 -0400 Use RedistributeLocal in post_timestep() in single-level case Source/Nyx.cpp commit c45af5654018ba75ff449a0dc455fe89580eae08 Author: Andrew Myers Date: Thu Apr 11 10:42:39 2019 -0700 add local version of Redistribute for Nyx Source/NyxParticleContainer.H commit a6ee51ea8b93276b3fc7eb681595270718fbf4d6 Author: Jean Sexton Date: Sun Sep 1 17:18:49 2019 -0400 Fix index bug in dark matter particles Source/DarkMatterParticleContainer.H Source/DarkMatterParticleContainer.cpp commit 5125c1fa760742c8367708bc1557ffd0b489b25a Author: Jean Sexton Date: Fri Aug 30 12:46:04 2019 -0400 Tweak redistribute call to check particles out of bounds Source/Nyx.cpp Source/NyxParticleContainer.H commit 64676b150d97d6a26e5fb87326956188a71c325e Author: Jean Sexton Date: Thu Aug 29 18:56:45 2019 -0400 Fixed value type for comoving_a and print_fortran_warnings to fix bug in compute_temp .gitignore Source/EOS/eos_hc.F90 Source/EOS/eos_stuff.F90 Source/Hydro/Nyx_ctu_fuse.cpp Source/Nyx.cpp Source/Nyx_F.H Source/Src_3d/compute_temp_3d.F90 commit 190da3cad7ef0e626ad899c2b4323106291e0512 Author: Jean Sexton Date: Tue Aug 27 19:46:47 2019 -0400 Fix use_const_species a factor in consup, add back in option for non-analytic riemann solve into hydro_convert=0 Source/Hydro/riemann_nd.F90 Source/HydroFortran/Nyx_advection_3d.f90 commit c4215b834207ba0e00c9a749575de81868f0ddb5 Author: Jean Sexton Date: Mon Aug 26 18:13:54 2019 -0400 Add 1cell version of analytic riemann to hydro_convert=1 Source/Hydro/riemann_nd.F90 Source/Hydro/riemann_util.F90 Source/Nyx.cpp commit 308dd181e822e062da26b23be6b20d2a0210502a Author: Jean Sexton Date: Mon Aug 26 17:43:25 2019 -0400 Added input flag for analytic riemann, added launchsafeguard for particles, tweaked redistribute call Source/DarkMatterParticleContainer.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 commit 6fb245afea05f4f1fb2ddb00b576f987c3d42015 Merge: 52d4f956 08ec506f Author: Jean M. Sexton Date: Wed Aug 14 07:53:11 2019 -0700 Merge branch 'gpu_hydro' of github.com:amrex-astro/Nyx into gpu_hydro. Rebased gpu_dev onto gpu_hydro, moved branch names as appropriate, match regression commit 52d4f95635ab22d067a0a01b3b08d826027cf426 Author: Jean Sexton Date: Tue Jul 23 12:39:01 2019 -0400 Fixed HEATCOOL ifdef location Source/Hydro/Nyx_ctu_fuse.cpp Source/Src_3d/compute_temp_3d.F90 commit fa8a5d3bff689810280c4e254c6638282a07dc2f Author: Jean M. Sexton Date: Fri Jul 19 14:12:45 2019 -0700 Fix seperate variables for fort_interp_to_this_z for the second strang call and compute_new_temp Source/EOS/atomic_rates.F90 Source/EOS/eos_hc.F90 Source/HeatCool/f_rhs.F90 Source/Hydro/Nyx_ctu_fuse.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/init_managed.F90 Source/Src_3d/compute_temp_3d.F90 Source/strang_hydro.cpp Source/strang_hydro_fuse.cpp commit 9be6f3dd7dcff978ab9408372e212a57e638578e Author: Jean M. Sexton Date: Fri Jul 19 06:24:57 2019 -0700 Add second set of z-dependent parameters in atomic_rates so that fhey can be set once per time-step in the fused loop case Source/EOS/atomic_rates.F90 Source/EOS/eos_hc.F90 Source/HeatCool/cvode_extras.F90 Source/HeatCool/f_rhs.F90 Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/Nyx_ctu_fuse.cpp commit 2c1ed79b644b0677e5c2bc21c856aca8bd8d88ce Author: Jean M. Sexton Date: Thu Jul 18 16:57:00 2019 -0700 Add prefetches for advance Source/Nyx_advance.cpp commit 78cebf7acd39542078d823420397b57b5ac1f79c Author: Jean M. Sexton Date: Thu Jul 18 16:28:34 2019 -0700 Convert MultiFab version of ext_src_old for fused version for the case when add_ext_src==0, add logic for nghost_state to fuse routines Source/Hydro/Nyx_ctu_fuse.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx_advance.cpp Source/strang_hydro_fuse.cpp commit c6aa376982852a609bbaae15adc72981a771a2ad Author: Jean M. Sexton Date: Thu Jul 18 15:38:14 2019 -0700 Add nyx.strang_fuse input flag to switch whether strang fuses the MFIter loops Source/Hydro/Make.package Source/Hydro/Nyx_ctu_fuse.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/Make.package Source/Nyx.H Source/Nyx.cpp Source/Nyx_advance.cpp Source/strang_hydro.cpp Source/strang_hydro_fuse.cpp commit 59b33d2fb8e5daf60beb77251b5abfc55e67a3e1 Author: Jean M. Sexton Date: Thu Jul 18 12:38:26 2019 -0700 Converted hydro_src MultiFab from strang_hydro.cpp into FArrayBox version Source/Hydro/Nyx_ctu_hydro.cpp Source/strang_hydro.cpp commit 9fa298b33cb93fb754fb43a04c7be5fc14b9dfcb Author: Jean M. Sexton Date: Thu Jul 18 06:49:57 2019 -0700 Testing moving update_state_with_sources into construct_ctu_hydro MFIter loop Source/Hydro/Nyx_ctu_hydro.cpp Source/strang_hydro.cpp commit 93a6c0645b027a5ae2720102275d9e54bc21d1ca Author: Jean M. Sexton Date: Wed Jul 17 18:18:13 2019 -0700 Testing patched version of 5.0.0-dev.1 Sundials with moving strang_first_step into construct_ctu_hydro mfiter loop Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/strang_hydro.cpp commit 331434bed67e9f578e89243119c9f831b5549724 Author: Jean M. Sexton Date: Wed Jul 17 17:15:16 2019 -0700 Added synchronizes to fix the oversubscribed MakeWithAllocator case Source/HeatCool/integrate_state_vec_3d.cpp commit c1001cb717a14799f4861c5b3ff2c1a282c42565 Author: Jean M. Sexton Date: Wed Jul 17 16:46:16 2019 -0700 Fix for missing #ifdef which was causing segfault Source/HeatCool/integrate_state_vec_3d.cpp commit fd3f41380f496d822a95d19ce14044518e3b3250 Author: Jean M. Sexton Date: Wed Jul 17 11:25:08 2019 -0700 Test with #define flag for selecting between NewManaged, MakeManaged and MakeWithAllocator for testing purposes, added prefetches Source/HeatCool/integrate_state_vec_3d.cpp commit 47aec258d3c903b8ba164316b729f82c42556ace Author: Jean M. Sexton Date: Wed Jul 17 09:03:23 2019 -0700 Made modular strang function and changed allocator/deallocator for sundials objects Source/HeatCool/integrate_state_vec_3d.cpp Source/Nyx.H commit 9cb503d2df9bfb2c189fa12ae19ae6a70884c680 Author: Jean M. Sexton Date: Tue Jul 16 13:42:55 2019 -0700 Move diag_eos indices from individual global static int to enum Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_cell_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp commit 76ec585d1f2315e0e5921a3808379b20d69bfd60 Author: Jean M. Sexton Date: Tue Jul 16 12:54:05 2019 -0700 Move state indices from individual global static int to enum Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_cell_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticleContainer.H commit 5a2966f421a74aac6b44277765364f0b60f68809 Author: Jean M. Sexton Date: Mon Jul 15 13:57:28 2019 -0700 Add LaunchSafeGuard for initcosmo, initdata, some of NyxParticles Source/NyxParticles.cpp commit 835181045847e84eafcdfd74ce44db184b5a4999 Author: Jean M. Sexton Date: Mon Jul 15 13:57:28 2019 -0700 Add LaunchSafeGuard for init Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp commit 1336e525a73bd6ee431c2118dd549647a90b4606 Author: Jean M. Sexton Date: Mon Jul 15 11:02:32 2019 -0700 Changed to LaunchSafeGuard in Nyx.cpp and nyx_main.cpp Source/Nyx.cpp Source/nyx_main.cpp commit 2196a4e41cc7ba0f984e2b06ae1085d284bd0d3e Author: Jean M. Sexton Date: Mon Jul 15 07:46:43 2019 -0700 Prefetch for correct gravity src Source/Nyx_advance.cpp commit a588a1dd6faa3adaac84b4867718c447ac225abc Author: Jean M. Sexton Date: Sun Jul 14 19:45:55 2019 -0700 LaunchSafeGuard for gravity Source/Gravity/Gravity.cpp commit 0ddaf44e0478677fe2658f890029fbe1e4445ff5 Author: Jean M. Sexton Date: Sun Jul 14 19:27:05 2019 -0700 Clean up particle launch region statements and add prefetch and launch safe guards for checkpoints and plotfiles Source/DerivedQuantities/ParticleDerive.cpp Source/Nyx.cpp Source/NyxParticleContainer.H Source/Nyx_output.cpp commit 0b4bbbdd42e05f2cb75338a80403f04f2c750c95 Author: Jean M. Sexton Date: Sun Jul 14 11:40:45 2019 -0700 Convert setlaunchregion to launchsafeguard for Nyx_advance and underlying hydro functions Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/Nyx_advance.cpp Source/strang_hydro.cpp Source/strang_reactions.cpp Source/update_state_with_sources.cpp commit 35304756452726c298bec024bdaf48660e4c7c5c Author: Jean M. Sexton Date: Thu Jul 11 14:44:39 2019 -0700 Revert "Remove prefetches for testing" This reverts commit 6c18e0ae18f1f53748f7b78d388f659ab46280ea. Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/Nyx_hydro.cpp Source/update_state_with_sources.cpp commit f385a4c66b0abdf642a7976fafdec1eec5de4714 Author: Jean M. Sexton Date: Wed Jun 26 14:16:06 2019 -0700 Remove prefetches for testing Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/Nyx_hydro.cpp Source/update_state_with_sources.cpp commit cc72774d45dec0f44c99c23264ff2c9a1cd78d54 Author: Jean M. Sexton Date: Wed Jun 26 12:58:37 2019 -0700 Revert "Summit prefers no prefetches and a synch in the construct_ctu_hydro driver" This reverts commit 440aed86fe54630d5d698aaa790587e3363eae67. Source/Hydro/Nyx_ctu_hydro.cpp commit 0503428820ae77d7f636ca615a54bb74c38d20a0 Author: Jean M. Sexton Date: Thu Jul 11 14:22:53 2019 -0700 Add input flag nyx.nghost_state for testing removal of S_old_tmp in strang_hydro, default is 1, setting this parameter to 4 means more data reuse Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_advance.cpp Source/strang_hydro.cpp commit bfe7b35e3f32517ad64739e6d83264cf72f26061 Author: Jean M. Sexton Date: Thu Jul 11 10:34:07 2019 -0700 Remove FillBoundary option in strang_hydro for single level runs Source/strang_hydro.cpp commit c805b08bcd39ddfaf10abc4bfdd6b739304a6490 Author: Jean M. Sexton Date: Wed Jun 26 13:17:18 2019 -0700 Revert "Revert "Summit prefers no prefetches and a synch in the construct_ctu_hydro driver"" This reverts commit 9a03c55927caae88c9aefee568083440faeb2147. Source/Hydro/Nyx_ctu_hydro.cpp commit 8efd6e67b2468a76d7c19f2e9127be339dfd4910 Author: Jean M. Sexton Date: Wed Jun 26 12:58:37 2019 -0700 Revert "Summit prefers no prefetches and a synch in the construct_ctu_hydro driver" This reverts commit 440aed86fe54630d5d698aaa790587e3363eae67. Source/Hydro/Nyx_ctu_hydro.cpp commit 71a4a8accb4e40a13ce38afed65c3439d919e934 Author: Jean Sexton Date: Thu Jun 20 06:38:18 2019 -0400 Clean up more memory Source/Gravity/Gravity.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/strang_hydro.cpp commit d8722a665bb8f7779ff43106dc1cdda18f6509a3 Author: Jean Sexton Date: Wed Jun 19 01:49:25 2019 -0400 Summit prefers no prefetches and a synch in the construct_ctu_hydro driver Source/Hydro/Nyx_ctu_hydro.cpp commit 92d050e625a9891e2dd5b00fb8edf9459aa0ab31 Author: Jean M. Sexton Date: Tue Jun 18 21:41:38 2019 -0700 Added more clears Source/Hydro/Nyx_ctu_hydro.cpp commit fd6a99c6c59e3894fd769e89bd8df310b5b45a8a Author: Jean M. Sexton Date: Tue Jun 18 20:26:55 2019 -0700 Move hydro_src declaration and clear more close to where it's used Source/Hydro/Nyx_ctu_hydro.cpp Source/strang_hydro.cpp commit 4a8187964d6c6cbceef2a84b8a413b91f77cd071 Author: Jean M. Sexton Date: Tue Jun 18 19:57:12 2019 -0700 Removed pre-allocated MultiFab for divu_cc for hydro_convert=1 version Source/Hydro/Nyx_ctu_hydro.cpp Source/Nyx.H Source/strang_hydro.cpp Source/update_state_with_sources.cpp commit 3a8a0d87b956790a081b7b073444521ccf4a15e5 Author: Jean M. Sexton Date: Tue Jun 18 14:28:26 2019 -0700 Remove 3 MultiFabs from construct_ctu_hydro, set QVAR and NQSRC to match initialization Source/Hydro/Nyx_ctu_hydro.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp Source/update_state_with_sources.cpp commit 54dfa22e3c6ca0afcc311b23f2785bfd6566a5b8 Author: Jean M. Sexton Date: Tue Jun 18 10:38:41 2019 -0700 Move consup Multifabs to large MFIter loop Source/Hydro/Nyx_ctu_hydro.cpp commit 59168fcc279c71cfd2431140a945c1d841e0a748 Author: Jean Sexton Date: Tue Jun 18 12:57:56 2019 -0400 Fix bug from #ifdef GRAVITY Source/Nyx_advance.cpp commit fb43903c1ada9cdd948df547aea9e5d2d2781ab5 Author: Jean M. Sexton Date: Mon Jun 17 20:01:00 2019 -0700 Added prefetch for cons_to_prim and update_state_with_sources Source/Hydro/Nyx_hydro.cpp Source/update_state_with_sources.cpp commit c4055bf7ce4507e9ab73b9f44d5246616efe9fab Author: Jean M. Sexton Date: Mon Jun 17 18:25:29 2019 -0700 Ensure some more dt, a_old, a_new passed by value Source/Hydro/Nyx_advection_util.F90 Source/Hydro/Nyx_ctu_hydro.cpp Source/Nyx_F.H commit 5c89c31d2488f89d6237b8eef62c54e1e61b5790 Author: Jean M. Sexton Date: Mon Jun 17 16:13:37 2019 -0700 Add prefetch to main hydro loop Source/Hydro/Nyx_ctu_hydro.cpp commit edbdd7392323fc9f74c502830f5a3ae2b1ab2281 Author: Jean Sexton Date: Sun Jun 16 15:26:17 2019 -0400 Added forgotten ifdef for freeing arena memory in non-gpu case Exec/Scaling/profile.sh Source/HeatCool/integrate_state_vec_3d.cpp commit 09b664bcf4012d89d7ca5b52dcb34446ab9a9d7b Author: Jean M. Sexton Date: Sun Jun 16 12:08:20 2019 -0700 Test using The_Managed_Arena and NV_MakeManaged_Cuda with sundials Source/HeatCool/integrate_state_vec_3d.cpp commit a721e33448fdef997923f224341354b6d9f833a8 Author: Jean M. Sexton Date: Sun Jun 16 11:21:31 2019 -0700 Remove redundant csml vs qaux MultiFab, ensure a passed by value in srctoprim Source/Hydro/Nyx_advection_util.F90 Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/Nyx_hydro.cpp Source/Nyx.H Source/Nyx_F.H commit ffc436c481267878124e3593eca69fb945cdfa98 Author: Jean M. Sexton Date: Sun Jun 16 10:53:56 2019 -0700 Remove area MultiFab, since for a single level area per cell is constant Source/Hydro/Nyx_advection_util.F90 Source/Hydro/Nyx_ctu_hydro.cpp Source/Nyx_F.H commit f222c3a821b976217d59f1e56d1e59a7edeb1bbe Author: Jean M. Sexton Date: Sun Jun 16 10:39:37 2019 -0700 Replace fabPtr for launched regions, tweaked setlaunchregion for post_init Source/Hydro/Nyx_hydro.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_advance.cpp Source/update_state_with_sources.cpp commit fd3315deb1331bdf06b7027a8f6391cf2556672c Author: Jean M. Sexton Date: Sat Jun 15 13:54:26 2019 -0700 Added clear() for elixirs, fixed order for memeory so that it's declared only before it's needed Source/Hydro/Nyx_ctu_hydro.cpp commit 5437aa6fdf13252c5ad7a0eb11a57d17bfd5891c Author: Jean M. Sexton Date: Sat Jun 15 12:31:24 2019 -0700 Change fabPtr to Array4 Source/Hydro/Nyx_ctu_hydro.cpp commit 7f17545b8ac2189a509ab6097af0c8f6cab1c88d Author: Jean M. Sexton Date: Tue Jun 11 08:06:13 2019 -0700 Port add_to_fluxes, expand launch region in advance_hydro_plus_particles Source/Gravity/Gravity.cpp Source/Nyx_advance.cpp commit 6a1758cf67832f4b8253280e7082da4164e55ea8 Author: Jean Sexton Date: Fri Jun 14 07:32:06 2019 -0400 Test for minimizing memory footprint of advance_Ctu_hydro Source/Hydro/Nyx_ctu_hydro.cpp commit 4d2df4b7eafd938f20603ce456cf12aecd5504ac Author: Jean Sexton Date: Fri Jun 14 07:29:59 2019 -0400 Revert "Test moving MLPoission define to post_regrid instead of every timestep" This reverts commit ed36c3e8713b300571cc6552c60b763267cd84d1. Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Nyx.cpp Source/Nyx_advance.cpp commit 19d76483eaf771d40377bc17fd919d6a9946e36b Author: Jean M. Sexton Date: Tue Jun 11 08:06:13 2019 -0700 Port add_to_fluxes, expand launch region in advance_hydro_plus_particles Source/Gravity/Gravity.cpp Source/Nyx_advance.cpp commit 8a787974192e9c3607a758c8cccbb5b2a531f37b Author: Jean M. Sexton Date: Tue Jun 11 06:54:32 2019 -0700 Test moving MLPoission define to post_regrid instead of every timestep Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Nyx.cpp commit b255c1bb1b96d00b8eb5b0149a7588627ab1094b Author: Jean M. Sexton Date: Sun Jun 9 12:06:15 2019 -0700 Added profiling var to track FillPatch in strang, fixed launch region in NyxParticleContainer.H Source/NyxParticleContainer.H Source/strang_hydro.cpp commit 28b8742aae8b94b4174058964474e65677bf08cb Merge: 96065a47 d9590c7a Author: Arnur Nigmetov Date: Tue Jul 30 15:58:23 2019 -0700 Fix merge commit 96065a47bc4880ddfbd4fc796ef3bacdea195621 Author: Arnur Nigmetov Date: Tue Jul 30 15:53:58 2019 -0700 Use unique_ptr for copies; discard ghost data. Util/reeber/src/reeber.cpp commit 08ec506f8e19ed63a746ce2fc1cee85db1404c27 Author: Jean Sexton Date: Tue Jul 23 12:39:01 2019 -0400 Fixed HEATCOOL ifdef location Source/Hydro/Nyx_ctu_fuse.cpp Source/Src_3d/compute_temp_3d.F90 commit d9590c7a0dca43ca2b15dd41fa5705fca3f65dcd Author: Jean M. Sexton Date: Mon Jul 22 17:39:50 2019 -0700 Fixed component names for AGN particle plotfile, added profile timers for halo functions and make guards for REEBER=FALSE case Exec/LyA_AGN/GNUmakefile Exec/Make.Nyx Source/AGNParticleContainer.H Source/Nyx.H Util/reeber/src/reeber.cpp commit a40a421059a967dc5525273c18a0345063a53bd9 Author: Arnur Nigmetov Date: Mon Jul 22 14:21:04 2019 -0700 fix assertion error Util/reeber/src/reeber.cpp commit f5b12c1e531c94fd25a08cef6ae800f260c93206 Author: Arnur Nigmetov Date: Fri Jul 19 23:47:59 2019 -0700 Interim, compiles. TODO: positions in true AMR Source/Nyx.H Source/Nyx_halos.cpp Util/reeber/include/reeber.H Util/reeber/src/reeber.cpp commit e6ea0715e27fc5e270024c4f4b8e68970be94e59 Author: Jean M. Sexton Date: Fri Jul 19 14:12:45 2019 -0700 Fix seperate variables for fort_interp_to_this_z for the second strang call and compute_new_temp Source/EOS/atomic_rates.F90 Source/EOS/eos_hc.F90 Source/HeatCool/f_rhs.F90 Source/Hydro/Nyx_ctu_fuse.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/init_managed.F90 Source/Src_3d/compute_temp_3d.F90 Source/strang_hydro.cpp Source/strang_hydro_fuse.cpp commit 9f99d9a667dca314196d111bb53d14551d03ce01 Author: Jean M. Sexton Date: Fri Jul 19 06:24:57 2019 -0700 Add second set of z-dependent parameters in atomic_rates so that fhey can be set once per time-step in the fused loop case Source/EOS/atomic_rates.F90 Source/EOS/eos_hc.F90 Source/HeatCool/cvode_extras.F90 Source/HeatCool/f_rhs.F90 Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/Nyx_ctu_fuse.cpp commit c38c867df7065327fb5c4341e619b1a359e54ea6 Author: Jean M. Sexton Date: Thu Jul 18 16:57:00 2019 -0700 Add prefetches for advance Source/Nyx_advance.cpp commit 7834d37665104627ca51287a239ee299241280ff Author: Jean M. Sexton Date: Thu Jul 18 16:28:34 2019 -0700 Convert MultiFab version of ext_src_old for fused version for the case when add_ext_src==0, add logic for nghost_state to fuse routines Source/Hydro/Nyx_ctu_fuse.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx_advance.cpp Source/strang_hydro_fuse.cpp commit 0b476171b65c363c25589b41ddc62236a4333d29 Author: Jean M. Sexton Date: Thu Jul 18 15:38:14 2019 -0700 Add nyx.strang_fuse input flag to switch whether strang fuses the MFIter loops Source/Hydro/Make.package Source/Hydro/Nyx_ctu_fuse.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/Make.package Source/Nyx.H Source/Nyx.cpp Source/Nyx_advance.cpp Source/strang_hydro.cpp Source/strang_hydro_fuse.cpp commit 41d6e71ca1191ace773de1de24a5f7260654b835 Author: Jean M. Sexton Date: Thu Jul 18 12:38:26 2019 -0700 Converted hydro_src MultiFab from strang_hydro.cpp into FArrayBox version Source/Hydro/Nyx_ctu_hydro.cpp Source/strang_hydro.cpp commit b3693982d5a7e3b41afb11bc576fa8b62bd38d69 Author: Jean M. Sexton Date: Thu Jul 18 06:49:57 2019 -0700 Testing moving update_state_with_sources into construct_ctu_hydro MFIter loop Source/Hydro/Nyx_ctu_hydro.cpp Source/strang_hydro.cpp commit d0897a629b8a98a270b90a9a309383d9a7d5b4a0 Author: Jean M. Sexton Date: Wed Jul 17 18:18:13 2019 -0700 Testing patched version of 5.0.0-dev.1 Sundials with moving strang_first_step into construct_ctu_hydro mfiter loop Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/strang_hydro.cpp commit 2eed42000fb22ef7e603df38d00d44537b6b9197 Author: Jean M. Sexton Date: Wed Jul 17 17:15:16 2019 -0700 Added synchronizes to fix the oversubscribed MakeWithAllocator case Source/HeatCool/integrate_state_vec_3d.cpp commit 111a9d2f8e15e550d88931797e8886c236f73729 Author: Jean M. Sexton Date: Wed Jul 17 16:46:16 2019 -0700 Fix for missing #ifdef which was causing segfault Source/HeatCool/integrate_state_vec_3d.cpp commit 82133d5b298b248f1d543fd4bb4c1931de006752 Author: Jean M. Sexton Date: Wed Jul 17 11:25:08 2019 -0700 Test with #define flag for selecting between NewManaged, MakeManaged and MakeWithAllocator for testing purposes, added prefetches Source/HeatCool/integrate_state_vec_3d.cpp commit 3c7df1f1044742d0086502526f95088713ad0dc8 Author: Jean M. Sexton Date: Wed Jul 17 09:03:23 2019 -0700 Made modular strang function and changed allocator/deallocator for sundials objects Source/HeatCool/integrate_state_vec_3d.cpp Source/Nyx.H commit 24049274843ef91e3b3650b550507738f0a90add Author: Arnur Nigmetov Date: Tue Jul 16 17:24:09 2019 -0700 interim, to save code Exec/LyA_AGN/GNUmakefile Source/Nyx_halos.cpp Util/reeber/src/reeber.cpp commit 61122f7d1f2c79070be49ac060b1574ef06eb266 Author: Jean M. Sexton Date: Tue Jul 16 13:42:55 2019 -0700 Move diag_eos indices from individual global static int to enum Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_cell_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp commit 8e2d18d5cc228c127863b3cbf5cf29c259ecd160 Author: Jean M. Sexton Date: Tue Jul 16 12:54:05 2019 -0700 Move state indices from individual global static int to enum Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_cell_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticleContainer.H commit 265407b690d2efc5dda1dd1f5b8ba8d52aacc729 Author: Arnur Nigmetov Date: Tue Jul 16 12:15:35 2019 -0700 First version with actual Reeber code compiles. Exec/LyA/GNUmakefile Exec/Make.Nyx Source/Nyx.H Util/reeber/Make.package Util/reeber/src/reeber.cpp commit b9a5a0e7eb949dfd39d58353788e199dc7503870 Merge: 837fe153 96a59e59 Author: Jean M. Sexton Date: Mon Jul 15 15:13:35 2019 -0700 Merge branch 'gpu_hydro' of https://github.com/AMReX-astro/Nyx into gpu_hydro commit 837fe1534713ba5791bd151cd19280a0e7c1897c Author: Jean M. Sexton Date: Mon Jul 15 15:13:21 2019 -0700 Update travis .travis.yml commit e1bc0d228d1575b6b675a624dd4d0d0b9f5158dd Author: Jean M. Sexton Date: Mon Jul 15 13:57:28 2019 -0700 Add LaunchSafeGuard for initcosmo, initdata, some of NyxParticles Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/NyxParticles.cpp commit 96a59e59127dff1707d43a9ace97b6ed71f9a215 Author: Jean M. Sexton Date: Mon Jul 15 13:57:28 2019 -0700 Add LaunchSafeGuard for init Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp commit d1025fc7d461873162fea59b2f313416f6451eb8 Author: Jean M. Sexton Date: Mon Jul 15 11:02:32 2019 -0700 Changed to LaunchSafeGuard in Nyx.cpp and nyx_main.cpp Source/Nyx.cpp Source/nyx_main.cpp commit 3ab32ea66df5603de5d0ec53679e3f2327a517c4 Author: Jean M. Sexton Date: Mon Jul 15 07:46:43 2019 -0700 Prefetch for correct gravity src Source/Nyx_advance.cpp commit 889d250ececf2f6e02afcd3a30cd583c3a938173 Author: Jean M. Sexton Date: Sun Jul 14 19:45:55 2019 -0700 LaunchSafeGuard for gravity Source/Gravity/Gravity.cpp commit 2f1aeb2d5475ba4d1a6d542164735c0cd8faf684 Author: Jean M. Sexton Date: Sun Jul 14 19:27:05 2019 -0700 Clean up particle launch region statements and add prefetch and launch safe guards for checkpoints and plotfiles Source/DerivedQuantities/ParticleDerive.cpp Source/Nyx.cpp Source/NyxParticleContainer.H Source/Nyx_output.cpp commit 16678285cac488ac55e1fa92933d27c098cc6496 Author: Jean M. Sexton Date: Sun Jul 14 11:40:45 2019 -0700 Convert setlaunchregion to launchsafeguard for Nyx_advance and underlying hydro functions Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/Nyx_advance.cpp Source/strang_hydro.cpp Source/strang_reactions.cpp Source/update_state_with_sources.cpp commit 7d7847ebf3c1a491e13491fb47150c46f23a69cd Author: Jean M. Sexton Date: Fri Jul 12 18:59:10 2019 -0700 Test adding ascent output to plotMF Exec/LyA/inputs Source/Nyx_output.cpp Source/write_info.cpp commit 19e40456acaaaf0ee6b386da382b35cf9a4e96b5 Author: Jean M. Sexton Date: Fri Jul 12 16:38:11 2019 -0700 Changed function arguments to util functions to pass a vector over levels of multifab pointers for the state data and for the dark matter particle mass and velocities.\nFixed inputs.rt in LyA_AGN to match LyA Exec/LyA_AGN/32.nyx Exec/LyA_AGN/inputs.rt Source/Nyx.H Source/Nyx_halos.cpp Util/reeber/src/reeber.cpp commit 571b9825fa848431dbc02ddd8c8ee85f03c9b018 Author: Jean M. Sexton Date: Fri Jul 12 15:41:15 2019 -0700 Added NPC directory to plotfiles and checkpoint files for NEUTRINO_DARK_PARTICLES case Source/Nyx.H Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_output.cpp commit 8140c0aa23399c4aab3c91833c543d10cae04da3 Author: Jean M. Sexton Date: Fri Jul 12 15:10:55 2019 -0700 Added Vector of unique pointers to vector of new state multifabs Source/.#Nyx.cpp Source/.#Nyx_halos.cpp Source/HeatCool/.#integrate_state_vec_3d.cpp Source/Nyx.cpp Source/Nyx_halos.cpp commit fc8e0ce53ce56ec7ca0f3490886de73d67d05c8d Author: Jean M. Sexton Date: Thu Jul 11 14:44:39 2019 -0700 Revert "Remove prefetches for testing" This reverts commit 6c18e0ae18f1f53748f7b78d388f659ab46280ea. Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/Nyx_hydro.cpp Source/update_state_with_sources.cpp commit 6c18e0ae18f1f53748f7b78d388f659ab46280ea Author: Jean M. Sexton Date: Wed Jun 26 14:16:06 2019 -0700 Remove prefetches for testing Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/Nyx_hydro.cpp Source/update_state_with_sources.cpp commit e4cc143d122d54f4d97d463cc091e08544141678 Author: Jean M. Sexton Date: Wed Jun 26 14:00:48 2019 -0700 Fix bug, test with prefetch commit 00d46bde15e0ec9e034fa16911e222159eee828b Author: Jean M. Sexton Date: Wed Jun 26 12:58:37 2019 -0700 Revert "Summit prefers no prefetches and a synch in the construct_ctu_hydro driver" This reverts commit 440aed86fe54630d5d698aaa790587e3363eae67. Source/Hydro/Nyx_ctu_hydro.cpp commit 6313df6c364ec16209acfc14e734bb503bcc02a8 Merge: 82177dd7 1bd57042 Author: Jean M. Sexton Date: Thu Jul 11 14:24:02 2019 -0700 Merge branch 'gpu_hydro' of ssh://github.com/Amrex-Astro/Nyx into gpu_hydro commit 1bd57042ec252ff9739c2acd9b57d8cc1fe77a54 Author: Jean M. Sexton Date: Thu Jul 11 14:22:53 2019 -0700 Add input flag nyx.nghost_state for testing removal of S_old_tmp in strang_hydro, default is 1, setting this parameter to 4 means more data reuse Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_advance.cpp Source/strang_hydro.cpp commit fd82d64621fda29810dee979134a74a603ad7c3c Author: Jean M. Sexton Date: Thu Jul 11 10:34:07 2019 -0700 Remove FillBoundary option in strang_hydro for single level runs Source/strang_hydro.cpp commit 1db4fdd81daa4a6e51db4346da9d5456e7df7771 Author: Jean M. Sexton Date: Tue Jul 9 12:58:18 2019 -0700 Testing different library include structure and more verbose mesh variable names Exec/LyA/GNUmakefile Exec/Make.Nyx Source/Nyx_output.cpp commit fe6ff9b64edb3764690f607d11907c19bcc3a0ff Merge: d4586e54 31f7c867 Author: Jean M. Sexton Date: Mon Jul 8 19:28:45 2019 -0400 Merge branch 'development' into ascent Conflicts: Exec/LyA/GNUmakefile commit 99e10339aa88178c60e3da22920d5bc656d65ae7 Author: Jean M. Sexton Date: Mon Jul 8 12:37:31 2019 -0700 Fixed particle file name bug in neutrino init Source/NyxParticles.cpp commit 31f7c8679b3b1572628704f467457ce217357b3f Author: Jean M. Sexton Date: Wed Jul 3 15:13:58 2019 -0700 Added BinaryMetaFile for neutrino testing, added derived plot vars for particle and neutrino velocities based off particle mass derived plot vars Exec/LyA_Neutrinos/inputs Exec/LyA_Neutrinos/inputs.no_hydro_64 Source/DerivedQuantities/ParticleDerive.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/NyxParticles.cpp Source/Nyx_output.cpp commit 710677495b0ed2a2ae2718606c2b62e3c99dfec5 Merge: eb20e13f c0ee00b3 Author: Jean M. Sexton Date: Wed Jul 3 13:54:01 2019 -0700 Merge branch 'development' into gpu_dev commit c0ee00b3e9bef70ad2e0f4ae867c9670e442d82e Author: Jean M. Sexton Date: Tue Jul 2 17:40:24 2019 -0700 Added compile flag to use dark matter functions instead of neutrino functions for non-relativistic neutrino case, added corresponding Exec/LyA_Neutrinos Exec/LyA_Neutrinos/32.nyx Exec/LyA_Neutrinos/64sssss_20mpc.nyx Exec/LyA_Neutrinos/GNUmakefile Exec/LyA_Neutrinos/Make.package Exec/LyA_Neutrinos/Nyx_error.cpp Exec/LyA_Neutrinos/Prob_3d.f90 Exec/LyA_Neutrinos/TREECOOL_middle Exec/LyA_Neutrinos/Tagging_3d.f90 Exec/LyA_Neutrinos/inputs Exec/LyA_Neutrinos/inputs.rt Exec/LyA_Neutrinos/inputs.small.dsc Exec/LyA_Neutrinos/inputs_gimlet_in_transit.dsc Exec/LyA_Neutrinos/probdata.f90 Exec/LyA_Neutrinos/probin Exec/LyA_Neutrinos/rhsfn.f90 Exec/Make.Nyx Source/Initialization/Nyx_initdata.cpp Source/NeutrinoParticleContainer.cpp Source/Nyx.H Source/NyxParticles.cpp commit e7f485016b36bd759d87879ff101f84ae6b87bb1 Author: Jean M. Sexton Date: Tue Jul 2 13:21:33 2019 -0700 Fixed make system to allow for exclusion of previously required library, added reeber interface template to Util Exec/LyA_AGN/GNUmakefile Exec/Make.Nyx Source/.#Nyx.cpp Source/.#Nyx_halos.cpp Source/HeatCool/.#integrate_state_vec_3d.cpp Source/Make.package Source/Nyx.H Source/Nyx.cpp Source/Nyx_halos.cpp Source/nyx_main.cpp Util/reeber/Make.package Util/reeber/include/ReeberAnalysis.H Util/reeber/include/reeber.H Util/reeber/src/reeber.cpp commit 82177dd7b0cd9f50e661a9b78d6b3c4e5fdc891f Author: Jean M. Sexton Date: Wed Jun 26 13:17:18 2019 -0700 Revert "Revert "Summit prefers no prefetches and a synch in the construct_ctu_hydro driver"" This reverts commit 9a03c55927caae88c9aefee568083440faeb2147. Source/Hydro/Nyx_ctu_hydro.cpp commit 9a03c55927caae88c9aefee568083440faeb2147 Author: Jean M. Sexton Date: Wed Jun 26 12:58:37 2019 -0700 Revert "Summit prefers no prefetches and a synch in the construct_ctu_hydro driver" This reverts commit 440aed86fe54630d5d698aaa790587e3363eae67. Source/Hydro/Nyx_ctu_hydro.cpp commit e47d8c82b2fd9d66e24b67f642c748a25c4573eb Author: Jean Sexton Date: Thu Jun 20 06:38:18 2019 -0400 Clean up more memory Source/Gravity/Gravity.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/strang_hydro.cpp commit 440aed86fe54630d5d698aaa790587e3363eae67 Author: Jean Sexton Date: Wed Jun 19 01:49:25 2019 -0400 Summit prefers no prefetches and a synch in the construct_ctu_hydro driver Source/Hydro/Nyx_ctu_hydro.cpp commit 0453ea4663d35604bb3325c35036cb59155c0f9d Author: Jean M. Sexton Date: Tue Jun 18 21:41:38 2019 -0700 Added more clears Source/Hydro/Nyx_ctu_hydro.cpp commit b125f1f9c27794807b21b9d48a4808ad6401d581 Author: Jean M. Sexton Date: Tue Jun 18 20:26:55 2019 -0700 Move hydro_src declaration and clear more close to where it's used Source/Hydro/Nyx_ctu_hydro.cpp Source/strang_hydro.cpp commit 7dd6d9fd3e5a6befb9419865f6e815356e3e48cc Author: Jean M. Sexton Date: Tue Jun 18 19:57:12 2019 -0700 Removed pre-allocated MultiFab for divu_cc for hydro_convert=1 version Source/Hydro/Nyx_ctu_hydro.cpp Source/Nyx.H Source/strang_hydro.cpp Source/update_state_with_sources.cpp commit 6142d5de71eab82b2300d3d87cf05cda15724b99 Author: Jean M. Sexton Date: Tue Jun 18 14:28:26 2019 -0700 Remove 3 MultiFabs from construct_ctu_hydro, set QVAR and NQSRC to match initialization Source/Hydro/Nyx_ctu_hydro.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp Source/update_state_with_sources.cpp commit 8847595cc40b43f739b8c7436c736d61a7a3251f Author: Jean M. Sexton Date: Tue Jun 18 10:38:41 2019 -0700 Move consup Multifabs to large MFIter loop Source/Hydro/Nyx_ctu_hydro.cpp commit bc21655acb54d4d6f88caca4ad35fa19d5e5631a Author: Jean Sexton Date: Tue Jun 18 12:57:56 2019 -0400 Fix bug from #ifdef GRAVITY Source/Nyx_advance.cpp commit 1f291e3fe7c8d46d225afa8192fac93798ceb125 Author: Jean M. Sexton Date: Mon Jun 17 20:01:00 2019 -0700 Added prefetch for cons_to_prim and update_state_with_sources Source/Hydro/Nyx_hydro.cpp Source/update_state_with_sources.cpp commit fcc51d1c6de61c72dacad8faf2904e07b3d4dda4 Author: Jean M. Sexton Date: Mon Jun 17 18:25:29 2019 -0700 Ensure some more dt, a_old, a_new passed by value Source/Hydro/Nyx_advection_util.F90 Source/Hydro/Nyx_ctu_hydro.cpp Source/Nyx_F.H commit 99f4da7664bc5feafd0d869713eb760238095ada Author: Jean M. Sexton Date: Mon Jun 17 16:13:37 2019 -0700 Add prefetch to main hydro loop Source/Hydro/Nyx_ctu_hydro.cpp commit e981b5d30ac8a3f769707d897f83a2aa2b45ffe4 Author: Jean Sexton Date: Sun Jun 16 15:26:17 2019 -0400 Added forgotten ifdef for freeing arena memory in non-gpu case Exec/Scaling/profile.sh Source/HeatCool/integrate_state_vec_3d.cpp commit 88f512a4c540e2490690c19b704b8b2ae94e6929 Author: Jean M. Sexton Date: Sun Jun 16 12:08:20 2019 -0700 Test using The_Managed_Arena and NV_MakeManaged_Cuda with sundials Source/HeatCool/integrate_state_vec_3d.cpp commit 1ba5b88afc23589bc53171e00a88e313945c1767 Author: Jean M. Sexton Date: Sun Jun 16 11:21:31 2019 -0700 Remove redundant csml vs qaux MultiFab, ensure a passed by value in srctoprim Source/Hydro/Nyx_advection_util.F90 Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/Nyx_hydro.cpp Source/Nyx.H Source/Nyx_F.H commit a0a7df45e799e87256dca30c95cc318d9b51a634 Author: Jean M. Sexton Date: Sun Jun 16 10:53:56 2019 -0700 Remove area MultiFab, since for a single level area per cell is constant Source/Hydro/Nyx_advection_util.F90 Source/Hydro/Nyx_ctu_hydro.cpp Source/Nyx_F.H commit 4bf1423326924e50a36577067eae7e61376053fa Author: Jean M. Sexton Date: Sun Jun 16 10:39:37 2019 -0700 Replace fabPtr for launched regions, tweaked setlaunchregion for post_init Source/Hydro/Nyx_hydro.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_advance.cpp Source/update_state_with_sources.cpp commit 23706fb063fd2c38f13f5024897c2bf2daf87bbc Author: Jean M. Sexton Date: Sat Jun 15 13:54:26 2019 -0700 Added clear() for elixirs, fixed order for memeory so that it's declared only before it's needed Source/Hydro/Nyx_ctu_hydro.cpp commit b4f86b3c7e2d1134d5aa9d507d5287e1401e77c7 Author: Jean M. Sexton Date: Sat Jun 15 12:31:24 2019 -0700 Change fabPtr to Array4 Source/Hydro/Nyx_ctu_hydro.cpp commit 09a42af79a88edc36f8840870cf2b3f3aa33b249 Author: Jean M. Sexton Date: Tue Jun 11 08:06:13 2019 -0700 Port add_to_fluxes, expand launch region in advance_hydro_plus_particles Source/Gravity/Gravity.cpp Source/Nyx_advance.cpp commit d51f543aec6f5361e158f6083e020f72be66f1c4 Author: Ann Almgren Date: Fri Jun 14 11:12:00 2019 -0700 change order of chapters Docs/sphinx_documentation/source/index.rst commit 0e656c145b84b1e8312ea2d423274ee941118c94 Author: Ann Almgren Date: Fri Jun 14 11:11:04 2019 -0700 add more detail to regression tests Docs/sphinx_documentation/source/NightlyTests.rst commit 9e600016a8094730f56ee55bc1c17424db29ab84 Author: Ann Almgren Date: Fri Jun 14 09:59:11 2019 -0700 FIx formatting Docs/sphinx_documentation/source/NightlyTests.rst commit 9560cc3fe0f2f07f976f5bf01264edd01e076a04 Author: Ann Almgren Date: Fri Jun 14 09:51:26 2019 -0700 Add description of regression tests -- still wrong but there Docs/sphinx_documentation/source/NightlyTests.rst Docs/sphinx_documentation/source/index.rst commit 04f09980cb5d7e24dbb2d612e780b4c4f3d8055e Author: Ann Almgren Date: Fri Jun 14 09:20:50 2019 -0700 Add default load balancing strategy Docs/sphinx_documentation/source/LoadBalancing.rst commit a45d95b6fd2bf666f7fb94569eec1e402208c49f Author: Ann Almgren Date: Fri Jun 14 09:14:28 2019 -0700 Meant to add this Docs/sphinx_documentation/source/LoadBalancing.rst commit 001de8ff367ab6451bb2af08ffec3bbe2ca1e25b Author: Ann Almgren Date: Fri Jun 14 09:11:36 2019 -0700 Add stuff about how to create grids Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst Docs/sphinx_documentation/source/index.rst commit 49a0de9a37b5129b89bd5f511bdb3c567313391b Author: Ann Almgren Date: Fri Jun 14 08:59:27 2019 -0700 fix formatting Docs/sphinx_documentation/source/InputsMultigrid.rst commit 0bf512155cd0c39ae4b46795232b1fcded26ab5e Author: Jean Sexton Date: Fri Jun 14 07:32:06 2019 -0400 Test for minimizing memory footprint of advance_Ctu_hydro Source/Hydro/Nyx_ctu_hydro.cpp commit fd59a9f896970d4935a4ad012d68cd1bb812e7f2 Author: Jean Sexton Date: Fri Jun 14 07:29:59 2019 -0400 Revert "Test moving MLPoission define to post_regrid instead of every timestep" This reverts commit ed36c3e8713b300571cc6552c60b763267cd84d1. Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Nyx.cpp Source/Nyx_advance.cpp commit 49643b38ffe566532dcc4d08bd5d4ec201c678e0 Author: Ann Almgren Date: Thu Jun 13 15:52:19 2019 -0700 fix formatting Docs/sphinx_documentation/source/InputsMultigrid.rst commit edb06e116f3ad07559142c9be02be9e880efb373 Author: Ann Almgren Date: Thu Jun 13 15:09:36 2019 -0700 fix formatting Docs/sphinx_documentation/source/InputsMultigrid.rst commit 5c8c5c0f089b30df7128ea713d626c11b7e7bc0d Author: Ann Almgren Date: Thu Jun 13 15:05:04 2019 -0700 Add multigrid inputs to documentation Docs/sphinx_documentation/source/InputsMultigrid.rst Docs/sphinx_documentation/source/index.rst commit d4fa8e661dadb79d393217dbf29f82ef0835d3d6 Author: Jean M. Sexton Date: Tue Jun 11 08:06:13 2019 -0700 Port add_to_fluxes, expand launch region in advance_hydro_plus_particles Source/Gravity/Gravity.cpp Source/Nyx_advance.cpp commit ed36c3e8713b300571cc6552c60b763267cd84d1 Author: Jean M. Sexton Date: Tue Jun 11 06:54:32 2019 -0700 Test moving MLPoission define to post_regrid instead of every timestep Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Nyx.cpp commit eb20e13f36033a3455c373c93bc67b0c19f89528 Author: Jean M. Sexton Date: Sun Jun 9 12:09:42 2019 -0700 Fix for AMR-density inputs and small_dens=0 assumption in MiniSB Exec/AMR-density/inputs.rt Exec/HydroTests/TurbForce/Nyx_setup.cpp Exec/MiniSB/Prob_3d.f90 Source/Nyx.cpp commit 41385a1325f1cde001ddf3ab3c3710190e38e173 Author: Jean M. Sexton Date: Sun Jun 9 12:06:15 2019 -0700 Added profiling var to track FillPatch in strang, fixed launch region in NyxParticleContainer.H Source/NyxParticleContainer.H Source/strang_hydro.cpp commit 004e1ae2a3dad510a4bf45a189f60fff09fa75c4 Author: Jean M. Sexton Date: Sat Jun 8 15:35:49 2019 -0700 HEAT_COOL=TRUE AMR-density matches, checked reset_internal_energy, copied over moveKickDrift based on current development code for matching Exec/AMR-density/inputs.rt Exec/LyA/inputs.rt Source/Gravity/Gravity.cpp Source/Nyx.cpp Source/strang_hydro.cpp Source/strang_reactions.cpp Source/sum_integrated_quantities.cpp Source/update_state_with_sources.cpp commit 1e8c7e86f00b76bfacc0d3f4881e131de5a3ceb5 Author: Jean M. Sexton Date: Sat Jun 8 08:18:38 2019 -0700 HEAT_COOL=FALSE LyA matches, copied over DarkMatterParticleContainer and Nyx_eos_given_RT based on current development code for matching Source/DarkMatterParticleContainer.cpp Source/EOS/eos_stuff.F90 Source/Nyx.cpp commit d928ddbbe711f2311b0e546d3ed75aad7e5ca3e7 Author: Jean M. Sexton Date: Sat Jun 8 06:53:26 2019 -0700 Copied HydroFortran to force matching, changed Prob_3d to use 0 instead of small density for matching Exec/AMR-density/Prob_3d.F90 Exec/HydroTests/Sedov/GNUmakefile Exec/LyA/GNUmakefile Exec/LyA/Prob_3d.F90 Exec/LyA/inputs.rt Exec/LyA/runlog Exec/Scaling/Prob_3d.F90 Source/Hydro/flatten_nd.F90 Source/Hydro/riemann_nd.F90 Source/HydroFortran/Make.package Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/analriem.f90 Source/HydroFortran/make_hydro_sources_3d.f90 Source/HydroFortran/ppm_3d.f90 Source/HydroFortran/trans_3d.f90 Source/Initialization/init_managed.F90 Source/Nyx.cpp Source/meth_params.F90 commit 1d110f1990d96c3cf6790c35439a59dbe77f8957 Author: Jean M. Sexton Date: Fri Jun 7 08:25:32 2019 -0700 Reset rt inputs and GNUmakefile to current development Exec/AMR-density/GNUmakefile Exec/AMR-density/inputs.rt Exec/HydroTests/DoubleRarefaction/inputs.regtest Exec/HydroTests/Sedov/inputs.regtest Exec/HydroTests/Sod/GNUmakefile Exec/HydroTests/Sod/inputs.regtest Exec/HydroTests/StrongShockTube/inputs.regtest Exec/LyA/GNUmakefile Exec/LyA/inputs.rt Exec/LyA/runlog commit 79b3c7dce97aadf9258ff898565ed27a32ac7f75 Author: Weiqun Zhang Date: Thu Jun 6 09:53:31 2019 -0700 Cuda::setLaunchRegion -> Gpu::setLaunchRegion Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_exact_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/Nyx_advance.cpp Source/nyx_main.cpp commit 778b4b467b38da72dd2cb9522fa6d07a55c208d7 Author: Weiqun Zhang Date: Thu Jun 6 16:41:14 2019 -0700 fix NyParticleContainer for gpu Source/NyxParticleContainer.H commit 86a8bb3eb4293338ea799085026b79ce7c0155b9 Author: Jean M. Sexton Date: Wed Jun 5 16:10:11 2019 -0700 Change ifdefs and scopes from Cuda to Gpu as appropriate Source/DerivedQuantities/ParticleDerive.cpp Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_cell_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Nyx.cpp Source/NyxParticleContainer.H Source/NyxParticles.cpp Source/Nyx_F.H Source/Nyx_advance.cpp Source/nyx_main.cpp Source/strang_hydro.cpp commit 414573d72f7037612072126ab45d7b2488907467 Author: Jean M. Sexton Date: Wed Jun 5 08:16:36 2019 -0700 Ported estTimeStep in NyxParticleContainer to GPU Source/NyxParticleContainer.H commit b7f8f708c957739ebe8226873fb7e95111a1f44c Author: Jean M. Sexton Date: Wed Jun 5 07:17:27 2019 -0700 Added GPU friendly constructs to estTimeStep in NyxParticleContainer Source/NyxParticleContainer.H commit 3d42a6d22ac2798eaeaa6ec2dc0d219b9e83dac8 Author: Jean M. Sexton Date: Tue Jun 4 18:56:38 2019 -0700 Added atomic Gpu version of compute_rho_temp and compute_gas_vol_frac Source/Nyx.cpp commit dfdd50be2ad62b6c28881540bc70f152319f3222 Author: Jean M. Sexton Date: Tue Jun 4 16:02:46 2019 -0700 Ported writeinfo to C++ Source/Nyx.cpp commit 2034eefc11d6d241382f521d9f7aa413d41238ce Author: Weiqun Zhang Date: Sat Jun 1 10:38:41 2019 -0700 use the MultiFab version of FineAdd Source/Gravity/Gravity.cpp commit 687dc68fe74aa81b579b2c222b24513cddb693ff Author: Jean M. Sexton Date: Mon Jun 3 22:12:19 2019 -0700 Fix some CPU page faults for copy, wrong launchregions, and using the Fab version of mult instead of the multifab version Source/Gravity/Gravity.cpp Source/Nyx.cpp Source/Nyx_advance.cpp Source/sum_utils.cpp commit 12a4f639abaab894e51ebf673eef2e50a5547c80 Author: Weiqun Zhang Date: Tue May 21 09:48:01 2019 -0700 prepare for upcoming changes in armex::Geometry Exec/HDF5_example/Nyx_output.cpp Exec/HydroTests/TurbForce/Nyx_setup.cpp Source/Gravity/Gravity.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp Source/Nyx_output.cpp commit 0df93a0eaf596a365efa65e7b8fd019dc96f9544 Author: Weiqun Zhang Date: Sat Jun 1 10:38:41 2019 -0700 use the MultiFab version of FineAdd Source/Gravity/Gravity.cpp commit b0ab85080f45984a9b563e460d229895b9f972ca Author: Jean M. Sexton Date: Sat Jun 1 07:44:55 2019 -0700 Initial transfer of moveKickDrift, remove setLaunchRegion(false) from multilevel solve Source/DarkMatterParticleContainer.H Source/DarkMatterParticleContainer.cpp Source/Gravity/Gravity.cpp commit baf2cb7e38678989849f7f8926c13771767b2df9 Author: Jean M. Sexton Date: Thu May 30 22:22:05 2019 -0700 Add option for using fillboundary instead of grown cells in first strang as input flag Source/Nyx.H Source/Nyx.cpp Source/strang_reactions.cpp commit 508a452ef0589dab6ef2c2cb9a3bb846671768f2 Merge: 55bcca3a 51933fa0 Author: zarija Date: Thu May 30 10:44:49 2019 -0600 Merge pull request #41 from burlen/development enable use of SENSEI for in situ commit d4586e540eda8cfbd21996f99879981646b3c6ad Author: Jean M. Sexton Date: Thu May 30 07:05:37 2019 -0700 Fix varnames Source/Nyx_output.cpp commit bdb61e145d5cb1d7f78506d701cdcd1f318700a9 Merge: 2ec007d9 55bcca3a Author: Jean M. Sexton Date: Thu May 30 06:48:09 2019 -0700 Merge branch 'development' into ascent commit af770df0fde127c5db9c7e5297ed30f6b0bf1635 Author: Jean M. Sexton Date: Thu May 30 05:59:30 2019 -0700 Hack for pgi/19.4 scope error, removes -gopt from F90FLAGS Exec/Make.Nyx commit 566a30f133e3f7fd77ed1c844d983814b6d75eef Author: Jean M. Sexton Date: Thu May 30 05:41:30 2019 -0700 Particle dt estimate on the gpu, add extra streamsynchronizes for safety, add matching example 256 input files in LyA and Scaling Exec/LyA/GNUmakefile Exec/LyA/inputs.256.noreduceverb Exec/Scaling/GNUmakefile Exec/Scaling/inputs.256.noreduceverb Source/Gravity/Gravity.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Nyx.cpp Source/NyxParticleContainer.H Source/NyxParticles.cpp Source/Nyx_advance.cpp Source/advance_particles.cpp Source/sdc_hydro.cpp Source/strang_hydro.cpp commit 5b0897fe8b4072adb3d7ecfdd262247a5b85230a Author: Jean M. Sexton Date: Wed May 29 11:33:08 2019 -0700 Don't use growntilebox in strang_first_step, fill boundary instead Source/strang_reactions.cpp commit 2ec007d9831a4a6ffd7bc1f0cef0e537f1db050c Author: Jean M. Sexton Date: Wed May 29 09:25:57 2019 -0700 Initial testing of blueprint, prints density, particle parts compile Exec/HydroTests/Sedov/GNUmakefile Exec/LyA/GNUmakefile Exec/LyA/inputs.rt Exec/Make.Nyx Source/Nyx.H Source/Nyx_output.cpp Source/write_info.cpp commit 2a261234bf67161902ff961ecaa46f94866b7b22 Author: Jean M. Sexton Date: Wed May 29 04:57:48 2019 -0700 Fix bug where multilevel solve for new phi is used when single-level should work Source/Nyx_advance.cpp commit 55bcca3a78e00d05c646050f20f6a2641956a11f Author: Andrew Myers Date: Tue May 28 17:09:40 2019 -0700 remove AMReX_Particles_F.H Header, which won't exist soon Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_advance.cpp Source/advance_particles.cpp Source/strang_hydro.cpp commit 51933fa055f4a292e887bfafa1a9ca7e5cdb4e04 Author: SENSEI SC18 VM Date: Tue May 28 15:26:21 2019 -0700 enable use of SENSEI for in situ Exec/LyA/GNUmakefile Exec/LyA/inputs Exec/Make.Nyx commit 20f92547c482d578768a3b45b067fc08a9d7e12a Author: Jean M. Sexton Date: Mon May 27 20:41:19 2019 -0700 Changing Sundials Cuda vectors to NewManaged from New is much faster Source/HeatCool/integrate_state_vec_3d.cpp commit 57668e30318caa15989815f25c11398fde714dc6 Author: Jean M. Sexton Date: Mon May 27 16:36:19 2019 -0700 Remove redundant files, check soundspeed Source/EOS/eos_hc.F90 Source/Nyx.cpp Source/Src_3d/EstDt_3d.F90 Source/Src_3d/Make.package commit 998a27e43f896f1e84453ffa242addc5ee015235 Author: Jean M. Sexton Date: Mon May 27 08:11:19 2019 -0700 Moved fort_estdt to C++ using amrex::ReduceMin as in the CNS tutorial Source/EOS/eos_hc.F90 Source/Nyx.cpp Source/Nyx_F.H Source/Src_3d/EstDt_3d.F90 Source/Src_3d/Make.package commit 55d911507711ea514aca7a0c6e665cd63764304c Author: Jean M. Sexton Date: Sun May 26 20:53:11 2019 -0700 Change vol_weight_sum to multifab operations Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/sum_utils.cpp commit 3aeae4dbe0d62d315aa6f20d6a0188ba11c550b1 Author: Jean M. Sexton Date: Sun May 26 16:41:52 2019 -0700 Removed redundant code, added option to do a reset_internal_energy without storing the reset_state Source/HeatCool/cvode_extras.F90 Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/riemann_nd.F90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Src_3d/reset_internal_energy_3d.F90 Source/strang_hydro.cpp Source/strang_reactions.cpp Source/update_state_with_sources.cpp commit 3832576ec3fa3dde5a3b431ab00a0ac2e699356f Author: Jean M. Sexton Date: Sun May 26 15:30:43 2019 -0700 Removed spurious logical flag dynamically allocated array in ctu_plm Source/Hydro/Nyx_ctu_nd.F90 commit 2264e7f0d9d9f6bbe91ef9e0a26e7bac2169dad2 Author: Jean M. Sexton Date: Sun May 26 13:14:54 2019 -0700 Made sure Nyx::init(old) is launched, tweak AddParticlesToRhs launches Source/Gravity/Gravity.cpp Source/Nyx.cpp Source/Nyx_advance.cpp Source/strang_hydro.cpp commit 85a339fb365fc8bdeeeaad32c36dd0405291efca Author: Jean M. Sexton Date: Sun May 26 11:06:27 2019 -0700 Update Sundials test in Nyx Util/SUNDIALS3/GNUmakefile Util/SUNDIALS3/Make.package Util/SUNDIALS3/atomic_rates.F90 Util/SUNDIALS3/cvode_extras.F90 Util/SUNDIALS3/eos_hc.F90 Util/SUNDIALS3/f_rhs.F90 Util/SUNDIALS3/init_managed.F90 Util/SUNDIALS3/inputs Util/SUNDIALS3/main.cpp Util/SUNDIALS3/meth_params.F90 Util/SUNDIALS3/myfunc_F.H Util/SUNDIALS3/reion_aux_module.F90 Util/SUNDIALS3/reion_aux_module.f90 Util/SUNDIALS3/vode_aux.F90 commit e37b60c0d80c46494b64144c049f03097b1b789d Author: Jean M. Sexton Date: Sat May 25 14:20:54 2019 -0500 Updated Makefile and initial condition for RayTracing Exec/RayTracing-NonComoving/GNUmakefile Exec/RayTracing-NonComoving/probin.3d.sph commit 0a5310e60d2012b1bfea3aa951e7f9a9696322d6 Author: Jean M. Sexton Date: Fri May 24 11:03:47 2019 -0700 Tweak launch in AddParticles, hardcode out new particle_est_time_step option, since other cfl conditions are on the CPU Source/Gravity/Gravity.cpp Source/NyxParticleContainer.H commit c6ba1fc907fb325ff6ec2246b91dcb8744d3bb3c Author: Jean M. Sexton Date: Fri May 24 10:09:23 2019 -0700 Add gravity sync_src and correct gpu launches, moved diagnostic max_temp norm inside if(verbos) in compute_new_temp Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_advance.cpp Source/SourceTerms/Make.package Source/SourceTerms/Nyx_grav_sources_3d.F90 commit 1f3c92570145aaa707545fc512d75f4d4a56944d Author: Jean M. Sexton Date: Fri May 24 08:43:38 2019 -0700 Remove launches from particle_est_time_step due to memory movement issues Source/NyxParticleContainer.H commit a1ad1a63ab0d8ae03f7abda4f42b1ad971a6c97f Author: Jean M. Sexton Date: Fri May 24 01:30:39 2019 -0700 Test seperating launches for trace routines into seperate calls Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/Nyx_ctu_nd.F90 Source/Nyx_F.H commit 9f498bb47042a860b80447019af46acdca296305 Author: Jean M. Sexton Date: Fri May 24 01:29:38 2019 -0700 Test rewriting particle cfl condition for est time step Source/NyxParticleContainer.H Source/NyxParticles.cpp commit 302f9460aba885e1b785788252c9d0a7ac475a95 Author: Zarija Lukic Date: Wed May 22 16:18:03 2019 -0700 Ray Tracing examples Exec/RayTracing-Expanding/GNUmakefile Exec/RayTracing-Expanding/Make.package Exec/RayTracing-Expanding/Nyx_error.cpp Exec/RayTracing-Expanding/Prob_3d.f90 Exec/RayTracing-Expanding/Tagging_3d.f90 Exec/RayTracing-Expanding/atomic_rates.f90 Exec/RayTracing-Expanding/inputs Exec/RayTracing-Expanding/probdata.f90 Exec/RayTracing-Expanding/probin Exec/RayTracing-Expanding/rhsfn.f90 Exec/RayTracing-NonComoving/GNUmakefile Exec/RayTracing-NonComoving/Make.package Exec/RayTracing-NonComoving/Nyx_error.cpp Exec/RayTracing-NonComoving/Prob_3d.f90 Exec/RayTracing-NonComoving/Tagging_3d.f90 Exec/RayTracing-NonComoving/bc_fill_3d.f90 Exec/RayTracing-NonComoving/inputs.3d.sph Exec/RayTracing-NonComoving/inputs.regtest Exec/RayTracing-NonComoving/probdata.f90 Exec/RayTracing-NonComoving/probin.3d.sph commit bcbf074f80f4254018399d0bc65e8987b2eca8ec Author: Jean M. Sexton Date: Wed May 22 09:00:23 2019 -0700 Tweak get_old_grav_vector call, add launch region for debug nan check Source/Gravity/Gravity.cpp Source/strang_hydro.cpp commit 3b7f48c5ecebba0612431f416eb8b2fefa2b9ce6 Author: Jean M. Sexton Date: Tue May 21 17:21:52 2019 -0700 Change travis files to use addons instead of sudo .travis.yml requirements.txt commit d4cea202058037cbeebd096f00ed719a6b975221 Author: Jean M. Sexton Date: Tue May 21 16:13:20 2019 -0700 Test changes to use more underlying gpu functions Exec/AMR-density/Make.package Exec/AMR-density/Prob_3d.F90 Source/Gravity/Gravity.cpp Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/Nyx_advection_util.F90 Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/Nyx_hydro.cpp Source/Hydro/enforce_nonnegative_species.F90 Source/Hydro/enforce_nonnegative_species_3d.F90 Source/Nyx.H Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_F.H Source/Nyx_advance.cpp Source/strang_hydro.cpp Source/strang_reactions.cpp Source/update_state_with_sources.cpp commit a6bac96c10a523698197943a3f7f9f004c4738c3 Author: Weiqun Zhang Date: Tue May 21 09:48:01 2019 -0700 prepare for upcoming changes in armex::Geometry Exec/HDF5_example/Nyx_output.cpp Exec/HydroTests/TurbForce/Nyx_setup.cpp Source/Gravity/Gravity.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp Source/Nyx_output.cpp commit 1c9279080429424755269b4e7679f109c1463cfc Author: Jean M. Sexton Date: Mon May 20 09:59:06 2019 -0700 Added .write form for binary convert Util/convert_amr/AmrElements.cpp commit 23680d03d5116c11a9b36701a40b418ee89372c5 Author: Jean Sexton Date: Fri May 17 15:52:44 2019 -0700 Remove amrex binary fab format write and read example, add mpi files, change component selection Util/convert_amr/AmrElements.cpp Util/convert_amr/GNUmakefile Util/convert_amr/inputs commit ac5c350ac0729f022435514ee778079d3cabc67c Author: Jean M. Sexton Date: Thu May 16 11:58:06 2019 -0700 Added missing openmp pragmas back to mfiter loop for compute_new_temp and fort_init_data, added nonnegative constraint to heat_cool_type=12, made openmp non-tiling for heat_cool_type=11 Source/HeatCool/integrate_state_cell_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/Nyx.cpp Source/NyxParticles.cpp commit a85c7001ef55011996b448408fc6affa78df1e86 Author: Jean Sexton Date: Thu May 16 11:00:14 2019 -0700 Add omp loop on f_rhs in heat_cool_type=11, moved cvode_mem constructor and destructor outside ijk loop Source/HeatCool/integrate_state_cell_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp commit e1d3b09429764d5639995654a794f33fe5fae530 Author: Jean M. Sexton Date: Wed May 15 19:53:02 2019 -0700 Test using OpenMP NVector in heat_cool_type=11 Exec/Make.Nyx Source/HeatCool/integrate_state_vec_3d.cpp commit ae4963edd87f448be0d8b82fee41b1c6b646b2e9 Author: Jean M. Sexton Date: Wed May 15 19:05:54 2019 -0700 Create heat_cool_type=12 for openmp similar to fortran interfaces Source/HeatCool/Make.package Source/HeatCool/integrate_state_box_3d_stubs.cpp Source/HeatCool/integrate_state_cell_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/Nyx.H Source/Nyx.cpp Source/comoving.cpp Source/strang_reactions.cpp commit d8cede0f6eb36f51e16ae01dbbe7c111bb0a2f45 Author: Jean M. Sexton Date: Wed May 15 18:47:01 2019 -0700 Add test script to util for manipulating leaf data from a multifab given a plotfile Util/convert_amr/AmrElements.cpp Util/convert_amr/GNUmakefile Util/convert_amr/Make.package Util/convert_amr/README Util/convert_amr/inputs commit cfaf2b7729d31dfbc02c31e998dd321028c1ffe4 Author: Jean M. Sexton Date: Wed May 15 13:56:49 2019 -0700 Removed extra setLaunch Exec/Make.Nyx Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/Nyx_hydro.cpp Source/NyxParticles.cpp Source/strang_reactions.cpp commit c2643b0e8b728c05bd931ce74f875caf67e8fd59 Author: Jean M. Sexton Date: Wed May 15 13:54:23 2019 -0700 Added OMP version of heat_cool_type=11 which is selected at compile-time, and prof vars for cvode Source/HeatCool/integrate_state_vec_3d.cpp commit 52c29477c8df5caeb96ab74ff7dbde55ca69baff Author: Jean M. Sexton Date: Tue May 14 16:47:58 2019 -0700 Make sure to initialize sum_state in enforce_min_density, uncommented OMP in heating-cooling Source/HeatCool/integrate_state_vec_3d.cpp Source/Hydro/enforce_minimum_density.F90 commit 9fdad5a976c43fcfca29f09d426a8e0d6c732190 Author: Jean M. Sexton Date: Tue May 14 16:45:58 2019 -0700 Seperate case for exact integration Source/HeatCool/Make.package Source/HeatCool/integrate_state_box_3d_stubs.cpp Source/HeatCool/integrate_state_exact_3d_stubs.cpp commit 4929b7f3db2f9f3aafad287b1b218e1635d2ccf2 Author: Jean M. Sexton Date: Tue May 14 12:46:00 2019 -0700 Fix extra debugging statements for multiple mpi Source/HeatCool/cvode_extras.F90 Source/HeatCool/integrate_state_vec_3d.cpp commit c61208dbf1f47631f256c28bfee0bb855bef1f7f Author: Jean M. Sexton Date: Mon May 13 19:37:13 2019 -0700 Moved fort_initdata to cuda for init_santa_barbara Exec/LyA/Make.package Exec/LyA/Prob_3d.F90 Exec/Scaling/GNUmakefile Exec/Scaling/Make.package Exec/Scaling/Prob_3d.F90 Source/NyxParticles.cpp Source/Nyx_F.H commit a80a2e612d6312a501a413504093dc2b9249d97b Author: Jean M. Sexton Date: Mon May 13 17:33:34 2019 -0700 Ensure specific particle functions are using the gpu version where possible Source/DerivedQuantities/ParticleDerive.cpp Source/Nyx.cpp Source/NyxParticleContainer.H Source/NyxParticles.cpp commit a7f9e3588f610bfd16f90594b3b3cd23b755844c Author: Jean M. Sexton Date: Mon May 13 16:20:45 2019 -0700 Fix for use_const_species=1 case Source/Hydro/enforce_minimum_density.F90 commit bf94cc19852ca154bdfe2e58d426a9d5f99683fa Author: Jean M. Sexton Date: Mon May 13 14:16:10 2019 -0700 Fix compile error for USE_HEATCOOL=FALSE Source/HeatCool/integrate_state_box_3d_stubs.cpp commit be16d3e12e942bc2f5ef6fd24515374d281b5d67 Merge: 98b4ff13 b3c82ec9 Author: Jean M. Sexton Date: Mon May 13 11:26:17 2019 -0700 Merge branch 'gpu_hydro' of https://github.com/AMReX-astro/Nyx into gpu_hydro commit 98b4ff139a4a86e5146953b5a97075307309b558 Author: Jean M. Sexton Date: Mon May 13 11:17:35 2019 -0700 Increased maximum step size and added constraint for positive internal energy Source/HeatCool/integrate_state_vec_3d.cpp commit af7e9c1b2412328e57cb0d5d8b10c7570eda6db7 Author: Jean Sexton Date: Sun May 12 21:39:05 2019 -0700 Remove extra debugging statements Source/strang_reactions.cpp commit afdccda9427441e9cf48eb39c3fc759dee8cff86 Author: Jean M. Sexton Date: Fri May 10 18:55:35 2019 -0700 Added exact integration method, currently uses vode for big/small T where power law doesn't match Source/EOS/eos_hc.f90 Source/HeatCool/Make.package Source/HeatCool/integrate_state_exact_3d.cpp Source/HeatCool/update.f90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/comoving.cpp Source/strang_reactions.cpp commit b3c82ec9c48ce9fed5f1728f6dc4f6032b526992 Author: Jean M. Sexton Date: Thu May 9 10:27:04 2019 -0700 Added plm check for hydro_convert=1 Exec/AMR-density/inputs Source/Nyx.cpp commit a1051334fed9d3272f0ab5df66ce2ae8e4a821ed Author: Jean M. Sexton Date: Wed May 8 17:10:49 2019 -0700 Change RedistributeLocal in post_timestep back to Redistribute, fixed bug in non-negative Source/Hydro/enforce_nonnegative_species.F90 Source/Nyx.cpp commit e9c0c27cb3705da21ad9e4eacbe011c0459b5269 Author: Jean M. Sexton Date: Wed May 8 17:10:04 2019 -0700 Clean up inputs files so default is primarily new hydro and vectorized cvode Exec/AMR-density/inputs Exec/AMR-density/inputs.rt Exec/LyA/inputs Exec/LyA/inputs_128 Exec/LyA/inputs_128_32grids Exec/LyA/inputs_hydro1.rt commit 3da322c92bdfe31a9d8feec9f5dd2a14de08d824 Author: Jean Sexton Date: Wed May 8 16:39:44 2019 -0400 Add temporary array for enforce_min_density to make it faster on GPUs Source/Hydro/Nyx_advection_util.F90 Source/Hydro/enforce_minimum_density.F90 Source/Nyx_F.H Source/update_state_with_sources.cpp commit e6deb8206d9685c767ece38e7d6f415c1beb1650 Author: Jean Sexton Date: Wed May 8 14:05:11 2019 -0400 Fix box use bug and remove extra debug statements Source/Hydro/Nyx_ctu_hydro.cpp Source/strang_hydro.cpp commit fa9b8fb52b5066f7ed0d4519cdf2c5438e07a5d8 Author: Jean M. Sexton Date: Tue May 7 19:09:34 2019 -0700 Moved enforce_min_density to device code, still has dynamic temporaries Source/Hydro/Make.package Source/Hydro/Nyx_advection_util.F90 Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/enforce_minimum_density.F90 Source/Hydro/enforce_nonnegative_species.F90 Source/Hydro/enforce_nonnegative_species_3d.F90 Source/update_state_with_sources.cpp commit 2c31a04d3222da57f78694d93d079d615e5b195f Author: Jean M. Sexton Date: Tue May 7 14:44:56 2019 -0700 Fix bug in trace (dx-> GpuArray), add Sedov inputs Exec/HydroTests/Sedov/inputs.3d.sph.testsuite Exec/HydroTests/Sod/GNUmakefile Source/Hydro/Nyx_ctu_hydro.cpp commit 69bd45a10012eaea2bb9c8ba3b0eba19aee2a405 Author: Jean Sexton Date: Tue May 7 13:09:53 2019 -0400 Added Array4 to hydro Source/DerivedQuantities/Derive_3d.f90 Source/Hydro/Nyx_advection_util.F90 Source/Hydro/Nyx_ctu_hydro.cpp Source/Initialization/Nyx_initdata.cpp Source/Nyx.H Source/Nyx_F.H Source/strang_hydro.cpp Source/update_state_with_sources.cpp commit 91261e884d24c3a223f3ffb7e848c64d9bc16e6d Author: Jean M. Sexton Date: Mon May 6 12:13:51 2019 -0700 Corrected extra setlaunch in ctoprim, changed makefile Exec/HydroTests/Sedov/GNUmakefile Source/Hydro/Nyx_hydro.cpp commit bd4add2883cdfc154749c9fa6b15a539192d90c2 Author: Jean Sexton Date: Mon May 6 13:50:37 2019 -0400 Fix bug with indexing f_rhs launch Source/HeatCool/integrate_state_vec_3d.cpp commit d3b5d62dde57fc1d17a98b03658db924b538091a Author: Jean Sexton Date: Fri May 3 16:18:49 2019 -0400 Seperate out enforce_min_density Source/Hydro/Nyx_advection_util.F90 Source/Nyx_F.H Source/update_state_with_sources.cpp commit 8a3e6752677bdf0b6df011ff17d20490faf7738e Author: Jean Sexton Date: Thu May 2 12:39:53 2019 -0400 Testing streamSynchronize Source/Hydro/Nyx_ctu_hydro.cpp commit 195b9958bcc3209de7f8cdbe2ac9e0326fab13ef Author: Jean Sexton Date: Wed May 1 14:20:00 2019 -0400 Add launched update with sources and grav Exec/AMR-density/GNUmakefile Exec/LyA/GNUmakefile Source/Hydro/Nyx_advection_util.F90 Source/Hydro/enforce_minimum_density.F90 Source/Hydro/make_hydro_sources_3d_test.f90 Source/Nyx_F.H Source/update_state_with_sources.cpp commit 06fccf99488f2a4572f7d59c400c667ebbbec936 Author: Jean Sexton Date: Tue Apr 30 12:15:56 2019 -0400 1D->3D in integrate_state_vec, works best when similar integration problems are solved together Source/HeatCool/integrate_state_vec_3d.cpp commit 2504c425a1db80a696fce72f03bb4a762d32903b Author: Jean Sexton Date: Sat Apr 27 11:09:17 2019 -0400 Moved setlaunchregion outside MFIter loop, added inputs/run scripts Exec/LyA/inputs_128_32grids Exec/LyA/run128.summit Exec/LyA/run128.summit.mpi Exec/LyA/run128.summit.mpi.nocuda Exec/LyA/run128.summit.nocuda Source/Hydro/Nyx_ctu_hydro.cpp commit 3872ba365f51e53fe6860b782f760bb0ae441c88 Author: Jean Sexton Date: Sat Apr 27 09:22:50 2019 -0400 Fixed bug where Prob_3d.f90 was setting initial density based on small_dens which was not yet defined Source/Initialization/Nyx_initdata.cpp commit 146b15bd57ace2953e5fd6f3c3428f1956404869 Author: Jean Sexton Date: Fri Apr 26 12:14:58 2019 -0400 Changed synchronizes to streamSynchronize, added launch for uflatten, moved setlaunchregion outside mfiter loops Source/HeatCool/integrate_state_box_3d.cpp Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/flatten_nd.F90 Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_F.H commit 0c908951ef1137022a0e6b6dfcde2f8023140734 Author: Jean Sexton Date: Thu Apr 25 15:29:04 2019 -0400 Renamed files for consistency, updated Make.package to match Source/Hydro/Make.package Source/Hydro/Nyx_ctu_hydro.cpp Source/Hydro/Nyx_ctu_nd.F90 Source/Hydro/Nyx_hydro.cpp Source/Hydro/riemann_nd.F90 commit 6a5ea361427082052088efc988844373335ff2cb Author: Jean Sexton Date: Thu Apr 11 17:35:52 2019 -0400 Changed synchronizes to streamSynchronize in Hydro, changed post_timestep Redistribute to local Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Castro_hydro.cpp Source/Nyx.cpp commit 039fce44cd0658a5e9283e8bbc6937cb757131e9 Merge: cc5037a2 e60823ca Author: Andrew Myers Date: Thu Apr 11 10:42:53 2019 -0700 Merge branch 'gpu_hydro' of github.com:AMReX-Astro/Nyx into gpu_hydro commit cc5037a2ed5fe149f1a6b1fff9d2496b4bf3cd98 Author: Andrew Myers Date: Thu Apr 11 10:42:39 2019 -0700 add local version of Redistribute for Nyx Source/NyxParticleContainer.H commit e60823cab7a4b94fecd489918288ca3f9775aeeb Author: Jean Sexton Date: Wed Apr 10 13:15:32 2019 -0400 Extra synchronizes to force particles to match in plt00000 LyA 128**3, updated make/inputs Exec/LyA/GNUmakefile Exec/LyA/inputs_128 Exec/LyA/inputs_hydro1.rt Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Nyx.cpp Source/NyxParticles.cpp commit 20dc8fa53f3a38fce1f2b8cb72581c2e477be32f Author: Andrew Myers Date: Mon Apr 8 17:45:34 2019 -0700 line length fix Source/Initialization/init_managed.F90 Source/meth_params.F90 commit ca869f0074afbd21e2bcd79e9363637af7ada402 Author: Jean Sexton Date: Mon Apr 8 14:58:48 2019 -0400 Move flux scaling with comoving a from consup to scale_flux to ensure correct box is used Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Nyx_advection_util.F90 Source/Nyx_F.H commit 71cf911068e3d90ac01919d8b643368ce6c9a2f3 Author: Ann Almgren Date: Fri Apr 5 16:42:36 2019 -0700 Add factor of a_half_inv to update for (rho q) Source/Hydro/Nyx_advection_util.F90 commit 9f1c3ae7949f0db7e7a272672c4ed8349b8e8bac Author: Ann Almgren Date: Fri Apr 5 16:40:54 2019 -0700 Add factor of a_half_inv to update for (rho q) Source/HydroFortran/Nyx_advection_3d.f90 commit b675caccd02eaadde2f2f4430fd9361e400f4fed Author: Jean Sexton Date: Thu Apr 4 15:53:39 2019 -0400 Fix ctoprim flux indexing error Tweak passive srcQ in ctoprim, trans, trace Add extra synchronizes for security Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Castro_hydro.cpp Source/Hydro/Nyx_advection_util.F90 Source/Hydro/trace_plm.F90 Source/Hydro/trans.F90 commit d5ec8a104450663465e1a73ee09508e9433072bc Author: Jean Sexton Date: Thu Apr 4 15:48:50 2019 -0400 Fix allocation bugs Source/EOS/atomic_rates.F90 Source/EOS/eos_hc.F90 Source/Initialization/init_managed.F90 Source/meth_params.F90 commit 7219246aec56a5434fc4f7b99a856173396a2b9b Author: Jean Sexton Date: Wed Apr 3 16:43:51 2019 -0400 Added launch for cmpflx_plus_godonuv Fix typo in ctoprim Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Castro_hydro.cpp Source/Hydro/riemann_nd.F90 Source/Hydro/riemann_util.F90 Source/Nyx_F.H commit 04e07c6cc19e0838c0ff271bcf5249e45947fa18 Author: Jean Sexton Date: Wed Apr 3 16:19:45 2019 -0400 Put in launches for trans.F90 Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/trans.F90 Source/Nyx_F.H commit d91c29b38e936b5d6d48de603bb04c790110dfec Author: Jean Sexton Date: Wed Apr 3 15:33:37 2019 -0400 Launch in ctoprim Source/EOS/eos_stuff.F90 Source/Hydro/Castro_hydro.cpp Source/Hydro/Nyx_advection_util.F90 Source/Nyx.H Source/Nyx_F.H commit e31e21769b23129acccf9c2531778ff09ed05bd4 Author: Jean Sexton Date: Wed Apr 3 14:06:18 2019 -0400 Added launch for normalize_species, tweaked normalize_species to use upass_map Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Nyx_advection_util.F90 Source/Nyx_F.H commit df239c7f90efb10150b946d90a35c37e0b72d30d Author: Jean Sexton Date: Wed Apr 3 13:24:29 2019 -0400 Removed intermediate Fortran test from transfering hydro Source/Hydro/Nyx_advection_util.F90 Source/HydroFortran/Make.package Source/HydroFortran/make_ca_hydro_sources_3d.f90 Source/Nyx_F.H Source/compute_hydro_sources.cpp Source/strang_hydro.cpp commit 35bc0b1571fbcb479e01146982965e33a52244ea Author: Jean Sexton Date: Wed Apr 3 13:01:22 2019 -0400 Conservation with vectorized cvode in LyA and new hydro Exec/LyA/inputs.rt Exec/LyA/inputs_hydro1.rt Source/HeatCool/integrate_state_vec_3d.cpp commit 2f8e5d327d5b53498a1101ef16ee259393cfe262 Author: Jean Sexton Date: Wed Apr 3 12:02:58 2019 -0400 Added launch for divu Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Nyx_advection_util.F90 Source/HydroFortran/make_ca_hydro_sources_3d.f90 Source/Nyx_F.H commit a4746b8b9a1333f08925d01743f4fab78dc8892e Author: Jean Sexton Date: Wed Apr 3 11:49:46 2019 -0400 Added launch for trace for ppm_type=0 Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Castro_ctu_nd.F90 Source/Hydro/Castro_hydro.cpp Source/Hydro/slope_nd.F90 Source/Hydro/trace_plm.F90 Source/Initialization/init_managed.F90 Source/Nyx_F.H Source/meth_params.F90 commit 724897e2b4158393da6fd7bec536bf71aff37110 Author: Jean Sexton Date: Wed Apr 3 11:16:38 2019 -0400 Using only gamma_minus_1 in Hydro instead of gamma_minus_1 and gamma_const Source/Hydro/Nyx_advection_util.F90 Source/Hydro/riemann_nd.F90 Source/Hydro/riemann_util.F90 Source/Hydro/trace_ppm.F90 Source/Hydro/trans.F90 commit d08fd3b97c58671cd561923a5e650815a95134bf Author: Jean Sexton Date: Wed Apr 3 10:38:24 2019 -0400 Add more managed variables, clean up riemann_nd extra variables Source/Hydro/riemann_nd.F90 Source/Initialization/init_managed.F90 Source/meth_params.F90 commit 16f8c6ee36542dd68776020bf5e92ed94f9a46af Author: Jean Sexton Date: Tue Apr 2 18:43:52 2019 -0400 Added FabArrayBox* use to most functions in construct_ctu_hydro Source/Hydro/Castro_ctu_hydro.cpp commit 6f9efb8d90df5b2e92155e988898d4bab9c7bc26 Author: Jean Sexton Date: Tue Apr 2 17:59:09 2019 -0400 Add launch on apply_av Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Nyx_advection_util.F90 Source/Initialization/init_managed.F90 Source/Nyx_F.H Source/meth_params.F90 commit d269bf4c06a912d3a665e1182f39112c54ba5bac Author: Jean Sexton Date: Tue Apr 2 17:17:31 2019 -0400 Remove extra deallocates if HEATCOOL=FALSE Source/Hydro/Castro_ctu_hydro.cpp Source/Initialization/init_managed.F90 Source/nyx_main.cpp commit 4310a1f88adb5322712d0cb0683ce0c39c37d5dd Author: Jean Sexton Date: Tue Apr 2 16:26:06 2019 -0400 Launched consup matches in Sedov and Sod Exec/HydroTests/Sod/inputs.regtest Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Castro_ctu_nd.F90 Source/Hydro/Nyx_advection_util.F90 Source/Initialization/init_managed.F90 Source/Nyx_F.H Source/meth_params.F90 commit b32390e67efc126bb960ca86ccd3bde22e8c4587 Author: Jean Sexton Date: Tue Apr 2 13:37:47 2019 -0400 Added device functions to eos_stuff Exec/HydroTests/Sedov/inputs.regtest Source/EOS/Make.package Source/EOS/eos_stuff.F90 commit b60c405bce35b6595cb2a532124511539e1937e3 Author: Jean Sexton Date: Tue Apr 2 11:04:11 2019 -0400 Changed compiler-specific nan check to equality check Source/Hydro/check_for_nan.f90 commit 87d62538aac3d9631e486fc12c3f0945a60624a4 Author: Jean M. Sexton Date: Mon Apr 1 16:20:15 2019 -0700 Test out different ways to subtract kinetic energy from total energy Source/Src_3d/reset_internal_energy_3d.F90 commit 954f07d4c8653d1135063e97d2ddaa4c6b1093e5 Author: Jean M. Sexton Date: Mon Apr 1 16:12:57 2019 -0700 Change inputs files for testing ppm_type=0 Exec/AMR-density/inputs.rt Exec/HydroTests/DoubleRarefaction/inputs.regtest Exec/HydroTests/StrongShockTube/inputs.regtest commit f6de4288344a04787d1506c5b24877effe200545 Author: Jean M. Sexton Date: Mon Apr 1 10:27:35 2019 -0700 Removed extraneous endif, added testing inputs Exec/LyA/GNUmakefile Exec/LyA/inputs Exec/LyA/test.sh Source/Hydro/riemann_nd.F90 commit 4c6e74af3f535a72476f13e8aafe341e3e84198c Author: Jean M. Sexton Date: Thu Mar 28 18:56:22 2019 -0700 Changed > to >= for matching using use_csmall_gamma flag Source/Hydro/riemann_nd.F90 commit fe617739aa9ae83b2a507315c49fded981db80eb Author: Jean M. Sexton Date: Thu Mar 28 16:02:32 2019 -0700 Added option to scale fluxes by area*dt pre-consup, fixed other option to use proper area2 and area3 in case they're distict Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Nyx_advection_util.F90 Source/Nyx_F.H Source/meth_params.F90 commit 1a83363d3f215517a7fd1cadae05a4271e96f1e2 Author: Jean M. Sexton Date: Thu Mar 28 14:11:12 2019 -0700 Fixed godnuv state used for pressure limiter, fixed rhoe in riemann to use gamma law Source/Hydro/riemann_nd.F90 Source/Hydro/trans.F90 commit 8d7e4eef098af0f5648835e40c7e32b17b58c6ce Author: Jean M. Sexton Date: Mon Mar 25 14:54:06 2019 -0700 Added final resets to trans Source/Hydro/trans.F90 commit 3da245045cb68b44797fa1251ca6fd35558dda47 Author: Jean M. Sexton Date: Mon Mar 25 14:32:32 2019 -0700 Added to resets to transz_on_x Source/Hydro/trans.F90 commit 8dc2b29fa59af1dc7a284e7a85b4691044acce11 Author: Jean M. Sexton Date: Mon Mar 25 12:10:43 2019 -0700 Added 6 resets Source/Hydro/trans.F90 commit 473662c01d1159b59ae9ecceea0c2e637d403167 Author: Jean M. Sexton Date: Mon Mar 25 11:13:32 2019 -0700 Added pressure limiter ins transxz Source/Hydro/trans.F90 commit 66f68c07a39c97c4b275265568df79e7cef2743f Author: Jean M. Sexton Date: Mon Mar 25 08:45:58 2019 -0700 Matched 3 more resets in trans, fixed typo in trace Source/Hydro/trace_plm.F90 Source/Hydro/trans.F90 commit a817559c1c7a0287f95ba81f04249a2083334adb Author: Jean M. Sexton Date: Mon Mar 25 07:32:44 2019 -0700 Removed max from trace before resetting, added more resets to trans Source/Hydro/trace_plm.F90 Source/Hydro/trans.F90 commit 310aec6cb6a400b4365fd3668643353a172c3bc2 Author: Jean M. Sexton Date: Sun Mar 24 22:03:37 2019 -0700 Add limiters to trace and transx_on_zstates Source/Hydro/trace_plm.F90 Source/Hydro/trans.F90 Source/meth_params.F90 commit 29f24ee4e9d22b15c8a32f78708fc5cce4499829 Author: Jean M. Sexton Date: Sun Mar 24 14:51:08 2019 -0700 Add csmall based on gamma Source/Hydro/riemann_nd.F90 commit 68084486704d32e09d704aba0b02e84f7249b61a Author: Jean M. Sexton Date: Fri Mar 22 18:10:04 2019 -0700 Added aborts to test small_pres and flags for testing evolving a and removing grav_vector Exec/Scaling/inputs Exec/Scaling/test.sh Source/Hydro/trans.F90 Source/strang_hydro.cpp commit 09039049387e5b259349ff20876c8572c3b9e2d5 Author: Jean M. Sexton Date: Fri Mar 22 10:21:50 2019 -0700 Fixed segfault for use_const_species=1 comparison test Source/Hydro/Nyx_advection_util.F90 commit 29de5371775589adf938679e70526ad941f809fe Author: Jean M. Sexton Date: Fri Mar 22 08:23:47 2019 -0700 Fix qmo indexing for srcQ Source/Hydro/Nyx_advection_util.F90 Source/Hydro/trans.F90 commit 34d1e02e201aada656466e1b5166949789f06878 Author: Jean M. Sexton Date: Thu Mar 21 11:11:11 2019 -0700 Added srcQ/a_old to transxy, transxz, transyz Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/trans.F90 Source/Nyx_F.H commit 5d05b45ee91aac8d1a6c62a548a8894adafebcb9 Author: Jean M. Sexton Date: Thu Mar 21 09:23:38 2019 -0700 Added a_old and a_new to factors dtdx and added flag for using srcQ in trace to new hydro Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Castro_ctu_nd.F90 Source/Hydro/trace_plm.F90 Source/Nyx_F.H Source/meth_params.F90 commit c044c07573c3d8a2b283df99187a9219b6046091 Merge: e1201cd2 62ac17d2 Author: Jean M. Sexton Date: Thu Mar 21 08:14:59 2019 -0700 Merge branch 'gpu_hydro' of github.com:amrex-astro/Nyx into gpu_hydro commit e1201cd2b2e0e08a1892bdfa529034fcae7b573a Author: Jean M. Sexton Date: Thu Mar 21 08:08:13 2019 -0700 Removed sources from trace_plm_orig and added limiter for pstar,ustar for non-analytic riemann in old Nyx Source/Hydro/trace_plm.F90 Source/HydroFortran/Nyx_advection_3d.f90 commit 62ac17d229dc30476a98204f34fe72217ab6a8d6 Merge: 902c513f 3675c297 Author: Ann Almgren Date: Wed Mar 20 19:23:05 2019 -0700 Merge branch 'development' into gpu_hydro commit 3675c297830ca13dae083123f84dc81ada21d98a Author: Ann Almgren Date: Wed Mar 20 19:20:43 2019 -0700 Remove all references to HPGMG and/or solving with anything besides the MLMG solver. Exec/AMR-density/inputs Exec/AMR-density/inputs.rt Exec/AMR-zoom/inputs Exec/HDF5_example/inputs Exec/Henson/amr-info/GNUmakefile Exec/Henson/extract-particles/GNUmakefile Exec/Henson/sample-analysis/GNUmakefile Exec/LyA/inputs Exec/LyA/inputs.rt Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA_AGN/inputs Exec/Make.Nyx Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.ref Exec/SantaBarbara/inputs Exec/Scaling/inputs Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit 902c513fcdb86230de2504a9abe769f26a50aa2b Author: Jean M. Sexton Date: Wed Mar 20 16:56:21 2019 -0700 Remove extra eos_module includes Source/Hydro/ppm_nd.F90 Source/Hydro/riemann_nd.F90 Source/Hydro/riemann_util.F90 Source/Hydro/trace_ppm.F90 commit 9ab5f2f15bae02356a20607c5d1c5110cee99931 Author: Jean M. Sexton Date: Wed Mar 20 16:27:11 2019 -0700 Neglected to commit testing analriem in Nyx new Source/Hydro/riemann_nd.F90 Source/HydroFortran/analriem.f90 commit 98a88b456e1eb031c308235729a9907add3a9f04 Author: Jean M. Sexton Date: Wed Mar 20 16:16:59 2019 -0700 Add Nyx old version of trace_plm with no reference Source/Hydro/Castro_ctu_nd.F90 Source/Hydro/trace_plm.F90 commit f629e1a03c2296bd7e52be8e67ba72d002b6c4a0 Author: Ann Almgren Date: Wed Mar 20 15:55:11 2019 -0700 Fix 1) dt weighting of source term in update for (rho e) 2) only multiply fluxes by a on valid faces Source/Hydro/Nyx_advection_util.F90 commit e67774a8fa2564fc886750b54423ae6f594aca1a Author: Ann Almgren Date: Wed Mar 20 15:51:58 2019 -0700 1) Remove radiation from Castro_ctu_hydro 2) Fix cxbx --> bx sent into the cmpflx call after transyz Source/Hydro/Castro_ctu_hydro.cpp commit 93bd6b7d1a43bd54b77f54049547a2d2d25c577a Merge: c89649f2 bef700da Author: Ann Almgren Date: Wed Mar 20 12:25:26 2019 -0700 Merge branch 'development' into gpu_hydro commit bef700da43ddf11fdd5db3165c655ceb6c37678b Author: Ann Almgren Date: Wed Mar 20 12:22:43 2019 -0700 When H = 0 we need to not call fort_integrate_comoving_a because it divides by H. Source/Nyx_F.H Source/comoving.cpp Source/comoving_nd.f90 commit c89649f2d73b2dc473da92005b2b3d4261453adb Author: Ann Almgren Date: Wed Mar 20 12:22:08 2019 -0700 Make default value of use_pressure_law_divu be 1 not 0 Source/meth_params.F90 commit d1b17bb449a869751dd9bc2eb5c44fcbf4eb87ef Author: Jean M. Sexton Date: Wed Mar 20 09:27:38 2019 -0700 Made both pdivu optional with flag Add option for not using analriem in old Nyx, using analriem in new Nyx has issues Source/Hydro/Nyx_advection_util.F90 Source/HydroFortran/Nyx_advection_3d.f90 Source/meth_params.F90 commit b504510af32bd21ea1a7ad861cf62016d7cab783 Author: Jean M. Sexton Date: Wed Mar 20 02:48:52 2019 -0700 Added pdivu using gamma_minus_1*e, since using stored pressure didn't match Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Castro_ctu_nd.F90 Source/Hydro/Nyx_advection_util.F90 Source/Nyx_F.H commit 123210676e6e979e5cb384e0a3c8c09b390f242e Merge: 071a3c97 91e94958 Author: Jean M. Sexton Date: Wed Mar 20 01:23:25 2019 -0700 Merge branch 'gpu_hydro' of github.com:amrex-astro/Nyx into gpu_hydro commit 91e9495893c3fbc6b5bf8c14687d77ed7af43f20 Author: Ann Almgren Date: Tue Mar 19 18:19:30 2019 -0700 1) set ppm_predict_gammae to 1 in order to match original Nyx algorithm -- since we know constant gamma this makes sense Note that with this commit, "new" hydro gives the same results as "old" hydro if we replace analriem in the "old" by the star states done as in the "new" Source/Hydro/trans.F90 Source/meth_params.F90 commit 071a3c97e920119d91616e392c4722b47e5fe87a Author: Jean M. Sexton Date: Tue Mar 19 13:49:48 2019 -0700 Added ppm flattening test, needs further verification Source/Hydro/Castro_ctu_nd.F90 Source/Hydro/ppm_nd.F90 Source/Hydro/trace_ppm.F90 Source/meth_params.F90 commit 8eecef496cf758bdc739a24f30bd3980b00d5f51 Author: Jean M. Sexton Date: Tue Mar 19 12:23:05 2019 -0700 Made corner_coupling default, removed version_2=3 and ppm_type=2 Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/ppm_3d.f90 Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/meth_params.F90 commit ded7c55740ef3875c56ae69c64e2cac06d42bbbb Author: Jean M. Sexton Date: Mon Mar 18 22:28:21 2019 -0700 Add flux registers for Sod Source/Hydro/Castro_ctu_hydro.cpp Source/Nyx.cpp commit f0dbdfddfe4f853a6944f2c1befe33549257a1b8 Author: Jean M. Sexton Date: Mon Mar 18 16:25:13 2019 -0700 Change area and dt scaling to match for Sedov Source/Hydro/Nyx_advection_util.F90 Source/Hydro/riemann_util.F90 Source/HydroFortran/make_ca_hydro_sources_3d.f90 Source/strang_hydro.cpp commit 866f0ef289509c12c1ffa82ff2c63e30a800d174 Author: Jean M. Sexton Date: Mon Mar 18 14:30:20 2019 -0700 Fixed index size and pressure in fluxes Source/Hydro/riemann_util.F90 Source/Nyx.cpp commit 676c78f077535c2b45955bff9b74a31a07302224 Author: Jean M. Sexton Date: Fri Mar 15 08:42:33 2019 -0700 Match arguments for Castro hydro into Nyx .gitignore Exec/Make.Nyx Source/Hydro/Castro_ctu_hydro.cpp Source/Hydro/Castro_ctu_nd.F90 Source/Hydro/Castro_hydro.cpp Source/Hydro/Make.package Source/Hydro/Nyx_advection_util.F90 Source/Hydro/check_for_nan.f90 Source/Hydro/make_hydro_sources_3d_test.f90 Source/Hydro/ppm_nd.F90 Source/Hydro/riemann_nd.F90 Source/Hydro/riemann_util.F90 Source/Hydro/slope_nd.F90 Source/Hydro/trace_plm.F90 Source/Hydro/trace_ppm.F90 Source/Hydro/trans.F90 Source/HydroFortran/make_ca_hydro_sources_3d.f90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/meth_params.F90 Source/prob_params.f90 Source/strang_hydro.cpp commit 67cada9a147604bc2c624cfb724ddff0a18caf58 Author: Jean M. Sexton Date: Fri Mar 15 08:43:29 2019 -0700 Revert "Changed make_hydro prototype to hide spacedim" This reverts commit cb32176a1b3bf21aadaad274b067a31aca09ea79. Source/Hydro/Nyx_advection_util.F90 Source/HydroFortran/make_ca_hydro_sources_3d.f90 commit cb32176a1b3bf21aadaad274b067a31aca09ea79 Author: Jean M. Sexton Date: Tue Mar 12 16:41:23 2019 -0700 Changed make_hydro prototype to hide spacedim Source/Hydro/Nyx_advection_util.F90 Source/HydroFortran/make_ca_hydro_sources_3d.f90 commit 956bf025a68fa1f5c171d42fee7b17939f1d4b53 Author: Jean M. Sexton Date: Tue Mar 12 14:56:13 2019 -0700 Fix gravity index Source/Hydro/Nyx_advection_util.F90 Source/HydroFortran/make_ca_hydro_sources_3d.f90 commit 47828a00eb66162f11c88050570e204df0f3ca5a Author: Jean M. Sexton Date: Tue Mar 12 11:33:14 2019 -0700 Transferred make_divu_nd Source/Hydro/Nyx_advection_util.F90 Source/HydroFortran/make_ca_hydro_sources_3d.f90 commit 1d7889a1ebd51400bc50a5ef8e5432543c87e96b Author: Jean M. Sexton Date: Tue Mar 12 11:19:54 2019 -0700 Moved over normalize_species_fluxes Source/Hydro/Nyx_advection_util.F90 Source/HydroFortran/make_ca_hydro_sources_3d.f90 commit 7828e06537947b1fd1591aa697349840e123743b Author: Jean M. Sexton Date: Tue Mar 12 10:52:27 2019 -0700 Added nyx.hydro_convert flag to choose whether standard hydro or hydro being converted is used Source/Hydro/Nyx_advection_util.F90 Source/Nyx.H Source/Nyx.cpp Source/compute_hydro_sources.cpp commit b2929ecd2fb5d52a86af2c039cb41bb9e80e78bc Author: Jean M. Sexton Date: Tue Mar 12 10:38:04 2019 -0700 Added seperate make_hydro_sources for transfer to preserve original behavior for comparison, transferred apply_av Source/Hydro/Make.package Source/Hydro/Nyx_advection_util.F90 Source/HydroFortran/Make.package Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/make_ca_hydro_sources_3d.f90 Source/HydroFortran/make_hydro_sources_3d.f90 Source/Nyx_F.H Source/compute_hydro_sources.cpp Source/prob_params.f90 commit d97dce9939ed0aefef06c90417729d788e96beea Author: Zarija Lukic Date: Mon Mar 11 17:49:22 2019 -0700 Memory profiling in the converter Util/zhi_converter/main.cpp commit 7e35296c93d5fb42527122eda93383f7c2235045 Author: Jean M. Sexton Date: Mon Mar 11 09:49:57 2019 -0700 Revert "Revert preliminary hydro changes" This reverts commit 6399b716008a495e5bf5bc8730299b43e1b2efe0. Exec/LyA/GNUmakefile Exec/Make.Nyx Source/Hydro/Make.package Source/Hydro/Nyx_advection_util.F90 Source/Hydro/flatten_nd.F90 Source/HydroFortran/Make.package Source/HydroFortran/make_hydro_sources_3d.f90 Source/Nyx_nd.f90 Source/meth_params.F90 commit b041173b7670cb5449d967510072ee7feaff6ef4 Author: Jean Sexton Date: Thu Mar 7 19:03:53 2019 -0500 Added cudaStreams Source/HeatCool/integrate_state_vec_3d.cpp commit 2c66c465592a45a81b0ed16611fe0f0870e15ecc Author: Jean Sexton Date: Thu Mar 7 17:12:36 2019 -0500 Test vectorizing by subsets of the i direction Source/HeatCool/integrate_state_vec_3d.cpp commit 9f6a12e97bd9b0e6a49c56098d5a6d7e44ceac30 Author: Jean Sexton Date: Thu Mar 7 12:41:50 2019 -0500 Use lambda for vectorizing in i Source/HeatCool/integrate_state_vec_3d.cpp commit 2b1208712a6bcb7c08a4cf7d1b583de7d5dc1fa5 Author: Jean Sexton Date: Thu Mar 7 12:41:01 2019 -0500 Commented out flush, removed singleton (first=.true.) check from atomic_rates for xl compatibility Source/EOS/atomic_rates.F90 Source/HeatCool/cvode_extras.F90 Source/HeatCool/integrate_state_farkode_3d.f90 Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_fcvode_vec_3d.f90 Source/HeatCool/integrate_state_fcvode_with_source_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 Source/HeatCool/integrate_state_with_source_3d.f90 Source/HydroFortran/Nyx_advection_3d.f90 Source/Src_3d/compute_temp_3d.F90 Source/Src_3d/reset_internal_energy_3d.F90 commit ddebacc01b0b1fb0124ae3613581b6aca1828c8b Author: Jean Sexton Date: Wed Mar 6 16:11:10 2019 -0500 Test unvectorized version with cuda Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_vec_3d.cpp Source/HydroFortran/trans_3d.f90 commit 4aebbbf5af696d6a0dcd799f298bc26c619cf883 Merge: 6399b716 e3cd5e6b Author: Jean Sexton Date: Wed Mar 6 13:07:11 2019 -0500 Add new vectorized version commit 6399b716008a495e5bf5bc8730299b43e1b2efe0 Author: Jean Sexton Date: Wed Mar 6 13:01:48 2019 -0500 Revert preliminary hydro changes Exec/LyA/GNUmakefile Exec/Make.Nyx Source/Hydro/Make.package Source/Hydro/Nyx_advection_util.F90 Source/Hydro/flatten_nd.F90 Source/HydroFortran/Make.package Source/HydroFortran/make_hydro_sources_3d.f90 Source/Nyx_nd.f90 Source/meth_params.F90 commit e3cd5e6b3b7f92f288db95dba8c3d104ca21b75d Author: Jean M. Sexton Date: Mon Mar 4 20:46:32 2019 -0800 More readable vectorized version Source/EOS/eos_hc.f90 Source/HeatCool/integrate_state_vec_3d.cpp commit 157553256768511187084733bbb39616b151950f Author: Jean M. Sexton Date: Mon Mar 4 19:10:59 2019 -0800 Macro version of C++ driver for heating-cooling Source/HeatCool/Make.package Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_box_3d_stubs.cpp Source/HeatCool/integrate_state_fcvode_vec_3d.f90 Source/HeatCool/integrate_state_vec_3d.cpp Source/Nyx.H Source/Nyx.cpp Source/comoving.cpp Source/strang_reactions.cpp commit 314f41b68ce3dbd4ed1fafe0d68cc080df7e60a7 Author: Jean M. Sexton Date: Mon Mar 4 09:42:45 2019 -0800 Cleaned up comments Source/Hydro/Nyx_advection_util.F90 Source/HydroFortran/make_hydro_sources_3d.f90 commit 46611665f355cd0fe6a47515bacd478d6bfecd84 Author: Jean M. Sexton Date: Mon Mar 4 09:39:53 2019 -0800 Transfered ctoprim and uflatten Exec/LyA/GNUmakefile Exec/Make.Nyx Source/Hydro/Make.package Source/Hydro/Nyx_advection_util.F90 Source/Hydro/flatten_nd.F90 Source/HydroFortran/Make.package Source/HydroFortran/make_hydro_sources_3d.f90 Source/Nyx_nd.f90 Source/meth_params.F90 commit d98f08c9c428b33b757fe3a1a155ebbf7f22e553 Author: Jean M. Sexton Date: Mon Mar 4 09:32:33 2019 -0800 Cleaned up if statements for compiling without heating-cooling Source/EOS/eos_hc.F90 Source/HeatCool/integrate_state_fcvode_vec_3d.f90 Source/Initialization/init_managed.F90 commit 5edf8d46b967bd1e2d8619b00c8b578747c128df Merge: 48691d4a 3b648cc3 Author: Jean M. Sexton Date: Sun Mar 3 08:38:23 2019 -0800 Merge remote-tracking branch 'origin/development' into gpu_hc commit 3b648cc318bfb287dd2a14cd23ec25e1b165e34a Author: Andrew Myers Date: Fri Feb 22 14:42:19 2019 -0800 when Redistributing after a regrid, account for the case that the number of levels has shrunk Source/NyxParticles.cpp commit 880fd1ac7020fc62a61ada3b998f77377375450d Merge: 7cfec554 f21c75d4 Author: Andrew Myers Date: Wed Feb 20 10:29:22 2019 -0800 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development commit f21c75d4554db501d740f7255c15f19de5b54572 Author: Jean M. Sexton Date: Thu Feb 14 07:40:18 2019 -0800 Changed all tracked inputs files to use e for exponent instead of d Exec/AMR-density/inputs Exec/AMR-density/inputs.rt Exec/DrivenTurbulence/inputs Exec/DrivenTurbulence/inputs.regtest Exec/GravityTests/MacLaurin/inputs Exec/GravityTests/zeldovich_dm/run/inputs_wmap7 Exec/HDF5_example/inputs Exec/HydroTests/DoubleRarefaction/inputs-test2-x Exec/HydroTests/DoubleRarefaction/inputs-test2-y Exec/HydroTests/DoubleRarefaction/inputs-test2-z Exec/HydroTests/DoubleRarefaction/inputs.regtest Exec/HydroTests/DoubleRarefaction/inputs.restarttest Exec/HydroTests/Sod/inputs-sod-x Exec/HydroTests/Sod/inputs-sod-y Exec/HydroTests/Sod/inputs-sod-z Exec/HydroTests/Sod/inputs.regtest Exec/HydroTests/StrongShockTube/inputs-x Exec/HydroTests/StrongShockTube/inputs-y Exec/HydroTests/StrongShockTube/inputs-z Exec/HydroTests/StrongShockTube/inputs.regtest Exec/HydroTests/TurbForce/inputs Exec/HydroTests/TurbForce/inputs.regtest Exec/LyA/inputs Exec/LyA/inputs.rt Exec/LyA/inputs.small.dsc Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA_AGN/inputs Exec/LyA_AGN/inputs.rt Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Exec/MiniSB/inputs.analysis Exec/SantaBarbara/inputs Exec/Scaling/inputs commit 71b32d96a5e0d6eb2bc8f25f34c01e89c56e6e07 Author: Weiqun Zhang Date: Fri Feb 1 14:34:35 2019 -0800 remove F_Interfaces from make and use amrex_pd_ioprocessor Exec/Make.Nyx Source/EOS/atomic_rates.f90 commit 48691d4ae269526480a604657f4db60e4777a5a4 Author: Jean Sexton Date: Thu Jan 31 13:04:01 2019 -0500 Remove verbose output, move deallocate to end Source/HeatCool/integrate_state_box_3d.cpp Source/nyx_main.cpp commit 0a8c985018ef2e2dbaf557d71ea199712a588e90 Author: Jean Sexton Date: Wed Jan 23 13:27:20 2019 -0500 Made compute, reset, init lambda launched Source/EOS/Make.package Source/EOS/eos_hc.F90 Source/EOS/reion_aux_module.F90 Source/EOS/reion_aux_module.f90 Source/HeatCool/cvode_extras.F90 Source/HeatCool/integrate_state_box_3d.cpp Source/Initialization/Make.package Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/init_e_from_t_3d.F90 Source/Initialization/init_managed.F90 Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_F.H Source/Src_3d/Make.package Source/Src_3d/compute_temp_3d.F90 Source/Src_3d/reset_internal_energy_3d.F90 Source/meth_params.F90 commit 9ba4b1cbb8b63491874ca9de0e85c906c9bd7da7 Author: Jean Sexton Date: Tue Jan 22 11:40:18 2019 -0500 Use macros Source/EOS/eos_hc.F90 Source/HeatCool/cvode_extras.F90 Source/HeatCool/f_rhs.F90 Source/HeatCool/integrate_state_vode_3d.f90 Source/Nyx_F.H Source/Src_3d/compute_temp_3d.f90 commit cb548cf5cde3705a53e168407b80f2d25c4b82ca Author: Jean Sexton Date: Mon Jan 21 13:36:51 2019 -0500 Second try at compute_new_temp Source/EOS/eos_hc.F90 Source/Src_3d/compute_temp_3d.f90 commit 8aa0d5557e9b0974113bc2f92930681d20710929 Author: Jean Sexton Date: Mon Jan 21 13:00:32 2019 -0500 Removed extra device ion_n Source/EOS/eos_hc.F90 commit 8e8f426b5617602757625f46745dcc3dd34b516b Merge: 56e3901a 36f80727 Author: Andrew Myers Date: Thu Jan 17 15:35:22 2019 -0800 Merge branch 'master' into development commit 36f807273144b83e68c12a420cda3265cea48f57 Author: Andrew Myers Date: Thu Jan 17 15:34:31 2019 -0800 update the where_width etc... for the dark matter only advance routine Source/DarkMatterParticleContainer.cpp Source/advance_particles.cpp commit 7cfec554cacba4adf58cc719656a76b4c97706c5 Merge: 8c4cb405 56e3901a Author: Andrew Myers Date: Thu Jan 17 14:15:09 2019 -0800 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development commit a0535bdbe2ba9a8a4207d971bbff72875ba84b32 Author: Jean Sexton Date: Wed Jan 16 17:24:58 2019 -0500 Add managed eos and iterate_ne Source/EOS/eos_hc.F90 Source/HeatCool/Make.package Source/HeatCool/cvode_extras.F90 Source/HeatCool/f_rhs.F90 Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_vode_3d.f90 Source/HeatCool/vode_aux.F90 Source/Nyx_F.H Source/Src_3d/compute_temp_3d.f90 commit 159d6b7d042f760ad47ee2ca7da129d56d193667 Author: Jean Sexton Date: Thu Jan 10 15:55:05 2019 -0500 Verified cuda nvector version with non-device f_rhs Source/EOS/eos_hc.F90 Source/HeatCool/cvode_extras.f90 Source/HeatCool/f_rhs.F90 Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/vode_aux.F90 Source/Initialization/init_managed.F90 Source/meth_params.F90 commit d5a48be3e0a5622998bd32246f99d66fd6c08988 Author: Jean Sexton Date: Thu Jan 10 11:23:21 2019 -0500 Same answer using cuda only in nvector linear ops Source/HeatCool/integrate_state_box_3d.cpp commit 53f82d5cf789167891c535dd8a4f0ed90b0ac0f7 Author: Jean Sexton Date: Thu Jan 10 09:55:33 2019 -0500 Added vode managed, takes twice as long .gitignore Source/HeatCool/vode_aux.F90 Source/Initialization/init_managed.F90 commit e0fec467f26c353a22d99ab01209d4f5e5479837 Author: Jean Sexton Date: Thu Jan 10 09:19:33 2019 -0500 Add managed Exec/LyA/GNUmakefile Source/EOS/atomic_rates.F90 Source/Initialization/init_managed.F90 Source/meth_params.F90 commit 8dc9b42c61a9f410bccc4d1bc1b42d7c1f64908e Author: Jean Sexton Date: Thu Jan 10 09:06:10 2019 -0500 Added constants Source/EOS/atomic_rates.F90 Source/Initialization/init_managed.F90 commit f0300d698394157b6acc6e1e8a5b2c668304d14e Author: Jean Sexton Date: Thu Jan 10 08:54:19 2019 -0500 Added gamma_minus_1 and XHYDROGEN, YHELIUM Source/EOS/atomic_rates.F90 Source/Initialization/init_managed.F90 Source/meth_params.F90 commit 32cc24a5e0400e303f50c1bc036d9eba4581cafe Author: Jean Sexton Date: Thu Jan 10 08:36:19 2019 -0500 Framework for adding allocated variables cleaned up Source/EOS/atomic_rates.F90 Source/HeatCool/integrate_state_box_3d.cpp Source/Initialization/Make.package Source/Initialization/Nyx_setup.cpp Source/Initialization/init_managed.F90 Source/Nyx.H Source/Nyx_F.H Source/nyx_main.cpp commit baa76cfffe5b9e76f5cd044d40865cc8b608fd25 Author: Jean Sexton Date: Wed Jan 9 13:57:57 2019 -0500 Change files to preprocessed Added new Make packages Source/EOS/Make.package Source/EOS/atomic_rates.F90 Source/EOS/eos_hc.F90 Source/HeatCool/Make.package Source/HeatCool/f_rhs.F90 Source/HeatCool/vode_aux.F90 Source/Initialization/Make.package Source/Make.package Source/meth_params.F90 commit fb1ea57b508f2a872b96e0a91dcc0f4170e5ef2a Author: Jean Sexton Date: Wed Jan 9 10:13:21 2019 -0500 Sanity check for USE_CUDA with no valid launch regions Exec/Scaling/inputs_short Exec/Scaling/run_cudashort.summit Exec/Scaling/run_short.summit Source/nyx_main.cpp commit 56e3901ab18a295d1674244b7065f013547b4aa2 Author: Ann Almgren Date: Thu Dec 20 14:15:25 2018 -0800 Update AGN stuff to use amrex_random instead of old RNGs. Source/AGN/agn_3d.f90 Source/AGNParticleContainer.cpp Source/Nyx.cpp Source/Nyx_halos.cpp commit 9b4c6487de3c026d216bf5ea5ea166f855d302e0 Author: Ann Almgren Date: Thu Dec 20 12:38:22 2018 -0800 One more bl --> amrex Source/Forcing/forcing_spect.f90 commit c99a2613c26ca456f3dd048dedaceff3ae65da24 Author: Ann Almgren Date: Thu Dec 20 12:28:27 2018 -0800 Convert to not using F_BaseLib Exec/HydroTests/TurbForce/Derive_3d.f90 Exec/HydroTests/TurbForce/Make.package Exec/HydroTests/TurbForce/Prob_3d.f90 Exec/HydroTests/TurbForce/integrate_state_force_3d.f90 Exec/HydroTests/TurbForce/turbforce.f90 Exec/HydroTests/TurbForce/turbinit.f90 commit f7fd1a8a4427973f71c51959915f9594a3bf77a4 Author: Ann Almgren Date: Thu Dec 20 12:05:39 2018 -0800 Convert bl_* --> amrex_* Exec/DrivenTurbulence/Derive_3d.f90 Exec/DrivenTurbulence/Prob_3d.f90 commit 80408d6764edecf8654ddc4aa8288c949d634e35 Author: Ann Almgren Date: Thu Dec 20 11:17:55 2018 -0800 Add amrex_error so we compile again Source/HeatCool/f_rhs.f90 Source/HeatCool/integrate_state_vode_3d.f90 commit ba67cf285b8b7009ebeb3920899b5cc567e77f71 Author: Ann Almgren Date: Thu Dec 20 11:01:16 2018 -0800 bl_error --> amrex_error Exec/HydroTests/Sedov/Prob_3d.f90 commit 34a1b7e7e2d972d47e9aae5cfaab620b1bdc3b28 Author: Jean M. Sexton Date: Wed Dec 19 09:01:53 2018 -0800 change bl_ to amrex_ Source/AGN/agn_3d.f90 Source/DerivedQuantities/Derive_3d.f90 Source/EOS/eos_stuff.f90 Source/Forcing/forcing_spect.f90 Source/Forcing/integrate_state_force_3d.f90 Source/Gravity/prescribe_grav_3d.f90 Source/HeatCool/cvode_extras.f90 Source/HeatCool/f_rhs.f90 Source/HeatCool/fcvode_extras_src.f90 Source/HeatCool/integrate_state_farkode_3d.f90 Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_fcvode_vec_3d.f90 Source/HeatCool/integrate_state_fcvode_with_source_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 Source/HeatCool/integrate_state_with_source_3d.f90 Source/Initialization/check_initial_species_3d.f90 commit a8cb90dd7459e0637f4addd2f00d26a3076a6533 Author: Jean M. Sexton Date: Tue Dec 18 06:16:33 2018 -0800 Fix Make.Nyx to include F_Interfaces correctly Exec/Make.Nyx commit f9d8b9ea689f3d3a9fc5c131da8f2cf723a13ca6 Author: Jean Sexton Date: Mon Dec 17 14:10:16 2018 -0500 Fix driver to match amrex gpu names Util/SUNDIALS3/GNUmakefile Util/SUNDIALS3/f_rhs.F90 Util/SUNDIALS3/main.cpp Util/SUNDIALS3/summitdev.sh commit 4e7c087734f65fe70b51651c21315a8f63404f9a Merge: e41c1fd7 16f6ec2b Author: Jean Sexton Date: Mon Dec 17 14:08:12 2018 -0500 Merge F_interface updates, tweak do_tiling test for GPU commit e41c1fd7a845d4ea39fdc8457b316d2c1d944763 Author: Jean Sexton Date: Mon Dec 17 13:40:13 2018 -0500 Update F_interfaces cleaner Exec/Make.Nyx Source/EOS/atomic_rates.f90 Source/EOS/eos_hc.f90 Source/EOS/eos_stuff.f90 Source/HeatCool/integrate_state_farkode_3d.f90 Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_fcvode_vec_3d.f90 Source/HeatCool/integrate_state_fcvode_with_source_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 Source/HeatCool/integrate_state_with_source_3d.f90 Source/Make.package commit 16f6ec2b19211b297c8bd3534a24ae02d63e978e Merge: 405cecf7 2620bace Author: Jean Sexton Date: Mon Dec 17 13:36:08 2018 -0500 Merge branch 'development' of github.com:/AMReX-Astro/Nyx into development commit 2620bace59ba5e990252a4735b9c396f5e77a403 Author: Jean M. Sexton Date: Wed Dec 12 11:38:13 2018 -0800 Changed order build_and_deploy.sh commit 114f503576b548aeee4ea397f82d469934155e97 Author: Jean M. Sexton Date: Wed Dec 12 11:03:11 2018 -0800 Change permissions build_and_deploy.sh id_rsa_travis.enc commit 1232df6fee0ec94e4a0b6927c38da5b3242d16eb Author: Jean M. Sexton Date: Wed Dec 12 10:03:35 2018 -0800 Testing keys build_and_deploy.sh id_rsa_travis.enc commit 2b521dd03d8982cdf8305a409db562af8f16de77 Author: Jean M. Sexton Date: Tue Dec 11 18:13:58 2018 -0800 Update key id_rsa_travis.enc commit 95ca4d5df90596a04bd423ff1a24cce03e3512ba Author: Jean M. Sexton Date: Tue Dec 11 18:03:35 2018 -0800 Removed tex build until macros are fixed build_and_deploy.sh commit cd697762ac9647d7043884f201d8c59b42b75dca Author: Jean M. Sexton Date: Tue Dec 11 17:54:56 2018 -0800 ipython .travis.yml commit cbf5cad0884df3dfc0b3645e2e353f484a1c9254 Author: Jean M. Sexton Date: Tue Dec 11 17:44:14 2018 -0800 Update pip packages documentation .travis.yml commit 6180a7e7cd1364c22ebc76677d2d899e32bc8e1d Author: Jean M. Sexton Date: Tue Dec 11 17:36:10 2018 -0800 Adding requirements for modules requirements.txt commit dfb2a880d44aa9dca1a94995daa6af6b70cafca8 Author: Jean M. Sexton Date: Tue Dec 11 17:29:46 2018 -0800 Moved documentation to sphinx_documentation in case of seperate documentation for Exec Docs/sphinx_documentation/Doxyfile Docs/sphinx_documentation/Makefile Docs/sphinx_documentation/converting_docs.txt Docs/sphinx_documentation/source/NyxEquations.rst Docs/sphinx_documentation/source/NyxGettingStarted.rst Docs/sphinx_documentation/source/NyxGravity.rst Docs/sphinx_documentation/source/NyxHeatCool.rst Docs/sphinx_documentation/source/NyxIntroduction.rst Docs/sphinx_documentation/source/NyxPreface.rst Docs/sphinx_documentation/source/Particles.rst Docs/sphinx_documentation/source/class/classAGNParticleContainer.rst Docs/sphinx_documentation/source/class/classDarkMatterParticleContainer.rst Docs/sphinx_documentation/source/class/classGravity.rst Docs/sphinx_documentation/source/class/classMemInfo.rst Docs/sphinx_documentation/source/class/classNyx.rst Docs/sphinx_documentation/source/class/classNyxBld.rst Docs/sphinx_documentation/source/class/classNyxParticleContainer.rst Docs/sphinx_documentation/source/class/classNyxParticleContainerBase.rst Docs/sphinx_documentation/source/class/classStochasticForcing.rst Docs/sphinx_documentation/source/classlist.rst Docs/sphinx_documentation/source/conf.py Docs/sphinx_documentation/source/file/AGNParticleContainer_8H.rst Docs/sphinx_documentation/source/file/AGNParticleContainer_8cpp.rst Docs/sphinx_documentation/source/file/AGN__sources_8cpp.rst Docs/sphinx_documentation/source/file/DarkMatterParticleContainer_8H.rst Docs/sphinx_documentation/source/file/DarkMatterParticleContainer_8cpp.rst Docs/sphinx_documentation/source/file/Derive__F_8H.rst Docs/sphinx_documentation/source/file/Forcing_8H.rst Docs/sphinx_documentation/source/file/Forcing_8cpp.rst Docs/sphinx_documentation/source/file/Forcing__init_8cpp.rst Docs/sphinx_documentation/source/file/Gravity_8H.rst Docs/sphinx_documentation/source/file/Gravity_8cpp.rst Docs/sphinx_documentation/source/file/Gravity__F_8H.rst Docs/sphinx_documentation/source/file/MemInfo_8H.rst Docs/sphinx_documentation/source/file/MemInfo_8cpp.rst Docs/sphinx_documentation/source/file/MersenneTwister_8cpp.rst Docs/sphinx_documentation/source/file/NeutrinoParticleContainer_8H.rst Docs/sphinx_documentation/source/file/NeutrinoParticleContainer_8cpp.rst Docs/sphinx_documentation/source/file/NyxBld_8cpp.rst Docs/sphinx_documentation/source/file/NyxParticleContainer_8H.rst Docs/sphinx_documentation/source/file/NyxParticles_8cpp.rst Docs/sphinx_documentation/source/file/Nyx_8H.rst Docs/sphinx_documentation/source/file/Nyx_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__F_8H.rst Docs/sphinx_documentation/source/file/Nyx__advance_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__error_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__error__F_8H.rst Docs/sphinx_documentation/source/file/Nyx__halos_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__initcosmo_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__initdata_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__output_8H.rst Docs/sphinx_documentation/source/file/Nyx__output_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__setup_8cpp.rst Docs/sphinx_documentation/source/file/Nyx__sources_8cpp.rst Docs/sphinx_documentation/source/file/ParticleDerive_8cpp.rst Docs/sphinx_documentation/source/file/advance__particles_8cpp.rst Docs/sphinx_documentation/source/file/agn__F_8H.rst Docs/sphinx_documentation/source/file/comoving_8cpp.rst Docs/sphinx_documentation/source/file/compute__hydro__sources_8cpp.rst Docs/sphinx_documentation/source/file/dm__F_8H.rst Docs/sphinx_documentation/source/file/main_8cpp.rst Docs/sphinx_documentation/source/file/nyx__main_8cpp.rst Docs/sphinx_documentation/source/file/read__plotfile_8cpp.rst Docs/sphinx_documentation/source/file/sdc__hydro_8cpp.rst Docs/sphinx_documentation/source/file/sdc__reactions_8cpp.rst Docs/sphinx_documentation/source/file/strang__hydro_8cpp.rst Docs/sphinx_documentation/source/file/strang__reactions_8cpp.rst Docs/sphinx_documentation/source/file/sum__integrated__quantities_8cpp.rst Docs/sphinx_documentation/source/file/sum__utils_8cpp.rst Docs/sphinx_documentation/source/file/testMemInfo_8cpp.rst Docs/sphinx_documentation/source/file/update__state__with__sources_8cpp.rst Docs/sphinx_documentation/source/file/write__info_8cpp.rst Docs/sphinx_documentation/source/filelist.rst Docs/sphinx_documentation/source/index.rst Docs/sphinx_documentation/source/mathsymbols.tex Docs/sphinx_documentation/source/namespace/namespace_0D20.rst Docs/sphinx_documentation/source/namespace/namespace_0D35.rst Docs/sphinx_documentation/source/namespace/namespace_0D39.rst Docs/sphinx_documentation/source/namespace/namespace_0D7.rst Docs/sphinx_documentation/source/namespace/namespaceamrex.rst Docs/sphinx_documentation/source/namespacelist.rst Docs/sphinx_documentation/source/runtime_parameters.rst commit 2301df635f5fa71f8553ba7fb001ee8064fca982 Author: Jean M. Sexton Date: Tue Dec 11 17:14:56 2018 -0800 Add key for build and deploy .travis.yml build_and_deploy.sh id_rsa_travis.enc commit 43ed300e312ea35bdb276c87bc1d7ba9726c060b Author: Jean M. Sexton Date: Tue Dec 11 12:49:22 2018 -0800 Update for macros, begin to add Travis structure .travis.yml Docs/source/NyxEquations.rst Docs/source/Particles.rst Docs/source/mathsymbols.tex build_and_deploy.sh commit cdf21b9da98c10a5db91b97b969b283fa307d6eb Author: Jean M. Sexton Date: Tue Dec 11 12:30:44 2018 -0800 Attempt to add mathjax Docs/source/conf.py commit 6a602054beca0fd0db6ff03ec03d691d92d72f4d Author: Jean M. Sexton Date: Tue Dec 11 10:27:19 2018 -0800 Added more detail to gravity description, some gravity options aren't exercised by Nyx Docs/source/NyxGravity.rst commit 1fb0c592db659cb8d648fc68ced6d914152ddff0 Author: Jean M. Sexton Date: Mon Dec 10 18:22:41 2018 -0800 Initial addition of hydro equations Docs/source/NyxEquations.rst Docs/source/index.rst commit ad167446606d41caaf6f62327f5b04c6e43c3523 Author: Jean M. Sexton Date: Mon Dec 10 18:17:26 2018 -0800 First draft of Particles, Gravity, and HeatCool added to documentation Docs/source/NyxGravity.rst Docs/source/NyxHeatCool.rst Docs/source/Particles.rst Docs/source/index.rst commit 45fcdc3c868e9fa9b4d40aadd9b06b045e363bda Author: Jean M. Sexton Date: Mon Dec 10 17:16:57 2018 -0800 Add first draft of tables and intro Docs/source/NyxGettingStarted.rst Docs/source/NyxIntroduction.rst Docs/source/NyxPreface.rst Docs/source/conf.py Docs/source/index.rst commit 9f9f1b7ae80217693ee9aec0ce25c2220632487b Author: Jean M. Sexton Date: Mon Dec 10 12:05:14 2018 -0800 Forgot to add file Docs/source/GettingStarted.rst commit 8c97ab76b4a37c9f8464c9ac317ded5edf3ad3bf Author: Jean M. Sexton Date: Mon Dec 10 12:02:56 2018 -0800 Added docs directory to development Docs/Doxyfile Docs/Makefile Docs/converting_docs.txt Docs/source/class/classAGNParticleContainer.rst Docs/source/class/classDarkMatterParticleContainer.rst Docs/source/class/classGravity.rst Docs/source/class/classMemInfo.rst Docs/source/class/classNyx.rst Docs/source/class/classNyxBld.rst Docs/source/class/classNyxParticleContainer.rst Docs/source/class/classNyxParticleContainerBase.rst Docs/source/class/classStochasticForcing.rst Docs/source/classlist.rst Docs/source/conf.py Docs/source/file/AGNParticleContainer_8H.rst Docs/source/file/AGNParticleContainer_8cpp.rst Docs/source/file/AGN__sources_8cpp.rst Docs/source/file/DarkMatterParticleContainer_8H.rst Docs/source/file/DarkMatterParticleContainer_8cpp.rst Docs/source/file/Derive__F_8H.rst Docs/source/file/Forcing_8H.rst Docs/source/file/Forcing_8cpp.rst Docs/source/file/Forcing__init_8cpp.rst Docs/source/file/Gravity_8H.rst Docs/source/file/Gravity_8cpp.rst Docs/source/file/Gravity__F_8H.rst Docs/source/file/MemInfo_8H.rst Docs/source/file/MemInfo_8cpp.rst Docs/source/file/MersenneTwister_8cpp.rst Docs/source/file/NeutrinoParticleContainer_8H.rst Docs/source/file/NeutrinoParticleContainer_8cpp.rst Docs/source/file/NyxBld_8cpp.rst Docs/source/file/NyxParticleContainer_8H.rst Docs/source/file/NyxParticles_8cpp.rst Docs/source/file/Nyx_8H.rst Docs/source/file/Nyx_8cpp.rst Docs/source/file/Nyx__F_8H.rst Docs/source/file/Nyx__advance_8cpp.rst Docs/source/file/Nyx__error_8cpp.rst Docs/source/file/Nyx__error__F_8H.rst Docs/source/file/Nyx__halos_8cpp.rst Docs/source/file/Nyx__initcosmo_8cpp.rst Docs/source/file/Nyx__initdata_8cpp.rst Docs/source/file/Nyx__output_8H.rst Docs/source/file/Nyx__output_8cpp.rst Docs/source/file/Nyx__setup_8cpp.rst Docs/source/file/Nyx__sources_8cpp.rst Docs/source/file/ParticleDerive_8cpp.rst Docs/source/file/advance__particles_8cpp.rst Docs/source/file/agn__F_8H.rst Docs/source/file/comoving_8cpp.rst Docs/source/file/compute__hydro__sources_8cpp.rst Docs/source/file/dm__F_8H.rst Docs/source/file/main_8cpp.rst Docs/source/file/nyx__main_8cpp.rst Docs/source/file/read__plotfile_8cpp.rst Docs/source/file/sdc__hydro_8cpp.rst Docs/source/file/sdc__reactions_8cpp.rst Docs/source/file/strang__hydro_8cpp.rst Docs/source/file/strang__reactions_8cpp.rst Docs/source/file/sum__integrated__quantities_8cpp.rst Docs/source/file/sum__utils_8cpp.rst Docs/source/file/testMemInfo_8cpp.rst Docs/source/file/update__state__with__sources_8cpp.rst Docs/source/file/write__info_8cpp.rst Docs/source/filelist.rst Docs/source/index.rst Docs/source/namespace/namespace_0D20.rst Docs/source/namespace/namespace_0D35.rst Docs/source/namespace/namespace_0D39.rst Docs/source/namespace/namespace_0D7.rst Docs/source/namespace/namespaceamrex.rst Docs/source/namespacelist.rst Docs/source/runtime_parameters.rst commit 405cecf7e7a2c1fe501fd3cb14b1e9aa3460a2e8 Author: Jean Sexton Date: Thu Nov 29 14:07:35 2018 -0500 Further fixes for F_interfaces Source/HeatCool/cvode_extras.f90 Source/HeatCool/integrate_state_box_3d.cpp Source/Nyx_advance.cpp Source/nyx_main.cpp commit b1cee32b827056c9dea65bf234e62987ae80f288 Author: Jean Sexton Date: Thu Nov 29 13:12:37 2018 -0500 Switched from F_BaseLib to F_Interfaces Exec/Make.Nyx Source/EOS/atomic_rates.f90 Source/EOS/eos_hc.f90 Source/HeatCool/integrate_state_farkode_3d.f90 Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_fcvode_vec_3d.f90 Source/HeatCool/integrate_state_fcvode_with_source_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 Source/HeatCool/integrate_state_with_source_3d.f90 Source/Make.package commit 363fcac29e9f0df1f5a77328485587db545e5e4f Author: Zarija Lukic Date: Mon Nov 26 18:28:16 2018 -0800 runlog: report time from the bigbang in years instead of the code timer Source/Nyx.H Source/Nyx_F.H Source/comoving.cpp Source/comoving_nd.f90 Source/write_info.cpp commit ff8ca0aec194895c5168f1f3801ad39d4305b45e Author: Ann Almgren Date: Thu Nov 15 18:01:46 2018 -0800 Add the writing of job_info to checkpoints -- it was already in plotfiles. Source/Nyx.H Source/Nyx_output.cpp commit 284f1271fa04494a784e43a9cc9f0e4c3ec7a216 Author: Ann Almgren Date: Thu Nov 8 18:16:29 2018 -0800 Bring NeutrinoParticleContainer up to date -- this now compiles and links and has the new AssignDensity routines modeled after the current versions in amrex. Source/DarkMatterParticleContainer.H Source/Make.package Source/NeutrinoParticleContainer.H Source/NeutrinoParticleContainer.cpp Source/NeutrinoParticles_F.H Source/Neutrino_Particle_mod_3d.F90 commit a9150660650014e767a12ef6247920e2ef998b5b Author: Andrew Myers Date: Thu Nov 8 13:45:12 2018 -0800 move the iterator typedefs into NyxParticleContainer, which knows the right template parameters. Source/NyxParticleContainer.H commit 975654aa892577655d532be08c7375c53c596137 Author: Jean M. Sexton Date: Wed Nov 7 09:48:11 2018 -0800 Removed erroneous header file Source/strang_reactions.cpp commit f20ee58775551ff11ce9689e3f8717019316e701 Author: Jean Sexton Date: Wed Nov 7 10:02:02 2018 -0500 Added serial box CVODE version with constraint checking in preparation for adding cuda N_Vector version Source/HeatCool/Make.package Source/HeatCool/cvode_extras.f90 Source/HeatCool/f_rhs.f90 Source/HeatCool/integrate_state_box_3d.cpp Source/HeatCool/integrate_state_box_3d_stubs.cpp Source/HeatCool/integrate_state_farkode_3d_stubs.f90 Source/HeatCool/integrate_state_fcvode_3d_stubs.f90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/comoving.cpp Source/strang_reactions.cpp commit 67d224e1e249c32eda3f00562d739c6c78d40247 Author: Jean Sexton Date: Fri Nov 2 14:36:08 2018 -0400 Tested growntilebox and removed extra arguments Util/SUNDIALS_serial_test/init_managed.f90 Util/SUNDIALS_serial_test/inputs Util/SUNDIALS_serial_test/main.cpp Util/SUNDIALS_serial_test/myfunc_F.H commit 0fcb0ee455dc51a1f2661efbc74c621dec8b5d53 Author: Jean Sexton Date: Thu Nov 1 21:21:02 2018 -0400 Ugly version of copy from diag_eos and integrate_state_box added. Update error messages for heating-cooling .gitignore Source/Nyx.cpp Util/SUNDIALS_cuda_cpu_compute/main.cpp Util/SUNDIALS_serial_test/init_managed.f90 Util/SUNDIALS_serial_test/main.cpp Util/SUNDIALS_serial_test/myfunc_F.H commit 8b0ac0574c905c52e6097b67b197ab964354a64e Author: Jean Sexton Date: Thu Nov 1 15:19:18 2018 -0400 Updated makefile and example submit scripts for non-debug case, changed default back to non-MPI Util/SUNDIALS3/GNUmakefile Util/SUNDIALS3/summitdev.sh Util/SUNDIALS_cuda_cpu_compute/GNUmakefile Util/SUNDIALS_cuda_cpu_compute/inputs_atomic Util/SUNDIALS_cuda_cpu_compute/summitdev.sh Util/SUNDIALS_serial_test/GNUmakefile Util/SUNDIALS_serial_test/inputs_atomic Util/SUNDIALS_serial_test/main.cpp Util/SUNDIALS_serial_test/summitdev.sh commit 96491a20c77c919a8fe4b82798da346f81d9a077 Author: Jean Sexton Date: Wed Oct 31 19:47:54 2018 -0400 Update gpu examples for amrex changes, debug fails due to thrust on summitdev Util/SUNDIALS3/GNUmakefile Util/SUNDIALS3/main.cpp Util/SUNDIALS_cuda_cpu_compute/GNUmakefile Util/SUNDIALS_cuda_cpu_compute/Make.package Util/SUNDIALS_cuda_cpu_compute/SetIC.f90 Util/SUNDIALS_cuda_cpu_compute/TREECOOL_middle Util/SUNDIALS_cuda_cpu_compute/atomic_rates.f90 Util/SUNDIALS_cuda_cpu_compute/comoving_nd.f90 Util/SUNDIALS_cuda_cpu_compute/comoving_params.f90 Util/SUNDIALS_cuda_cpu_compute/constants_cosmo.f90 Util/SUNDIALS_cuda_cpu_compute/constants_mod.f90 Util/SUNDIALS_cuda_cpu_compute/eos_hc.f90 Util/SUNDIALS_cuda_cpu_compute/eos_params.f90 Util/SUNDIALS_cuda_cpu_compute/f_rhs.f90 Util/SUNDIALS_cuda_cpu_compute/fcvode_extras.f90 Util/SUNDIALS_cuda_cpu_compute/init_managed.f90 Util/SUNDIALS_cuda_cpu_compute/inputs Util/SUNDIALS_cuda_cpu_compute/main.cpp Util/SUNDIALS_cuda_cpu_compute/meth_params.f90 Util/SUNDIALS_cuda_cpu_compute/misc_params.f90 Util/SUNDIALS_cuda_cpu_compute/myfunc_F.H Util/SUNDIALS_cuda_cpu_compute/reion_aux_module.f90 Util/SUNDIALS_cuda_cpu_compute/summitdev.sh Util/SUNDIALS_cuda_cpu_compute/vode_aux.f90 Util/SUNDIALS_serial_test/GNUmakefile Util/SUNDIALS_serial_test/main.cpp commit 340403a5773b92e46cd85e164f6f81130dbe6479 Merge: 25670158 b29eccaf Author: Zarija Lukic Date: Fri Oct 26 13:59:53 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 25670158d4507d0cc32cc9708e898bc18d5bffd3 Author: Zarija Lukic Date: Fri Oct 26 13:59:24 2018 -0700 HDF5 converter for Nbody runs Util/convert_nbody/AmrDerive.cpp Util/convert_nbody/GNUmakefile Util/convert_nbody/Make.package commit b29eccafd4c49a0816078abd3b055182bf8d6731 Author: Jean Sexton Date: Wed Oct 24 19:44:37 2018 -0400 Cleaned up previous compiler warnings, added final output printing Util/SUNDIALS3/main.cpp Util/SUNDIALS3/summitdev.sh Util/SUNDIALS_serial_test/main.cpp Util/SUNDIALS_serial_test/summitdev.sh commit 2b8e66ab0479cb1b26a22204535f7fd17577fef6 Author: Jean Sexton Date: Wed Oct 24 18:51:13 2018 -0400 Testing with patched version gives comparable answers and number of steps Util/SUNDIALS3/main.cpp Util/SUNDIALS_serial_test/main.cpp commit 1ce70ecd56884423f64435beca1d2aaa737cc1e4 Author: Jean Sexton Date: Tue Oct 23 19:19:43 2018 -0400 Updated make to match current amrex make system, added testing Util/SUNDIALS3/GNUmakefile Util/SUNDIALS3/main.cpp Util/SUNDIALS_serial_test/GNUmakefile Util/SUNDIALS_serial_test/main.cpp commit 7c3d9d527a5c56ecb77d2180fb0f7bba012dff23 Author: Jean M. Sexton Date: Wed Oct 17 17:57:21 2018 -0700 Removed extra warning print statements from eos call Source/EOS/eos_hc.f90 commit 60e45037acd21cea52df51ca82fe4010d1605526 Merge: b0f23d5e 9c1ff442 Author: Zarija Lukic Date: Tue Oct 16 23:00:06 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 9c1ff442dd879d06a643d8a9347376292bb77735 Author: Jean M. Sexton Date: Mon Oct 15 10:41:42 2018 -0700 Fixed missing dummy function error Source/HeatCool/integrate_state_fcvode_3d_stubs.f90 commit 159ec528a4f8c0cc5cdc5d989d17d3929c284787 Author: Jean Sexton Date: Fri Oct 12 21:15:04 2018 -0400 Incremental fix Source/HeatCool/integrate_state_3d.f90 commit 5c81c003541c8b9694d3f0366faf729ccf8dc553 Author: Jean Sexton Date: Fri Oct 12 18:40:31 2018 -0400 Changed CVDense to CVDiag in fcvode integration, adding additional functionality to heating-cooling Source/HeatCool/Make.package Source/HeatCool/farkode_extras.f90 Source/HeatCool/integrate_state_3d.f90 Source/HeatCool/integrate_state_farkode_3d.f90 Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_fcvode_with_source_3d.f90 Source/Nyx.cpp Util/SUNDIALS3/GNUmakefile commit cb0a9997b6daf2054867cca67cbf0dfc094a093a Author: Jean Sexton Date: Fri Oct 12 13:43:02 2018 -0400 Test with comparison against serial box-by-box version Util/SUNDIALS3/main.cpp Util/SUNDIALS_serial_test/GNUmakefile Util/SUNDIALS_serial_test/Make.package Util/SUNDIALS_serial_test/SetIC.f90 Util/SUNDIALS_serial_test/TREECOOL_middle Util/SUNDIALS_serial_test/atomic_rates.f90 Util/SUNDIALS_serial_test/comoving_nd.f90 Util/SUNDIALS_serial_test/comoving_params.f90 Util/SUNDIALS_serial_test/constants_cosmo.f90 Util/SUNDIALS_serial_test/constants_mod.f90 Util/SUNDIALS_serial_test/eos_hc.f90 Util/SUNDIALS_serial_test/eos_params.f90 Util/SUNDIALS_serial_test/f_rhs.f90 Util/SUNDIALS_serial_test/fcvode_extras.f90 Util/SUNDIALS_serial_test/init_managed.f90 Util/SUNDIALS_serial_test/inputs Util/SUNDIALS_serial_test/main.cpp Util/SUNDIALS_serial_test/meth_params.f90 Util/SUNDIALS_serial_test/misc_params.f90 Util/SUNDIALS_serial_test/myfunc_F.H Util/SUNDIALS_serial_test/reion_aux_module.f90 Util/SUNDIALS_serial_test/vode_aux.f90 commit df4f1c71ba896233e60d2719adc1746bcb015d45 Author: Jean Sexton Date: Thu Oct 11 17:42:01 2018 -0400 Fixed f kernel from previous commit history, added compile flags for sundials versions Util/SUNDIALS3/GNUmakefile Util/SUNDIALS3/f_rhs.F90 Util/SUNDIALS3/main.cpp Util/SUNDIALS3/ode_mod.f90 commit 8781b80bfc4d7d66417d77c4b95a7bb31835e94b Author: Jean Sexton Date: Wed Oct 10 14:11:15 2018 -0400 Test small versions Util/SUNDIALS3/main.cpp commit d0c1298fdeefae6a88246d09e5553ccb64ed510a Author: Jean Sexton Date: Wed Oct 10 11:53:58 2018 -0400 Works for 32^3 box with synchronize statements Util/SUNDIALS3/GNUmakefile Util/SUNDIALS3/main.cpp commit 051ac60108344182c4d9aa08df90fc59d3171867 Author: Jean Sexton Date: Mon Oct 8 20:06:57 2018 -0400 Works for threading where max_grid<=8, otherwise works for <<<1,1>>> and max_grid=anything Util/SUNDIALS3/eos_hc.F90 Util/SUNDIALS3/f_rhs.F90 Util/SUNDIALS3/init_managed.F90 Util/SUNDIALS3/main.cpp Util/SUNDIALS3/ode_mod.f90 commit 669989fdb0eaf8384101f66d9f4ffd17d4151f61 Author: Jean Sexton Date: Mon Oct 8 16:46:50 2018 -0400 Fixed z and a mixup, validating with one example Util/SUNDIALS3/GNUmakefile Util/SUNDIALS3/eos_hc.F90 Util/SUNDIALS3/f_rhs.F90 Util/SUNDIALS3/main.cpp Util/SUNDIALS3/ode_mod.f90 commit c517b54895ad284790bf2ec60069f1c772b5d9b8 Author: Jean Sexton Date: Sun Oct 7 21:29:54 2018 -0400 Final solution has errors Util/SUNDIALS3/f_rhs.F90 Util/SUNDIALS3/init_managed.F90 Util/SUNDIALS3/main.cpp Util/SUNDIALS3/ode_mod.f90 commit 0afe5d9aaa4c78809c7f19dafb1578357cbe70ae Author: Jean Sexton Date: Sun Oct 7 20:04:55 2018 -0400 Passing userdata seems workable, testing using explicit copies Util/SUNDIALS3/init_managed.F90 Util/SUNDIALS3/main.cpp Util/SUNDIALS3/ode_mod.f90 commit 673e3be8609ed217ceaa0e36299f057b291c7e92 Author: Jean Sexton Date: Sat Oct 6 13:13:09 2018 -0400 Adding example of C++ CVode driver with f_rhs kernel Util/SUNDIALS3/GNUmakefile Util/SUNDIALS3/Make.package Util/SUNDIALS3/SetIC.f90 Util/SUNDIALS3/TREECOOL_middle Util/SUNDIALS3/atomic_rates.F90 Util/SUNDIALS3/comoving_nd.f90 Util/SUNDIALS3/comoving_params.f90 Util/SUNDIALS3/constants_cosmo.f90 Util/SUNDIALS3/constants_mod.f90 Util/SUNDIALS3/eos_hc.F90 Util/SUNDIALS3/eos_params.f90 Util/SUNDIALS3/f_rhs.F90 Util/SUNDIALS3/init_managed.F90 Util/SUNDIALS3/inputs Util/SUNDIALS3/inputs_atomic Util/SUNDIALS3/inputs_non_vectorized Util/SUNDIALS3/main.cpp Util/SUNDIALS3/meth_params.F90 Util/SUNDIALS3/misc_params.f90 Util/SUNDIALS3/myfunc_F.H Util/SUNDIALS3/ode_mod.f90 Util/SUNDIALS3/reion_aux_module.f90 Util/SUNDIALS3/vode_aux.F90 commit e1d9bb7af245734c6272b246a3700700c9de72ac Merge: 0b5ceaf4 a584fb53 Author: Jean Sexton Date: Sat Oct 6 12:23:55 2018 -0400 Merge branch 'development' of ssh://github.com/amrex-astro/Nyx into development commit 8c4cb405b8f7f60b16824c5bab00f268ca4c8f50 Merge: c587fa43 a584fb53 Author: Andrew Myers Date: Thu Oct 4 11:38:21 2018 -0700 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development commit d31397361115bc9268da4e6addd3d3e77cc4798e Merge: 110a5c38 b0f23d5e Author: Zarija Lukic Date: Mon Oct 1 23:34:51 2018 -0700 Merge branch 'development' commit b0f23d5e7785ea36784e80f56bc197cae3ac74d7 Merge: a584fb53 110a5c38 Author: Zarija Lukic Date: Mon Oct 1 23:33:51 2018 -0700 Merge branch 'master' into development commit a584fb532a755ec7195751d84ef89ed6ba7a4757 Author: Zarija Lukic Date: Mon Oct 1 23:32:45 2018 -0700 Fix compiling problem in AGN Source/AGNParticleContainer.cpp Source/Nyx_halos.cpp commit 8745e9b2229f969c3d5a2e8d26721f1f093ad99f Merge: 25e7fa76 afb52ed3 Author: Zarija Lukic Date: Mon Oct 1 17:38:28 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 0b5ceaf49365b927268229f9053a6cd0967208f9 Author: Jean Sexton Date: Sat Sep 29 21:18:41 2018 -0400 Added looping structures to test multiple inputs at a time, cvode interface version compiles with gfortran and xlf Util/VODE3_gpu/Makefile Util/VODE3_gpu/fmain.f90 Util/VODE3_gpu/fmain_gpu_atomic.cuf Util/VODE3_gpu/fmain_vode.f90 Util/VODE3_gpu/integrate_state_vode_3d.f90 commit bb9a21a84d3157ff33a38c85df2d5ebb2ef15d29 Author: Jean Sexton Date: Sat Sep 29 21:15:28 2018 -0400 Preliminary cleaning up efforts Util/VODE3_gpu/eos_hc.cuf Util/VODE3_gpu/eos_hc.f90 Util/VODE3_gpu/f_rhs.cuf Util/VODE3_gpu/f_rhs.f90 Util/VODE3_gpu/fmain_gpu_atomic.cuf Util/VODE3_gpu/fmain_vode.f90 Util/VODE3_gpu/inputs_hc commit afb52ed35ab30fbc9bd1a1743bbce37f7d5a9a66 Author: Jean Sexton Date: Sat Sep 29 11:12:11 2018 -0400 Fixed f_rhs_host to call cleaner device functions Util/VODE3_gpu/Makefile Util/VODE3_gpu/eos_hc.cuf Util/VODE3_gpu/f_rhs.cuf Util/VODE3_gpu/inputs_hc_short Util/VODE3_gpu/integrate_state_vode_3d.cuf Util/VODE3_gpu/integrate_state_vode_3d.f90 commit ce2283d1b321d3212a8effecaf7d3a5219ea6c1f Author: Jean Sexton Date: Fri Sep 28 20:54:16 2018 -0400 Ugly version of f kernel wrapping runs on gpu to correct/comparable solution to CPU-only, iteration count incorrect Util/VODE3_gpu/atomic_rates.cuf Util/VODE3_gpu/f_rhs.cuf Util/VODE3_gpu/fmain_gpu_atomic.cuf Util/VODE3_gpu/integrate_state_vode_3d.f90 Util/VODE3_gpu/vode_aux.cuf commit d5a0a83fde3a6740253cc4eab908d02a6848a2a2 Author: Jean Sexton Date: Fri Sep 28 12:10:18 2018 -0400 Hardcoded ion calls into nyx_eos_T_given_Re, final e_out and T_out answer correct Util/VODE3_gpu/Makefile Util/VODE3_gpu/eos_hc.cuf Util/VODE3_gpu/eos_hc.f90 Util/VODE3_gpu/fmain_gpu_atomic.cuf Util/VODE3_gpu/fmain_vode.f90 commit e87caea37e5d8cf98ac28b9b19f36d5570d11993 Author: Jean Sexton Date: Fri Sep 28 11:12:11 2018 -0400 e_out matches with a relative difference around 1e-16, T_out still doesn't match Util/VODE3_gpu/eos_hc.cuf Util/VODE3_gpu/eos_hc.f90 Util/VODE3_gpu/f_rhs.cuf Util/VODE3_gpu/fmain_gpu_atomic.cuf Util/VODE3_gpu/fmain_vode.f90 commit a0e68812682551af4b776b4ff9fd675917df9687 Author: Jean Sexton Date: Thu Sep 27 19:57:15 2018 -0400 Same answer at end of integration for first 3 digits Util/VODE3_gpu/Makefile Util/VODE3_gpu/atomic_rates.cuf Util/VODE3_gpu/eos_hc.cuf Util/VODE3_gpu/eos_hc.f90 Util/VODE3_gpu/f_rhs.cuf Util/VODE3_gpu/f_rhs.f90 Util/VODE3_gpu/fmain_gpu_atomic.cuf commit 426ef6657cc7784b4d7723426e81f5027b198192 Author: Jean Sexton Date: Thu Sep 27 17:18:24 2018 -0400 Incremental testing of cuda fortran kernel Util/VODE3_gpu/Makefile Util/VODE3_gpu/atomic_rates.cuf Util/VODE3_gpu/eos_hc.cuf Util/VODE3_gpu/fmain_gpu.cuf Util/VODE3_gpu/fmain_gpu_atomic.cuf commit 25e7fa769a26a490d434d408cf1f6b09ab53b2fb Merge: 1c7e91ef fde2bebd Author: Zarija Lukic Date: Thu Sep 27 09:09:38 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 9410e5f62eca9cf659a5a79e50b399d401cfe6e7 Author: Jean Sexton Date: Wed Sep 26 17:49:45 2018 -0400 Compiles with ion_n on device, output not identical Util/VODE3_gpu/Makefile Util/VODE3_gpu/atomic_rates.cuf Util/VODE3_gpu/eos_hc.cuf Util/VODE3_gpu/f_rhs.f90 Util/VODE3_gpu/fmain_gpu_atomic.cuf Util/VODE3_gpu/meth_params.cuf commit 1aca9be649a40970bb66d771613a62f29b751d13 Author: Jean Sexton Date: Wed Sep 26 15:22:27 2018 -0400 Runs full fmain test with some tables managed Util/VODE3_gpu/Makefile Util/VODE3_gpu/fmain_gpu_atomic.cuf commit 13c6216a75572a4a274eeb0fd1a4ff92e2068e28 Author: Jean Sexton Date: Wed Sep 26 11:50:54 2018 -0400 Doing fort_tablulate_rates on host and can modify on device and see change back on host Util/VODE3_gpu/Makefile Util/VODE3_gpu/atomic_rates.cuf Util/VODE3_gpu/fmain_gpu_atomic.cuf commit fde2bebd6758ac2a845714efade0e5954455dbdf Author: Jean Sexton Date: Tue Sep 25 18:43:06 2018 -0400 First step for translating heating cooling integration structure, working on getting atomic rates table on GPU Util/VODE3_gpu/Makefile Util/VODE3_gpu/fmain_gpu.cuf Util/VODE3_gpu/fmain_vode.f90 commit 796f16cf90227e04cd5763cf0930b96174526269 Author: Jean Sexton Date: Tue Sep 25 11:47:38 2018 -0400 Added Util/VODE3_gpu test directory with Makefile for summitdev, no gpu code yet Util/VODE3_gpu/Makefile Util/VODE3_gpu/TREECOOL_middle Util/VODE3_gpu/arkode_interface.f90 Util/VODE3_gpu/atomic_rates.f90 Util/VODE3_gpu/comoving_nd.f90 Util/VODE3_gpu/comoving_params.f90 Util/VODE3_gpu/constants_cosmo.f90 Util/VODE3_gpu/constants_mod.f90 Util/VODE3_gpu/cvode_interface.f90 Util/VODE3_gpu/eos_hc.f90 Util/VODE3_gpu/eos_params.f90 Util/VODE3_gpu/example_hc.out Util/VODE3_gpu/f_rhs.f90 Util/VODE3_gpu/farkode.f90 Util/VODE3_gpu/fcvode.f90 Util/VODE3_gpu/fcvode_extras.f90 Util/VODE3_gpu/fmain.f90 Util/VODE3_gpu/fmain_vode.f90 Util/VODE3_gpu/fnvector_serial.f90 Util/VODE3_gpu/fnvector_serial_fprefix.f90 Util/VODE3_gpu/fsunlinsol_dense.f90 Util/VODE3_gpu/fsunmat_dense.f90 Util/VODE3_gpu/inputs_atomic Util/VODE3_gpu/inputs_hc Util/VODE3_gpu/integrate_state_vode_3d.f90 Util/VODE3_gpu/meth_params.f90 Util/VODE3_gpu/misc_params.f90 Util/VODE3_gpu/reion_aux_module.f90 Util/VODE3_gpu/vode_aux.f90 commit 8acb44d2a51c5d7467958c15a90b235c0468f1b4 Author: Jean M. Sexton Date: Mon Sep 24 15:51:14 2018 -0700 Added USE_SUNDIALS3 to HeatCool Make.package and tested for LyA Exec/LyA/GNUmakefile Source/HeatCool/Make.package Source/Nyx.cpp commit bb1c7c292ae4bb7e1439ce5b35fd89de681d0316 Author: Ann Almgren Date: Fri Sep 21 08:40:43 2018 -0700 Update the Scaling/inputs file. Exec/Scaling/inputs commit c587fa43c9a619d2705285a534a8b50f5bc70049 Merge: fe35ad01 528f6134 Author: Andrew Myers Date: Tue Sep 18 10:16:02 2018 -0700 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development commit 528f6134d35544d47ee6e4df61864373afc87116 Merge: 6b7d1c51 4380458b Author: Ann Almgren Date: Wed Sep 12 15:46:57 2018 -0700 Merge branch 'development' of https://github.com/amrex-astro/nyx into development commit 6b7d1c51385cc365faf811b51ddd5cf0b8be9016 Author: Ann Almgren Date: Wed Sep 12 15:46:42 2018 -0700 removed accidentally-committed print statement Source/Nyx_nd.f90 commit 4380458ba23817403346a617fdc4574ba434803d Author: Andrew Myers Date: Wed Sep 12 15:42:15 2018 -0700 after regrid, account for particles that might be off of the level in the multilevel solve Source/Nyx.cpp commit 5bb0ae072ac43d7674c1e2c5fb3dddd850f7c8b6 Author: Andrew Myers Date: Wed Sep 12 13:21:29 2018 -0700 fix for regrid_int < ref_ratio Source/NyxParticles.cpp commit 01b05a9187bc2e0c4ae02b940826f813b666594f Author: Andrew Myers Date: Wed Sep 12 12:26:30 2018 -0700 pass ngrow into AssignDensity Source/NyxParticleContainer.H commit fe35ad01575e7cfbdd1c774f8dbb47148d76cdf4 Merge: 48f1c02b 62bc2c8a Author: Andrew Myers Date: Tue Sep 11 11:04:09 2018 -0700 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development commit 62bc2c8a7e6deebc36d627c8857e3da969a99bce Author: Jean M. Sexton Date: Thu Sep 6 16:45:07 2018 -0700 Added ghost cells to srcQ using NUM_GROW to allow version_2=2 to work Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/make_hydro_sources_3d.f90 Source/sdc_hydro.cpp Source/strang_hydro.cpp commit 110a5c38ea01fbee7be8a1d3fce6d8ee6581dc1c Merge: 48f1c02b 1c7e91ef Author: Zarija Lukic Date: Tue Sep 4 15:53:33 2018 -0700 Merge branch 'development' commit 1c7e91ef23406cc61996fa042f0b9cbcaf216d56 Merge: 20d1afcf 48f1c02b Author: Zarija Lukic Date: Tue Sep 4 15:52:47 2018 -0700 Merge branch 'master' into development commit 20d1afcf812efeb2bcc3b4f0d3b7a3605f3de30d Author: Zarija Lukic Date: Tue Sep 4 14:18:59 2018 -0700 Reeber cannot use OMP Exec/LyA_AGN/GNUmakefile commit 1e2aff2511a297fd998c73d2dbe09eed62454131 Author: Zarija Lukic Date: Tue Sep 4 14:10:40 2018 -0700 updating README README.md commit 9a676bf60586eb0de2f8be2a4b1d97a2c6b075a6 Author: Zarija Lukic Date: Tue Sep 4 12:11:51 2018 -0700 Fixed typecheck errors in MacLaurin Exec/GravityTests/MacLaurin/Tagging_3d.f90 commit 535d8b05e5cb9b671589a52f442dbcba2e284d0a Author: Ann Almgren Date: Wed Aug 22 06:26:56 2018 -0700 We don't have D_new if no hydro ... Source/Initialization/Nyx_initdata.cpp commit a7d82529df9e2e197b3cedb1ef1336bb85ce2baf Author: Ann Almgren Date: Wed Aug 22 06:06:57 2018 -0700 1) Remove HPGMG option from all GNUmakefiles 2) Update RegressionTest/Prob_3d.f90 so it works when do_hydro = 0 Exec/AMR-density/GNUmakefile Exec/AMR-zoom/GNUmakefile Exec/HDF5_example/GNUmakefile Exec/LyA/GNUmakefile Exec/LyA_AGN/GNUmakefile Exec/MiniSB/GNUmakefile Exec/RegressionTest/GNUmakefile Exec/RegressionTest/Prob_3d.f90 Exec/SanityCheck/GNUmakefile Exec/SantaBarbara/GNUmakefile Exec/Scaling/GNUmakefile commit fb80b7f353f349611fd3e89a559b2be637558093 Author: Ann Almgren Date: Wed Aug 22 06:01:36 2018 -0700 Get this working again when NO_HYDRO is not defined but nyx.do_hydro = 0. Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx_nd.f90 commit 1781bc2df027adeb9e5e46ab5baa0de2f4308ccf Author: Ann Almgren Date: Tue Aug 21 17:21:41 2018 -0700 Another oops -- I missed one when I fixed the pragma omp lines. Source/sum_utils.cpp commit d57f27a9297870e21e2edc5383d200b13b7d2e3e Author: Jean M. Sexton Date: Tue Aug 21 15:04:13 2018 -0700 Tweaked new_a and new_dummy_a use for new da and dt definitions to better match previously existing swaps Source/comoving.cpp Source/comoving_nd.f90 commit 5502bdc7f6723567324e87635be6539d6caedc1a Merge: ad573125 aa2489f8 Author: Jean M. Sexton Date: Tue Aug 21 12:45:45 2018 -0700 Merge branch 'development' of github.com:amrex-astro/Nyx into development commit ad5731258a27aaf345fcd073a2b3bc4034657842 Author: Jean M. Sexton Date: Tue Aug 21 12:45:08 2018 -0700 Remove extra print statements Source/comoving.cpp Source/comoving_nd.f90 commit 1719c7e0fc9a810456438223c1ccfb76bbff29e3 Author: Jean M. Sexton Date: Tue Aug 21 12:39:12 2018 -0700 Added dt modification to mimic HACC da/dt subcycling Source/Nyx.H Source/Nyx_F.H Source/comoving.cpp Source/comoving_nd.f90 commit aa2489f8e5ae8e45639c7304ccb74b9899d8fd24 Author: Ann Almgren Date: Fri Aug 17 07:50:33 2018 -0700 Remove particles.write_in_plotfile from inputs file -- it no longer does anything Exec/AMR-density/inputs Exec/AMR-density/inputs.rt Exec/AMR-zoom/inputs Exec/HDF5_example/inputs Exec/LyA/inputs Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA_AGN/inputs Exec/RegressionTest/inputs.mass.nosub Exec/RegressionTest/inputs.mass.sub Exec/Scaling/inputs commit d4f9551841ee4d6a819222030488d35caf7f0596 Author: Ann Almgren Date: Fri Aug 17 07:11:39 2018 -0700 Fix oops. This works: pragma omp parallel if (!system::regtest_reduction) reduction(+:sum) This doesn't: pragma omp if (!system::regtest_reduction) parallel reduction(+:sum) Source/sum_utils.cpp commit 4c82e12b23c6d66f78572cfe8d399333b502246e Author: Jean M. Sexton Date: Thu Aug 16 11:12:47 2018 -0700 Added fixed da input flag, default still relative. Positive absolute max change in a flag uses fixed da instead of enforcing a relative percent change Source/Nyx.H Source/Nyx_F.H Source/comoving.cpp Source/comoving_nd.f90 commit 48f1c02bc5ed3a32182099f7be5921a62942ee39 Merge: ea33412f 414d821e Author: Ann Almgren Date: Thu Aug 16 08:23:24 2018 -0700 Merge branch 'development' commit 414d821e0f292016a84ea35a63c1780fc8f74bff Author: Ann Almgren Date: Wed Aug 15 17:04:07 2018 -0700 Update inputs files to use nyx.add_ext_src = 0 since we don't need it when we don't have additional sources besides heating/cooling and gravity Exec/AMR-density/inputs Exec/AMR-density/inputs.rt Exec/AMR-zoom/inputs Exec/LyA/inputs Exec/LyA/inputs.rt Exec/LyA/inputs.small.dsc Exec/LyA/inputs_gimlet_in_transit.dsc Exec/Scaling/inputs commit 7410da42f389937720c0d2884d468a5489484988 Author: Ann Almgren Date: Wed Aug 15 16:47:37 2018 -0700 Update so that we don't use get_old_source and get_new_source when we don't need to -- ie for runs without additional source terms (other than heating/cooling and gravity) nyx.add_ext_src should be set to 0. Previously this generated an error message; this shouldn't have been happening. We changed the interpretation of add_ext_src when we converted from just_the_hydro to strang_hydro and sdc_hydro. Source/Nyx.cpp Source/SourceTerms/Nyx_sources.cpp commit 457c11088b80450d9ec4d0d60a0dbc74ae156397 Author: Ann Almgren Date: Tue Aug 14 16:13:40 2018 -0700 Oops -- forgot that src has 4 components -- these commits actually compile Exec/HydroTests/TurbForce/ext_src_3d.f90 Source/SourceTerms/ext_src_3d.f90 Source/SourceTerms/ext_src_add_3d.f90 commit ed82a1cad1a5fad78b1338bd0282e68666176e99 Author: Ann Almgren Date: Tue Aug 14 15:56:52 2018 -0700 When we set "src" to 0 in ext_src*3d.f90, make sure to only set it to zero on the tile we're working on, not the whole array. Exec/HydroTests/TurbForce/ext_src_3d.f90 Source/SourceTerms/ext_src_3d.f90 Source/SourceTerms/ext_src_add_3d.f90 commit b812b4c54f5d1c5a941974ba96b4b345e02056ad Author: Wolfram Schmidt Date: Mon Aug 13 18:28:09 2018 +0200 Development (#38) * Added some more stuff to .gitignore. * Fixed calls of fort_interp_to_this_z in external sources if nyx.heat_cool_type = 0. Added 32.nyx to LyA for regression testing. * Cleaning up in DrivenTurbulence and TurbForce. .gitignore Exec/DrivenTurbulence/GNUmakefile Exec/DrivenTurbulence/Make.package Exec/DrivenTurbulence/heat_cool_stubs.f90 Exec/HydroTests/TurbForce/Make.package Exec/HydroTests/TurbForce/Nyx_setup.cpp Exec/LyA/32.nyx Source/HeatCool/heat_cool_stubs.f90 commit be1ce08d92ff001204cb96beeafa82d8cc5e5b85 Author: Ann Almgren Date: Wed Aug 8 16:09:08 2018 -0700 Add system.regtest=1 to inputs.2line in Nyx/Exec/RegressionTest to address OpenMP variability identified in LyA-OMP test Exec/LyA/inputs.rt Exec/RegressionTest/inputs.2line commit 92913c93159f97e832bd25f67ab88dda262e5c61 Author: Ann Almgren Date: Tue Aug 7 13:53:24 2018 -0700 Add test on system::regtest_reduction to sum calls in sum_util.cpp and sums in Gravity.cpp Source/Gravity/Gravity.cpp Source/sum_utils.cpp commit 360691e3fc20c8d95295da95caa7d38eadfb762b Author: Ann Almgren Date: Tue Aug 7 13:51:33 2018 -0700 Add system.regtest_reduction = 1 in order for this to be able to pass the regression tests when using OpenMP Exec/LyA/inputs.rt commit 2b2e711d38c4bd670eba2bce1e51764d87da4cc2 Author: Ann Almgren Date: Mon Aug 6 11:35:33 2018 -0700 Fix bug in dimensioning divu_cc in the Fortran hydro -- specifically starting with the call to make_hydro_sources -- we were creating divu_cc as a MultiFab but internally it was still getting dimensioned with the tilesize -- this resulted in incorred results in the (rho e) update when run with tiling. Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/make_hydro_sources_3d.f90 commit c5a3c0c7aed53316cfc84e3945da2c665ee12a28 Author: Ann Almgren Date: Mon Jul 30 04:32:21 2018 -0700 Remove two-partice advance and multipole gravity. Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Gravity/set_dirichlet_bcs_3d.f90 Source/Make.package Source/two_particle_advance.cpp commit 219a7e324f978272b76266abb16e90ad78c76317 Author: Andrew Myers Date: Thu Jul 26 17:42:39 2018 -0700 update these function names to reflect change in amrex Source/NyxParticleContainer.H commit 4b64ea5e1c3597c821a2532bfed71c09eeddfe31 Author: Ann Almgren Date: Fri Jul 6 19:46:29 2018 -0700 Add comment in GNUMakefile that this problem is not thread-safe. Exec/DrivenTurbulence/GNUmakefile Exec/DrivenTurbulence/inputs.regtest commit 7a20aaaccf55c084bade8a8dee1df5e5c378287d Author: Ann Almgren Date: Fri Jul 6 17:25:38 2018 -0700 Re-enable the source terms in ext_src_3d.f90 -- the default is 0 but you can create a new ext_src_3d.f90 to define new source terms. We have eliminated the ability to treat heating/cooling source termss as predicted/corrected contributions. Source/HeatCool/Make.package Source/HeatCool/ext_src_hc_3d.f90 Source/HeatCool/heat_cool_stubs.f90 Source/HeatCool/integrate_state_fcvode_3d_stubs.f90 Source/HeatCool/integrate_state_fcvode_vec_3d_stubs.f90 Source/HeatCool/integrate_state_fcvode_with_source_3d_stubs.f90 Source/SourceTerms/ext_src_3d.f90 Source/sdc_hydro.cpp Source/strang_hydro.cpp commit 2137e14d76130b381fccae1b063a98a9c27af7bf Author: Ann Almgren Date: Fri Jul 6 14:49:09 2018 -0700 Make this work with USE_SDC = TRUE and USE_HEATCOOL = FALSE. Source/HeatCool/Make.package Source/HeatCool/heat_cool_stubs.f90 Source/HeatCool/integrate_state_fcvode_with_source_3d_stubs.f90 commit 0cbf564471facc415424c47a27d2e7188e935e1f Author: Ann Almgren Date: Wed Jun 27 17:25:18 2018 -0700 Remove the line setting strang_split to 1. Then this runs fine. Exec/HydroTests/TurbForce/inputs.regtest commit edf5dd6ef987e534905b75b830d6d97a7ec61fd8 Author: Ann Almgren Date: Wed Jun 27 17:23:07 2018 -0700 Remove IOIOIO cout statements for pre-creating directories. Source/Nyx.cpp commit eef469a60602143b0d09b327558b5fb60a355626 Author: Andrew Myers Date: Mon Jun 25 16:32:00 2018 -0700 update Nyx to reflect changes in AMReX Source/NyxParticleContainer.H commit fb3a30ed42c64c6b5f1ccabc33a44cb0ac71563f Author: Jean M. Sexton Date: Wed May 30 14:59:44 2018 -0700 Removed extra reset in write_info Source/write_info.cpp commit 14facdebffd819473450aa652d6d394003c46718 Author: Jean M. Sexton Date: Wed May 23 17:17:14 2018 -0700 Added missing sdc file Source/HeatCool/fcvode_extras_src.f90 Source/HeatCool/integrate_state_with_source_3d.f90 commit cb5c04792a599046722cde4b628b379f03fc6316 Author: Jean M. Sexton Date: Wed May 23 15:33:33 2018 -0700 Extra heating cooling files for sdc and associated makefile updates Exec/Make.Nyx Source/HeatCool/Make.package Source/HeatCool/f_rhs.f90 Source/HeatCool/integrate_state_fcvode_with_source_3d.f90 Source/HeatCool/integrate_state_fcvode_with_source_3d_stubs.f90 Source/HeatCool/integrate_state_with_source_3d.f90 Source/HeatCool/vode_aux.f90 Source/sdc_hydro.cpp commit e937e67142e2a85efb0c1a48724c3a48fbf5df72 Author: Zarija Lukic Date: Tue May 22 18:32:24 2018 -0700 Fix typos in atomic_rates Source/EOS/atomic_rates.f90 commit 6ff5e8bceb303a5aee2904cd43bdfdfc5bc2059f Author: Zarija Lukic Date: Tue May 22 17:56:05 2018 -0700 HDF5 converter Util/convert_lyaf/AmrDerive.cpp Util/convert_lyaf/GNUmakefile Util/convert_lyaf/Make.package commit 6ecbc158ffe62d4bd6daf3f32820fe5161e1d26f Merge: 350daadd ab058c9d Author: zarija Date: Thu May 10 12:01:51 2018 -0700 Merge pull request #37 from mrzv/henson Henson update commit ab058c9df5c711795dc8677771431fe25b6f6f46 Author: Dmitriy Morozov Date: Thu May 10 10:35:15 2018 -0700 Move chai scripts from Exec/LyA to Exec/Henson Exec/Henson/all.chai Exec/Henson/amr-info.chai Exec/Henson/nyx-only.chai Exec/Henson/particles.chai Exec/Henson/simple.chai commit 0b47351544164ba60107b7e9d78ff621089bc9dd Author: Dmitriy Morozov Date: Mon May 7 15:37:49 2018 -0700 Add neighbors to Exec/Henson/amr-info Exec/Henson/amr-info/main.cpp commit 518a11108f887abc1488f4b67d377c33c101bbb1 Author: Dmitriy Morozov Date: Tue May 8 20:58:56 2018 -0700 Add compiler variable in chai scripts Exec/LyA/all.chai Exec/LyA/amr-info.chai Exec/LyA/nyx-only.chai Exec/LyA/particles.chai Exec/LyA/simple.chai commit 84e4c6e905ed6e75d6ddb5f2c5bf095cc212f8ed Author: Dmitriy Morozov Date: Tue May 8 20:57:08 2018 -0700 Compile puppets (under Henson) as shared libraries, to avoid headaches on Linux Exec/Make.Nyx commit 350daadd7d6db36ddd5508206c9d9eba1f57bdb9 Author: Ann Almgren Date: Wed May 9 14:33:39 2018 -0700 Updated reset_internal_energy that collects the reset_source to be used in SDC algorithm Source/Src_3d/reset_internal_energy_3d.f90 commit 02a0a119c7b5363fbe9373468045a598f80500a7 Author: Ann Almgren Date: Wed May 9 14:16:20 2018 -0700 Add initialization stuff for SDC. Source/Initialization/Nyx_setup.cpp commit 4ea45b3a6423de4c9ed80c50b13b0c68f362b3f9 Author: Ann Almgren Date: Wed May 9 14:12:41 2018 -0700 Remove file "1" Source/HydroFortran/1 commit 92173ba1a3d473590b91a48de19580eeb7da03f9 Author: Ann Almgren Date: Wed May 9 08:50:50 2018 -0700 Fix mistake with the flux registers Source/compute_hydro_sources.cpp commit f304f07d479e0f9b99eb1b8e80f71213c29f1bbd Author: Ann Almgren Date: Wed May 9 00:16:56 2018 -0700 Oops - forgot to remove cflLoc from the argument list Source/Nyx_F.H Source/compute_hydro_sources.cpp commit 20481db33b08cbfed36f3a121cf4fc7c24a8ab08 Author: Ann Almgren Date: Tue May 8 23:45:17 2018 -0700 Oops - the flux stuff is in compute_hydro_sources not in strang_hydro Source/strang_hydro.cpp commit ebbba5b0f600f80c2fd2a6670a261fd2699c3e08 Author: Ann Almgren Date: Tue May 8 21:53:58 2018 -0700 more bl_ --> amrex_ Source/SourceTerms/Nyx_sources_3d.f90 Source/Src_3d/enforce_nonnegative_species_3d.f90 commit 50ca90b1add02bc37cc7a90c9163c9ecbb646765 Author: Ann Almgren Date: Tue May 8 21:49:24 2018 -0700 1) strang_hydro now makes the sources before adding them -- we will see order of operations changes 2) change bl_ --> amrex_ everywhere Source/HydroFortran/1 Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/README Source/HydroFortran/add_grav_source_3d.f90 Source/HydroFortran/flatten_3d.f90 Source/HydroFortran/make_hydro_sources_3d.f90 Source/HydroFortran/ppm_3d.f90 Source/HydroFortran/slope_3d.f90 Source/HydroFortran/trace_3d.f90 Source/HydroFortran/trace_ppm_3d.f90 Source/HydroFortran/trans_3d.f90 Source/Nyx_F.H Source/Nyx_nd.f90 Source/SourceTerms/Nyx_grav_sources_3d.f90 Source/Src_3d/compute_temp_3d.f90 Source/Src_3d/update_particles_3d.f90 Source/comoving_nd.f90 Source/compute_hydro_sources.cpp Source/strang_hydro.cpp commit 967c1d68c75c6b7833da8821529fa6532c43ec93 Author: Ann Almgren Date: Tue May 8 19:24:18 2018 -0700 Make the divu_cc term in the source term for (rho e) be fully explicit rather than time-centered. Source/HydroFortran/Nyx_advection_3d.f90 commit eaf9fb5d72ec0fb41eaf43bf6edd418fcf7950e5 Author: Ann Almgren Date: Tue May 8 17:47:24 2018 -0700 1) Remove old comments from a number of files 2) Move add_grad_source out of advance_gas and call it from the C++ in anticipation of moving to the SDC option. This makes O(10^-6) changes in LyA plt00354. Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/add_grav_source_3d.f90 Source/HydroFortran/enforce_minimum_density_3d.f90 Source/HydroFortran/flatten_3d.f90 Source/HydroFortran/normalize_species_3d.f90 Source/HydroFortran/ppm_3d.f90 Source/HydroFortran/slope_3d.f90 Source/HydroFortran/trace_3d.f90 Source/HydroFortran/trace_colglaz_3d.f90 Source/HydroFortran/trace_ppm_3d.f90 Source/HydroFortran/trace_src_3d.f90 Source/HydroFortran/trans_3d.f90 Source/Nyx_F.H Source/strang_hydro.cpp commit b6a32b6c88c653bb027038ebe6d698c4a53a21f0 Author: Ann Almgren Date: Tue May 8 16:50:42 2018 -0700 Minor cleanup in prep for testing the move to the source term version -- this gives identical results on the LyA test. Source/HydroFortran/Nyx_advection_3d.f90 Source/Nyx_F.H Source/strang_hydro.cpp commit 5099d3829ae0b9bb2c187fdf599362c85a68588a Author: Zarija Lukic Date: Mon May 7 14:30:14 2018 -0700 HDF5 example Exec/HDF5_example/64sssss_20mpc.nyx Exec/HDF5_example/GNUmakefile Exec/HDF5_example/Make.package Exec/HDF5_example/Nyx_error.cpp Exec/HDF5_example/Nyx_output.cpp Exec/HDF5_example/Prob_3d.f90 Exec/HDF5_example/TREECOOL_middle Exec/HDF5_example/Tagging_3d.f90 Exec/HDF5_example/inputs Exec/HDF5_example/knl.sl Exec/HDF5_example/probdata.f90 Exec/HDF5_example/probin Exec/HDF5_example/rhsfn.f90 Source/Nyx.H commit e4dc687e142dc0abea4db9c9b93d9411d5e65211 Merge: 5eb27b38 db52c362 Author: zarija Date: Mon May 7 13:38:21 2018 -0700 Merge pull request #34 from luminosa42/new_agn Cleaned agn model commit 5eb27b383ef714ada454c3322bae57a33a510707 Merge: 6dfe7172 4ef408e3 Author: zarija Date: Mon May 7 13:37:55 2018 -0700 Merge pull request #36 from mrzv/henson Henson capability commit ea33412f72a0fb5057482d0e51c7d41a6871f444 Merge: dee4a4bd 6dfe7172 Author: Zarija Lukic Date: Mon May 7 13:31:33 2018 -0700 Merge branch 'development' commit 6dfe7172f1adff63467e72b94f84ce01e597ff7d Author: Zarija Lukic Date: Mon May 7 13:29:49 2018 -0700 license info in README README.md commit 43aaa244f7e924417c215bbd0ffe1450d90bbc81 Author: Zarija Lukic Date: Mon May 7 13:28:55 2018 -0700 updating setups Exec/AMR-density/GNUmakefile Exec/LyA/inputs commit 4ef408e3ae18397a0a9a3d9ca4fe8c8b4ecec5e2 Author: Dmitriy Morozov Date: Sun May 6 19:57:38 2018 -0700 Add Exec/LyA/all.chai Exec/LyA/all.chai commit fce80a59eb74bd80653c727c17d513ff644fa030 Author: Dmitriy Morozov Date: Sat May 5 19:47:52 2018 -0700 Add Exec/Henson/amr-info Exec/Henson/amr-info/GNUmakefile Exec/Henson/amr-info/Make.package Exec/Henson/amr-info/Prob_3d.f90 Exec/Henson/amr-info/Tagging_3d.f90 Exec/Henson/amr-info/main.cpp Exec/Henson/amr-info/probdata.f90 Exec/LyA/amr-info.chai commit 227ef3ce9eeded83e9f780ff7c4d9c7e3b1315b7 Author: Dmitriy Morozov Date: Sun May 6 20:48:35 2018 -0700 Add Exec/Henson/extract-particles Exec/Henson/extract-particles/GNUmakefile Exec/Henson/extract-particles/Make.package Exec/Henson/extract-particles/Prob_3d.f90 Exec/Henson/extract-particles/Tagging_3d.f90 Exec/Henson/extract-particles/main.cpp Exec/Henson/extract-particles/probdata.f90 Exec/LyA/particles.chai commit 7d5a0aa4e81fc964d3dad8f9656ef291e3c00243 Author: Dmitriy Morozov Date: Sun May 6 20:26:45 2018 -0700 Add Exec/Henson/sample-analysis Exec/Henson/sample-analysis/GNUmakefile Exec/Henson/sample-analysis/Make.package Exec/Henson/sample-analysis/Prob_3d.f90 Exec/Henson/sample-analysis/Tagging_3d.f90 Exec/Henson/sample-analysis/main.cpp Exec/Henson/sample-analysis/probdata.f90 Exec/LyA/simple.chai commit 9a395d989694c2ec011196535aca93a9b67c250b Author: Dmitriy Morozov Date: Sat May 5 09:56:57 2018 -0700 Add USE_HENSON=FALSE in Exec/LyA Exec/LyA/GNUmakefile commit 5772056ae089272db1ba48495411716e4274e2b5 Author: Dmitriy Morozov Date: Sun May 6 20:26:25 2018 -0700 Fiddle with Exec/Make.Nyx Exec/Make.Nyx commit f633848f31c1ee16cff43d2779aaf3420961b20e Author: Dmitriy Morozov Date: Sun May 6 20:10:17 2018 -0700 Add henson_yield() to Nyx Source/Make.package Source/nyx_main.cpp commit 186c09019584e9a2bd53bcb97b1cb5f6299c86fe Author: Ann Almgren Date: Wed May 2 13:44:27 2018 -0700 Oops -- missed one of the pp --> pp_nyx Source/Nyx.cpp commit f2e24e89e9fc17e8cfdb932f0a25ae1ec3a977ab Author: Ann Almgren Date: Wed May 2 13:29:43 2018 -0700 1) Some cleanup 2) We need to use the boxArray and DistributionMap of the right level when constructing reset_e_src so we use S_new.boxArray and S_new.DistributionMap rather than grids and dmap. Source/Initialization/Nyx_initdata.cpp Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_F.H Source/Nyx_advance.cpp Source/Src_3d/reset_internal_energy_3d.f90 Source/sdc_reactions.cpp Source/strang_hydro.cpp Source/strang_reactions.cpp Source/sum_integrated_quantities.cpp Source/write_info.cpp commit b53170510fff6b9e31416012fcc9ec0c50e7a829 Author: Ann Almgren Date: Wed May 2 12:08:40 2018 -0700 More sync-ing of current code with SDC version. Specifically we separate the call to reset_internal_energy out of the call to compute_new_temp. In the call to reset_internal_energy we pass reset_e_src which holds the amount by which we have changed e in the process of resetting it. Source/HydroFortran/Nyx_advection_3d.f90 Source/Initialization/Nyx_initdata.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_advance.cpp Source/Nyx_nd.f90 Source/SourceTerms/Nyx_grav_sources_3d.f90 Source/sdc_reactions.cpp Source/strang_hydro.cpp Source/strang_reactions.cpp Source/sum_integrated_quantities.cpp Source/write_info.cpp commit aa36777d635c8885baaec8271c4fb086ccebcb3c Author: Ann Almgren Date: Wed May 2 10:26:06 2018 -0700 These changes should not change the answer at all, but they are structural changes in prep for merging in the SDC stuff. Source/HeatCool/integrate_state_3d.f90 Source/HydroFortran/Make.package Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/add_grav_source_3d.f90 Source/HydroFortran/make_hydro_sources_3d.f90 Source/Make.package Source/Nyx.H Source/Nyx_F.H Source/Nyx_advance.cpp Source/compute_hydro_sources.cpp Source/sdc_hydro.cpp Source/sdc_reactions.cpp Source/strang_hydro.cpp Source/strang_reactions.cpp Source/update_state_with_sources.cpp commit d0db7c65c81e5a552961a4d63aaabd2ecb2d9d9b Author: Weiqun Zhang Date: Wed Apr 25 13:36:56 2018 -0700 use a different version of complementIn Source/NeutrinoParticleContainer.cpp commit 7d42ce6470f37e66a4e7b531b1e3d04035e19322 Author: Ann Almgren Date: Fri Apr 20 14:56:05 2018 -0700 Use the Fortran version of multilevel AssignDensity. Source/NyxParticleContainer.H commit 61e579b10f29af971f3a355e4f673261310a1f5b Author: Ann Almgren Date: Fri Apr 20 14:24:41 2018 -0700 1) Remove calls to fill_ec_grow 2) Clean up some stuff so we can remove F_BaseLib dependency in the long run Source/Constants/constants_cgs.f90 Source/EOS/eos_stuff.f90 Source/Forcing/forcing_spect.f90 Source/Gravity/Gravity.cpp Source/Network/network.f90 Source/Network/nyx_burner.f90 commit 3e69c2c6403c00bfa8512df413c532d40305168e Author: Weiqun Zhang Date: Wed Apr 18 10:31:39 2018 -0700 mempool_module --> amrex_mempool_module Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/ppm_3d.f90 Source/HydroFortran/trans_3d.f90 commit 71c5efd3c89e0d89c506372d8b80976d40f2b5bd Author: Weiqun Zhang Date: Wed Apr 11 12:59:49 2018 -0700 USE_CVODE --> AMREX_USE_CVODE Exec/HydroTests/TurbForce/Nyx_setup.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp Source/nyx_main.cpp commit a178c299f98c43a0993f33095d0426fb5a73dfc5 Author: Ann Almgren Date: Mon Apr 9 21:29:56 2018 -0700 We have to redefine grav_n_grow to allow for the fact that ghost particles were created on the coarser level which means they may be (iteration-1) cells further out than ghost_width which means we need to grow grav_n_grow to reflect that. Source/Nyx_advance.cpp commit dee4a4bda55efee25839431a5f1846a90089b6cd Merge: 4bac2574 752d5c92 Author: Zarija Lukic Date: Sat Apr 7 23:26:29 2018 -0700 Merge branch 'development' commit 752d5c92143bc9a73d7d531ee31623b51d8bff10 Author: Ann Almgren Date: Sat Apr 7 12:20:34 2018 -0700 Don't need Source/MG any more Exec/Make.Nyx commit 9a35b50c46a485c7ae21910633b49a5724c4f328 Author: Ann Almgren Date: Sat Apr 7 12:17:58 2018 -0700 Get rid of local MG directory which was used in the past for constant coefficient F90 solves Source/MG/cc_smoothers.f90 Source/MG/cc_stencil_apply.f90 Source/MG/mg_tower_smoother.f90 commit e56ac9d1df4bfd22e77d04a89c1da4f7fcbd235c Author: Andrew Myers Date: Fri Apr 6 14:12:17 2018 -0700 fix typo. Source/NyxParticleContainer.H commit c7417adc4ac0c6336088ea1675256049d7d93bac Merge: 2170ec74 90e029c7 Author: Andrew Myers Date: Fri Apr 6 11:14:12 2018 -0700 merging. commit 90e029c7bc5e58ba7182e24212d5925dba802ac4 Author: Ann Almgren Date: Tue Apr 3 07:13:08 2018 -0700 Removed too much when removing sidecars Source/nyx_main.cpp commit 80e16adf8ca54c03672da400fc5dc49df4b1e082 Author: Weiqun Zhang Date: Mon Apr 2 19:19:17 2018 -0700 remove unused array Source/Gravity/Gravity.H commit 92c3698fe0b63a6c5af325b6d93a2eda3b8091b7 Author: Weiqun Zhang Date: Mon Apr 2 19:14:53 2018 -0700 fix compilation Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit d0b78955a6cc3bea4daf8678be3c8daf1ed308bb Author: Ann Almgren Date: Mon Apr 2 18:06:37 2018 -0700 Remove use of F90 or single-level C++ solvers (use MLMG as default instead) Exec/Make.Nyx Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit 658757279d2f580455c3a902d1d49ea706ac9369 Merge: a03478e0 7375cde9 Author: Weiqun Zhang Date: Mon Apr 2 17:29:14 2018 -0700 Merge branch 'rmsidecar' into development commit a03478e021fd39965ce1e6b92c5e3c7b77240414 Author: Zarija Lukic Date: Mon Apr 2 11:26:26 2018 -0700 Zoom AMR case Exec/AMR-zoom/64_cref_l1.nyx Exec/AMR-zoom/GNUmakefile Exec/AMR-zoom/Make.package Exec/AMR-zoom/Nyx_error.cpp Exec/AMR-zoom/Prob_3d.f90 Exec/AMR-zoom/TREECOOL_middle Exec/AMR-zoom/Tagging_3d.f90 Exec/AMR-zoom/inputs Exec/AMR-zoom/probdata.f90 Exec/AMR-zoom/probin Exec/AMR-zoom/rhsfn.f90 commit 18eea2b91e2e7e036936ab1317850fcf11c38299 Author: Zarija Lukic Date: Mon Apr 2 11:25:30 2018 -0700 adjusting inputs in AMR problem Exec/AMR-density/inputs commit 7375cde9b97812d5618a8fdd2dca2469d869ae0f Author: Weiqun Zhang Date: Mon Apr 2 11:13:34 2018 -0700 remove sidecar Exec/HydroTests/TurbForce/Nyx_setup.cpp Exec/LyA/inputs.small.dsc Exec/LyA/inputs_gimlet_in_transit.dsc Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxBld.cpp Source/NyxParticles.cpp Source/Nyx_halos.cpp Source/nyx_main.cpp UsersGuide/PostProcessing/NyxPostProcessing.tex commit 9be8320ace9d4fb6649b627560cd77d265dc57ed Author: Ann Almgren Date: Fri Mar 30 15:52:22 2018 -0700 Add inputs.rt for regression testing Exec/AMR-density/inputs.rt commit a30fb05cefc8afe331c23b98508ef8a6750cfd8b Author: Ann Almgren Date: Fri Mar 30 14:49:47 2018 -0700 Modify the AssignDensity routine in amrex and the interfaces and calling routines so that we can pass in the number of grow cells used to define the array that will hold the particle deposition. Some previous calls defaulted to 1 ghost cell which is not big enough if valid particles live in ghost cells themselves (eg if starting the second level 1 solve of a subcycled level 0-1-2 simulation.) Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Nyx.cpp Source/NyxParticleContainer.H Source/Nyx_advance.cpp commit ee4d992c94c07814ec51a5d29876b37d72347792 Author: Zarija Lukic Date: Tue Mar 27 15:40:50 2018 -0700 dynamic AMR example Exec/AMR-density/64sssss_20mpc.nyx Exec/AMR-density/GNUmakefile Exec/AMR-density/Make.package Exec/AMR-density/Nyx_error.cpp Exec/AMR-density/Prob_3d.f90 Exec/AMR-density/TREECOOL_middle Exec/AMR-density/Tagging_3d.f90 Exec/AMR-density/inputs Exec/AMR-density/probdata.f90 Exec/AMR-density/probin Exec/AMR-density/rhsfn.f90 commit 4bac257414933362b6e2ef565f19ab75a6235859 Author: Ann Almgren Date: Wed Mar 7 20:24:39 2018 -0800 Don't test using ZHI_COMP unless you know you're doing inhomo_reion Source/Src_3d/compute_temp_3d.f90 commit 0f178dbab0db87389124c0b2a27c4357002f6343 Author: Ann Almgren Date: Mon Feb 26 14:05:51 2018 -0800 Add USE_HENSON flag Exec/Make.Nyx commit 532cf0f1d0db75c4788de982a2aaa0b1fa1378f4 Author: Ann Almgren Date: Mon Feb 26 13:29:34 2018 -0800 Replace existing main by nyx_main so that we can have an optional main in cases where an external program wants to use its own main Source/Make.package Source/main.cpp Source/nyx_main.cpp commit ed5ae52ce3cad81ac9246338b90e32f68484dfa6 Author: Jean M. Sexton Date: Wed Feb 7 18:48:06 2018 -0800 Cleaned up added files Util/VODE_test/f_rhs.f90 Util/VODE_test/fmain.f90 Util/VODE_test/fmain_vode.f90 commit a09d0c4c6478eded8aebb24e7b59adb811c82470 Author: Jean M. Sexton Date: Wed Feb 7 18:40:46 2018 -0800 Added input files for VODE_test Util/VODE_test/atomic_rates.f90 Util/VODE_test/fmain.f90 Util/VODE_test/inputs_atomic Util/VODE_test/inputs_hc commit a32443bd5d75a253861166d7a98d4461b770288f Author: Jean M. Sexton Date: Mon Feb 5 16:45:11 2018 -0800 Fixed this_z interpolation, number of vode functions matches Util/VODE_test/eos_hc.f90 Util/VODE_test/fmain.f90 Util/VODE_test/fmain_vode.f90 commit 4180e198ae03ebdf7d5a1f003576c25d87afaa23 Author: Jean M. Sexton Date: Mon Feb 5 15:33:14 2018 -0800 Fixed gamma issue Util/VODE_test/Makefile Util/VODE_test/eos_hc.f90 Util/VODE_test/f_rhs.f90 Util/VODE_test/fmain.f90 Util/VODE_test/fmain_vode.f90 commit 2bd6352eac67c325a99877b0e65411db67bc79f0 Author: Jean M. Sexton Date: Mon Feb 5 10:12:02 2018 -0800 Fixed Makefile ordering Util/VODE_test/Makefile Util/VODE_test/f_rhs Util/VODE_test/f_rhs.f90 commit 502c133990fcd4573a9285c784eba63969f151f1 Author: Jean Sexton Date: Mon Feb 5 10:39:22 2018 -0600 Added standalone test for VODE and FCVODE integration as VODE_test in Util Util/VODE_test/Makefile Util/VODE_test/TREECOOL_middle Util/VODE_test/atomic_rates.f90 Util/VODE_test/comoving_nd.f90 Util/VODE_test/comoving_params.f90 Util/VODE_test/constants_cosmo.f90 Util/VODE_test/constants_mod.f90 Util/VODE_test/cvode_interface.f90 Util/VODE_test/eos_hc.f90 Util/VODE_test/eos_params.f90 Util/VODE_test/f_rhs Util/VODE_test/f_rhs.f90 Util/VODE_test/fcvode_extras.f90 Util/VODE_test/fmain.f90 Util/VODE_test/fmain_vode.f90 Util/VODE_test/fnvector_serial.f90 Util/VODE_test/integrate_state_vode_3d.f90 Util/VODE_test/meth_params.f90 Util/VODE_test/misc_params.f90 Util/VODE_test/reion_aux_module.f90 Util/VODE_test/vode_aux.f90 commit 2170ec74da15058f7f0081b6545f03d4427e131d Author: Andrew Myers Date: Sat Jan 27 16:14:32 2018 -0800 Removing some code duplication from the Nyx particle containers. Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/NyxParticleContainer.H commit eeb75a975faba901e0aaebeb1f9d7195a888fb8a Author: Andrew Myers Date: Fri Jan 26 21:21:56 2018 -0800 remove now-removed template parameter from Nyx Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp commit c1468c0aa28586e51c68b012de048728980640f1 Author: Andrew Myers Date: Fri Jan 26 12:32:51 2018 -0800 removing Nyx_slice - this functionality is in amrex now. Source/Nyx_slice.cpp commit 896ee2bc6560ca3583ee97a5e11402b1db0c7653 Author: Andrew Myers Date: Fri Jan 26 12:23:27 2018 -0800 Have AGNParticleContainer inherit the neighbor functionality from amrex Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/NyxParticleContainer.H commit 36c76cebea8dc6e5d9b851c5ec8c210f5fc07a60 Author: Weiqun Zhang Date: Thu Jan 25 14:58:18 2018 -0800 minor Source/Gravity/Gravity.cpp commit 0feb0cc857b3225dd32a5d550fa6b6c43571f854 Merge: d5f59cc9 b0e246e6 Author: Andrew Myers Date: Tue Jan 23 17:42:32 2018 -0800 add in Nyx slice commit b0e246e68800e5a2495a378150a6aa528a413894 Author: Weiqun Zhang Date: Tue Jan 23 11:27:23 2018 -0800 Array --> Vector Source/Nyx_slice.cpp commit db52c3620f319f9df720cec53329606cf499f5c9 Author: Yinghe Lu Date: Thu Dec 21 15:05:18 2017 -0800 got rid of the test routine Source/Nyx_halos.cpp commit 24048c94fdcc8493b3aeab2b30a0294690132974 Author: vince Date: Thu Dec 21 15:03:38 2017 -0800 optimized i/o support for AGN. Source/Nyx.H Source/Nyx.cpp Source/Nyx_output.cpp commit 46dd6b9085dccb8ab823eb49935a4dbeac36dc47 Author: Yinghe Lu Date: Thu Dec 21 15:03:33 2017 -0800 added merging parameters into probin file Exec/LyA_AGN/GNUmakefile Exec/LyA_AGN/Prob_3d.f90 Exec/LyA_AGN/inputs Exec/LyA_AGN/probin Source/AGN/agn_3d.f90 Source/Nyx_halos.cpp Source/agn_params.f90 commit 06b9fa6d2b7c5e149b9cae2cdd49e29bf415aca8 Author: vince Date: Mon Dec 18 15:50:01 2017 -0800 example code to make a plotfile from a slice multifab. Util/SliceUtils/GNUmakefile Util/SliceUtils/Make.package Util/SliceUtils/slice_00340/Diag_x_D_00001 Util/SliceUtils/slice_00340/Diag_x_D_00003 Util/SliceUtils/slice_00340/Diag_x_D_00005 Util/SliceUtils/slice_00340/Diag_x_D_00007 Util/SliceUtils/slice_00340/Diag_x_H Util/SliceUtils/slice_00340/Diag_y_D_00002 Util/SliceUtils/slice_00340/Diag_y_D_00003 Util/SliceUtils/slice_00340/Diag_y_D_00006 Util/SliceUtils/slice_00340/Diag_y_D_00007 Util/SliceUtils/slice_00340/Diag_y_H Util/SliceUtils/slice_00340/Diag_z_D_00004 Util/SliceUtils/slice_00340/Diag_z_D_00005 Util/SliceUtils/slice_00340/Diag_z_D_00006 Util/SliceUtils/slice_00340/Diag_z_D_00007 Util/SliceUtils/slice_00340/Diag_z_H Util/SliceUtils/slice_00340/State_x_D_00001 Util/SliceUtils/slice_00340/State_x_D_00003 Util/SliceUtils/slice_00340/State_x_D_00005 Util/SliceUtils/slice_00340/State_x_D_00007 Util/SliceUtils/slice_00340/State_x_H Util/SliceUtils/slice_00340/State_y_D_00002 Util/SliceUtils/slice_00340/State_y_D_00003 Util/SliceUtils/slice_00340/State_y_D_00006 Util/SliceUtils/slice_00340/State_y_D_00007 Util/SliceUtils/slice_00340/State_y_H Util/SliceUtils/slice_00340/State_z_D_00004 Util/SliceUtils/slice_00340/State_z_D_00005 Util/SliceUtils/slice_00340/State_z_D_00006 Util/SliceUtils/slice_00340/State_z_D_00007 Util/SliceUtils/slice_00340/State_z_H Util/SliceUtils/sliceutils.cpp commit bcf411ab929806af91b560ac4138520c09364b4f Merge: b69474e2 8b42e758 Author: vince Date: Wed Dec 13 16:30:34 2017 -0800 Merge branch 'development' into partio commit 8b42e7582243b372e50bd4046e40442017098389 Merge: 951619b2 2acf53f4 Author: zarija Date: Wed Dec 13 15:07:19 2017 -0800 Merge pull request #30 from luminosa42/submittest New AGN merging criterion commit 2acf53f4b008584ad7899c08c9c252c83999d190 Author: Yinghe Lu Date: Wed Dec 13 13:18:53 2017 -0800 Modified AGN model Source/AGN/agn_3d.f90 commit b69474e208eb4971c44c0dde62acbeaa5af0abb7 Merge: 7cb12e79 951619b2 Author: vince Date: Wed Dec 13 12:13:13 2017 -0800 Merge branch 'development' into partio commit 951619b288ef52a764a6ddc24e15dfee1c554550 Author: Ann Almgren Date: Tue Dec 12 15:18:11 2017 -0800 This version actually compiles Source/Src_3d/compute_temp_3d.f90 commit ea6e2a5f2bb00cb546d64a8330671427edd6ce11 Author: Ann Almgren Date: Tue Dec 12 15:13:49 2017 -0800 Don't use ZHI (which is -1) if flag is not true Source/Src_3d/compute_temp_3d.f90 commit 7cb12e79bf55134e8dc6cb54d9f5464bf989c562 Author: vince Date: Fri Dec 8 12:42:07 2017 -0800 fix for not precreating directories. Source/Nyx.cpp commit 17a0c37c22a75c59875063af11ff3e7a6dda9df0 Merge: 9d86d280 2824eccd Author: vince Date: Thu Dec 7 16:26:28 2017 -0800 Merge branch 'partio' of https://github.com/AMReX-Astro/Nyx into partio commit 9d86d280598c58404a59438fa5f5b14073ef397e Author: vince Date: Thu Dec 7 16:26:06 2017 -0800 remove diagnostics. Source/Nyx_output.cpp commit 9bad77f7810e99919d687d1d30699e223bbec4c0 Author: vince Date: Thu Dec 7 12:37:03 2017 -0800 prepost updates for plotfiles. Source/Nyx.H Source/Nyx_output.cpp commit 5449928232e6023263b1aaf10b2552716e3ff7bf Author: vince Date: Fri Dec 1 18:07:02 2017 -0800 only print on ioproc. Source/Initialization/read_plotfile.cpp commit 2824eccdeb7c79b821de30cee5ab84ab01208b2e Merge: 8e0c6947 1a189320 Author: Zarija Lukic Date: Mon Nov 20 00:38:40 2017 -0800 Merge branch 'development' into partio commit 1a18932094ccf2a24e4ea3fb7e80b2dbc0e7db56 Author: Zarija Lukic Date: Sun Nov 19 23:46:40 2017 -0800 Add gas fractions Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Src_3d/compute_temp_3d.f90 Source/write_info.cpp commit 9969b98d8e24741917be5edb0e8920abc8725202 Author: Zarija Lukic Date: Sun Nov 19 19:34:19 2017 -0800 Profile init_zhi() Source/Initialization/Nyx_initdata.cpp commit 20ba4b820ababba70cb653f11d6cf7360cb7b147 Author: Zarija Lukic Date: Sun Nov 19 19:25:39 2017 -0800 Use fixed T for reionization Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 commit 08bc4566a178ec7b7a3c8f44f4232d7041078815 Author: Zarija Lukic Date: Sun Nov 19 19:02:29 2017 -0800 Thread-safe warnings from F Source/EOS/eos_hc.f90 Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_fcvode_vec_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 commit 8e0c6947ba4ea07afbbb744376ba7db2ea2561c6 Merge: 5c9e89af cefe4418 Author: Zarija Lukic Date: Sun Nov 19 00:57:28 2017 -0800 Merge branch 'development' into partio commit cefe44186c893967ff596db9d753caa89ef7c47e Author: Zarija Lukic Date: Sun Nov 19 00:56:48 2017 -0800 fixed int overflow Util/zhi_converter/main.cpp commit 3e0edbef506739c5f5be856f24b48a7105c8f3eb Merge: 7652381f 76af2d84 Author: Zarija Lukic Date: Sat Nov 18 10:47:00 2017 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 5c9e89aff54c4f31e86c7565f3b1e65c8c6b63b3 Author: vince Date: Fri Nov 17 18:44:11 2017 -0800 remove diagnostic. Source/Nyx.cpp commit ee3446f391edc7cf742b7f95381ad3cefbbe154c Merge: a9b2988f 76af2d84 Author: vince Date: Fri Nov 17 13:26:23 2017 -0800 Merge branch 'development' into partio commit 76af2d844297f4a11de2219d519ffc8bd82f5586 Author: Weiqun Zhang Date: Thu Nov 16 15:12:34 2017 -0800 amrex renamed a funciton Source/Gravity/Gravity.cpp commit a9b2988f3f9cb90024fb16282863af8604da19b4 Merge: 49d36aff 3d66c999 Author: vince Date: Mon Nov 13 16:52:42 2017 -0800 merge fixes. commit 3d66c999ad67c1c04a6fe3015938b1da46041943 Author: vince Date: Mon Nov 13 16:35:50 2017 -0800 additions for pre and post checkpoint functions for i/o optimization. Source/Nyx.H Source/Nyx_output.cpp commit 71784d1800be77b41804fd2ba010010e634c7ea4 Author: Weiqun Zhang Date: Mon Nov 13 13:03:12 2017 -0800 use mlmg in some regression tests Exec/LyA/inputs.rt Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.ref commit e6c916c73aa27af2728a2ae423591f6a7c6acb00 Author: Weiqun Zhang Date: Fri Nov 10 11:55:53 2017 -0800 MLMG: update due to amrex change Source/Gravity/Gravity.cpp commit d96214f0ea0011c2b2a1e160ec230e74c0684ec2 Author: vince Date: Wed Nov 8 14:51:37 2017 -0800 remove sentinel from dmap. Source/Nyx_slice.cpp commit 25114108110edd1ed4f862e5cef4ea7a7eb76c8a Author: Weiqun Zhang Date: Wed Nov 8 09:50:01 2017 -0800 MLMG: it turns we have always been using agglomeration and consolidation due to a bug in AMReX Source/Gravity/Gravity.cpp commit 7652381f560f8163768bd74c8e323f21c0698e2f Merge: 906d9e9e e0bdaefd Author: Zarija Lukic Date: Sat Nov 4 19:40:07 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit e0bdaefd73ef30ae24bd5418458c46417089110d Merge: 2e0b8e1e 10a0b45b Author: zarija Date: Sat Nov 4 19:34:38 2017 -0700 Merge pull request #29 from AMReX-Astro/mlmg Option to use AMReX's MLMG linear solver commit 10a0b45b92905beae0eb198bb48eee14bd91c9a5 Author: Weiqun Zhang Date: Sat Nov 4 15:51:29 2017 -0700 Array -> Vector Source/Gravity/Gravity.cpp commit 76cf45e9b79a16e6a000040ed742c6a667c0d86c Merge: b828425c 2e0b8e1e Author: Weiqun Zhang Date: Sat Nov 4 14:36:47 2017 -0700 Merge branch 'development' into mlmg commit 2e0b8e1ec3d72b1bb00a4a02eb5a0e5cc7fde250 Merge: 01846a3c 500cdd0b Author: Weiqun Zhang Date: Sat Nov 4 14:35:09 2017 -0700 Merge branch 'development' of ssh://github.com/AMReX-Astro/Nyx into development commit 01846a3c64b44b04f4641684974a731790b52b39 Author: Weiqun Zhang Date: Sat Nov 4 14:34:19 2017 -0700 need to move the HPGMG block to a place before Make.defs is included, otherwise Make.hpgmg include by Make.defs will not see them in time Exec/Make.Nyx commit 906d9e9e68f0967cc92ee34ce953406f4b7a2cf2 Author: Zarija Lukic Date: Fri Nov 3 18:12:00 2017 -0700 Set tempInit to be the same as in Prob_3d Source/Initialization/Nyx_initcosmo.cpp commit b828425c24e4d7eabb3252e997f18aed0ef1500b Author: Weiqun Zhang Date: Fri Nov 3 15:53:20 2017 -0700 fix level index Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit be991611cc9a10110dfae143b03f590d53b504ee Author: Weiqun Zhang Date: Fri Nov 3 14:59:08 2017 -0700 multi-level solve Source/Gravity/Gravity.cpp commit e9b0670674f3cf305bb05df160a0a3c819d0bb2b Author: Weiqun Zhang Date: Fri Nov 3 14:31:25 2017 -0700 solve for delta phi with mlmg Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit 262cfa2de3dca0c0779003ac7190bf1d8a473308 Author: Weiqun Zhang Date: Fri Nov 3 13:14:52 2017 -0700 solve_with_MLMG in solve_for_phi Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit b98ac0e3d37625b954f5abe21c4d4dd725fb397a Merge: a5603e45 500cdd0b Author: Zarija Lukic Date: Fri Nov 3 09:27:20 2017 -0700 Merge branch 'development' commit 500cdd0b00cbafebecf6f90361ee13d7cc0fbdc6 Author: Zarija Lukic Date: Fri Nov 3 09:26:38 2017 -0700 Correct reference README.md commit a5603e4565ad1ea9ead13fae3f3dd97adc067306 Merge: df3201f1 140e7a07 Author: Zarija Lukic Date: Fri Nov 3 09:06:59 2017 -0700 Merge branch 'development' commit 140e7a07077d8bb5bc93cb13f02385b90948b833 Author: Zarija Lukic Date: Fri Nov 3 00:09:08 2017 -0700 Readme update README.md commit 886e923d125984435d6253cb66937f69edbf6068 Author: Zarija Lukic Date: Thu Nov 2 22:30:45 2017 -0700 Updated README README.md commit 2e84a9c2ee9a7987048d0e8caba2d4875a9a6bdb Author: Zarija Lukic Date: Thu Nov 2 22:18:01 2017 -0700 Citation CITATION commit ec69c781075a1b16db16f4af77b5eb586686f680 Author: Zarija Lukic Date: Thu Nov 2 22:14:41 2017 -0700 updating GNUMakefiles Exec/LyA/GNUmakefile Exec/LyA_AGN/GNUmakefile Exec/Scaling/GNUmakefile commit dd9020b13807e3d14e9c8e7223166a3ded5b5d81 Merge: 8166baae 22cf5f65 Author: Zarija Lukic Date: Thu Nov 2 21:53:05 2017 -0700 Merge PR 28 commit 22cf5f65f721876c29a3a1034293ff77e37d4484 Author: Zarija Lukic Date: Thu Nov 2 21:52:37 2017 -0700 Minor changes to PR 28 Exec/LyA_AGN/GNUmakefile Source/AGN/agn_3d.f90 commit 3a228caeb5cb09f357fee54bb5321e677cd4bd2a Author: Weiqun Zhang Date: Thu Nov 2 14:02:32 2017 -0700 compile MLMG if DIM=3 and gravity is on Exec/Make.Nyx commit 0581064349508a02d3e173717ee23f1a7867eaab Author: Yinghe Lu Date: Wed Nov 1 22:47:08 2017 -0700 modified AGN module Exec/LyA_AGN/GNUmakefile Source/AGN/agn_3d.f90 Source/Nyx_halos.cpp commit 49d36affae1efc6a7f53def74270a6b48872406c Merge: f8bb4581 8166baae Author: vince Date: Fri Oct 27 12:00:31 2017 -0700 Merge branch 'development' into partio commit 8166baae27f5f515acc6ecb5cd2375262c0f2596 Author: Ann Almgren Date: Fri Oct 27 06:03:59 2017 -0700 Changes so that Wolfram's forcing stuff works -- shouldn't change anything else. Exec/DrivenTurbulence/Prob_3d.f90 Exec/HydroTests/TurbForce/Nyx_setup.cpp Exec/HydroTests/TurbForce/Nyx_sources.cpp Exec/HydroTests/TurbForce/Prob_3d.f90 Exec/HydroTests/TurbForce/ext_src_force_3d.f90 Source/SourceTerms/Nyx_sources.cpp Source/strang_splitting.cpp commit 1b8c07a74df4802b8ca8811a496c9680a419e2d0 Author: Zarija Lukic Date: Thu Oct 26 13:53:19 2017 -0700 Change triple-negation in the error message. Source/main.cpp commit 50daa4853eacce582d4e319d998408926dc77123 Author: vince Date: Wed Oct 25 17:20:46 2017 -0700 added slice test to write just a fab. this is just a test. Source/Nyx.cpp commit 991cf7c0ac516f4bf7d77f210582f277c6d0ce2c Merge: 28f8b8ab bcc9fe1b Author: vince Date: Wed Oct 25 16:22:57 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit 188904a591ff7bb8e535a7193c791b628e9f4099 Author: vince Date: Mon Oct 23 18:08:56 2017 -0700 experiment to write slices faster. dir fix. Source/Nyx.cpp commit 8ff529f18c00c088703edaadf51b5dcd9c5d5de6 Author: vince Date: Mon Oct 23 17:44:09 2017 -0700 experiment to write slices faster. Source/Nyx.cpp commit bcc9fe1b4948ae0f8f3b22e9190c1589bcfd0356 Author: Andrew Myers Date: Mon Oct 23 17:04:02 2017 -0700 always disable tiling when initialization from the Morton file. Source/DarkMatterParticleContainer.cpp commit 28f8b8ab6879a09c01bbc69bc6ad48e6e3aa98dd Merge: 484a49ef 44387929 Author: vince Date: Mon Oct 23 14:57:01 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit fe1e6a17e4fd017f29f0e2edae8c500f04634270 Merge: f8bb4581 44387929 Author: Zarija Lukic Date: Sat Oct 21 11:55:00 2017 -0700 Merge branch 'development' into partio commit 443879299f8cc78adb0e83b97569d0c05d850627 Author: Zarija Lukic Date: Sat Oct 21 11:43:48 2017 -0700 More slice control on inputs Source/Nyx.cpp commit 1223f2f8736be6b7aec84e5440f3200e4627bcd0 Author: Zarija Lukic Date: Sat Oct 21 11:42:35 2017 -0700 remove unused declaration Source/HeatCool/integrate_state_vode_3d.f90 commit d5f59cc96615a3c17b61856f57cb037539c3d1cd Author: Andrew Myers Date: Fri Oct 20 15:00:28 2017 -0700 remove Nyx version of slicing stuff - moved to amrex. Source/Make.package Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_slice.H Source/Nyx_slice.cpp Source/Src_3d/Make.package Source/Src_3d/fill_slice_3d.f90 commit fee62b81ed02cc151e81dabdb9fd894261d40395 Author: Andrew Myers Date: Fri Oct 20 14:57:41 2017 -0700 switch over to using amrex's version of get_slice_data. Source/Nyx.cpp commit 1df39b51dc8924e429c41b064a0e3c26cd578538 Author: Andrew Myers Date: Fri Oct 20 14:57:16 2017 -0700 fix this construction to work with Debug on. Source/Src_3d/compute_temp_3d.f90 commit f8bb45813fafcc228a26d3fb58da7780ad8c301d Author: vince Date: Fri Oct 20 14:26:52 2017 -0700 more support for precreate directories. Source/Nyx_output.cpp commit 5deb11982ead7c44c03da3a26ef91a1ba11784d9 Author: vince Date: Fri Oct 20 13:37:33 2017 -0700 more support for precreate directories. Source/Nyx.H Source/Nyx.cpp Source/Nyx_output.cpp commit 9c4ee65716ad8feb309bff34eabc82ee9ab9fa64 Author: vince Date: Fri Oct 20 12:59:19 2017 -0700 fix comment Source/NyxBld.cpp commit a4da7cae55258d0ea4289121fa10a9869de447b5 Author: vince Date: Fri Oct 20 12:56:10 2017 -0700 fix comment Source/Gravity/Gravity.cpp commit 17507a2cf60c8016194d46bb671203e8651d8bb1 Author: vince Date: Fri Oct 20 12:55:52 2017 -0700 fix comment Source/DarkMatterParticleContainer.H commit 67fd217d3a8137753a259c2a1db963be6b5f94b9 Author: Zarija Lukic Date: Fri Oct 20 10:45:02 2017 -0700 Fix folders for slices Source/Nyx.cpp commit 484a49eff36c7210fc7dbc22383d0a5310a09524 Merge: f2f5c585 d57a44f4 Author: vince Date: Fri Oct 20 09:50:30 2017 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/Nyx into development commit d57a44f4ad44276aa00f652e26cd352e7e6bab9a Author: Zarija Lukic Date: Thu Oct 19 23:58:51 2017 -0700 More work on slices Source/Nyx.cpp commit 3c8d2b22fd0a8dee13549d3c3f52b097b1ce0dea Author: Zarija Lukic Date: Thu Oct 19 21:21:57 2017 -0700 Consistent T jump in vode and cvode Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 commit b3eb3fb247b92d01468bb7f2df5d31399fe1c854 Author: Zarija Lukic Date: Thu Oct 19 20:53:33 2017 -0700 Ignore all executables .gitignore commit 9879d5fb44f04f85baccca0fc5cfe6259340dedf Author: Zarija Lukic Date: Thu Oct 19 19:49:50 2017 -0700 Another fix for diag_eos size Source/Nyx_hydro.cpp commit 7a1693ca6cbf4b67f3db0606f40d1225b59c75dd Merge: a07eb705 ed7e0d7d Author: zarija Date: Thu Oct 19 19:48:49 2017 -0700 Merge pull request #26 from ghweber/development Two minor fixes commit ed7e0d7dc965d8446d72523ef4ddcae6c432b609 Author: Gunther H. Weber Date: Thu Oct 19 18:20:38 2017 -0700 Fixed include guard mismatch. Source/Nyx_slice.H commit e31f8b639543a4f80105562c69e63b28614c0252 Author: Gunther H. Weber Date: Thu Oct 19 18:19:02 2017 -0700 Ignore Nyx executables. .gitignore commit a07eb70526f38f456f4a2f9333b57479d2537280 Author: Zarija Lukic Date: Thu Oct 19 16:28:40 2017 -0700 Use NDIAG instead of hard-coded 2 Source/Src_3d/reset_internal_energy_3d.f90 commit fc8a7b1bbcfd8bfdba9bf1343b5dccc435d64889 Author: Zarija Lukic Date: Thu Oct 19 16:17:15 2017 -0700 add z_HI to the list of outputs Source/Initialization/Nyx_setup.cpp commit 678db4ac6d6a0a78de6a03e79348c25b3ce751f3 Author: Ann Almgren Date: Thu Oct 19 13:08:17 2017 -0700 Add the ability to write 2-d slices of 3-d data every "slice_int" coarse time steps. This only writes slices of data at the level 0 resolution -- it is called from postCoarseTimeStep. Source/Make.package Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_slice.H Source/Nyx_slice.cpp Source/Src_3d/Make.package Source/Src_3d/fill_slice_3d.f90 commit 9d2425ce5759b2a0104cbaad430b5d3a6ce8aa94 Author: Andrew Myers Date: Wed Oct 18 15:45:18 2017 -0700 move this call to the right place. Source/Initialization/Nyx_initdata.cpp Source/Nyx.cpp commit 72268701db278aacfc34f3b6b3af0357bdff7dd6 Author: Andrew Myers Date: Wed Oct 18 15:15:17 2017 -0700 also read in zhi on restart Source/Initialization/Nyx_initdata.cpp commit c283b5b7934fde61c6626c8be68bdac7831706be Author: Andrew Myers Date: Wed Oct 18 14:49:06 2017 -0700 fix bug in init_zhi Source/Initialization/Nyx_initdata.cpp commit 81e6d5d23a25c805a8305bc38b79be6999886442 Author: Zarija Lukic Date: Fri Oct 13 22:32:36 2017 -0700 zhi file converter Util/zhi_converter/GNUmakefile Util/zhi_converter/Make.package Util/zhi_converter/main.cpp commit e7b5c340d3bfc87be7c417824838de8c24d1dc9b Author: Zarija Lukic Date: Thu Oct 12 18:40:58 2017 -0700 HPGMG poisson solver update Exec/Make.Nyx Source/Gravity/Gravity.cpp Util/hpgmg/finite-volume/source/defines.h Util/hpgmg/finite-volume/source/mg.h Util/hpgmg/finite-volume/source/mg_hpgmg.c commit f2f5c5857840fcb87708a1284b8d6c44dd9ab84c Merge: 5e91a79f 53e787e9 Author: vince Date: Tue Oct 10 14:56:45 2017 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/Nyx into development commit 53e787e99c18603ade52ac0b8c550409d2a8d025 Merge: d1c1c4bc be1879eb Author: Andrew Myers Date: Mon Oct 9 10:24:32 2017 -0700 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development commit d1c1c4bcdc646d0a6e41cf08a9f05d1c27619f28 Author: Andrew Myers Date: Mon Oct 9 10:22:35 2017 -0700 add an assertion to check that the domain resolution is larger than the file res Source/Initialization/Nyx_initdata.cpp commit 0b84f850c056ae3bff96bc4d07e36bf1c9c7ad1a Author: Andrew Myers Date: Mon Oct 9 10:17:04 2017 -0700 add option to initialize zhi from a file. Source/Initialization/Nyx_initdata.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_F.H Source/Nyx_nd.f90 commit be1879eb0e74edca1782321748022c127ec2e88c Author: Weiqun Zhang Date: Mon Oct 9 08:51:40 2017 -0700 Array --> Vector Diagnostics/AmrDerive.cpp Exec/DrivenTurbulence/Nyx_error.cpp Exec/GravityTests/zeldovich_dm/build/Nyx_error.cpp Exec/HydroTests/DoubleRarefaction/Nyx_error.cpp Exec/HydroTests/Sedov/Nyx_error.cpp Exec/HydroTests/Sod/Nyx_error.cpp Exec/HydroTests/StrongShockTube/Nyx_error.cpp Exec/HydroTests/TurbForce/Nyx_error.cpp Exec/HydroTests/TurbForce/Nyx_setup.cpp Exec/LyA/Nyx_error.cpp Exec/LyA_AGN/Nyx_error.cpp Exec/MiniSB/Nyx_error.cpp Exec/RegressionTest/Nyx_error.cpp Exec/SantaBarbara/Nyx_error.cpp Exec/Scaling/Nyx_error.cpp Source/AGN/AGN_sources.cpp Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/DarkMatterParticleContainer.H Source/DarkMatterParticleContainer.cpp Source/DerivedQuantities/ParticleDerive.cpp Source/Forcing/Forcing_init.cpp Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/read_plotfile.cpp Source/NeutrinoParticleContainer.H Source/NeutrinoParticleContainer.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticleContainer.H Source/NyxParticles.cpp Source/Nyx_output.cpp Source/Tagging/Nyx_error.cpp Source/sum_integrated_quantities.cpp Source/two_particle_advance.cpp commit df3201f187381590a636e3653a2b86eebf5aadab Merge: 71556d77 4ee8f072 Author: Zarija Lukic Date: Fri Oct 6 13:49:22 2017 -0700 Merge branch 'development' commit a466fc0ad47801eedd866f484693dae38fdc700c Merge: f006e4a5 4ee8f072 Author: Andrew Myers Date: Fri Oct 6 13:08:50 2017 -0700 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development commit 5e91a79fead2281b5d3a4afcad1afb16c4c1cf5f Merge: 842c7de5 4ee8f072 Author: vince Date: Fri Oct 6 12:10:53 2017 -0700 merge fix. commit 842c7de5a226b968bf41f0aaa64020bc4c1ee409 Author: vince Date: Fri Oct 6 12:09:20 2017 -0700 prof fix. Exec/LyA/GNUmakefile Exec/LyA/inputs Source/NyxParticleContainer.H Source/advance_particles.cpp commit 4ee8f072120ad0294a4aa026c295a7ea9f90af12 Author: Zarija Lukic Date: Fri Oct 6 00:08:04 2017 -0700 Added density dependent UVB heating option Exec/LyA/inputs Exec/LyA_AGN/inputs Exec/Scaling/inputs Source/EOS/atomic_rates.f90 Source/HeatCool/f_rhs.f90 commit dd347c5aa048ae1b63e1eba9e3dcceb28dc2149e Author: Zarija Lukic Date: Thu Oct 5 22:46:57 2017 -0700 Adjust reionization heating in vode and cvode Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 commit c8bf32534eb5bfe4997dc1fbb8aa40ee772d0175 Author: Zarija Lukic Date: Thu Oct 5 22:10:42 2017 -0700 Set redshift to half the timestep in second strang Source/strang_splitting.cpp commit f006e4a58b3b37e6a54ddf7c38583a207404f154 Merge: 575e0ac5 20193a16 Author: Andrew Myers Date: Thu Oct 5 13:12:47 2017 -0700 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development commit 20193a1601726fa5927444bcaa8d97ae59883344 Author: Zarija Lukic Date: Thu Oct 5 00:53:13 2017 -0700 heating setup in vode Source/HeatCool/integrate_state_vode_3d.f90 commit 66c10d72cf0589937d1d39950487b4122a115013 Author: Zarija Lukic Date: Wed Oct 4 08:11:50 2017 -0700 ifdef guards to tabulate_rates() call Source/Initialization/Nyx_setup.cpp commit cbb791b9a19bc5f6111784883155edc465a270b7 Author: Zarija Lukic Date: Tue Oct 3 22:28:36 2017 -0700 eos_hc organization, optional species Source/EOS/eos_hc.f90 commit 6a68c0327c5d5d7a5488c602ce43a10c9beafd78 Author: Zarija Lukic Date: Tue Oct 3 19:51:24 2017 -0700 Correction lost in merge... Source/HeatCool/integrate_state_vode_3d.f90 commit ed3765c8acff935ccf2db1984c00d9895f39dbfd Author: zarija Date: Tue Oct 3 19:02:59 2017 -0700 Merge PR 23 Source/EOS/atomic_rates.f90 Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_fcvode_3d_stubs.f90 Source/HeatCool/integrate_state_fcvode_vec_3d.f90 Source/HeatCool/integrate_state_fcvode_vec_3d_stubs.f90 Source/Initialization/Nyx_setup.cpp Source/Initialization/check_initial_species_3d.f90 Source/Nyx_F.H Source/Nyx_nd.f90 commit 5916e51214a10222ab0ae9e3209f35b8d2606571 Author: Zarija Lukic Date: Tue Oct 3 11:20:08 2017 -0700 ZHI template in Prob_3d Exec/LyA/Prob_3d.f90 Exec/LyA_AGN/Prob_3d.f90 Exec/Scaling/Prob_3d.f90 commit ce1673c1663be35f0899ff924122406f1532dda3 Author: Zarija Lukic Date: Mon Oct 2 21:28:41 2017 -0700 Updated GNUmakefiles Exec/DrivenTurbulence/GNUmakefile Exec/GravityTests/MacLaurin/GNUmakefile Exec/HydroTests/DoubleRarefaction/GNUmakefile Exec/HydroTests/Sedov/GNUmakefile Exec/HydroTests/Sod/GNUmakefile Exec/HydroTests/StrongShockTube/GNUmakefile Exec/HydroTests/TurbForce/GNUmakefile Exec/LyA/GNUmakefile Exec/LyA_AGN/GNUmakefile Exec/MiniSB/GNUmakefile Exec/RegressionTest/GNUmakefile Exec/SantaBarbara/GNUmakefile Exec/Scaling/GNUmakefile commit aaf3593aadc5ee5ad3dd83978d6b54e35f260010 Author: Zarija Lukic Date: Mon Oct 2 21:25:17 2017 -0700 Added missing vode stub in DrivenTurbulence setup Exec/DrivenTurbulence/heat_cool_stubs.f90 commit b0cdb13567bba62568d4d2bc49795bb97e38f92f Merge: 0f720576 65722fcf Author: Ann Almgren Date: Mon Oct 2 19:58:08 2017 -0700 Merge branch 'development' of https://www.github.com/AMReX-Astro/Nyx into development commit 0f720576ba512e5764375ba637edce74235d0ded Author: Ann Almgren Date: Mon Oct 2 19:57:52 2017 -0700 Need to test logicals using eqv not eq Source/HeatCool/integrate_state_vode_3d.f90 Source/Src_3d/compute_temp_3d.f90 commit 65722fcf3026eeb53695e5f35fbc7a28da5a6df3 Author: Zarija Lukic Date: Mon Oct 2 19:56:34 2017 -0700 Fix eg -> eqv for gnu Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 Source/Src_3d/compute_temp_3d.f90 commit 32c3a861d4b538626e901a73f1b2be874b85ac79 Author: Zarija Lukic Date: Mon Oct 2 19:19:59 2017 -0700 Different UVB options Source/EOS/eos_hc.f90 Source/EOS/eos_stuff.f90 Source/HeatCool/f_rhs.f90 Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 Source/HeatCool/vode_aux.f90 Source/Src_3d/compute_temp_3d.f90 commit 02314011e0c527e8fd02a28582cc2e331845bb70 Author: Zarija Lukic Date: Mon Oct 2 16:22:10 2017 -0700 Reionization reorganization... Exec/LyA/inputs Exec/LyA_AGN/inputs Exec/Scaling/inputs Source/EOS/Make.package Source/EOS/atomic_rates.f90 Source/EOS/reion_aux_module.f90 commit 8c8fbf794a7e365b9e051fa8bae2b805d01ae4e4 Author: Zarija Lukic Date: Mon Oct 2 11:43:59 2017 -0700 Remove dysfunctional heat_cool_type = 1 Source/HeatCool/Make.package Source/HeatCool/cooling.f90 Source/HeatCool/ext_src_hc_3d.f90 Source/HeatCool/integrate_state_3d.f90 Source/HeatCool/integrate_state_hc_3d.f90 commit 8291094bd6389bd5ee76ec99c2645402182ac356 Author: Zarija Lukic Date: Mon Oct 2 09:51:37 2017 -0700 Unused rates in f_rhs removed Source/HeatCool/f_rhs.f90 commit 4ed2020b8526def0022556f80b5e4c233f499762 Author: Zarija Lukic Date: Sat Sep 30 20:05:05 2017 -0700 Temp fix in vector version of EOS Source/EOS/eos_hc.f90 commit 727af56ef1e9a88972a0afad118f6f62ef0ab33c Merge: 33dcdb36 de0d63b7 Author: zarija Date: Fri Sep 29 13:54:44 2017 -0700 Merge pull request #25 from bcfriesen/fix_simd_width HeatCool, CVODE: misc SIMD width fixes commit 33dcdb361ab4cd10ccfa7242b4020dddd4cf1d6d Merge: e8d2f4ee 05e41f46 Author: zarija Date: Fri Sep 29 13:54:23 2017 -0700 Merge pull request #24 from bcfriesen/update_CVODE_docs UserGuide: add a chapter about HeatCool, VODE, and CVODE commit de0d63b772e229a18c51b2c5397bf47ca7645c35 Author: Brian Friesen Date: Thu Sep 28 14:01:18 2017 -0700 HeatCool: remove unnecessary simd_width "use" statement from a few functions Source/HeatCool/vode_aux.f90 Source/Initialization/cvode_simd.f90 commit 57bda797c33cbfe6d9687d125de26ec194754b6e Author: Brian Friesen Date: Thu Sep 28 14:00:35 2017 -0700 HeatCool: print the correct indices in SIMD CVODE if we have bad energy value Source/HeatCool/integrate_state_fcvode_vec_3d.f90 commit 2bb9daa86cf32a8073bd5d7b1de071a9fff17b55 Author: Brian Friesen Date: Thu Sep 28 13:59:49 2017 -0700 HeatCool: wrap some comment text so it doesn't run on for so many columns Source/HeatCool/integrate_state_fcvode_vec_3d.f90 commit 4b5d39f3172d5f7910dc291714601294f53ac981 Author: Brian Friesen Date: Thu Sep 28 13:59:24 2017 -0700 HeatCool: use explicit array-slicing bounds for a few SIMD CVODE statements Source/HeatCool/f_rhs.f90 commit d78188a025e6b1e6fa0ebd7b0364fe367427611b Author: Brian Friesen Date: Thu Sep 28 13:51:40 2017 -0700 HeatCool: document our way out of the simd_width+blocking problem When we use the SIMD ODE integration method, we loop over the x-direction of each box/tile in strides of simd_width. However, if the number of cells in the x-direction is not a multiple of simd_width, we fall off the end of the box and compute garbage. One way to fix this is to make simd_width adaptive so that, if the modulus of the x-length and simd_width is not zero, it shortens itself on the last iteration so that it stays within the box. However, doing so would require tearing down the existing CVODE solver scratch memory and reinitializing it with the shorter size to do the last iteration of the x-direction, then tear down the solver memory again and reinitialize it again with the original simd_width. This extra work would likely destroy any speedup that we otherwise gain from using the SIMD solver method over the scalar cell-by-cell method. So instead, we simply quit with an error if the modulus is not zero, and require the user to build boxes that are appropriately sized. Source/HeatCool/integrate_state_fcvode_vec_3d.f90 commit e8d2f4ee6ccc2ebdb97581889bc571b121b429f7 Author: Zarija Lukic Date: Wed Sep 27 21:31:49 2017 -0700 Use dynamic tiling in source integration Source/SourceTerms/Nyx_sources.cpp commit 2caf5d0b836d5061e0bf6a85f794b3dfc5c5591f Author: Zarija Lukic Date: Tue Sep 26 17:09:55 2017 -0700 Correcting compile time ifdefs... Source/Nyx.cpp Source/comoving.cpp commit 679f856bb8c6720607688a19bc0e1a9bdf7f8c31 Author: Zarija Lukic Date: Tue Sep 26 13:09:09 2017 -0700 Don't call interp_to_this_z() when HEATCOOL is off Source/Nyx.cpp Source/comoving.cpp commit e77eb031364d053eba764299a877ddb0d702ee4c Author: Zarija Lukic Date: Tue Sep 26 09:20:57 2017 -0700 Use Base instead of F_Interfaces Exec/Make.Nyx Source/EOS/atomic_rates.f90 commit f7eaca50bed1d1f91ee2208f21efd87a7704f942 Author: Zarija Lukic Date: Mon Sep 25 21:45:08 2017 -0700 TREECOOL info in inputs Exec/LyA/inputs Exec/LyA/inputs.rt Exec/LyA_AGN/inputs Exec/Scaling/inputs Source/EOS/atomic_rates.f90 commit 61f3541b0f119d32b1813e9db14278b7a0753cb3 Author: Zarija Lukic Date: Mon Sep 25 21:43:27 2017 -0700 add amrex's F_Interfaces/Base to compile list Exec/Make.Nyx commit 35d2eeffd064185709b6fab4773ac54609f50ab3 Merge: 9520517b c4365277 Author: Andrew Myers Date: Sat Sep 23 22:57:21 2017 -0700 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development commit 9520517bdf312a6e240c7c853428d740903becee Author: Andrew Myers Date: Sat Sep 23 22:57:04 2017 -0700 be more memory efficient in the morton file reader. Source/DarkMatterParticleContainer.cpp commit c4365277ba28df9959cfb03d3cc8066a7fa877d9 Author: petermcLBL Date: Fri Sep 22 19:11:48 2017 -0700 Initial sumBoundary is for agn_density_old, not for agn_density. Source/Nyx_halos.cpp commit 14d829efba667b9fc39a5e135235fe6b99da71a6 Author: Ann Almgren Date: Fri Sep 22 15:51:57 2017 -0700 We were missing a SumBoundary call after the first call to AssignDensity for the old halos -- this was a bug where the mass of a halo near a grid boundary was not getting fully added but was getting fully subtracted Source/Nyx_halos.cpp commit 5e72d6a96abd130b11d394b44b36e48122bda1cc Author: Ann Almgren Date: Fri Sep 22 15:51:13 2017 -0700 Fix the loop indices over particles in compute_overlap. Source/AGN/agn_3d.f90 commit 05e41f469afc0575037fd130ba61a4f59e2520a2 Author: Brian Friesen Date: Fri Sep 22 10:58:10 2017 -0400 UserGuide: add some words about the numerical tolerances in HeatCool integration UsersGuide/HeatCool/NyxHeatCool.tex commit 14c1b51c85fb7f94bb35dce87c20e4ddc865088e Author: Brian Friesen Date: Fri Sep 22 09:58:07 2017 -0400 UserGuide: add a chapter about HeatCool, VODE, and CVODE UsersGuide/HeatCool/NyxHeatCool.tex UsersGuide/HeatCool/heatcool.bib UsersGuide/NyxUserGuide.tex commit ec839e1bf183da2d15ce0af2940e25c91757715b Author: Zarija Lukic Date: Thu Sep 21 00:04:21 2017 -0700 hpgmg flags in problem setups Exec/LyA/GNUmakefile Exec/LyA/inputs Exec/LyA_AGN/GNUmakefile Exec/LyA_AGN/inputs Exec/Scaling/GNUmakefile Exec/Scaling/inputs commit 869f977f18c261e79cd6259f15517e31f69e8369 Author: Zarija Lukic Date: Wed Sep 20 23:35:27 2017 -0700 memory leaks fixes in hpgmg Util/hpgmg/finite-volume/source/level.c Util/hpgmg/finite-volume/source/mg_hpgmg.c commit a9893330f436d055ac1616d42c315ddbb2e6f0da Author: Zarija Lukic Date: Wed Sep 20 23:30:19 2017 -0700 Brian's HPGMG branch Util/hpgmg/LICENSE Util/hpgmg/README Util/hpgmg/finite-volume/README Util/hpgmg/finite-volume/local.mk Util/hpgmg/finite-volume/source/Make.package Util/hpgmg/finite-volume/source/Makefile Util/hpgmg/finite-volume/source/README Util/hpgmg/finite-volume/source/TODO Util/hpgmg/finite-volume/source/call_hpgmg_setup.c Util/hpgmg/finite-volume/source/compile Util/hpgmg/finite-volume/source/defines.h Util/hpgmg/finite-volume/source/hpgmg-fv.c Util/hpgmg/finite-volume/source/hpgmg_setup.c Util/hpgmg/finite-volume/source/level.c Util/hpgmg/finite-volume/source/level.h Util/hpgmg/finite-volume/source/local.mk Util/hpgmg/finite-volume/source/mg.h Util/hpgmg/finite-volume/source/mg_hpgmg.c Util/hpgmg/finite-volume/source/operators.27pt.c Util/hpgmg/finite-volume/source/operators.7pt.c Util/hpgmg/finite-volume/source/operators.fv2.c Util/hpgmg/finite-volume/source/operators.fv4.c Util/hpgmg/finite-volume/source/operators.h Util/hpgmg/finite-volume/source/operators.old.c Util/hpgmg/finite-volume/source/operators.old/aggregate.mpi/chebyshev.c Util/hpgmg/finite-volume/source/operators.old/aggregate.mpi/gsrb.c Util/hpgmg/finite-volume/source/operators.old/aggregate.mpi/jacobi.c Util/hpgmg/finite-volume/source/operators.old/apply_op.c Util/hpgmg/finite-volume/source/operators.old/chebyshev.c Util/hpgmg/finite-volume/source/operators.old/gsrb.c Util/hpgmg/finite-volume/source/operators.old/iterators.c Util/hpgmg/finite-volume/source/operators.old/jacobi.c Util/hpgmg/finite-volume/source/operators.old/misc.c Util/hpgmg/finite-volume/source/operators.old/residual.c Util/hpgmg/finite-volume/source/operators.old/symgs.c Util/hpgmg/finite-volume/source/operators/apply_op.c Util/hpgmg/finite-volume/source/operators/blockCopy.c Util/hpgmg/finite-volume/source/operators/boundary_fd.c Util/hpgmg/finite-volume/source/operators/boundary_fv.c Util/hpgmg/finite-volume/source/operators/chebyshev.c Util/hpgmg/finite-volume/source/operators/exchange_boundary.c Util/hpgmg/finite-volume/source/operators/gsrb.c Util/hpgmg/finite-volume/source/operators/interpolation_p0.c Util/hpgmg/finite-volume/source/operators/interpolation_p1.c Util/hpgmg/finite-volume/source/operators/interpolation_p2.c Util/hpgmg/finite-volume/source/operators/interpolation_v2.c Util/hpgmg/finite-volume/source/operators/interpolation_v4.c Util/hpgmg/finite-volume/source/operators/jacobi.c Util/hpgmg/finite-volume/source/operators/misc.c Util/hpgmg/finite-volume/source/operators/problem.fv.c Util/hpgmg/finite-volume/source/operators/problem.p4.c Util/hpgmg/finite-volume/source/operators/problem.p6.c Util/hpgmg/finite-volume/source/operators/problem.sine.c Util/hpgmg/finite-volume/source/operators/rebuild.c Util/hpgmg/finite-volume/source/operators/residual.c Util/hpgmg/finite-volume/source/operators/restriction.c Util/hpgmg/finite-volume/source/operators/symgs.c Util/hpgmg/finite-volume/source/solvers.c Util/hpgmg/finite-volume/source/solvers.h Util/hpgmg/finite-volume/source/solvers/bicgstab.c Util/hpgmg/finite-volume/source/solvers/cabicgstab.c Util/hpgmg/finite-volume/source/solvers/cacg.c Util/hpgmg/finite-volume/source/solvers/cg.c Util/hpgmg/finite-volume/source/solvers/matmul.c Util/hpgmg/finite-volume/source/timers.c Util/hpgmg/finite-volume/source/timers.h Util/hpgmg/finite-volume/source/timers/mpi.c Util/hpgmg/finite-volume/source/timers/omp.c Util/hpgmg/finite-volume/source/timers/x86.c commit 551c803ce29997c84b4715d6b39b0dac094be115 Author: Peter McCorquodale Date: Tue Sep 19 13:17:34 2017 -0700 Convert to primitive variables before adding and subtracting density. Then convert back to conserved variables after density has been updated, because the conserved variables are primitive variables multiplied by density. Source/Nyx_halos.cpp commit 58e21829bc02072e2ecb10bf6e0911278eea199e Author: Peter McCorquodale Date: Tue Sep 19 13:15:20 2017 -0700 Added explanatory comments. Source/AGN/agn_3d.f90 commit f7352b96e8e210ad38286533886c8321062c9cef Merge: fcbe72e5 b8b3c505 Author: Peter McCorquodale Date: Tue Sep 19 13:12:36 2017 -0700 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development Conflicts: Source/HeatCool/integrate_state_vode_3d.f90 commit fcbe72e56165bd84a7dae3266cc88abe5b043f07 Author: Peter McCorquodale Date: Tue Sep 19 11:26:39 2017 -0700 More informative debugging info. Source/AGN/agn_3d.f90 commit 7771244a8a0f6c7eaf8a7db2b41b6ea9734152d3 Author: Peter McCorquodale Date: Tue Sep 19 11:25:16 2017 -0700 Deposit particle masses onto grid density before adding new particles. Will be removed after adding new particles. Source/Nyx_halos.cpp commit e885bdc3d150504765090b234d503f801cb52b33 Author: Peter McCorquodale Date: Tue Sep 19 11:24:31 2017 -0700 Write out density if energy is negative. Source/HeatCool/integrate_state_vode_3d.f90 commit b8b3c5059a09d01cdc1bc20d6a15b87e5c7030fc Author: Zarija Lukic Date: Sat Sep 16 15:21:08 2017 -0700 Keeping only one binary file in the repo Exec/LyA_AGN/64sssss_20mpc.nyx commit c023838eecb27f8d527254cc18937e4c046bd96f Author: Ann Almgren Date: Sat Sep 16 09:15:11 2017 -0700 Same fix as last commit -- nd .ge. 2 rather than nd .eq. 2 Exec/LyA_AGN/Prob_3d.f90 Exec/Scaling/Prob_3d.f90 commit 3581523a24c5d44f90d1d24cc29dfac7667f0418 Author: Ann Almgren Date: Sat Sep 16 09:12:34 2017 -0700 Need to test on nd .ge. 2 not nd .eq. 2 Exec/LyA/Prob_3d.f90 commit 258ce2a368a52dcdae749cd9bc8f9671f562baef Author: Zarija Lukic Date: Fri Sep 15 23:54:10 2017 -0700 New field setup in diag_eos Exec/LyA/inputs Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/meth_params.f90 commit 5d132c72d03b63739d0f08e7ffa0135b5c6b9777 Author: Ann Almgren Date: Fri Sep 15 18:29:18 2017 -0700 We now define NDIAG in Nyx_setup.cpp and pass the value through to the Fortran. Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 commit 761dc8d34912c9cf075bc1ab3fa9a125bd020191 Author: Ann Almgren Date: Fri Sep 15 18:14:03 2017 -0700 Replace 2 by NDIAG / D.nComp() everywhere that DiagEOS (in C++) or diag_eos (in Fortran) is defined or in FillPatch etc ... Source/AGN/AGN_sources.cpp Source/AGN/agn_3d.f90 Source/Forcing/integrate_state_force_3d.f90 Source/HeatCool/integrate_state_3d.f90 Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_fcvode_3d_stubs.f90 Source/HeatCool/integrate_state_fcvode_vec_3d.f90 Source/HeatCool/integrate_state_fcvode_vec_3d_stubs.f90 Source/HeatCool/integrate_state_hc_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_hydro.cpp Source/Nyx_nd.f90 Source/SourceTerms/Nyx_sources.cpp Source/Src_3d/compute_temp_3d.f90 Source/meth_params.f90 commit 2519e33f5adecd28a047a14b1aa19e910487b15a Author: Ann Almgren Date: Fri Sep 15 15:47:10 2017 -0700 Remove nyx.small_pres from the inputs file since it is no longer set that way Exec/LyA/inputs Exec/LyA/inputs.rt Exec/LyA/inputs.small.dsc Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA_AGN/inputs Exec/LyA_AGN/inputs.rt Exec/SantaBarbara/inputs commit 191b920b0d1012014f2e4c48081597fe09dd1653 Author: Ann Almgren Date: Fri Sep 15 15:43:05 2017 -0700 Remove show_timings since it is no longer used anywhere. Exec/DrivenTurbulence/inputs Exec/DrivenTurbulence/inputs.regtest Exec/LyA/inputs Exec/LyA/inputs.rt Exec/LyA/inputs.small.dsc Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA_AGN/inputs Exec/LyA_AGN/inputs.rt Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Exec/MiniSB/inputs.analysis Exec/SantaBarbara/inputs Exec/Scaling/inputs Source/Gravity/Gravity.H commit 15967281d6f547a8719a42c2f30a788ee673f6b7 Author: Ann Almgren Date: Fri Sep 15 15:26:25 2017 -0700 1) Move all of the integrate*f90 files from LyA into Source/HeatCool 2) Clean up the individual GNUmakefiles by moving much of the commonality into Exec/Make.Nyx Exec/LyA/GNUmakefile Exec/LyA/Make.package Exec/LyA_AGN/GNUmakefile Exec/Make.Nyx Exec/MiniSB/GNUmakefile Exec/SantaBarbara/GNUmakefile Exec/Scaling/GNUmakefile Source/HeatCool/Make.package Source/HeatCool/fcvode_extras.f90 Source/HeatCool/integrate_state_fcvode_3d.f90 Source/HeatCool/integrate_state_fcvode_vec_3d.f90 commit 497ba068af47e6c2cfc9479818d41cb61866b935 Author: Zarija Lukic Date: Thu Sep 14 22:10:13 2017 -0700 Calculating more temperature summaries Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Src_3d/compute_temp_3d.f90 Source/write_info.cpp commit 1815df0626c052c7bc452eaaac9cb3731f801746 Author: Zarija Lukic Date: Thu Sep 14 19:47:24 2017 -0700 Set initial T on adiabatic cooling relation Exec/LyA/Prob_3d.f90 Exec/LyA_AGN/Prob_3d.f90 Exec/Scaling/Prob_3d.f90 commit bda81460d398c26e7aa7d87b507dbaa00eba1f0d Author: Zarija Lukic Date: Thu Sep 14 19:44:25 2017 -0700 Unifying LyA, LyA_AGN, and Scaling problems (LyA_AGN mostly unchanged), their inputs. Exec/LyA/32.nyx Exec/LyA/64sssss_20mpc.nyx Exec/LyA/inputs Exec/LyA_AGN/inputs Exec/Scaling/inputs commit 8544539ed0cd01ad1c0e415ab5cf207c09cd4687 Author: Zarija Lukic Date: Thu Sep 14 18:53:22 2017 -0700 simplifying integrate_state_vode_3d mess Exec/LyA/integrate_state_vode_3d.f90 Exec/LyA_AGN/integrate_state_vode_3d.f90 Exec/Scaling/integrate_state_vode_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 commit f2088668b7260b3d48c91fce371a12d8c93cf776 Author: Zarija Lukic Date: Thu Sep 14 17:14:29 2017 -0700 fixed missing rt type Source/HeatCool/integrate_state_vode_3d.f90 commit 8f532481ed79661300abc027cafc3f76fd042638 Author: Zarija Lukic Date: Thu Sep 14 15:23:21 2017 -0700 updating GNUmakefiles in test problems Exec/LyA/GNUmakefile Exec/LyA_AGN/GNUmakefile Exec/Scaling/GNUmakefile commit 90ffc622f0c37367eb9e60c0661e6c576dab3ba7 Author: Brian Friesen Date: Thu Sep 14 12:52:23 2017 -0700 Initialization: fix the #define which calls fort_setup_eos_params() (#22) This occurs with regular VODE, not just CVODE. So this should happen if HEATCOOL is defined, not just CVODE. Source/Initialization/Nyx_initdata.cpp commit 980ce423df5e236e3b380059fb42a8af60966cf5 Author: Ann Almgren Date: Wed Sep 13 21:09:00 2017 -0700 Make the end subroutine match the subroutine statement Source/HeatCool/integrate_state_fcvode_vec_3d_stubs.f90 commit 6c4d379f34f793f37ba0043a72072fcdff4c6356 Author: Brian Friesen Date: Wed Sep 13 21:08:00 2017 -0700 HeatCool: add stubs for SIMD CVODE function if USE_HEATCOOL=FALSE (#21) Source/HeatCool/Make.package Source/HeatCool/integrate_state_fcvode_vec_3d_stubs.f90 commit 594db2cc7aa6106a8766bbc9171224b4f828b3d4 Author: Brian Friesen Date: Wed Sep 13 20:11:37 2017 -0700 EOS, HeatCool: implement SIMD ODE integration (v2) (#20) * EOS: add SIMD function nyx_eos_given_RT_vec() This is a SIMD version of nyx_eos_given_RT() * EOS: add SIMD function ion_n_vec() This is a SIMD version of the function ion_n() * EOS: add SIMD function iterate_ne_vec() This is a SIMD version of the function iterate_ne(). * EOS: add SIMD function nyx_eos_T_given_Re_vec() This is a SIMD version of the function nyx_eos_T_given_Re(). * Src_3d: added SIMD function fort_compute_temp_vec() This is a SIMD version of the function fort_compute_temp() * Initialization: add Nyx::set_simd_width() and Fortran set_simd() functions These set the SIMD width. * EOS: add subroutine iterate_ne_vec() This is a SIMD version of the function iterate_ne(). * EOS: add function nyx_eos_T_given_Re_vec() This is a SIMD version of the function nyx_eos_T_given_Re(). * EOS: add subroutine hc_rates_vec() This is a SIMD version of the subroutine hc_rates(). * HeatCool, LyA: add functions f_rhs_vec() and RhsFn_vec() These are SIMD versions of the functions f_rhs() and RhsFn(). * HeatCool: add array versions of misc VODE variables These will only be used with the SIMD functions. * Src_3d: add subroutine fort_compute_temp_vec() This is a SIMD version of the subroutine fort_compute_temp(). * LyA: add subroutine fcvode_wrapper_vec() This is a SIMD version of the subroutine fcvode_wrapper(). * LyA: add subroutine integrate_state_fcvode_vec() This is a SIMD version of the function integrate_state_fcvode(). * Nyx::read_params(): add a few sanity checks for the SIMD CVODE solver * EOS: replace missing TCOOLMIN_R and TCOOLMAX_R that got dropped during merge These are the real values (not log10 values) of TCOOLMIN and TCOOLMAX. * Nyx: print "SIMD CVODE" to STDOUT when using SIMD CVODE integrator * HeatCool, EOS: revert back to original SIMD versions of compute_temp * LyA: fix two memory leaks in integrate_state_fcvode_vec() * LyA: minor formatting fixes; no functional changes * LyA: get the # of eqns for SIMD CVODE from the "simd_width" parameter * CVODE: make misc SIMD functions public instead of protected We will need to call them from main() instead of within a Nyx object (due to problems with Nyx objects going out of scope during a restart), so we need them to be public. * CVODE: allocate SIMD vectors in main() instead of in Nyx member functions During a checkpoint restart, there were problems with Nyx objects going out of scope and so these arrays were in the wrong allocation state. * CVODE: fix a few typos being printed to STDOUT * EOS: don't assign vec_count at declaration It gets initialized in the function body, so no reason to initialize it at declaration. * EOS: remove commented-out print statement * HeatCool: set length of dummy arrays explicitly in hc_rates_vec() Since we know what it is, there is no reason to make the compiler guess. * HeatCool: make "e_in" dummy argument in f_rhs_vec() more in line with its behavior in f_rhs() f_rhs() sets e_in to TINY() if it enters the function with a negative value. In the original version of f_rhs_vec() the value of e_in() was copied to a local variable "e" which was then set to TINY if negative. But it is less confusing for the two functions to have the same behavior. * HeatCool: add SAVE attribute to the SIMD versions of the misc vars in vode_aux This way they have the same behavior as their scalar counterparts. * Initialization: allocate vode_aux arrays in an OpenMP parallel region These are threadprivate variables, so we need to allocate them in a parallel region or else they will be allocated only on the master thread. * LyA, CVODE: switch from dense solver to diagonal solver for SIMD COVDE The Jacobian matrix of a "system" of independent equations is diagonal, so let's use that to avoid computing all the off-diagonal elements which are all zero anyway. * comoving_a_post_restart(): add missed check for SIMD CVODE mode (heat_cool_type=7) * EOS: make interpolation err msg in iterate_ne()/iterate_ne_vec() more descriptive * EOS, HeatCool, VODE: make all tolerance parameters run-time inputs The tolerances used in the heating/cooling integration affect results differently depending on whether one uses the scalar or SIMD implementation. Since it will take some work to find tolerances that yield the same result in both approaches, it will be convenient to be able to specify these at run time. These tolerances are specified by three parameters: - nyx.eos_nr_eps: tolerance for computing Newton-Raphson iteration in iterate_ne() - nyx.vode_rtol: relative tolerance in VODE integration - nyx.vode_atol_scaled: absolute tolerance in VODE integration, scaled by the initial value of the independent variable in the ODE * HeatCool: add code path for SIMD CVODE in ext_src_hc() Missed this code path earlier when adding the SIMD CVODE runtime option. * Nyx::read_params(): print the percent sign "%" the correct way * Nyx::read_params(): add warning message about experimental nature of SIMD CVODE * HeatCool, CVODE: fix case of uninitialized bool "hot" in SIMD CVODE * LyA, CVODE: fix SIMD function name in error messages * EOS: add stubs for SIMD functions if called without USE_CVODE=TRUE and USE_HEATCOOL=TRUE * CVODE: don't compile CVODE-relevant code unless USE_CVODE=TRUE Exec/LyA/fcvode_extras.f90 Exec/LyA/integrate_state_fcvode_vec_3d.f90 Source/EOS/atomic_rates.f90 Source/EOS/eos_hc.f90 Source/EOS/eos_stuff.f90 Source/HeatCool/Make.package Source/HeatCool/cooling.f90 Source/HeatCool/ext_src_hc_3d.f90 Source/HeatCool/f_rhs.f90 Source/HeatCool/heat_cool_stubs.f90 Source/HeatCool/integrate_state_3d.f90 Source/HeatCool/vode_aux.f90 Source/Initialization/Make.package Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/cvode_simd.f90 Source/Make.package Source/Nyx.H Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/Src_3d/compute_temp_3d.f90 Source/comoving.cpp Source/main.cpp Source/misc_params.f90 commit f61e3d11b7c553f204ec523892d6b808196cf0b8 Merge: 60879508 aee1b5a3 Author: WeiqunZhang Date: Tue Sep 12 10:39:34 2017 -0700 Merge pull request #18 from bcfriesen/fix_threading_bugs Fix threading bugs commit aee1b5a3ea35cf27ff49a8430be74ff2015072c4 Author: Brian Friesen Date: Tue Sep 12 10:33:04 2017 -0700 Nyx::just_the_hydro(): restore manual initialization of reduction variables If OpenMP is disabled, the variables "e_added" and "ke_added" still should be initialized to zero, so initialize them outside of the OpenMP parallel region. Source/Nyx_hydro.cpp commit 090197c8db51dbd08702393e5635df85336acdb1 Author: Brian Friesen Date: Tue Sep 12 10:17:58 2017 -0700 Nyx::just_the_hydro(): remove manual initialization of reduction variables In commit f3bdfe4 ("Nyx::just_the_hydro(): add OpenMP reduction construct to e_added,ke_added") I moved initialization of the reduction variables "e_added" and "ke_added" to inside the OpenMP parallel region. However, while this code is not wrong, it is unnecessary because the OpenMP spec requires that the default initializer for the "+" reduction is zero, which is what this code already does by hand. So we can remove it. Source/Nyx_hydro.cpp commit 6087950868e6293e60de1c46bbd2c9d245c82ce5 Merge: 3b1d1585 ec9fa886 Author: WeiqunZhang Date: Tue Sep 12 09:56:05 2017 -0700 Merge pull request #17 from bcfriesen/fix_derived_quantities Initialization: remove entropy from list of derived quantities commit 3b1d1585357dfa67dccd245a214b42be29193acd Author: Weiqun Zhang Date: Tue Sep 12 08:47:40 2017 -0700 Nyx doesn't need to call parallel_initialize because amrex already did it Exec/HydroTests/TurbForce/Nyx_setup.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx_F.H Source/Nyx_nd.f90 commit 58a9c53151acb50d1e430d9e331a6d1721d08237 Author: Brian Friesen Date: Sun Sep 10 22:09:36 2017 -0700 EOS, HeatCool: move z_vode update to fort_interp_to_this_z() This removes a race condition in updating z_vode. Exec/LyA/fcvode_extras.f90 Exec/LyA/integrate_state_vode_3d.f90 Source/EOS/atomic_rates.f90 Source/HeatCool/integrate_state_vode_3d.f90 commit 50b4890bd28c50a35817e17b3fb57e6cfd4902d6 Author: Brian Friesen Date: Sun Sep 10 21:46:45 2017 -0700 EOS, HeatCool: fix naming mixups between "interp_to_this_z()" and "fort_interp_to_this_z()" The convention is to add the "fort_" prefix to Fortran functions if they are called from C++. I messed this up at some point, so now it's all consistent. Source/EOS/atomic_rates.f90 Source/Forcing/ext_src_force_3d.f90 Source/HeatCool/ext_src_hc_3d.f90 Source/HeatCool/integrate_state_fcvode_3d_stubs.f90 Source/Nyx.cpp Source/Nyx_F.H Source/SourceTerms/Nyx_sources.cpp Source/comoving.cpp Source/strang_splitting.cpp commit e7efe86d4c093a0b03b8afd83b5e6809c3ab6816 Author: Brian Friesen Date: Thu Sep 7 12:17:12 2017 -0700 Nyx::strang_second_step(): add OpenMP reduction construct to min_iter, max_iter This fixes a race condition in the min/max comparisons of these variables. Source/strang_splitting.cpp commit f3bdfe4d3c88be4e75a53d21aecfebcfad427400 Author: Brian Friesen Date: Thu Sep 7 12:15:48 2017 -0700 Nyx::just_the_hydro(): add OpenMP reduction construct to e_added,ke_added This fixes a race condition, which is that they were added together without atomics or using thread-private copies. Source/Nyx_hydro.cpp commit 6a081a3bb208ee538cb9a7eac40a16f128018621 Author: Brian Friesen Date: Thu Sep 7 12:00:38 2017 -0700 EOS: move Fortran calls to interp_to_this_z() to C++ The C++ calls to interp_to_this_z() are all done in serial regions, so the race condition of calling interp_to_this_z() from a threaded region is gone. Exec/LyA/fcvode_extras.f90 Exec/LyA/integrate_state_fcvode_3d.f90 Exec/LyA/integrate_state_vode_3d.f90 Source/EOS/atomic_rates.f90 Source/HeatCool/ext_src_hc_3d.f90 Source/HeatCool/integrate_state_hc_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 Source/Nyx.cpp Source/Nyx_F.H Source/SourceTerms/Nyx_sources.cpp Source/Src_3d/compute_temp_3d.f90 Source/comoving.cpp Source/strang_splitting.cpp commit 8c8c310efc9cf8c0cf42884d1b4347e3e2ee645d Author: Brian Friesen Date: Tue Sep 5 12:19:12 2017 -0700 EOS: add BIND(C) attribute to interp_to_this_z() function, and add C++ function prototype This function modifies public variables stored in modules, so we want to have control over which threads execute this function; if multiple threads execute it simultaneously, then there is a race condition. The OpenMP semantics should be in the C++ code, not Fortran, so we will move calls to this function out of existing Fortran functions and into C++ code instead. Source/EOS/atomic_rates.f90 Source/Nyx_F.H commit 0d00f6b873d2d450eb84953b43875452c2b9bd93 Author: Andrew Myers Date: Sat Sep 9 11:34:35 2017 -0700 add option to downsample particle initial conditions from the Morton-ordered file. Source/DarkMatterParticleContainer.H Source/DarkMatterParticleContainer.cpp Source/Nyx.H Source/NyxParticles.cpp commit 38af20060fcb905a87336bd15a9e6d4a9c79a17b Merge: 40664bae 32c44e5e Author: Andrew Myers Date: Fri Sep 8 17:08:07 2017 -0700 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development commit 40664bae5a8d23795ea8861896a467abfa7b4633 Author: Andrew Myers Date: Fri Sep 8 17:06:10 2017 -0700 Checking the the version of the Morton reader uses the split-up files. Source/DarkMatterParticleContainer.H Source/DarkMatterParticleContainer.cpp commit ec9fa8860d0055189cfd46da2712928ed536c382 Author: Brian Friesen Date: Tue Sep 5 14:29:05 2017 -0700 Initialization: remove entropy from list of derived quantities We do not compute the entropy (the relevant code in derentropy() is commented out) so it should not be included as a derived quantity, because the result is wrong. Source/Initialization/Nyx_setup.cpp commit 71556d77952c2de6354fcd879c3c599d188af7bc Merge: 73438977 32c44e5e Author: Ann Almgren Date: Tue Sep 5 09:58:55 2017 -0700 Merge branch 'development' commit 3d62c831d17f846b8d35ac271aa1384fb753ffb5 Author: Andrew Myers Date: Thu Aug 31 18:27:33 2017 -0700 check for Morton files on init Source/Initialization/Nyx_initdata.cpp commit 718795cc7e4eedfb7204547da4b3c3af229e8401 Author: Andrew Myers Date: Thu Aug 31 15:07:44 2017 -0700 use the ParIter in estTimeStep. Source/NyxParticleContainer.H commit da5273522c7e6a310398565db70b2f7c78f35098 Author: Andrew Myers Date: Thu Aug 31 15:07:05 2017 -0700 parse whether we want to the morton-ordered file from the inputs script. Source/NyxParticles.cpp commit c6f335d98123c5d6eba940d1631dd4240620c156 Author: Andrew Myers Date: Thu Aug 31 15:06:18 2017 -0700 Add method for initializing particles from Morton-ordered binary file. Source/DarkMatterParticleContainer.H Source/DarkMatterParticleContainer.cpp commit 32c44e5e8c8e8a524d5ed2b074e8f867a5e6b4f9 Author: Ann Almgren Date: Thu Aug 31 13:39:57 2017 -0700 Remove particles.do_tiling and particles.tile_size -- we want to use the defaults for these Exec/LyA/inputs Exec/LyA/inputs.rt Exec/Scaling/inputs commit 575e0ac54f54685a5d41095863c316386b32e44f Merge: c7574f71 b18a2721 Author: Andrew Myers Date: Thu Aug 31 10:42:24 2017 -0700 Merge branch 'development' of github.com:AMReX-Astro/Nyx into development commit b18a27213eb8b4056bbc56cd08dd1e0671be1c11 Author: Weiqun Zhang Date: Sat Aug 26 14:33:09 2017 -0700 omp critical --> reduction Source/Nyx.cpp Source/Nyx_hydro.cpp commit c6a7c8a34a09a1a7fd45945e0bc7f32d7bddf174 Author: Weiqun Zhang Date: Sat Aug 26 14:24:24 2017 -0700 Revert "Update the way we handle estdt with OMP -- before we had a serial section" This reverts commit 40a61250329aa260f750fcc0afcbddfd64845a74. Source/Nyx.cpp commit 2d7062bdd28630dd0031a80ecbff09c018e2c727 Author: Weiqun Zhang Date: Sat Aug 26 14:24:07 2017 -0700 Revert "Add omp parallel redution(max:courno) in Nyx_hydro loop" This reverts commit b6fbbdb690ecc6230ce02391eeb33720256b62e4. Source/Nyx_hydro.cpp commit b6fbbdb690ecc6230ce02391eeb33720256b62e4 Author: Ann Almgren Date: Sat Aug 26 13:26:20 2017 -0700 Add omp parallel redution(max:courno) in Nyx_hydro loop Source/Nyx_hydro.cpp commit 40a61250329aa260f750fcc0afcbddfd64845a74 Author: Ann Almgren Date: Sat Aug 26 13:12:02 2017 -0700 Update the way we handle estdt with OMP -- before we had a serial section of code here, now we use omp parallel reduction(min:) Source/Nyx.cpp commit 75117b3400260a0ef03f61db3ed6b786fa46934e Author: Ann Almgren Date: Tue Aug 15 18:53:27 2017 -0700 Remove final line referring to PROFILE. Exec/Make.Nyx commit 4e9ac969c0b0f3bacb052b12d6291c24eb5d1a0b Author: Andrew Myers Date: Tue Aug 15 14:50:54 2017 -0700 use the particle_real type here to allow for single precision. Source/particle_mod.f90 commit f16c3bca40a1906efe783ac9c8f3c0d7a2f21ddd Author: Ann Almgren Date: Mon Aug 14 14:55:35 2017 -0700 No longer need the specialized stuff here for PROFILE = TRUE -- that has been moved into the amrex build system. Exec/Make.Nyx commit 8905fe07bf7f5cc0d977b09732334dac5b7aba13 Author: Ann Almgren Date: Sun Aug 13 12:52:13 2017 -0700 Cleanup Source/Gravity/Gravity.cpp commit 7f2608dcab09eed3ef9d8aa85bd1999d58c8b398 Author: Ann Almgren Date: Sun Aug 13 12:51:03 2017 -0700 Replace std::cout by amrex::Print() Source/NyxParticles.cpp commit e94fc5c957bb2309562781f2801112ed7f366f36 Author: Ann Almgren Date: Sun Aug 13 10:46:22 2017 -0700 Replace std::cout by amrex::Print() Source/Gravity/Gravity.cpp commit e4763aefd9095878a41f06679fbd1c60a4572576 Merge: 7e4d0045 447c8de2 Author: Ann Almgren Date: Sat Aug 12 15:29:29 2017 -0700 Merge branch 'development' of https://www.github.com/AMReX-Astro/Nyx into development commit 7e4d0045c5b8ed5c090630877b2bf679340aa210 Author: Ann Almgren Date: Sat Aug 12 15:29:12 2017 -0700 Add extra lines to build with PROFILE = TRUE Exec/Make.Nyx commit 447c8de24db86a2be8b592968ed97636508b333a Author: Ann Almgren Date: Sat Aug 12 11:54:24 2017 -0700 Clarify print statements in particle_redistribute Source/NyxParticles.cpp commit 3c1e76141cd063350263f2be17196b2aeeae5940 Author: Ann Almgren Date: Sat Aug 12 10:51:48 2017 -0700 If "redistributed because changed", identify whether the BoxArray or the Distribution Map has changed Source/NyxParticles.cpp commit 734389778e0b6e3334e9fe8efea6e9c6246ecebf Merge: abfd2e30 74ce1cc5 Author: Ann Almgren Date: Thu Aug 10 09:23:10 2017 -0700 Merge branch 'development' commit c7574f719d190acf79d8c93cfd241528e3957cd4 Author: Andrew Myers Date: Fri Jul 21 14:04:18 2017 -0700 use the amrex_particle_real type in the particle type definitions to allow for single precision particles. Source/particle_mod.f90 commit 74ce1cc53253b6304aeb91ea8beb6dbb3a1a852d Merge: af6f9b48 148aa44c Author: Ann Almgren Date: Fri Jul 14 11:47:56 2017 -0700 Merge branch 'development' of https://www.github.com/AMReX-Astro/Nyx into development Conflicts: Exec/AssignDensityTest/Prob_3d.f90 Exec/AssignDensityTest/inputs Exec/AssignDensityTest/probin commit af6f9b48101c5941dff0eb048a331ca2aa18d292 Author: Ann Almgren Date: Fri Jul 14 11:46:22 2017 -0700 Remove AssignDensityTest Exec/AssignDensityTest/GNUmakefile Exec/AssignDensityTest/Make.package Exec/AssignDensityTest/Nyx_error.cpp Exec/AssignDensityTest/Prob_3d.f90 Exec/AssignDensityTest/Tagging_3d.f90 Exec/AssignDensityTest/inputs Exec/AssignDensityTest/probdata.f90 Exec/AssignDensityTest/probin commit 148aa44cbfd0635563ba095a3bbdd0d3b616ce06 Merge: 8515a34c 32d24f77 Author: petermcLBL Date: Fri Jul 14 10:37:51 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/Nyx into development Moving comoving_OmM, comoving_OmB, and comoving_h from probin to inputs. commit 8515a34ca9577d2e335131ccf9389c072624d934 Author: petermcLBL Date: Thu Jul 13 18:31:25 2017 -0700 reverted last change Exec/LyA_AGN/GNUmakefile commit a5d7a0809b64c597bde9e63099be14663c08e883 Author: petermcLBL Date: Thu Jul 13 18:26:06 2017 -0700 Moved comoving parameters from probin to inputs. Exec/GravityTests/zeldovich_dm/run/inputs_wmap7 Exec/GravityTests/zeldovich_dm/run/probin_wmap7 commit 3a921ca4f6b1c872f8c1d0f0d397d7a2a05c01bc Author: petermcLBL Date: Thu Jul 13 18:25:46 2017 -0700 This is in the Source directory. Exec/GravityTests/zeldovich_dm/build/NyxParticles.cpp commit 9e6da0af463d415c35f00220637bb87348d85a1d Author: petermcLBL Date: Thu Jul 13 18:24:21 2017 -0700 Moved comoving_OmB, comoving_OmM, comoving_h from probin to inputs. Exec/AssignDensityTest/Prob_3d.f90 Exec/AssignDensityTest/inputs Exec/AssignDensityTest/probin Exec/DrivenTurbulence/Prob_3d.f90 Exec/DrivenTurbulence/inputs Exec/DrivenTurbulence/inputs.regtest Exec/DrivenTurbulence/probin Exec/GravityTests/MacLaurin/Prob_3d.f90 Exec/GravityTests/MacLaurin/inputs Exec/GravityTests/MacLaurin/probin Exec/GravityTests/zeldovich_dm/build/Nyx_error.cpp Exec/GravityTests/zeldovich_dm/build/Prob_3d.f90 Exec/GravityTests/zeldovich_dm/run/inputs Exec/GravityTests/zeldovich_dm/run/probin Exec/HydroTests/DoubleRarefaction/Prob_3d.f90 Exec/HydroTests/DoubleRarefaction/inputs-test2-x Exec/HydroTests/DoubleRarefaction/inputs-test2-y Exec/HydroTests/DoubleRarefaction/inputs-test2-z Exec/HydroTests/DoubleRarefaction/inputs.regtest Exec/HydroTests/DoubleRarefaction/inputs.restarttest Exec/HydroTests/DoubleRarefaction/probin-test2-x Exec/HydroTests/DoubleRarefaction/probin-test2-y Exec/HydroTests/DoubleRarefaction/probin-test2-z Exec/HydroTests/Sedov/Prob_3d.f90 Exec/HydroTests/Sedov/inputs.3d.sph Exec/HydroTests/Sedov/inputs.regtest Exec/HydroTests/Sedov/probin.3d.sph Exec/HydroTests/Sod/Prob_3d.f90 Exec/HydroTests/Sod/inputs-sod-x Exec/HydroTests/Sod/inputs-sod-y Exec/HydroTests/Sod/inputs-sod-z Exec/HydroTests/Sod/inputs.regtest Exec/HydroTests/Sod/probin-sod-x Exec/HydroTests/Sod/probin-sod-y Exec/HydroTests/Sod/probin-sod-z Exec/HydroTests/StrongShockTube/Prob_3d.f90 Exec/HydroTests/StrongShockTube/inputs-x Exec/HydroTests/StrongShockTube/inputs-y Exec/HydroTests/StrongShockTube/inputs-z Exec/HydroTests/StrongShockTube/inputs.regtest Exec/HydroTests/StrongShockTube/probin-test3-x Exec/HydroTests/StrongShockTube/probin-test3-y Exec/HydroTests/StrongShockTube/probin-test3-z Exec/HydroTests/TurbForce/Prob_3d.f90 Exec/HydroTests/TurbForce/inputs Exec/HydroTests/TurbForce/inputs.regtest Exec/HydroTests/TurbForce/probin Exec/LyA/Prob_3d.f90 Exec/LyA/inputs Exec/LyA/inputs.rt Exec/LyA/inputs.small.dsc Exec/LyA/inputs_gimlet_in_transit.dsc Exec/LyA/probin Exec/LyA_AGN/GNUmakefile Exec/LyA_AGN/Prob_3d.f90 Exec/LyA_AGN/inputs Exec/LyA_AGN/inputs.rt Exec/LyA_AGN/probin Exec/MiniSB/Prob_3d.f90 Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Exec/MiniSB/inputs.analysis Exec/MiniSB/probin Exec/RegressionTest/Prob_3d.f90 Exec/RegressionTest/inputs.2line Exec/RegressionTest/inputs.2line.restarttest Exec/RegressionTest/inputs.mass.nosub Exec/RegressionTest/inputs.mass.sub Exec/RegressionTest/probin Exec/SantaBarbara/Prob_3d.f90 Exec/SantaBarbara/inputs Exec/SantaBarbara/probin Exec/Scaling/GNUmakefile Exec/Scaling/Prob_3d.f90 Exec/Scaling/inputs Exec/Scaling/probin Source/Initialization/Nyx_initcosmo.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_F.H Source/Nyx_output.cpp Source/comoving_nd.f90 commit 32d24f774351b68be007f07ca4981dde052ea31a Author: Ann Almgren Date: Thu Jul 13 18:21:20 2017 -0700 Replace test on grids.contains(domain) by test on grids.numPts() == domain.numPts() Source/Gravity/Gravity.cpp commit 8136cb9a4683dfb5786bb7f2c5fdf872bf1be360 Author: Andrew Myers Date: Tue Jul 11 14:20:03 2017 -0700 Always use the fortran version for single-level deposition, even in the context of sub-cycling. Source/NyxParticleContainer.H commit cf01559c59f9176f96f0e5dbb59be138eabbbba5 Author: Brian Friesen Date: Sun Jul 9 14:55:24 2017 -0700 Particle: add OpenMP to the particle loops in moveKick() and moveKickDrift() (#14) Source/DarkMatterParticleContainer.cpp commit 336d1f7521aa919ba00979ab36a47dd769c86bda Author: petermcLBL Date: Fri Jul 7 19:30:43 2017 -0700 formatting UsersGuide/AGN/AGN.tex commit 7ef7ee19760e185ed6334d926f0bb4860ff2ba4b Author: petermcLBL Date: Fri Jul 7 19:23:28 2017 -0700 new AGN chapter UsersGuide/NyxUserGuide.tex commit 4be258d52a30a8a7c5999601f01a675a80ea3f18 Author: petermcLBL Date: Fri Jul 7 19:23:11 2017 -0700 formatting UsersGuide/Inputs/NyxInputs.tex commit 4fe40e87c29f35bb19777409573c1f1032b47a1d Author: petermcLBL Date: Fri Jul 7 19:22:55 2017 -0700 formatting UsersGuide/Gravity/NyxGravity.tex commit bd745706c50964d8d7be9e921509cdc42428679f Author: petermcLBL Date: Fri Jul 7 19:22:17 2017 -0700 New chapter on AGN. UsersGuide/AGN/AGN.tex commit db833c8337423f666e9a68e000ec8d487d1c8b93 Author: petermcLBL Date: Fri Jul 7 19:21:11 2017 -0700 formatting UsersGuide/GettingStarted/NyxGettingStarted.tex commit bf72dba710449da30eb5f552c6a36b79f773345b Author: petermcLBL Date: Fri Jul 7 19:20:46 2017 -0700 formatting UsersGuide/EOSNetwork/EOSNetwork.tex commit de725cb079564c759c3ad3c0faaa8aad221e39fc Author: petermcLBL Date: Fri Jul 7 19:20:26 2017 -0700 formatting UsersGuide/Particles/Particles.tex commit 208739e298a5e672a2bc889fd5817a5724783ecb Author: petermcLBL Date: Fri Jul 7 19:19:58 2017 -0700 formatting UsersGuide/UnitsAndConstants/NyxUnits.tex commit 74ea3db01dec5b0a80b09d328dbdd1071983705f Author: petermcLBL Date: Fri Jul 7 19:18:18 2017 -0700 Added mass_halo_min and mass_seed as Nyx fields and inputs, rather than having them hard-coded. Source/Nyx.H Source/Nyx.cpp Source/Nyx_halos.cpp commit 3859985516bb7e636782ecbefe35ffa1d0f5e0c5 Author: petermcLBL Date: Fri Jul 7 19:15:44 2017 -0700 Corrected bug here: condition is (vrelsq * r) < Gconst * larger_mass), not (vrelsq * r2) < (Gconst * larger_mass)**2, which has incompatible units. Source/AGN/agn_3d.f90 commit a92fdc14efb6616a8969f0550f09aa9330ca65e6 Author: petermcLBL Date: Fri Jul 7 19:14:39 2017 -0700 Write this (with the #ifndefs) in such a way as to avoid repetition of code. Source/write_info.cpp commit c7fdbbb72b639ffe99de3778dd0c6905fd5d52f6 Author: petermcLBL Date: Fri Jul 7 19:14:13 2017 -0700 not such a long single line Exec/LyA_AGN/Prob_3d.f90 commit 2267881da704d8188ac4838d4b1988bba37e277f Merge: 5bd685c6 f184c3fa Author: petermcLBL Date: Fri Jul 7 18:49:04 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/Nyx into development updating commit 5bd685c61b472f35f0a16e1857d707cba838ced7 Author: petermcLBL Date: Fri Jul 7 18:46:14 2017 -0700 explanatory line for reeber.halo_int Exec/LyA_AGN/inputs commit abfd2e308d30eda0d6b3cf603ecc8a45d89b4c42 Merge: e359f698 f184c3fa Author: Ann Almgren Date: Fri Jun 30 13:05:14 2017 -0700 Merge branch 'development' commit f184c3faf434e993f6331785be7de65a2b9c4308 Author: Ann Almgren Date: Fri Jun 30 10:34:45 2017 -0700 Revert to AssignDensitySingleLevel if single-level solve not at level = 0 Source/NyxParticleContainer.H commit be839ce32123359cfd46a731d744b460e3c0d398 Author: Ann Almgren Date: Fri Jun 30 10:12:14 2017 -0700 Only call the new AssignDensityFort if doing a level = 0 solve (for now) Source/NyxParticleContainer.H commit 11a995642831dbba3f7811d143632280fe54f9f9 Author: Ann Almgren Date: Thu Jun 29 15:43:05 2017 -0700 No reason to keep a batch script for hopper Exec/LyA/pbs_hopper commit 06045fff091600b2742f65a641250b8f3d98c134 Author: Ann Almgren Date: Thu Jun 29 12:49:44 2017 -0700 Update how grids are created (2.5.5) UsersGuide/Inputs/NyxInputs.tex commit 96581653f16c1a211f3fc8aa471b204ab6e6df47 Author: Ann Almgren Date: Wed Jun 28 17:01:20 2017 -0700 Add Forcing chapter from Wolfram. UsersGuide/Forcing/NyxForcing.tex UsersGuide/Forcing/force.bib UsersGuide/NyxUserGuide.tex commit 821e9cd1fde6bbef7c0b7afce661a6807d25459b Author: Ann Almgren Date: Tue Jun 27 21:32:01 2017 -0700 Remove all "show_timings" Source/Gravity/Gravity.cpp commit aede6591a86f1cfe94e3a563eecdf523ffc84e0a Author: Ann Almgren Date: Tue Jun 27 21:18:15 2017 -0700 abs-->std::abs Source/comoving.cpp commit fcff294b79d1ec0633e88d2ccad266753bbbb276 Author: Ann Almgren Date: Tue Jun 27 18:42:41 2017 -0700 Set particles.do_tiling = 1 Exec/LyA/inputs Exec/LyA/inputs.rt commit 92694da8fc910f0b1b2de13a1c1f7dd98033e352 Author: Ann Almgren Date: Tue Jun 27 18:37:16 2017 -0700 Run the non-debug executable. Exec/Scaling/cori.knl commit 0771b97abd9f8b4eebfb415ab0c29722ea9e396a Merge: 511cb928 d97f0b00 Author: Ann Almgren Date: Tue Jun 27 18:35:08 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/Nyx into development commit 511cb92825073d632c0cad4707736727ea9a621b Author: Ann Almgren Date: Tue Jun 27 18:34:51 2017 -0700 Modify the AMREX_HOME spec Exec/Scaling/GNUmakefile commit d97f0b00db9ffd5fcbc3e0ed7b19778b8e267ca1 Merge: e319199a 2baca005 Author: Ann Almgren Date: Tue Jun 27 18:33:45 2017 -0700 Merge branch 'development' of https://www.github.com/AMReX-Astro/Nyx into development commit e319199aa0dc12a05cf430ae55b811a33291883a Author: Ann Almgren Date: Tue Jun 27 18:33:07 2017 -0700 Add the option for RandomPerCell -- this particle_init_type generates one particle per cell, randomly positioned within that cell Source/NyxParticles.cpp commit 2baca005d96216376325fbfade01c4a2bbec289e Author: Ann Almgren Date: Tue Jun 27 18:27:08 2017 -0700 This is the up-to-date Scaling setup for this case. Exec/Scaling/GNUmakefile Exec/Scaling/TREECOOL_middle Exec/Scaling/cori.knl Exec/Scaling/inputs commit 7f9f1a3c68962d61c32107b7ce69316dc2bf7cf7 Merge: 6533c46b 7590d89e Author: Ann Almgren Date: Tue Jun 27 17:17:16 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/Nyx into development commit 6533c46b3e1ef3c843f3c0e695ce5f3fe0bcbb20 Author: Ann Almgren Date: Tue Jun 27 17:16:12 2017 -0700 Add Cori-KNL batch script Exec/Scaling/cori.knl commit 7590d89e594eba55d0ba193f1fd8d1372468deda Author: Ann Almgren Date: Tue Jun 27 16:13:45 2017 -0700 Remove write_particles_in_plotfile and always write the particles. Source/Nyx.H Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_output.cpp commit deeab4317916c7dfcc2268bd35e66d5cf80874d6 Author: Ann Almgren Date: Tue Jun 27 16:13:20 2017 -0700 Update documentation UsersGuide/GettingStarted/NyxGettingStarted.tex UsersGuide/NyxUserGuide.tex UsersGuide/Visualization/NyxVisualization.tex commit e35ca7dd3712483c6f2a0fcaab34d7409161aea7 Author: Ann Almgren Date: Tue Jun 27 09:11:54 2017 -0700 Replace missing semicolon Source/Gravity/Gravity.cpp commit 7ed09c5410810eb9f8abe12eebbe349728444ec4 Author: Ann Almgren Date: Sun Jun 25 12:38:50 2017 -0700 Now call the Fortran-based AssignDensity routines ... also a little more profiling stuff. Source/AGN/AGN_sources.cpp Source/NyxParticleContainer.H Source/NyxParticles.cpp Source/SourceTerms/Nyx_sources.cpp commit 6be6aa2d765c1fc92e226836967a4e200fcd8031 Author: Ann Almgren Date: Sun Jun 25 10:18:14 2017 -0700 Remove all show_timings stuff and replace with BL_PROFILE timers. Source/AGNParticleContainer.cpp Source/DarkMatterParticleContainer.cpp Source/Forcing/Forcing.H Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp Source/Gravity/Gravity.cpp Source/NeutrinoParticleContainer.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxParticleContainer.H Source/Nyx_advance.cpp Source/Nyx_halos.cpp Source/Nyx_hydro.cpp Source/advance_particles.cpp commit 10ca2f602958bf7263714fcec632fc03ec24d440 Author: Ann Almgren Date: Sat Jun 24 20:58:31 2017 -0700 Have the Nyx AssignDensity single level calls use the OpenMP-threaded version. Source/NyxParticleContainer.H commit cfa73b2de081a0c1d378ffabe23cb65e2d16b11a Merge: a9d97d55 871fb2e9 Author: petermcLBL Date: Tue Jun 20 17:28:28 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/Nyx into development momentum/kinetic feedback commit a9d97d5531ced33e88117cd4d352e7f154c2ea9e Author: petermcLBL Date: Tue Jun 20 17:27:23 2017 -0700 including first draft of momentum/kinetic feedback Exec/LyA_AGN/Prob_3d.f90 Exec/LyA_AGN/probin Source/AGN/agn_3d.f90 Source/AGN/agn_F.H Source/Make.package Source/Nyx.cpp Source/agn_params.f90 Source/uniform01.f90 commit 871fb2e9c8534cf7f2f42086bf62290fe2bbd32c Author: Brian Friesen Date: Tue Jun 20 15:03:08 2017 -0700 CVODE fixes (#12) * CVODE: fix thread safety of the yvec array Originally, yvec was (mistakenly) not thread-private, leading to a race condition when using CVODE with OpenMP. Now it is declared on a thread-private heap within integrate_state_fcvode(). * LyA: merge RHS function and CVode Fortran wrapper into single module "fcvode_extras" * LyA: change 'stop' commands to amrex_abort() for more graceful exit in MPI Exec/LyA/Make.package Exec/LyA/fcvode_extras.f90 Exec/LyA/integrate_state_fcvode_3d.f90 commit 0d22228d02bc6c2b989da6da8779cca32abea405 Author: petermcLBL Date: Fri Jun 16 19:33:37 2017 -0700 Added real variable names to checkpoint and plotfile output. Simplified this for NyxParticleContainer. Source/AGNParticleContainer.H Source/DarkMatterParticleContainer.H Source/NyxParticleContainer.H Source/Nyx_output.cpp commit 74d674ac832630aba96747b55f0ca2ea93f2be67 Author: petermcLBL Date: Fri Jun 16 19:32:42 2017 -0700 Took out call to writeAllAtLevel. Source/Nyx_halos.cpp commit ab0c8c3907f6dcd688024e7a913cc3eee3829049 Author: petermcLBL Date: Fri Jun 16 19:32:14 2017 -0700 Added mdot field for AGN particles. Source/AGN/agn_3d.f90 commit b6e9d05d188fd8069bbac8d7d391befb413032fd Author: petermcLBL Date: Fri Jun 16 19:31:30 2017 -0700 Added mdot field for AGN particles. Source/AGNParticleContainer.cpp Source/particle_mod.f90 commit e0d5e0a276a193eae52ff1ae1eae74952fbadbb6 Author: petermcLBL Date: Wed Jun 14 15:37:53 2017 -0700 Use pout() instead of cout. Source/AGNParticleContainer.cpp Source/Nyx_halos.cpp commit ec6f868244b0bb8a9e309cd5df3f3f1574fb81c0 Author: Ann Almgren Date: Thu Jun 8 17:46:22 2017 -0700 We were dividing the state by density twice before entering halo_merge -- turns out we only need to do the conserved--primitive and primitive--conserved conversion inside halo_accrete since that is the only place we need it. Source/Nyx_halos.cpp commit 2479ded0d35e2adda50b8ed72a64c44a313a9a5e Author: Ann Almgren Date: Thu Jun 8 17:01:05 2017 -0700 Get rid of unused code Source/Nyx.cpp commit 4811351c0f972434d53a75c9dc5c1fc67c657e03 Author: Yinghe Lu Date: Wed Jun 7 12:25:13 2017 -0700 Yinghe AGN (#11) * added a few missing constants under cgs unit * small bug fixes for the code to work with USE_AGN=FALSE * removed all the tmp_build_dir stuff * removed print statement * also removed the duplicated input file Exec/LyA_AGN/GNUmakefile Exec/LyA_AGN/Prob_3d.f90 Source/AGN/Make.package Source/AGN/agn_3d.f90 Source/Constants/constants_cgs.f90 Source/Make.package Source/agn_params.f90 commit 3275a16e47e7dc632f29f73e7baa81956d5ebe0a Merge: b97b775c e2d57a2f Author: asalmgren Date: Wed Jun 7 10:37:31 2017 -0700 Merge pull request #10 from bcfriesen/cvode_fixes CVode fixes commit b97b775c78401695d5f7162040442577e902fa56 Author: Michael Zingale Date: Tue Jun 6 20:44:29 2017 -0400 add a .gitignore from Castro to help prevent PRs from including build temporaries .gitignore commit e2d57a2f85f76fe188f956fefdbdadaf789e0165 Author: Brian Friesen Date: Tue Jun 6 14:43:47 2017 -0700 LyA: fix bugs in how Fortran and C arrays store data for CVODE solver Exec/LyA/fcvode_wrapper.f90 Exec/LyA/integrate_state_fcvode_3d.f90 commit 14110f2aa0d45292b35ee5bdc5a0cd130e3e267a Author: Brian Friesen Date: Tue Jun 6 08:26:19 2017 -0700 LyA: add 0 return value to RHS function for CVODE integration CVODE checks for a 0 return code from the RHS, or else it assumes the RHS failed and will spam warning messages to STDOUT (even though it continues with the integration). Exec/LyA/rhsfn.f90 commit a88aa5f1991094d82a432eb9766f51ca6c8056ed Author: Brian Friesen Date: Tue Jun 6 08:25:21 2017 -0700 HeatCool: fix source term bounds arg names given to integrate_state_fcvode() Source/HeatCool/ext_src_hc_3d.f90 commit 9fcf1881b08c02df1e89aec89785d105b786b5c1 Merge: 16aa8d7e 747b1a37 Author: asalmgren Date: Mon Jun 5 20:36:19 2017 -0700 Merge pull request #8 from bcfriesen/add_f03_cvode Add Fortran 2003 CVODE interface commit 747b1a370d86a2765b00f8e39509b857cdd4f3b2 Author: Brian Friesen Date: Thu Jun 1 17:31:40 2017 -0700 HeatCool: implement new Fortran interface to CVODE using iso_c_bindings Exec/LyA/GNUmakefile Exec/LyA/Make.package Exec/LyA/fcvfun.f90 Exec/LyA/fcvode_wrapper.f90 Exec/LyA/integrate_state_fcvode_3d.f90 Exec/LyA/rhsfn.f90 commit 16aa8d7e162817a69ff8e40266cda066487a6677 Author: Ann Almgren Date: Sun Jun 4 14:21:37 2017 -0700 Fix spelling error in comment Source/Nyx.cpp Source/Nyx_output.cpp commit d68c9b14f03ab0e1a87ff2606497d33b4b1b68d4 Author: petermcLBL Date: Thu Jun 1 17:34:51 2017 -0700 Use probin and module agn_params_module for parameters: eps_rad, eps_coupling, T_min, bondi_boost, max_frac_removed Exec/LyA_AGN/Prob_3d.f90 Exec/LyA_AGN/probin Source/AGN/Make.package Source/AGN/agn_3d.f90 Source/AGN/agn_F.H Source/AGN/agn_params.f90 Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/Nyx_halos.cpp commit 9d2a63389914b2355b8f14cbbfa77d46229e585f Author: petermcLBL Date: Thu Jun 1 15:30:52 2017 -0700 Add 3^3 particles instead of 2^3 of them. Source/Nyx_halos.cpp commit e7ad9cc89296375499e179b63ad9256612e4ceb3 Author: petermcLBL Date: Thu Jun 1 15:29:00 2017 -0700 more informative about updating particle energy. Source/AGN/agn_3d.f90 commit 0110956279131ea109e8dd0fd913d3d597df5109 Author: petermcLBL Date: Wed May 31 14:37:07 2017 -0700 Added ability to restart with AGN. Source/NyxParticles.cpp commit 5b5615f78b1b94e78a7ae3e27520c19952b95450 Author: Ann Almgren Date: Wed May 31 12:25:19 2017 -0700 Add the variable names for the particle attributes in plotfiles and checkpoints. Source/Nyx_output.cpp commit 1e5552abb5f27a590bbaae6ab3bacff21e00448e Author: Ann Almgren Date: Wed May 31 11:52:24 2017 -0700 Add AGN particles to plotfiles and checkpoints. Source/Nyx_output.cpp commit f33fe4c6131a67ee11c46401257621fd29ef57ca Merge: 8809145f 5f1d3e4b Author: Ann Almgren Date: Tue May 30 19:26:23 2017 -0700 Merge branch 'development' of https://www.github.com/AMReX-Astro/Nyx into development commit 8809145f8584233ab4abbe78e2b3e3baca7bde3e Author: Ann Almgren Date: Tue May 30 19:26:13 2017 -0700 Update comment Exec/Make.Nyx commit 5f1d3e4b02116d9646b15988ecc842a0684a49cf Merge: ce607307 63f54e16 Author: asalmgren Date: Mon May 29 17:58:02 2017 -0700 Merge pull request #7 from wolfram-schmidt/development Development commit 63f54e16ab86ca1b26111d3605c739e320f1e7b0 Merge: b33d09dc ce607307 Author: Wolfram Schmidt Date: Mon May 29 13:05:35 2017 +0200 Merge remote-tracking branch 'upstream/development' into development commit b33d09dcc938653c0881d26a3d1c19db65192d46 Author: Wolfram Schmidt Date: Mon May 29 13:00:34 2017 +0200 Added strang splitting for stochastic forcing and improved performance of integrate_state_force. Exec/DrivenTurbulence/Derive_3d.f90 Exec/DrivenTurbulence/Make.package Exec/DrivenTurbulence/heat_cool_stubs.f90 Exec/DrivenTurbulence/inputs Exec/DrivenTurbulence/inputs.regtest Exec/DrivenTurbulence/probin Source/Forcing/Forcing.H Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp Source/Forcing/forcing_spect.f90 Source/Forcing/integrate_state_force_3d.f90 Source/HeatCool/heat_cool_stubs.f90 Source/HeatCool/integrate_state_3d.f90 Source/Nyx_F.H Source/strang_splitting.cpp commit ce6073071e8cf8f6945f3e737709df3d5f4c6de0 Author: petermcLBL Date: Fri May 26 14:27:53 2017 -0700 Simplified using Fortran 90 tricks. Source/AGN/agn_3d.f90 commit 54addf5352119ef02a5f9ba271a3478451f59ea9 Author: Ann Almgren Date: Fri May 26 13:21:18 2017 -0700 oops -- fix typo in write statement Source/AGNParticleContainer.cpp commit 3754f9689bbfdb8488d1ac9fda9571e91c364ee6 Author: Ann Almgren Date: Fri May 26 13:18:51 2017 -0700 1) Rename Ghosts --> Neighbors in the context of fillGhosts --> fillNeighbors etc. This is to eliminate confusion with the "ghost" particles which are copies of particles living at a coarser grid. 2) We need to shift the position of neighbor particles when they live outside of a periodic domain -- this now happens in the packNeighbors routine. Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/Nyx_halos.cpp commit f77e82a06c28fd363b67f00cdf721242f6fc4e20 Author: petermcLBL Date: Thu May 25 19:15:19 2017 -0700 Make new_state the one that is saved, and orig_state the one that is a copy. Source/Nyx_halos.cpp commit 20ad0bc0995f0c7ea6b649da3f66c3b9e87bfffe Author: petermcLBL Date: Thu May 25 19:14:01 2017 -0700 agn_release_energy takes corners of D state. Source/AGN/agn_3d.f90 Source/AGN/agn_F.H Source/AGNParticleContainer.cpp commit 99c549e7caa845898d193f30d56a153bb9e91f26 Author: petermcLBL Date: Thu May 25 19:13:45 2017 -0700 formatting Source/AGNParticleContainer.H commit 0151facb930ac424e35ddda0ae19eaa810ee096b Author: petermcLBL Date: Thu May 25 15:06:16 2017 -0700 Use the right threshold for releasing energy from particles. Source/AGN/agn_3d.f90 Source/AGN/agn_F.H Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/Nyx_halos.cpp commit 66510ceaf0df59b9c151f608e681ae6f7b6d1f73 Author: petermcLBL Date: Wed May 24 19:31:58 2017 -0700 Don't calculate E unless you need it. Source/AGN/agn_3d.f90 commit 597fc7e12dd26b56f9b6a90d308a6355fecd6c0f Author: petermcLBL Date: Wed May 24 19:30:35 2017 -0700 Calling functions to convert between conserved and primitive variables. Adding deposition from particles. Source/Nyx_halos.cpp commit 5fe0f4ae0b91cca553157a0f12f3b188a4211777 Author: petermcLBL Date: Wed May 24 19:26:12 2017 -0700 Added new functions for converting conserved variables to primitive and vice versa. Source/Nyx.H commit 2d4b895329f956e63d9084381b7f0484ddf5c5c5 Author: petermcLBL Date: Wed May 24 19:25:33 2017 -0700 Added periodicity. Source/NyxParticleContainer.H commit 2003eaa6c1958529b77a404c5bd4a1f045a4e0fc Author: petermcLBL Date: Wed May 24 19:24:55 2017 -0700 Added periodicity. Source/AGNParticleContainer.cpp commit db91667739540ba70525766ebb8ae75af519f110 Merge: d7028523 207425c0 Author: petermcLBL Date: Tue May 23 13:40:34 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/Nyx into development Made halo calculations clearer (I think). Also added thermal energy feedback. commit d70285236abc3cfb80ad4dc7a02c3be8c433661f Author: petermcLBL Date: Tue May 23 13:39:01 2017 -0700 Clearer (I think) way of doing halo operations. Also added thermal energy feedback. Source/AGN/agn_3d.f90 Source/AGN/agn_F.H Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/Nyx_halos.cpp commit 207425c0b45adf9efb462fedfa5849924287209e Author: Zarija Lukic Date: Tue May 23 10:55:29 2017 -0700 cleanup in LyA_AGN Exec/LyA_AGN/32.nyx Exec/LyA_AGN/GNUmakefile commit 4fe8b444116e82f3f9ff0f7e8051bc0a1fc1ec8c Author: Zarija Lukic Date: Tue May 23 10:46:00 2017 -0700 correcting the probin file Exec/LyA_AGN/probin commit 267114a11410300867c494e8095d9be668d32e44 Author: Andrew Myers Date: Mon May 22 17:50:03 2017 -0700 simply call std::map's clear method here. Source/AGNParticleContainer.cpp commit 5658ac4363431c0d96a854bb9d1412b44a105117 Author: Ann Almgren Date: Mon May 22 13:19:54 2017 -0700 More efficient version of clearGhosts Source/AGNParticleContainer.cpp commit eab02abe4cbb5cdd7897986033b3907433d2bf6d Author: Ann Almgren Date: Mon May 22 12:49:07 2017 -0700 Fix the clearGhosts routine. Source/AGNParticleContainer.cpp commit 6a5aa8251748e94e1f75bef8656e75cbecdb04f5 Author: Wolfram Schmidt Date: Mon May 22 13:09:28 2017 +0200 Improved performance of integrate_state_force_3d. Source/EOS/eos_stuff.f90 Source/Forcing/Forcing_init.cpp Source/Forcing/forcing_spect.f90 Source/Forcing/integrate_state_force_3d.f90 commit dc84f2e9ffeeebce8348904191008ec479ec0bd6 Author: Andrew Myers Date: Fri May 19 13:13:02 2017 -0700 Set up mask for ghost particles and allow for variable numbers of ghost cells. Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/Nyx.H Source/NyxParticles.cpp commit 98df2d979e87e139a2d0cec15b57861dcbfb1372 Author: Brian Friesen Date: Wed May 17 15:42:16 2017 -0700 Source: print which heating/cooling integration scheme we use Source/Nyx.cpp commit a960a247931f1820bda3451a1639dd8b1d11197e Author: Brian Friesen Date: Wed May 17 15:40:46 2017 -0700 HeatCool: add support for CVODE integration VODE has not been updated in a long time; all new development is in CVODE (part of SUNDIALS). So now we can use CVODE instead. Exec/LyA/GNUmakefile Exec/LyA/Make.package Exec/LyA/fcvfun.f90 Exec/LyA/integrate_state_fcvode_3d.f90 Source/HeatCool/Make.package Source/HeatCool/ext_src_hc_3d.f90 Source/HeatCool/integrate_state_3d.f90 Source/HeatCool/integrate_state_fcvode_3d_stubs.f90 Source/HeatCool/vode_aux.f90 Source/Nyx.cpp Source/Nyx_nd.f90 Source/comoving.cpp commit 1a9badc0534b6881228d34c0715d72d736a76413 Author: Wolfram Schmidt Date: Wed May 17 16:17:49 2017 +0200 Added restarting capability for stochastic forcing. Exec/DrivenTurbulence/Derive_3d.f90 Source/Forcing/Forcing.H Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp Source/Forcing/MersenneTwister.cpp Source/Forcing/integrate_state_force_3d.f90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_output.cpp commit 3a3dfa7ce22ea6b2a16d858e277157c432145c92 Author: Andrew Myers Date: Tue May 16 15:19:01 2017 -0700 skip invalid particles in update. Source/Src_3d/update_particles_3d.f90 commit 12c8b964a1e531cc6f99931781bd727ae7372873 Author: Ann Almgren Date: Tue May 16 12:23:50 2017 -0700 Move the moveKickDrift and moveKick operations into DarkMatterParticleContainer and AGNParticleContainer so we can get the expansion constants out of amrex (among other reasons) Source/AGN/Make.package Source/AGN/agn_3d.f90 Source/AGN/agn_F.H Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/DarkMatterParticleContainer.H Source/DarkMatterParticleContainer.cpp Source/Make.package Source/NyxParticleContainer.H Source/Nyx_advance.cpp Source/Src_3d/Make.package Source/Src_3d/update_particles_3d.f90 Source/dm_F.H Source/particle_mod.f90 commit 793bbbd99c63e1dc1f7715e2a1ab2049941d6bdc Author: Wolfram Schmidt Date: Tue May 16 13:31:59 2017 +0200 Incorporated bug fix in ext_src_hc into ext_src_force. Exec/DrivenTurbulence/Derive_3d.f90 Exec/DrivenTurbulence/Make.package Exec/DrivenTurbulence/ext_src_3d.f90 Exec/HydroTests/TurbForce/ext_src_3d.f90 Exec/HydroTests/TurbForce/ext_src_force_3d.f90 Exec/HydroTests/TurbForce/integrate_state_force_3d.f90 Source/Forcing/Make.package Source/Forcing/ext_src_force_3d.f90 Source/Forcing/forcing_spect.f90 Source/Forcing/integrate_state_force_3d.f90 Source/Initialization/Nyx_setup.cpp commit e2d82acf1e4adca17c1c25594d9d414e96fab270 Merge: b4b314c8 becea0ce Author: Wolfram Schmidt Date: Tue May 16 10:25:05 2017 +0200 Merge remote-tracking branch 'upstream/development' into development commit b4b314c8ec3814f4373fccc4f37004e54aad2216 Author: Wolfram Schmidt Date: Tue May 16 10:24:24 2017 +0200 Test version of stochastic forcing completed (except for restarts). Exec/DrivenTurbulence/Derive_3d.f90 Exec/DrivenTurbulence/Make.package Exec/DrivenTurbulence/Prob_3d.f90 Exec/DrivenTurbulence/Tagging_3d.f90 Exec/DrivenTurbulence/ext_src_3d.f90 Exec/DrivenTurbulence/ext_src_force_3d.f90 Exec/DrivenTurbulence/integrate_state_force_3d.f90 Exec/DrivenTurbulence/turbforce.f90 Exec/DrivenTurbulence/turbinit.f90 Exec/HydroTests/TurbForce/Derive_3d.f90 Exec/HydroTests/TurbForce/Nyx_setup.cpp Source/Forcing/Forcing.H Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp Source/Forcing/Make.package Source/Forcing/forcing_spect.f90 Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_advance.cpp commit becea0ce708a0d7d65380ce144bedbafe4bf4cdd Merge: 2e75f55a 8a978b3c Author: Peter McCorquodale Date: Mon May 15 17:16:16 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/Nyx into development Issues with Reeber on. commit 2e75f55af7c5d4031674e9ec446de19fe7094c8a Author: Peter McCorquodale Date: Mon May 15 17:15:27 2017 -0700 Write out diagnostic before crash occurs. Source/Nyx_halos.cpp commit 6372bcafe45065c994b0e0edc980bf4f2dc00a1d Author: Peter McCorquodale Date: Mon May 15 17:14:34 2017 -0700 Corrected the order of arguments for MultiFab constructor. Source/main.cpp commit 8a978b3c482ea0f952604cc5fb83a2586ff356a7 Author: Andrew Myers Date: Mon May 15 17:02:28 2017 -0700 Fix logic for redistributing active particles in post time step. Source/Nyx.cpp commit e53df6f71c3ac991ac8d3286c9b96db545dcb6c8 Author: Ann Almgren Date: Mon May 15 16:17:23 2017 -0700 fixed to work with reeber Source/Nyx_halos.cpp commit db2f99e7992d7038310f774f98e7212028c63848 Merge: 8c4f8318 49971df2 Author: Ann Almgren Date: Mon May 15 16:12:16 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/Nyx into development commit 8c4f83189fcf96b07bd99724c09191274c50d2d4 Author: Ann Almgren Date: Mon May 15 16:11:38 2017 -0700 Getting this to work with REEBER ... Source/Nyx_halos.cpp commit 49971df219e9630099692b28b20109d3a7df994c Merge: c43abd2b 2b488e53 Author: Ann Almgren Date: Mon May 15 15:48:33 2017 -0700 Merge branch 'development' of https://www.github.com/AMReX-Astro/Nyx into development commit c43abd2b3708c487d87ad37e2e15db84571b821b Author: Ann Almgren Date: Mon May 15 15:48:20 2017 -0700 BoxLib-->amrex inside ifdef REEBER Source/Nyx_halos.cpp commit e359f698fc27eb09cce87712808a7e5b4201b446 Author: Weiqun Zhang Date: Mon May 15 12:29:47 2017 -0700 add copyright notice and update license Conflicts: license.txt copyright.txt license.txt commit 2b488e53e460feb8ae334a656a10893f91548644 Author: Weiqun Zhang Date: Mon May 15 12:29:47 2017 -0700 add copyright notice and update license copyright.txt license.txt commit 13fc50b8d5b680748338d9f9cebf4a53a0bd282f Author: Ann Almgren Date: Mon May 15 12:16:38 2017 -0700 Fix typo Source/HeatCool/ext_src_hc_3d.f90 commit a8f8d33669656fd27e3689b713a6802620426794 Author: Ann Almgren Date: Mon May 15 12:14:53 2017 -0700 Fix how we call the ext_src routines within a tiled loop -- we need to explicitly define the growntilebox(ext_src.nGrow()) from the call rather than overwriting the loop indices inside ext_src_*.f90 with the full array bounds. Source/HeatCool/ext_src_hc_3d.f90 Source/SourceTerms/Nyx_sources.cpp commit 6b82358ea9eaae94547d45cf5b8c5974bff28275 Author: Ann Almgren Date: Mon May 15 09:34:46 2017 -0700 This change fixes the regresion test but I don't understand why it's the right thing to do. Source/Nyx.cpp commit 50435d45799d2fda33af5a0b88bd407231ab7aa0 Author: Ann Almgren Date: Sat May 13 18:38:03 2017 -0700 Clean up how we compute "grav_n_grow" Source/Nyx.H Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_advance.cpp Source/advance_particles.cpp commit d9a394865c31e4576f0d01c1428a763061a0655c Author: Ann Almgren Date: Tue May 9 19:21:11 2017 -0700 Fix error write statement Source/NyxParticles.cpp commit 6ebd48bdae2670852e6a7aab1c4031e81e1a8b6b Author: Andrew Myers Date: Tue May 9 13:04:08 2017 -0700 Update Nyx to reflect changes to AMReX's particle initialization API. Source/NyxParticles.cpp commit 8671fca6589aaa0fffd9eb28b78b44bbc1408aca Merge: af94d0f5 fe00d49b Author: Wolfram Schmidt Date: Tue May 9 10:01:09 2017 +0200 Merge remote-tracking branch 'upstream/development' into development commit af94d0f5b7fd5465256cbd4a8c4402ef892c4ae7 Author: Wolfram Schmidt Date: Mon May 8 17:48:45 2017 +0200 Added class StochasticForcing in Source/Forcing. Added Exec/DrivenTurbulence, which is still equivalent to Exec/HydroTests/TurbForce, but evolves already the forcing spectrum without making use of it. Exec/DrivenTurbulence/Derive_3d.f90 Exec/DrivenTurbulence/GNUmakefile Exec/DrivenTurbulence/Make.package Exec/DrivenTurbulence/Nyx_error.cpp Exec/DrivenTurbulence/Prob_3d.f90 Exec/DrivenTurbulence/Tagging_3d.f90 Exec/DrivenTurbulence/ext_src_3d.f90 Exec/DrivenTurbulence/ext_src_force_3d.f90 Exec/DrivenTurbulence/integrate_state_force_3d.f90 Exec/DrivenTurbulence/probdata.f90 Exec/DrivenTurbulence/turbforce.f90 Exec/DrivenTurbulence/turbinit.f90 Exec/HydroTests/TurbForce/GNUmakefile Exec/Make.Nyx Source/Forcing/Forcing.H Source/Forcing/Forcing.cpp Source/Forcing/Forcing_init.cpp Source/Forcing/Make.package Source/Forcing/MersenneTwister.cpp Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_advance.cpp Source/sum_integrated_quantities.cpp commit fe00d49b0ca4c0a40e41236264f36ee162a6411e Author: Ann Almgren Date: Sun May 7 17:20:48 2017 -0700 Update the derive_dat type. Source/Nyx_halos.cpp commit a2fa2eb19e0a3c069bfa2d1b7ce5edb5caa23238 Author: Ann Almgren Date: Sun May 7 17:11:05 2017 -0700 Update the size of ghost particles so that ghost particles always have the same size as valid particles. Source/AGNParticleContainer.H Source/agn_3d.f90 Source/agn_particle_mod.f90 commit 786ab774c3ee70ac93d23669f79b845cbeebca50 Author: Weiqun Zhang Date: Sat May 6 22:09:04 2017 -0700 add #ifdef __cplusplus Source/Nyx_F.H commit a9021de742527b1c1331d5ce650f6d677caab10e Author: Weiqun Zhang Date: Sat May 6 22:06:50 2017 -0700 changing size_t to int to match Fortran integer Source/AGNParticleContainer.cpp Source/agn_F.H commit 507bfe487727db3e6e299b6c13ef7369b217bd8e Author: Ann Almgren Date: Sat May 6 11:06:32 2017 -0700 Add _rt to the constant Source/Constants/constants_cosmo.f90 commit 6cc802c904f534cb43ed31231060427fcac71143 Author: Zarija Lukic Date: Fri May 5 22:37:40 2017 -0700 accretion rates fix Source/agn_3d.f90 commit 00e20e22fc2051f042653f4a3aeec34de690c670 Author: Zarija Lukic Date: Fri May 5 20:56:05 2017 -0700 fixed constants Source/Constants/constants_cosmo.f90 commit 9eeb3bc17c92089077e11a5fe1198be5c4961316 Author: Ann Almgren Date: Fri May 5 15:14:37 2017 -0700 Add print statement in order to debug Eddington limit Source/AGN/Make.package Source/agn_3d.f90 commit 5a27b3eeecc89a57cbc5f5adac7c01417c389358 Author: Ann Almgren Date: Fri May 5 15:10:48 2017 -0700 Remove old AGN stuff we weren't using Source/AGN/Makefile Source/AGN/agn_geometry.f90 Source/AGN/agn_mesh.f90 Source/AGN/agn_models.f90 Source/AGN/agn_params.f90 Source/AGN/agn_random.f90 Source/AGN/agnug.f90 commit 4500b0994564e70eec8acc73ad79078e1d159599 Author: Ann Almgren Date: Thu May 4 13:16:50 2017 -0700 Put the ghosts into the new particle format. All seems to work ... Source/AGNParticleContainer.cpp Source/agn_3d.f90 Source/agn_F.H Source/agn_particle_mod.f90 commit 7267e28dfd3d1c717d91f0ef10e54627ccc18169 Author: Ann Almgren Date: Thu May 4 12:32:23 2017 -0700 1) Finish using the new particle format 2) Modify ghosts to take all 8 (3 postion + mass + velocity + energy) components Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/agn_3d.f90 Source/agn_F.H commit e9c5980a5c4ce8c3401649ad40e262f1e61eb8e5 Merge: ac37c4ec 36f4699d Author: Ann Almgren Date: Thu May 4 12:05:55 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/Nyx into development commit ac37c4ec9e270268b355f1fc1f7647d5f1256a61 Author: Ann Almgren Date: Thu May 4 12:04:04 2017 -0700 moving to the new particle format Source/AGNParticleContainer.cpp Source/agn_3d.f90 Source/agn_F.H commit 36f4699d6838585fdbd35b2bbf871100cbbc7090 Author: Michael Zingale Date: Thu May 4 14:53:48 2017 -0400 sync up the job info with Castro Exec/Make.Nyx Source/Nyx_output.cpp commit 8a25f48b9a6d11ac21681e1d5c79f738787691ae Author: Ann Almgren Date: Thu May 4 11:42:50 2017 -0700 Moving towards using the new particle structure in the Fortran for much easier readability. Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/Constants/constants_cosmo.f90 Source/Make.package Source/Nyx_halos.cpp Source/agn_3d.f90 Source/agn_F.H Source/agn_particle_mod.f90 commit 73089b4ac205330e4a39c31575a780b09763c581 Author: Ann Almgren Date: Thu May 4 10:23:45 2017 -0700 Updated license. license.txt commit 9fe94c66f6bebe21c8558c64b8598a0072ceba67 Author: Ann Almgren Date: Wed May 3 20:17:53 2017 -0700 Fix the AGN stuff -- initial energy to zero, set the Thomson cross section ... Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/Constants/constants_cosmo.f90 Source/NyxParticleContainer.H Source/Nyx_halos.cpp Source/agn_3d.f90 Source/agn_F.H commit 861f2e2bf9a1655d08b1d6c9645ec5891dc3ef4d Author: Ann Almgren Date: Wed May 3 18:25:48 2017 -0700 Add the Eddington limit in the accretion and update the energy as well as the velocity of the particle. Source/NyxParticleContainer.H Source/Nyx_halos.cpp Source/agn_3d.f90 commit 4555a1119dcb6ab3241297997bb7b0378869a0d0 Author: Ann Almgren Date: Wed May 3 17:51:04 2017 -0700 Got the mass and momentum conservation working! Even have accretion appearing to work now. Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/Nyx_halos.cpp Source/agn_3d.f90 Source/agn_F.H commit 61614804f31f6c8f968779f28a47134a5f3aa75d Author: Ann Almgren Date: Wed May 3 15:50:00 2017 -0700 Update README for correct github.io location README.md commit 3ad102982f0a0a6c930737fcefe2f19f86b448e9 Author: Ann Almgren Date: Wed May 3 15:50:00 2017 -0700 Update README for correct github.io location README.md commit cecd1cef503728b6da7a404464fe68b4e3c67443 Author: petermcLBL Date: Wed May 3 15:23:33 2017 -0700 scaling by cell volume Source/agn_3d.f90 commit 8fea459fc198474910641c2baa996b6cfc9be9f3 Author: petermcLBL Date: Wed May 3 15:23:15 2017 -0700 momentum update Source/Nyx_halos.cpp commit 36e785e8ca864de5d5659c5e862895133ff1d14d Author: petermcLBL Date: Wed May 3 12:21:49 2017 -0700 different symbol for static member UsersGuide/Classes/classes.eps commit 0b1163393001146b7e144d420ef248019c134146 Author: petermcLBL Date: Wed May 3 12:21:21 2017 -0700 different symbol for static member UsersGuide/Classes/classes.fig commit e0cec3c61eddf410c2a27a0f0c64900e280d68bf Author: Ann Almgren Date: Tue May 2 18:15:19 2017 -0700 Add comment about still need to add the Eddington limit Source/agn_3d.f90 commit c00cf36e3d058d225fe77c38fbb9120b8ef26266 Author: Ann Almgren Date: Tue May 2 18:13:46 2017 -0700 Added the capability to merge AGN particles and to accrete mass onto AGN particles. This still needs lots of testing and we still need to extract the momentum from the gas before defining the velocity of the particle. Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/Constants/constants_cosmo.f90 Source/Nyx.H Source/Nyx.cpp Source/Nyx_halos.cpp Source/agn_3d.f90 Source/agn_F.H commit 0b64251878d86df2936b9885b1998567a17b2c88 Author: Ann Almgren Date: Tue May 2 17:04:16 2017 -0700 Add a routine that checks for mergers *before* new AGN particles are created. Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/Make.package Source/Nyx.H Source/Nyx_halos.cpp Source/agn_3d.f90 Source/agn_F.H Source/agn_overlap_3d.f90 commit 21f299270172de97a1321cdada3f6d508a4a0897 Author: Ann Almgren Date: Tue May 2 14:51:55 2017 -0700 Implement the code to set the velocity of the AGN Particles. Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/NyxParticleContainer.H Source/Nyx_halos.cpp Source/agn_F.H Source/agn_overlap_3d.f90 commit ddd00d4ced069d8aab442696426e379a8abe593b Merge: 10cd49ac 0c4a4d50 Author: Ann Almgren Date: Tue May 2 07:11:45 2017 -0700 Merge branch 'development' commit 8a59f4a82409865ca24f18907e5b6f1abbc02326 Merge: b38c413f 0c4a4d50 Author: Wolfram Schmidt Date: Tue May 2 16:01:22 2017 +0200 Merge remote-tracking branch 'upstream/development' into development commit 0c4a4d50d44d4300e8aaef5e13b9ba5a470feb26 Author: Ann Almgren Date: Fri Apr 28 17:36:57 2017 -0700 Update info about github.io README.md commit 10cd49ac6418caaf185d9d5277b3957eb20b3e53 Author: Ann Almgren Date: Fri Apr 28 17:36:57 2017 -0700 Update info about github.io README.md commit eee646a4d08faeb05800ebddf8d50b72f46c911b Author: Ann Almgren Date: Fri Apr 28 17:16:21 2017 -0700 Update AMReX info Conflicts: README.md README.md commit df1aea38ce96ae4c9f23af88aedce4dac8a2bf32 Author: Ann Almgren Date: Fri Apr 28 17:16:21 2017 -0700 Update AMReX info README.md commit e378eb507ab0edc2fc297e7cd7cff59d64c71836 Author: petermcLBL Date: Wed Apr 26 18:11:32 2017 -0700 Diagram of class hierarchy. UsersGuide/Classes/classes.eps UsersGuide/Classes/classes.fig commit c648fd9dd4a7999487c14cc50b81e01432babf4a Author: petermcLBL Date: Wed Apr 26 17:52:50 2017 -0700 new write function Source/Nyx_halos.cpp commit 599a47ebb92bb5ec0f756221669c1a5c06ecd28c Author: petermcLBL Date: Wed Apr 26 17:52:18 2017 -0700 new function writeAllAtLevel Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp commit b826f06b8c81d47852cb759fe0d65960b4477888 Author: petermcLBL Date: Wed Apr 26 17:51:40 2017 -0700 set particle id of new particles to -1 Source/agn_overlap_3d.f90 commit adc0b22bf344290d7a501ad5e5253da76f0b83aa Author: petermcLBL Date: Wed Apr 26 17:51:06 2017 -0700 avoid irritating warning message when MPI is off Source/main.cpp commit c618afba7fdba83b8122c29989bd37685306fd4a Merge: aed6742b f0f74dab Author: petermcLBL Date: Wed Apr 26 16:50:10 2017 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/Nyx into development Conflicts: Source/Nyx_halos.cpp commit aed6742b353a9c23ec0301579ebd0b034bc1ca87 Author: petermcLBL Date: Wed Apr 26 16:45:47 2017 -0700 starting loop over particles Source/Nyx_halos.cpp commit f0f74dabf233afd9b9921cd76f38707a6e45b26f Author: Ann Almgren Date: Wed Apr 26 16:35:05 2017 -0700 Add the capability to subtract density from the grid when we create new particles. Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/Nyx_halos.cpp Source/agn_F.H Source/agn_overlap_3d.f90 commit 79324f29bf9f059c3ae14cb6f2f295fe1ccf9a45 Author: Ann Almgren Date: Wed Apr 26 16:12:16 2017 -0700 Remove the REEBER version of redistributing the halos -- that is now made obsolete by our redistribution of particles. Source/Nyx_halos.cpp commit 2d97e786d4d57226c24857d87b47c1fc047afb5b Author: Ann Almgren Date: Wed Apr 26 15:34:24 2017 -0700 Destroy the AGN particles that are in the same locations as previously created particles Exec/LyA_AGN/inputs Source/AGNParticleContainer.H Source/AGNParticleContainer.cpp Source/Make.package Source/Nyx_halos.cpp Source/agn_F.H Source/agn_overlap_3d.f90 commit b53afa19c24f8757ac490c2ee04ba0f0a1b1bead Author: Ann Almgren Date: Wed Apr 26 14:14:20 2017 -0700 Fix typo Source/NeutrinoParticleContainer.H commit 82d6567d66b7a28b4a5ae2b8b2de4c739e060c7d Author: Ann Almgren Date: Wed Apr 26 12:49:27 2017 -0700 Fix the call to Redistribute -- we had the wrong arguments there. Source/Nyx_halos.cpp commit dd711bb1579ecde41db933db8f999b25e1e5b012 Author: Ann Almgren Date: Wed Apr 26 12:27:08 2017 -0700 Uncomment the computation of the particle mass from the halo mass Source/Nyx_halos.cpp commit 474ef397e301b4ec475ef6d87ae49bdb141a603c Merge: 2a928c7c 307ae390 Author: petermcLBL Date: Wed Apr 26 12:05:12 2017 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/Nyx into development blank commit 307ae3908e04a97e6e3e8590ced1c3e7642ccfed Author: Ann Almgren Date: Wed Apr 26 11:03:21 2017 -0700 Fxi TurbForce *.f90 files to compile. Exec/HydroTests/TurbForce/Prob_3d.f90 Exec/HydroTests/TurbForce/ext_src_3d.f90 commit b38c413f7249216ab067df5b108c067f3eab6e3c Author: Wolfram Schmidt Date: Wed Apr 26 15:27:20 2017 +0200 Postsync fixes in Exec/HydroTests/TurbForce. Exec/HydroTests/TurbForce/Prob_3d.f90 Exec/HydroTests/TurbForce/ext_src_3d.f90 commit 2a928c7c4b2d6b29806ffe280dee71ebb35a94db Author: petermcLBL Date: Tue Apr 25 18:28:39 2017 -0700 was ParticleDeposition.cpp Source/NeutrinoParticleContainer.cpp commit a49659610e1083b68696aa7ee7af2065bc913f7c Author: petermcLBL Date: Tue Apr 25 18:28:12 2017 -0700 changed to NeutrinoParticleContainer.cpp Source/Make.package Source/ParticleDeposition.cpp commit 0edd033f761556f2d5fd78911bbdb5de71129a9e Author: petermcLBL Date: Tue Apr 25 13:41:20 2017 -0700 Make AGNParticleContainer a class, not a typedef. Source/AGNParticleContainer.H Source/Make.package Source/Nyx.H commit 31379e0103b4b5a8d53236ce0356ab33dfae45b3 Author: petermcLBL Date: Tue Apr 25 11:49:00 2017 -0700 New DarkMatterParticleContainer class. Source/DarkMatterParticleContainer.H Source/DarkMatterParticleContainer.cpp Source/Initialization/Make.package Source/Make.package Source/Nyx.H Source/NyxParticleContainer.H Source/ParticleDeposition.cpp commit 1412fca7fcc4404c58f1dd444344702c093d88bd Author: Ann Almgren Date: Mon Apr 24 17:23:05 2017 -0700 Update the Users Guide UsersGuide/GNUmakefile UsersGuide/GettingStarted/NyxGettingStarted.tex UsersGuide/NyxUserGuide.tex UsersGuide/NyxVerification/Verification.tex UsersGuide/Particles/Particles.tex UsersGuide/PostProcessing/NyxPostProcessing.tex UsersGuide/Software/NyxSoftware.tex UsersGuide/Visualization/NyxVisualization.tex commit d4f23a3c92c7c8f0051833b4983e587c1c65899e Author: Ann Almgren Date: Mon Apr 24 17:23:05 2017 -0700 Update the Users Guide UsersGuide/GNUmakefile UsersGuide/GettingStarted/NyxGettingStarted.tex UsersGuide/NyxUserGuide.tex UsersGuide/NyxVerification/Verification.tex UsersGuide/Particles/Particles.tex UsersGuide/PostProcessing/NyxPostProcessing.tex UsersGuide/Software/NyxSoftware.tex UsersGuide/Visualization/NyxVisualization.tex commit 1d51f8202e7cfe5d423cd5276fb713fb31b84043 Author: Ann Almgren Date: Mon Apr 24 16:56:02 2017 -0700 Stop pointing to boxlib repo README.md commit f88730293cd961b334bb6577ab4ae289ea272acd Author: Ann Almgren Date: Mon Apr 24 16:56:02 2017 -0700 Stop pointing to boxlib repo README.md commit d9b4f97eb33623603ba8a1edd353d7f24b70f5f3 Author: Ann Almgren Date: Mon Apr 24 16:14:36 2017 -0700 Wrap everything AGN-related inside ifdef AGN Source/DerivedQuantities/ParticleDerive.cpp Source/NyxParticles.cpp commit 1cb0177f700102a46bb364b47a0a37fbf53918c8 Author: Ann Almgren Date: Mon Apr 24 16:07:58 2017 -0700 1) Extract the NeutrinoParticle stuff from NyxParticleContainer.H and make a new file, NeutrinoParticleContainer.H 2) Wrap everything related to neutrinos inside #ifdef NEUTRINO_PARTICLES Source/DerivedQuantities/ParticleDerive.cpp Source/Make.package Source/NeutrinoParticleContainer.H Source/Nyx.H Source/NyxParticleContainer.H Source/NyxParticles.cpp commit 2ce384bdc4a23d657b0e90196d2710531e00e471 Author: Ann Almgren Date: Mon Apr 24 15:56:45 2017 -0700 Update NyxParticleContainer to work with the new AMReX ParticleContainer stuff in which you can carry four rather than three types of data: 1) AoS Real 2) AoS Integer 3) SoA Real 4) SoA Integer Source/NyxParticleContainer.H commit 95cb3ddfe0358018ea1722ca037f11f42d09f5bd Author: Ann Almgren Date: Wed Apr 19 07:21:47 2017 -0700 Need to bind the bc functions local to Sedov Exec/HydroTests/Sedov/bc_fill_3d.f90 commit 96565162cdaff8f95f5d24912a361ba1bad5c7a1 Author: Ann Almgren Date: Tue Apr 18 16:05:09 2017 -0700 This at least creates the new particles -- very much a work in progress. Source/Nyx_halos.cpp commit 3ea37a0aaf57b61470c8adca8e20e6963b489501 Author: Ann Almgren Date: Tue Apr 18 09:48:46 2017 -0700 Get this compiling again. Source/HeatCool/heat_cool_stubs.f90 Source/Nyx_F.H Source/SourceTerms/Nyx_sources.cpp Source/SourceTerms/ext_src_3d.f90 Source/SourceTerms/ext_src_add_3d.f90 commit dad12abd52e70f177c0c6b48bdcdc9ae47681a9c Author: Ann Almgren Date: Mon Apr 17 18:07:48 2017 -0700 We can now add particles without REEBER defined but we still get a floating exception if we don't stop right after adding them. Source/Nyx.cpp Source/Nyx_halos.cpp commit 23210a896be0478de9ee7fa316cc4f0e046d15e4 Author: Ann Almgren Date: Mon Apr 17 17:50:11 2017 -0700 This version compiles Source/Nyx_halos.cpp commit 51731cd7592a6914b007a596879fc69f3da92e23 Author: Ann Almgren Date: Mon Apr 17 17:42:37 2017 -0700 Changes along the way to make the AGN particle creation work. Source/NyxParticleContainer.H Source/NyxParticles.cpp Source/Nyx_halos.cpp commit 2b4311973924a166be3f3bd2bcad6c32c713623d Author: Ann Almgren Date: Mon Apr 17 16:16:31 2017 -0700 Replace all the BL_FORT_PROC... wrappers with C bindings. Exec/AssignDensityTest/Prob_3d.f90 Exec/GravityTests/MacLaurin/Prob_3d.f90 Exec/GravityTests/zeldovich_dm/build/Prob_3d.f90 Exec/HydroTests/DoubleRarefaction/Prob_3d.f90 Exec/HydroTests/Sedov/Prob_3d.f90 Exec/HydroTests/Sod/Prob_3d.f90 Exec/HydroTests/StrongShockTube/Prob_3d.f90 Exec/HydroTests/TurbForce/Prob_3d.f90 Exec/LyA/Prob_3d.f90 Exec/LyA_AGN/Prob_3d.f90 Exec/MiniSB/Prob_3d.f90 Exec/RegressionTest/Prob_3d.f90 Exec/SantaBarbara/Prob_3d.f90 Exec/Scaling/Prob_3d.f90 Source/AGN/AGN_sources.cpp Source/EOS/atomic_rates.f90 Source/Gravity/Gravity.cpp Source/Gravity/Gravity_nd.f90 Source/HeatCool/integrate_state_3d.f90 Source/HydroFortran/Nyx_advection_3d.f90 Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/check_initial_species_3d.f90 Source/Initialization/init_e_from_rhoe_3d.f90 Source/Initialization/init_e_from_t_3d.f90 Source/Nyx.cpp Source/NyxParticles.cpp Source/Nyx_F.H Source/Nyx_advance.cpp Source/Nyx_hydro.cpp Source/Nyx_nd.f90 Source/Nyx_output.cpp Source/SourceTerms/Nyx_grav_sources_3d.f90 Source/SourceTerms/Nyx_sources.cpp Source/SourceTerms/Nyx_sources_3d.f90 Source/Src_3d/EstDt_3d.f90 Source/Src_3d/Make.package Source/Src_3d/Nyx_sums_3d.f90 Source/Src_3d/bc_fill_3d.f90 Source/Src_3d/compute_temp_3d.f90 Source/Src_3d/enforce_consistent_e_3d.f90 Source/Src_3d/enforce_nonnegative_species_3d.f90 Source/Src_3d/fort_avgdown_3d.f90 Source/Src_3d/reset_internal_energy_3d.f90 Source/comoving.cpp Source/comoving_nd.f90 Source/strang_splitting.cpp Source/sum_integrated_quantities.cpp Source/sum_utils.cpp Source/two_particle_advance.cpp commit 6393f21409677e425ba0e562c9294a8b64009a28 Author: Ann Almgren Date: Mon Apr 17 10:33:51 2017 -0700 Modified to make MacLaurin now compile. Exec/GravityTests/MacLaurin/set_dirichlet_bcs_3d.f90 Source/Tagging/Nyx_error.cpp commit 37b7a1f781458bb8e3e528a55654ea66bd39128f Author: Ann Almgren Date: Mon Apr 17 10:10:23 2017 -0700 Remove local version of Nyx_setup.cpp in MacLaurin Exec/GravityTests/MacLaurin/Nyx_setup.cpp commit 2d31367256c9dc8c9b9b745c74b31db741c990c2 Author: Ann Almgren Date: Sat Apr 15 19:27:25 2017 -0700 Fix Nyx_error.cpp, Prob_3d.f90 and integrate* so that they work with amrex. Now modify inputs so we can run a small problem in serial for testing. Exec/Scaling/Nyx_error.cpp Exec/Scaling/Prob_3d.f90 Exec/Scaling/inputs Exec/Scaling/integrate_state_vode_3d.f90 commit 37913e518bd07e40a4a214c6a6269cd9298ce4c5 Author: Ann Almgren Date: Sat Apr 15 19:26:38 2017 -0700 Add the option to call InitRandomPerBox which we use for scaling studies in which we want to replicate the random particle generation from one box to multiple boxes. Source/NyxParticles.cpp commit 01938ed60081e9ced0476d124baafeb7fba1ddf0 Author: Ann Almgren Date: Sat Apr 15 17:56:16 2017 -0700 1) Shouldn't have committed AMReX_buildInfo.cpp 2) Add init_random_count_per_box Exec/Scaling/AMReX_buildInfo.cpp Source/Nyx.H commit 097b53b691104465d8378c3b550e0b9db32a5f19 Author: Ann Almgren Date: Sat Apr 15 17:54:48 2017 -0700 Oops -- should never have committed tmp_build_dir. Exec/Scaling/Nyx.H Exec/Scaling/Nyx.cpp Exec/Scaling/NyxParticles.cpp Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_ABecLaplacian.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_ABec_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_ABec_UTIL.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_ARRAYLIM_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Amr.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_AmrCore.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_AmrData.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_AmrLevel.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_AmrMesh.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Arena.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_AuxBoundaryData.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BArena.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BCRec.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BLBackTrace.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BLBoxLib_F.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BLParmParse_F.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BLProfiler.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BLProfiler_F.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BLutil_F.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BaseFab.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BndryData.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BndryRegister.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Box.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BoxArray.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BoxDomain.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BoxIterator.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BoxList.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_CArena.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_CGSolver.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_COORDSYS_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Cluster.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_CoordSys.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_DataServices.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Derive.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_DistributionMapping.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_ErrorList.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Extrapolater.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FABUTIL_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FArrayBox.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FILCC_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FLUXREG_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FMultiGrid.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FPC.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FabArrayBase.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FabConv.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FabSet.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FillPatchUtil.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FluxRegister.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Geometry.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_IArrayBox.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_INTERPBNDRYDATA_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_INTERP_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_IndexType.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_IntVect.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_InterpBndryData.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Interpolater.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_LO_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_LO_UTIL.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_LP_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Laplacian.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_LinOp.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_MAKESLICE_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_MFCopyDescriptor.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_MFIter.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_MGT_Solver.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_MG_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_MacBndry.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Mask.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_MemPool.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_MultiFab.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_MultiFabUtil.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_MultiGrid.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_MultiMask.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_NFiles.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Orientation.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_ParallelDescriptor.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_ParmParse.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Particles_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Periodicity.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_PhysBCFunct.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_PlotFileUtil.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_RealBox.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_RealVect.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_StateData.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_StateDescriptor.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_TagBox.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_TracerParticles.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Utility.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_VisMF.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_buildInfo.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_error_fi.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_iMultiFab.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_parmparse_fi.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/Gravity.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/MemInfo.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/MultiFab_C_F.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/Nyx.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/NyxBld.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/NyxParticles.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/Nyx_advance.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/Nyx_error.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/Nyx_halos.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/Nyx_hydro.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/Nyx_initcosmo.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/Nyx_initdata.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/Nyx_output.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/Nyx_setup.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/Nyx_sources.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/ParticleDeposition.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/ParticleDerive.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/ParticleInit.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/advance_particles.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/backtrace_c.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/comoving.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dacopy.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/daxpy.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dcopy.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/ddot.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dewset.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dgbfa.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dgbsl.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dgefa.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dgesl.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dscal.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dumach.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dvhin.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dvindy.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dvjac.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dvjust.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dvnlsd.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dvnorm.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dvode.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dvset.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dvsol.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/dvstep.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/f90.depends Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/fabio_c.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/idamax.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/iumach.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/ixsav.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/main.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/read_plotfile.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/strang_splitting.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/sum_integrated_quantities.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/sum_utils.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/timer_c.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/two_particle_advance.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/write_info.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/xerrwd.d Exec/Scaling/tmp_build_dir/f/3d.gnu.MPI.OMP.EXE/F90PP-AMReX_Particle_mod_3d.F90 Exec/Scaling/tmp_build_dir/f/3d.gnu.MPI.OMP.EXE/F90PP-AMReX_error_mod.F90 Exec/Scaling/tmp_build_dir/f/3d.gnu.MPI.OMP.EXE/F90PP-AMReX_fort_mod.F90 Exec/Scaling/tmp_build_dir/f/3d.gnu.MPI.OMP.EXE/F90PP-AMReX_omp_mod.F90 Exec/Scaling/tmp_build_dir/f/3d.gnu.MPI.OMP.EXE/F90PP-AMReX_parmparse_mod.F90 Exec/Scaling/tmp_build_dir/f/3d.gnu.MPI.OMP.EXE/F90PP-AMReX_string_mod.F90 Exec/Scaling/tmp_build_dir/o/3d.gnu.MPI.OMP.EXE/NyxBld.o Exec/Scaling/tmp_build_dir/o/3d.gnu.MPI.OMP.EXE/Nyx_advance.o Exec/Scaling/tmp_build_dir/o/3d.gnu.MPI.OMP.EXE/Nyx_halos.o Exec/Scaling/tmp_build_dir/o/3d.gnu.MPI.OMP.EXE/ParticleDeposition.o Exec/Scaling/tmp_build_dir/o/3d.gnu.MPI.OMP.EXE/advance_particles.o commit ac7a2382dd936d7826d9b0c5beed94f855218041 Author: Ann Almgren Date: Thu Apr 13 22:17:06 2017 -0700 More cleanup ... completing the replacement of "double precision" and "real(dp_t)" by real(rt) from amrex. At this point MacLauren and Scaling don't compile yet. Exec/AssignDensityTest/Prob_3d.f90 Exec/GravityTests/MacLaurin/GNUmakefile Exec/GravityTests/MacLaurin/Nyx_error.cpp Exec/GravityTests/MacLaurin/Nyx_setup.cpp Exec/GravityTests/MacLaurin/Prob_3d.f90 Exec/GravityTests/MacLaurin/Tagging_3d.f90 Exec/GravityTests/MacLaurin/probdata.f90 Exec/GravityTests/MacLaurin/set_dirichlet_bcs_3d.f90 Exec/GravityTests/zeldovich_dm/build/GNUmakefile Exec/GravityTests/zeldovich_dm/build/Prob_3d.f90 Exec/GravityTests/zeldovich_dm/build/Tagging_3d.f90 Exec/GravityTests/zeldovich_dm/build/probdata.f90 Exec/HydroTests/DoubleRarefaction/Prob_3d.f90 Exec/HydroTests/DoubleRarefaction/Tagging_3d.f90 Exec/HydroTests/DoubleRarefaction/probdata.f90 Exec/HydroTests/Sedov/Prob_3d.f90 Exec/HydroTests/Sedov/Tagging_3d.f90 Exec/HydroTests/Sedov/bc_fill_3d.f90 Exec/HydroTests/Sedov/probdata.f90 Exec/HydroTests/Sod/Prob_3d.f90 Exec/HydroTests/Sod/Tagging_3d.f90 Exec/HydroTests/Sod/probdata.f90 Exec/HydroTests/StrongShockTube/Prob_3d.f90 Exec/HydroTests/StrongShockTube/Tagging_3d.f90 Exec/HydroTests/StrongShockTube/probdata.f90 Exec/HydroTests/TurbForce/Derive_3d.f90 Exec/HydroTests/TurbForce/Prob_3d.f90 Exec/HydroTests/TurbForce/Tagging_3d.f90 Exec/HydroTests/TurbForce/ext_src_3d.f90 Exec/HydroTests/TurbForce/ext_src_force_3d.f90 Exec/HydroTests/TurbForce/integrate_state_force_3d.f90 Exec/HydroTests/TurbForce/probdata.f90 Exec/HydroTests/TurbForce/turbforce.f90 Exec/HydroTests/TurbForce/turbinit.f90 Exec/LyA/GNUmakefile Exec/LyA/Prob_3d.f90 Exec/LyA/Tagging_3d.f90 Exec/LyA/integrate_state_vode_3d.f90 Exec/LyA_AGN/Prob_3d.f90 Exec/LyA_AGN/Tagging_3d.f90 Exec/LyA_AGN/integrate_state_vode_3d.f90 Exec/MiniSB/Prob_3d.f90 Exec/MiniSB/Tagging_3d.f90 Exec/RegressionTest/Prob_3d.f90 Exec/RegressionTest/Tagging_3d.f90 Exec/SantaBarbara/Prob_3d.f90 Exec/SantaBarbara/Tagging_3d.f90 Exec/Scaling/AMReX_buildInfo.cpp Exec/Scaling/GNUmakefile Exec/Scaling/Nyx.H Exec/Scaling/Nyx.cpp Exec/Scaling/NyxParticles.cpp Exec/Scaling/Nyx_error.cpp Exec/Scaling/Particles.H Exec/Scaling/Prob_3d.f90 Exec/Scaling/Tagging_3d.f90 Exec/Scaling/integrate_state_vode_3d.f90 Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_ABecLaplacian.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_ABec_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_ABec_UTIL.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_ARRAYLIM_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Amr.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_AmrCore.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_AmrData.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_AmrLevel.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_AmrMesh.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Arena.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_AuxBoundaryData.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BArena.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BCRec.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BLBackTrace.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BLBoxLib_F.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BLParmParse_F.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BLProfiler.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BLProfiler_F.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BLutil_F.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BaseFab.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BndryData.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BndryRegister.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Box.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BoxArray.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BoxDomain.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BoxIterator.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_BoxList.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_CArena.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_CGSolver.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_COORDSYS_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Cluster.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_CoordSys.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_DataServices.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Derive.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_DistributionMapping.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_ErrorList.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Extrapolater.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FABUTIL_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FArrayBox.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FILCC_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FLUXREG_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FMultiGrid.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FPC.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FabArrayBase.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FabConv.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FabSet.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FillPatchUtil.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_FluxRegister.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Geometry.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_IArrayBox.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_INTERPBNDRYDATA_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_INTERP_3D.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_IndexType.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_IntVect.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_InterpBndryData.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_Interpolater.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/AMReX_LO_3D.d 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Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/f90.depends Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/fabio_c.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/idamax.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/iumach.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/ixsav.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/main.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/read_plotfile.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/strang_splitting.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/sum_integrated_quantities.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/sum_utils.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/timer_c.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/two_particle_advance.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/write_info.d Exec/Scaling/tmp_build_dir/d/3d.gnu.MPI.OMP.EXE/xerrwd.d Exec/Scaling/tmp_build_dir/f/3d.gnu.MPI.OMP.EXE/F90PP-AMReX_Particle_mod_3d.F90 Exec/Scaling/tmp_build_dir/f/3d.gnu.MPI.OMP.EXE/F90PP-AMReX_error_mod.F90 Exec/Scaling/tmp_build_dir/f/3d.gnu.MPI.OMP.EXE/F90PP-AMReX_fort_mod.F90 Exec/Scaling/tmp_build_dir/f/3d.gnu.MPI.OMP.EXE/F90PP-AMReX_omp_mod.F90 Exec/Scaling/tmp_build_dir/f/3d.gnu.MPI.OMP.EXE/F90PP-AMReX_parmparse_mod.F90 Exec/Scaling/tmp_build_dir/f/3d.gnu.MPI.OMP.EXE/F90PP-AMReX_string_mod.F90 Exec/Scaling/tmp_build_dir/o/3d.gnu.MPI.OMP.EXE/NyxBld.o Exec/Scaling/tmp_build_dir/o/3d.gnu.MPI.OMP.EXE/Nyx_advance.o Exec/Scaling/tmp_build_dir/o/3d.gnu.MPI.OMP.EXE/Nyx_halos.o Exec/Scaling/tmp_build_dir/o/3d.gnu.MPI.OMP.EXE/ParticleDeposition.o Exec/Scaling/tmp_build_dir/o/3d.gnu.MPI.OMP.EXE/advance_particles.o Source/AGN/AGN_sources.cpp Source/DerivedQuantities/Derive_3d.f90 Source/DerivedQuantities/Derive_F.H Source/EOS/eos_stuff.f90 Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/NyxParticles.cpp Source/Nyx_F.H Source/SourceTerms/Nyx_sources.cpp Source/SourceTerms/ext_src_3d.f90 commit 8e0393471b102c42ebec827520cf5713e8d93e94 Author: Ann Almgren Date: Thu Apr 13 15:37:56 2017 -0700 Replace real(dp_t) and double precision by real(rt) with the line use amrex_fort_module, only : rt => amrex_real Source/AGN/agn_geometry.f90 Source/AGN/agn_mesh.f90 Source/AGN/agn_models.f90 Source/AGN/agn_params.f90 Source/AGN/agn_random.f90 Source/AGN/agnug.f90 Source/Constants/constants_cgs.f90 Source/Constants/constants_cosmo.f90 Source/DerivedQuantities/Derive_3d.f90 Source/EOS/atomic_rates.f90 Source/EOS/eos_hc.f90 Source/EOS/eos_stuff.f90 Source/Gravity/Gravity_3d.f90 Source/Gravity/Gravity_nd.f90 Source/Gravity/prescribe_grav_3d.f90 Source/Gravity/set_dirichlet_bcs_3d.f90 Source/HeatCool/cooling.f90 Source/HeatCool/ext_src_hc_3d.f90 Source/HeatCool/f_rhs.f90 Source/HeatCool/heat_cool_stubs.f90 Source/HeatCool/integrate_state_3d.f90 Source/HeatCool/integrate_state_hc_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 Source/HeatCool/vode_aux.f90 Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/add_grav_source_3d.f90 Source/HydroFortran/analriem.f90 Source/HydroFortran/enforce_minimum_density_3d.f90 Source/HydroFortran/flatten_3d.f90 Source/HydroFortran/normalize_species_3d.f90 Source/HydroFortran/ppm_3d.f90 Source/HydroFortran/slope_3d.f90 Source/HydroFortran/trace_3d.f90 Source/HydroFortran/trace_colglaz_3d.f90 Source/HydroFortran/trace_ppm_3d.f90 Source/HydroFortran/trace_src_3d.f90 Source/HydroFortran/trans_3d.f90 Source/Initialization/check_initial_species_3d.f90 Source/Initialization/init_e_from_rhoe_3d.f90 Source/Initialization/init_e_from_t_3d.f90 Source/Initialization/interpolate.f90 Source/MG/cc_smoothers.f90 Source/MG/cc_stencil_apply.f90 Source/MG/mg_tower_smoother.f90 Source/Make.package Source/Network/network.f90 Source/Network/nyx_burner.f90 Source/Nyx_nd.f90 Source/SourceTerms/Nyx_grav_sources_3d.f90 Source/SourceTerms/Nyx_sources_3d.f90 Source/SourceTerms/ext_src_3d.f90 Source/SourceTerms/ext_src_add_3d.f90 Source/Src_3d/EstDt_3d.f90 Source/Src_3d/Nyx_sums_3d.f90 Source/Src_3d/ang_mom_sums_3d.f90 Source/Src_3d/bc_fill_3d.f90 Source/Src_3d/compute_temp_3d.f90 Source/Src_3d/enforce_consistent_e_3d.f90 Source/Src_3d/enforce_nonnegative_species_3d.f90 Source/Src_3d/fort_avgdown_3d.f90 Source/Src_3d/reset_internal_energy_3d.f90 Source/Tagging/Tagging_3d.f90 Source/comoving_nd.f90 Source/comoving_params.f90 Source/eos_params.f90 Source/meth_params.f90 Source/project_S.f90 commit 5091f8195fea1688d17a37a1664c087c77a237fa Merge: 6e503109 85bb44e6 Author: asalmgren Date: Thu Apr 13 12:34:11 2017 -0700 Merge pull request #4 from wolfram-schmidt/development TurbForce commit 85bb44e6f9c71989ef857f58bcfd55b2efdba771 Merge: be5337d2 6e503109 Author: asalmgren Date: Thu Apr 13 12:33:49 2017 -0700 Merge branch 'development' into development commit c7c02ce79f60416042d927cc4c25b4ccc512cf99 Merge: 82e3f804 6e503109 Author: Ann Almgren Date: Wed Apr 12 17:31:40 2017 -0700 Merge branch 'development' commit 6e503109c13e7ba2b4ae09ba184100e1b807a21a Author: Ann Almgren Date: Wed Apr 12 17:29:52 2017 -0700 Add DERFORCEX, DERFORCEY, DERFORCEZ Source/DerivedQuantities/Derive_F.H commit 3cf3943faf46d2f3a81a0a40be2f4bb230fcee8d Author: Ann Almgren Date: Wed Apr 12 17:29:14 2017 -0700 Clean up the eos slightly to remove redundant computation. Source/EOS/eos_stuff.f90 commit 82e3f8046dca61b9278297a80b292b0a3b311e58 Merge: c09627c1 9102bf46 Author: Ann Almgren Date: Wed Apr 12 17:20:04 2017 -0700 Merge branch 'development' commit 9102bf46add14ecb63cd9e485636fb79e9856eb2 Author: Ann Almgren Date: Wed Apr 12 17:02:23 2017 -0700 Oops -- we forgot to define Sborder_old and Dborder_old in Nyx_sources.cpp Source/SourceTerms/Nyx_sources.cpp commit be5337d2fc7a1b75538d6bb3abb1d990a28b986e Author: Wolfram Schmidt Date: Wed Apr 12 15:43:13 2017 +0200 Ported TurbForce to new AMReX version; bug fixes in Nyx_sources.cpp and Derive_F.H Exec/HydroTests/TurbForce/GNUmakefile Exec/HydroTests/TurbForce/Nyx_error.cpp Exec/HydroTests/TurbForce/Nyx_setup.cpp Exec/HydroTests/TurbForce/Prob_3d.f90 Source/DerivedQuantities/Derive_F.H Source/SourceTerms/Nyx_sources.cpp commit 535b518375455ad717c5a214fb14b3d893895f58 Merge: 8af82282 dc34a3e4 Author: Wolfram Schmidt Date: Wed Apr 12 12:01:02 2017 +0200 Merge remote-tracking branch 'upstream/development' into development Conflicts: Exec/LyA/GNUmakefile Source/SourceTerms/Nyx_sources.cpp commit c09627c17067ab298659237d5b97dff26d222444 Author: Ann Almgren Date: Tue Apr 11 08:46:55 2017 -0700 Add directions to use development branch of amrex -- we got out of sync README.md commit 8af822820b17113214df870e9a7fca8dd043b347 Author: Wolfram Schmidt Date: Tue Apr 11 12:42:22 2017 +0200 Added files for TurbForce regression test. Exec/HydroTests/TurbForce/inputs.regtest Exec/HydroTests/TurbForce/probin commit 3b0caf26ce4c7f060607e2322136f274735458dd Author: Wolfram Schmidt Date: Thu Apr 6 15:19:05 2017 +0200 Checked MPI/OMP consistency of cooling loop in integrate_state_force; fixed bug in call of integrate_state_hc in ext_src_hc; changed data types in eos_stuff to double precision and modified computation of eint to avoid unnecessary operations. Exec/HydroTests/TurbForce/Derive_3d.f90 Exec/HydroTests/TurbForce/GNUmakefile Exec/HydroTests/TurbForce/Prob_3d.f90 Exec/HydroTests/TurbForce/atomic_rates.f90 Exec/HydroTests/TurbForce/ext_src_3d.f90 Exec/HydroTests/TurbForce/ext_src_force_3d.f90 Exec/HydroTests/TurbForce/inputs Exec/HydroTests/TurbForce/integrate_state_force_3d.f90 Exec/HydroTests/TurbForce/probdata.f90 Exec/HydroTests/TurbForce/probin Exec/HydroTests/TurbForce/turbinit.f90 Exec/LyA/GNUmakefile Source/DerivedQuantities/Derive_3d.f90 Source/EOS/eos_stuff.f90 Source/HeatCool/ext_src_hc_3d.f90 Source/SourceTerms/Nyx_sources_3d.f90 Source/sum_integrated_quantities.cpp commit dc34a3e4a1a89b41446ef8e8e8c983ecdf81f5b2 Author: Ann Almgren Date: Fri Apr 7 18:14:37 2017 -0700 Add details about moving to AMReX README.md commit 4aabfb21ecf9664720a81a4aeab20a2fbd0d4707 Merge: 0a0c699d 8fb11344 Author: Ann Almgren Date: Fri Apr 7 17:56:18 2017 -0700 Merge branch 'development' Conflicts: Source/Nyx.H Source/Nyx.cpp commit 8fb113448dd6f9f81b21a9409b30a80b6313e7da Author: Ann Almgren Date: Fri Apr 7 16:52:25 2017 -0700 Update the Sborder and Dborder defines to work with amrex Source/SourceTerms/Nyx_sources.cpp commit 863b545078b1a6b2f912438cab1623f7723c9c6d Merge: 5e000a36 faf42e1c Author: Ann Almgren Date: Fri Apr 7 16:43:42 2017 -0700 Merge branch 'amrex' into development commit 0a0c699dd9c49021578679098aebdc5a01be9350 Merge: 74ab88a2 5e000a36 Author: Ann Almgren Date: Fri Apr 7 16:37:22 2017 -0700 Merge remote-tracking branch 'origin/development' commit faf42e1c02f4415926bd7a322b74c87048837da9 Author: Weiqun Zhang Date: Wed Apr 5 15:16:38 2017 -0700 add const due to amrex change Exec/AssignDensityTest/Nyx_error.cpp Exec/HydroTests/DoubleRarefaction/Nyx_error.cpp Exec/HydroTests/Sedov/Nyx_error.cpp Exec/HydroTests/Sod/Nyx_error.cpp Exec/HydroTests/StrongShockTube/Nyx_error.cpp Exec/LyA/Nyx_error.cpp Exec/MiniSB/Nyx_error.cpp Exec/RegressionTest/Nyx_error.cpp Exec/SantaBarbara/Nyx_error.cpp Source/Nyx.H commit 6bd5432dcbb99247a093829610248f9b3b92aba1 Author: Wolfram Schmidt Date: Fri Mar 31 15:57:05 2017 +0200 Ann's bug fix in Nyx_sources; added forcing components to derived fields; small changes in output to log files. Source/DerivedQuantities/Derive_3d.f90 Source/DerivedQuantities/Derive_F.H Source/SourceTerms/Nyx_sources.cpp Source/sum_integrated_quantities.cpp commit c3ade75b1021ddc3519699d810ae3469b2d43270 Author: Wolfram Schmidt Date: Fri Mar 31 15:53:58 2017 +0200 Inserted linear heating/cooling around equilibrium temperature temp0 with coefficient alpha in integrate_state_force. Exec/HydroTests/TurbForce/integrate_state_force_3d.f90 commit db87a0bce6acd13987ec47225af62fad45350fc7 Author: Wolfram Schmidt Date: Fri Mar 31 14:34:18 2017 +0200 Added Exec/HydroTests/TurbForce for random turbulent forcing in approximately isothermal gas; integrate_state_force is only a dummy which does not change the state yet. Exec/HydroTests/TurbForce/GNUmakefile Exec/HydroTests/TurbForce/Make.package Exec/HydroTests/TurbForce/Nyx_error.cpp Exec/HydroTests/TurbForce/Nyx_setup.cpp Exec/HydroTests/TurbForce/Prob_3d.f90 Exec/HydroTests/TurbForce/Tagging_3d.f90 Exec/HydroTests/TurbForce/atomic_rates.f90 Exec/HydroTests/TurbForce/ext_src_3d.f90 Exec/HydroTests/TurbForce/ext_src_force_3d.f90 Exec/HydroTests/TurbForce/integrate_state_force_3d.f90 Exec/HydroTests/TurbForce/probdata.f90 Exec/HydroTests/TurbForce/turbforce.f90 Exec/HydroTests/TurbForce/turbinit.f90 commit 5e000a3623554f5003ff3dcce036ff7a578aa165 Author: Ann Almgren Date: Wed Mar 29 10:42:41 2017 -0700 We need to define temporary multifabs with 4 ghost cells in order to call these particular ext_src routines. Source/SourceTerms/Nyx_sources.cpp commit 74ab88a2998cb3885c88ee98c1f1cbe6fca1360c Merge: 8b45b483 1a081587 Author: asalmgren Date: Mon Mar 6 15:30:03 2017 -0800 Merge pull request #3 from ghweber/master Return halos from Reeber to simulation commit 1a0815877795ca896f42347908b4759423419971 Author: Gunther H. Weber Date: Mon Mar 6 15:25:50 2017 -0800 Return halos from Reeber to simulation Source/Nyx.cpp commit 8ddcb5e7cf8e1432f785a706deac31b623c4bc9b Author: Andrew Myers Date: Sun Mar 5 10:15:02 2017 -0800 SingleLevelWhere has been removed. Source/NyxParticleContainer.H commit adb3bec6e0234f8d54fec809fd9773edbfe1f053 Author: Andrew Myers Date: Wed Mar 1 14:03:41 2017 -0800 Make these variables OpenMP private Source/Initialization/ParticleInit.cpp Source/NyxParticleContainer.H commit 4cb15c0d34af5edb32766b58d58c422e2286e2b5 Author: Andrew Myers Date: Wed Mar 1 12:20:27 2017 -0800 Fix a bug I just introduced. Source/NyxParticles.cpp commit 75411457f5a3c287f24d2530c0738dad44542e0c Author: Andrew Myers Date: Wed Mar 1 11:14:26 2017 -0800 Update Nyx to reflect particle API changes. Source/NyxParticleContainer.H Source/NyxParticles.cpp commit 31a987dec6d9ab91babf1753a45a2a5156d55097 Author: Andrew Myers Date: Wed Mar 1 10:33:09 2017 -0800 update Nyx to reflect the new form of Redistribute() Source/Nyx.cpp Source/NyxParticleContainer.H commit 13a43b4c2e7a2e5bcba829fced534c9e4a4f7197 Author: Andrew Myers Date: Wed Mar 1 10:05:04 2017 -0800 update Nyx to reflect recent API changes. Source/Initialization/ParticleInit.cpp Source/NyxParticleContainer.H commit 750ef2a4fc7d08f2492db9f570d75dc32777c487 Author: Andrew Myers Date: Wed Mar 1 09:56:20 2017 -0800 Fix compilation errors when OpenMP is turned on. Source/Initialization/ParticleInit.cpp Source/NyxParticleContainer.H commit 48b19387dec99fa285961af6c81f39d22744457d Author: Andrew Myers Date: Tue Feb 28 18:04:21 2017 -0800 Fix a problematic assert. Source/NyxParticleContainer.H commit d9a7c24b2e3093a43b359c107b9f6d3d6b139494 Author: Andrew Myers Date: Tue Feb 28 17:31:02 2017 -0800 Updating Nyx to work with the particle_refactor branch of amrex. Source/Initialization/ParticleInit.cpp Source/Nyx.cpp Source/NyxParticleContainer.H Source/NyxParticles.cpp commit f5d2d80094e5f696809e0c7d04ee86ea24f6e323 Author: Andrew Myers Date: Mon Feb 27 14:51:21 2017 -0800 Remove obsolete fortran-threaded version of enforce_nonnegative species. Source/Src_3d/enforce_nonnegative_species_3d.f90 commit 8b45b483cbcd272e814f1ee760d98a78287031dc Merge: 157526bd 66dbd684 Author: asalmgren Date: Thu Feb 23 17:11:01 2017 -0800 Merge pull request #2 from ghweber/master Updated paths for Reeber on Cori commit 66dbd6843f9c50d8749bd2d463b742031571dd3f Author: Gunther H. Weber Date: Thu Feb 23 17:06:50 2017 -0800 Updated paths for Reeber on Cori Exec/LyA/GNUmakefile Exec/Make.Nyx commit 157526bd014d5c13b11e53e5e3d63da5aaa20c6b Merge: ae352aff 30d11363 Author: asalmgren Date: Wed Feb 22 16:17:55 2017 -0800 Merge pull request #1 from ghweber/master Updated and improved Reeber analysis commit 30d11363bb381a03c1b808575757f5faef0cf283 Author: Gunther H. Weber Date: Tue Jan 17 17:29:37 2017 -0800 Updated and improved Reeber analysis Exec/LyA/GNUmakefile Exec/Make.Nyx Exec/MiniSB/GNUmakefile Exec/MiniSB/inputs.analysis Source/Make.package Source/Nyx.H Source/Nyx.cpp Source/main.cpp commit ae352affada763c0ea56ccc929365aa275030cd8 Author: Ann Almgren Date: Tue Feb 21 14:29:16 2017 -0800 Use analysis_z_values to decide doAnalysisNow() ... Source/Nyx.H Source/Nyx.cpp commit 6aa6893197c115e4cc990db42afb4a9af23650da Author: Ann Almgren Date: Tue Feb 21 13:50:04 2017 -0800 We now have analysis_z_values that are analogous to plot_z_values but they are for determining when to do analysis as opposed to when to write plotfiles Source/Nyx.H Source/Nyx.cpp Source/comoving.cpp commit 958d6be9a87324968e0a7ea453d469417a00db50 Author: Weiqun Zhang Date: Fri Jan 27 10:33:39 2017 -0800 migration step 10 Source/DerivedQuantities/Derive_F.H Source/Gravity/Gravity.H Source/Gravity/Gravity_F.H Source/Initialization/Nyx_initcosmo.cpp Source/Nyx.H Source/NyxParticleContainer.H Source/Nyx_F.H Source/Tagging/Nyx_error_F.H commit 03f88b88462f44d1c1c62fdd4d111e8cf30cfab1 Author: Zarija Lukic Date: Mon Jan 16 01:08:57 2017 -0800 Add scaling problem Exec/Scaling/GNUmakefile Exec/Scaling/Make.package Exec/Scaling/Nyx.H Exec/Scaling/Nyx.cpp Exec/Scaling/NyxParticles.cpp Exec/Scaling/Nyx_error.cpp Exec/Scaling/Particles.H Exec/Scaling/Prob_3d.f90 Exec/Scaling/Tagging_3d.f90 Exec/Scaling/inputs Exec/Scaling/integrate_state_vode_3d.f90 Exec/Scaling/probdata.f90 Exec/Scaling/probin commit a0cec45c104d5e7a940805b72984d5bc07e66e52 Author: Weiqun Zhang Date: Sat Jan 14 17:32:01 2017 -0800 fix a new bug: grids needs to be reference Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit bdbc535e2a11056c3a3f84440b3eb0ebf1e76b1a Author: Weiqun Zhang Date: Sat Jan 14 12:42:33 2017 -0800 migration step 9 Source/DerivedQuantities/ParticleDerive.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_output.cpp Source/sum_utils.cpp commit fc5d97628596cf86fb1fadc3f0c60993c3c9595d Author: Weiqun Zhang Date: Sat Jan 14 12:15:14 2017 -0800 migration step 8 Diagnostics/AmrDerive.cpp Exec/AssignDensityTest/Nyx_error.cpp Exec/GravityTests/MacLaurin/Nyx_error.cpp Exec/GravityTests/MacLaurin/Nyx_setup.cpp Exec/GravityTests/zeldovich_dm/build/Nyx_error.cpp Exec/HydroTests/DoubleRarefaction/Nyx_error.cpp Exec/HydroTests/Sedov/Nyx_error.cpp Exec/HydroTests/Sod/Nyx_error.cpp Exec/HydroTests/StrongShockTube/Nyx_error.cpp Exec/LyA/Nyx_error.cpp Exec/Make.Nyx Exec/MiniSB/Nyx_error.cpp Exec/RegressionTest/Nyx_error.cpp Exec/SantaBarbara/Nyx_error.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/read_plotfile.cpp Source/Nyx.cpp Source/Nyx_advance.cpp Source/Nyx_hydro.cpp Source/Nyx_output.cpp Source/Tagging/Nyx_error.cpp Source/advance_particles.cpp Source/main.cpp Source/strang_splitting.cpp Source/two_particle_advance.cpp commit 9414fe396918cf2490fc7197ac2b7930f90c83f4 Author: Weiqun Zhang Date: Sat Jan 14 12:13:08 2017 -0800 migration step 7 Exec/AssignDensityTest/Prob_3d.f90 Exec/GravityTests/MacLaurin/Prob_3d.f90 Exec/GravityTests/zeldovich_dm/build/Prob_3d.f90 Exec/HydroTests/DoubleRarefaction/Prob_3d.f90 Exec/HydroTests/Sedov/Prob_3d.f90 Exec/HydroTests/Sod/Prob_3d.f90 Exec/HydroTests/StrongShockTube/Prob_3d.f90 Exec/LyA/Prob_3d.f90 Exec/MiniSB/Prob_3d.f90 Exec/RegressionTest/Prob_3d.f90 Exec/SantaBarbara/Prob_3d.f90 commit b94d932719ce771f2e813e56dbcd055749535ce5 Author: Weiqun Zhang Date: Sat Jan 14 09:41:27 2017 -0800 migration step 6 Diagnostics/AmrDerive.cpp Source/DerivedQuantities/ParticleDerive.cpp Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxBld.cpp Source/NyxParticleContainer.H Source/NyxParticles.cpp Source/Nyx_advance.cpp Source/Nyx_hydro.cpp Source/Nyx_output.cpp Source/ParticleDeposition.cpp Source/advance_particles.cpp Source/main.cpp Source/sum_utils.cpp commit cc693e876cb7337fa3c7e78972b9abd9b1b73f41 Author: Weiqun Zhang Date: Fri Jan 13 13:03:15 2017 -0800 migration step 5 Diagnostics/AmrDerive.cpp Exec/AssignDensityTest/Nyx_error.cpp Exec/GravityTests/MacLaurin/Nyx_error.cpp Exec/GravityTests/MacLaurin/Nyx_setup.cpp Exec/GravityTests/zeldovich_dm/build/NyxParticles.cpp Exec/GravityTests/zeldovich_dm/build/Nyx_error.cpp Exec/HydroTests/DoubleRarefaction/Nyx_error.cpp Exec/HydroTests/Sedov/Nyx_error.cpp Exec/HydroTests/Sod/Nyx_error.cpp Exec/HydroTests/StrongShockTube/Nyx_error.cpp Exec/LyA/Nyx_error.cpp Exec/MiniSB/Nyx_error.cpp Exec/RegressionTest/Nyx_error.cpp Exec/SantaBarbara/Nyx_error.cpp Source/AGN/AGN_sources.cpp Source/DerivedQuantities/ParticleDerive.cpp Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/ParticleInit.cpp Source/Initialization/read_plotfile.cpp Source/Monitors/MemInfo.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxBld.cpp Source/NyxParticleContainer.H Source/NyxParticles.cpp Source/Nyx_advance.cpp Source/Nyx_hydro.cpp Source/Nyx_output.cpp Source/ParticleDeposition.cpp Source/SourceTerms/Nyx_sources.cpp Source/Tagging/Nyx_error.cpp Source/advance_particles.cpp Source/comoving.cpp Source/main.cpp Source/strang_splitting.cpp Source/sum_integrated_quantities.cpp Source/sum_utils.cpp Source/two_particle_advance.cpp Source/write_info.cpp commit af7682abab42405c7cf167a2d0c860177bf78ab6 Author: Weiqun Zhang Date: Fri Jan 13 12:24:07 2017 -0800 migration step 4 Diagnostics/GNUmakefile Exec/AssignDensityTest/GNUmakefile Exec/GravityTests/MacLaurin/GNUmakefile Exec/GravityTests/zeldovich_dm/build/GNUmakefile Exec/HydroTests/DoubleRarefaction/GNUmakefile Exec/HydroTests/Sedov/GNUmakefile Exec/HydroTests/Sod/GNUmakefile Exec/HydroTests/StrongShockTube/GNUmakefile Exec/LyA/GNUmakefile Exec/Make.Nyx Exec/MiniSB/GNUmakefile Exec/RegressionTest/GNUmakefile Exec/SantaBarbara/GNUmakefile commit 3ddb1cd270906e0e6ce8213004b6ecbb00d28f24 Author: Weiqun Zhang Date: Fri Jan 13 12:15:52 2017 -0800 migration steps 2 and 3 Diagnostics/AmrDerive.cpp Exec/AssignDensityTest/Nyx_error.cpp Exec/GravityTests/MacLaurin/Nyx_error.cpp Exec/GravityTests/MacLaurin/Nyx_setup.cpp Exec/GravityTests/zeldovich_dm/build/NyxParticles.cpp Exec/GravityTests/zeldovich_dm/build/Nyx_error.cpp Exec/GravityTests/zeldovich_dm/build/Prob_3d.f90 Exec/HydroTests/DoubleRarefaction/Nyx_error.cpp Exec/HydroTests/Sedov/Nyx_error.cpp Exec/HydroTests/Sedov/bc_fill_3d.f90 Exec/HydroTests/Sod/Nyx_error.cpp Exec/HydroTests/StrongShockTube/Nyx_error.cpp Exec/LyA/Nyx_error.cpp Exec/MiniSB/Nyx_error.cpp Exec/RegressionTest/Nyx_error.cpp Exec/SantaBarbara/Nyx_error.cpp Source/DerivedQuantities/Derive_F.H Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Gravity/Gravity_F.H Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/read_plotfile.cpp Source/Monitors/MemInfo.cpp Source/Nyx.H Source/Nyx.cpp Source/NyxBld.cpp Source/NyxParticleContainer.H Source/NyxParticles.cpp Source/Nyx_F.H Source/Nyx_advance.cpp Source/Nyx_hydro.cpp Source/Src_3d/bc_fill_3d.f90 Source/Tagging/Nyx_error.cpp Source/Tagging/Nyx_error_F.H Source/advance_particles.cpp Source/main.cpp Source/strang_splitting.cpp Source/two_particle_advance.cpp commit 55feca3a50a9372b69431b525a6486e984751aeb Author: Weiqun Zhang Date: Fri Jan 13 12:11:24 2017 -0800 migration step 1 Diagnostics/GNUmakefile Exec/AssignDensityTest/GNUmakefile Exec/GravityTests/MacLaurin/GNUmakefile Exec/GravityTests/zeldovich_dm/build/GNUmakefile Exec/HydroTests/DoubleRarefaction/GNUmakefile Exec/HydroTests/Sedov/GNUmakefile Exec/HydroTests/Sod/GNUmakefile Exec/HydroTests/StrongShockTube/GNUmakefile Exec/LyA/GNUmakefile Exec/Make.Nyx Exec/MiniSB/GNUmakefile Exec/RegressionTest/GNUmakefile Exec/SantaBarbara/GNUmakefile commit bd0873876b9e8cdabba7161fda7c04c438a5a27c Merge: 7b600a8b c5174d77 Author: Weiqun Zhang Date: Fri Jan 13 11:27:03 2017 -0800 Merge branch 'master' into experimental Conflicts: Source/Gravity/Gravity.cpp commit c5174d77cfbaaa1ea84e53e62afa8936fc47f8af Merge: cfc2e769 38b872b6 Author: Weiqun Zhang Date: Fri Jan 13 10:48:16 2017 -0800 Merge branch 'development' commit 38b872b6e7fbe3ae65a0cdfbadbce3f35d7b91e2 Author: Michael Zingale Date: Mon Dec 12 14:39:19 2016 -0500 the BoxLib C++ build system no longer distinguishes COMP and FCOMP, so remove FCOMP from job_info. Exec/Make.Nyx Source/Nyx_output.cpp commit 16a2118e06ef1499c7eb281ca4ccebaf8a148403 Author: Ann Almgren Date: Tue Dec 6 13:23:05 2016 -0800 If, in the multilevel solver (actual_multilevel_solve) we are solving just at level = 0 then we enable the HPGMG solver just as in the level solve. Source/Gravity/Gravity.cpp commit 9dbfe11c2eda532b83f03a041dbff91291b89873 Author: Weiqun Zhang Date: Wed Nov 30 11:11:02 2016 -0800 fix dangling pointers Source/Initialization/ParticleInit.cpp commit ea2850996d1bb7263008ff1c41fca58de8f32627 Author: Weiqun Zhang Date: Wed Nov 9 09:28:22 2016 -0800 add C_AmrCoreLib to make explicitly Exec/Make.Nyx commit 7b600a8b5d44c9b76801c100c1e5efb1250dbb08 Author: Weiqun Zhang Date: Sun Nov 13 17:30:40 2016 -0800 rm PArray according to changes in BoxLib experimental branch Exec/GravityTests/zeldovich_dm/build/NyxParticles.cpp Source/DerivedQuantities/ParticleDerive.cpp Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Nyx.cpp Source/NyxParticleContainer.H Source/NyxParticles.cpp Source/ParticleDeposition.cpp Source/sum_integrated_quantities.cpp Source/sum_utils.cpp commit cfc2e7696edf4a59091c9323c914048fd56bd5f1 Merge: de69126f 16898a8e Author: Ann Almgren Date: Wed Nov 9 14:27:32 2016 -0800 Merge branch 'development' commit 2f35f5dfabe6d5b1828120266518a60a6818cebd Author: Weiqun Zhang Date: Wed Nov 9 09:28:22 2016 -0800 add C_AmrCoreLib to make explicitly Exec/Make.Nyx commit 16898a8e206d9004c27b5a5c026110c1dde9f4d6 Author: Brian Friesen Date: Mon Nov 7 15:46:26 2016 -0800 Exec: remove OpenMP parallel directives from loop in integrate_state_vode() in LyA I removed them from the integrate_state_vode() that lives in Source/HeatCool, but the LyA problem uses this version instead. This routine is called within a tiled loop already so we don't want more OpenMP threads here. Exec/LyA/integrate_state_vode_3d.f90 commit aa16c5ca81e3b0d2ec5549f61b115a10349cc573 Author: Ann Almgren Date: Thu Oct 27 15:26:23 2016 -0700 Added the regression testing script to Util/regression_testing. Util/regression_testing/Nyx-tests.ini commit 8a4a3ce557eb2e04cc13a861d8b19ef8056d5fb2 Author: Weiqun Zhang Date: Fri Oct 21 21:18:17 2016 -0700 call AmrLevel::postCoarseTimeStep to sync up StateData times; this may result in roundoff difference Source/Nyx.cpp commit b2d35eebb33e1e75458917865196070d951cb5f7 Author: Weiqun Zhang Date: Fri Oct 14 12:38:37 2016 -0700 update to BoxLib changes Source/Initialization/Nyx_initcosmo.cpp commit bbaff8a5d5a674ca89567cf27321c4481fdf8f15 Author: Weiqun Zhang Date: Tue Oct 11 16:51:37 2016 -0700 update to BoxLib amrcore branch Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/ParticleInit.cpp Source/NyxParticleContainer.H commit 02879a403714fc5ef04bc8b13909733b4dd9b068 Author: Brian Friesen Date: Mon Oct 10 10:57:29 2016 -0700 EOS, HydroFortran, Src_3d: remove unused array "pt_index" Source/EOS/eos_hc.f90 Source/EOS/eos_stuff.f90 Source/HydroFortran/Nyx_advection_3d.f90 Source/Src_3d/compute_temp_3d.f90 Source/Src_3d/reset_internal_energy_3d.f90 commit 34e813bfa01e3963836160d6404416f718e8282b Author: Brian Friesen Date: Wed Aug 31 15:19:13 2016 -0700 Nyx::just_the_hydro(): add timings for first Strang splitting call Source/Nyx_hydro.cpp commit e96f1c482d248b1c25319a6e3a186f1238b7c761 Author: Weiqun Zhang Date: Sat Oct 8 16:35:33 2016 -0700 fix a bug in last commit Source/NyxParticleContainer.H commit f32e7051d4d6d92f63d18f21ab7dccf5343f929c Author: Weiqun Zhang Date: Sat Oct 8 16:30:33 2016 -0700 move some Particle stuff from BoxLib to Nyx Source/Nyx.H Source/NyxParticleContainer.H Source/NyxParticles.cpp commit fa9ffd13dd1d60f07f47169f68563f722c08edd2 Author: Weiqun Zhang Date: Tue Oct 4 12:56:38 2016 -0700 update due to changes in BoxLib Particle Exec/Make.Nyx commit de69126f24d939df18cd7af3db53452e2fa5a394 Author: Ann Almgren Date: Mon Oct 3 16:07:20 2016 -0700 Remove files that weren't meant to be committed. Source/Gravity/Gravity.ann Source/Gravity/Gravity.tried commit 800e6297c2e20dfab4d1d677e1c08cc683c71ed6 Author: Ann Almgren Date: Mon Oct 3 16:06:53 2016 -0700 Remove files that weren't meant to be committed. Source/Gravity/Gravity.ann Source/Gravity/Gravity.tried commit eb8eecf0f7ffa3adba12f09bc7681d499a1b7f26 Merge: f666d744 34462259 Author: Ann Almgren Date: Mon Oct 3 15:47:10 2016 -0700 Merge branch 'development' of github.com:BoxLib-Codes/Nyx into development commit f666d7447ac65ce9b77f6263c59942663d37200e Author: Ann Almgren Date: Mon Oct 3 15:46:38 2016 -0700 Make sure the new routines compile with NEUTRINO_PARTICLES = TRUE and NEUTRINO_PARTICLES = FALSE Source/NyxParticleContainer.H Source/ParticleDeposition.cpp commit 34462259e94e89e4b399a0f2719687bace173b9e Author: Weiqun Zhang Date: Mon Oct 3 15:30:49 2016 -0700 fix override Source/NyxParticleContainer.H commit 2196023d3fdfa2b0ae8a0189a37407890f51fd28 Merge: 12626fb2 cd0b9ccf Author: Ann Almgren Date: Mon Oct 3 14:54:46 2016 -0700 Merge branch 'development' of github.com:BoxLib-Codes/Nyx into development commit 12626fb2441eabf6c6cccd2ddb8ea2788503a9ea Author: Ann Almgren Date: Mon Oct 3 14:53:52 2016 -0700 Move code out of BoxLib's Particles.H and into here since the deposition is relativistic for neutrinos -- this is too general for BoxLib. Source/Make.package Source/Nyx.H Source/NyxParticleContainer.H Source/ParticleDeposition.cpp commit cd0b9ccfd2c53ae79dd8fc824da9ab9cc9a5295e Author: Weiqun Zhang Date: Mon Oct 3 12:49:06 2016 -0700 move USE_PARTICLES=TRUE before include Make.defs Exec/Make.Nyx commit f06320568ca28f709879a28dcbc3af6659fcf811 Author: Ann Almgren Date: Mon Oct 3 07:10:06 2016 -0700 Remove assertion: BL_ASSERT(N >= BL_SPACEDIM+1); Source/Initialization/ParticleInit.cpp commit 1326781603cd6548fe41385a1150f8d64b5efa53 Author: Ann Almgren Date: Sun Oct 2 16:55:50 2016 -0700 Mv NyxParticleInit.cpp --> ParticleInit.cpp Source/Initialization/Make.package Source/Initialization/ParticleInit.cpp commit 67e42b11181aea337cb974fb58c470a0b3eb8ae3 Author: Ann Almgren Date: Sun Oct 2 16:18:02 2016 -0700 Moved the ParticleContainer::InitCosmo... routines out of BoxLib and into the Nyx repo since they are specific to cosmology applications. DarkMatterParticleContainer is now a derived class rather than a typedef. Source/Initialization/Make.package Source/Initialization/NyxParticleInit.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Make.package Source/Nyx.H Source/NyxParticleContainer.H commit 7ea8ef71f12d5a013bb85418e953a781477a8e61 Author: Ann Almgren Date: Tue Sep 6 10:15:11 2016 -0700 Add a file that tells how to cite the use of this code. CITATION commit 892ce1bf51852658ff44945eff5135747063fe85 Author: Brian Friesen Date: Wed Aug 31 09:24:52 2016 -0700 Make.Nyx: add support (and requirement) for OpenMP in Gimlet Exec/Make.Nyx commit 0a84a9df4f8827264105e6b9559ae9d955ae8760 Author: Brian Friesen Date: Tue Aug 30 13:18:17 2016 -0700 main: wrap sidecar-specific stuff in BL_USE_MPI ifdefs After merging in the sidecar stuff we couldn't compile in serial anymore. Now we should be able to do it. Source/main.cpp commit 6eca61be0a4d02715a1a9cd8ec9849f3b0351334 Author: Weiqun Zhang Date: Thu Aug 25 17:36:45 2016 -0700 remove calls to BoxLib::fill_boundary because it is deprecated Source/Gravity/Gravity.cpp commit 4e5374dfc9f9f1a953e0ba6668291f399f861b03 Author: Weiqun Zhang Date: Thu Aug 25 16:59:28 2016 -0700 replace Geometry::FillPeriodicBoundary because BoxLib is about to remove the function Source/AGN/AGN_sources.cpp Source/Gravity/Gravity.cpp Source/Initialization/Nyx_initcosmo.cpp Source/Nyx_hydro.cpp Source/SourceTerms/Nyx_sources.cpp commit ebede83aaa9dc9d6d7b99599fd22e6e8b42ef8ff Author: Brian Friesen Date: Thu Aug 25 11:02:52 2016 -0700 Util: added example SLURM script showing how to use the burst buffer on Cori at NERSC Util/sample_run_scripts/run_Nyx_LyA_10Mpc_256_Cori_test_burst_buffer.sh commit 215d0339d5d9f32973700059ae7b3c1efcedd481 Author: Brian Friesen Date: Wed Aug 17 21:05:53 2016 -0700 main: replace "Time w/o init" print statement lost in the sidecar merge Source/main.cpp commit d106ebba07d579086a92ff8caa5a06e9005f99de Author: Brian Friesen Date: Sat Aug 13 12:09:57 2016 -0700 Nyx: remove some debugging sizeof() print statements Source/Nyx.cpp commit acdfe3e98d0f6130cb436d7ef457e1c60a490728 Author: Weiqun Zhang Date: Thu Aug 25 11:13:26 2016 -0700 use FabArray::copy for periodic copy Source/Gravity/Gravity.cpp commit 9e6b4146bd10bf4173d02eb6d77b22753995bff7 Author: Brian Friesen Date: Fri Aug 12 14:10:04 2016 -0700 LyA: turn off Gimlet compilation by default Exec/LyA/GNUmakefile commit 8b41945f906877ade35f051ad2494bd11b15625f Merge: 56812d9c 8241e4a0 Author: Brian Friesen Date: Fri Aug 12 13:58:15 2016 -0700 Merge branch 'dynamicsidecars' into development commit 8241e4a0cf2c70141d76a3a51d32955878903573 Merge: a1a8cc2b 92e06bb8 Author: Brian Friesen Date: Fri Aug 12 13:52:57 2016 -0700 Merge branch 'sidecar_docs_update' into dynamicsidecars commit 92e06bb8dbb620e5aad930be374ec6a6dee9dd24 Author: Brian Friesen Date: Fri Aug 12 13:43:25 2016 -0700 UsersGuide: start adding chapter about post-processing UsersGuide/NyxUserGuide.tex UsersGuide/PostProcessing/NyxPostProcessing.tex commit 43e50cb580bbcc0bce9d763a8937c4c939aa67c2 Author: Brian Friesen Date: Fri Aug 12 13:12:34 2016 -0700 README: add blurb about post-processing with Gimlet and Reeber README.md commit a1a8cc2b20e69160994759c36df4f95eb060ad43 Author: Brian Friesen Date: Fri Aug 12 12:56:44 2016 -0700 inputs: minor fixes to small example in-transit inputs file Exec/LyA/inputs.small.dsc commit 12a5f447c221399810853486022ad2982de76790 Author: Brian Friesen Date: Fri Aug 12 12:45:34 2016 -0700 main: make halo_int and gimlet_int global variables Source/Nyx.H Source/Nyx.cpp Source/main.cpp commit 2eec5d64c993fe2c1e64f6439d21152a0eb87ef6 Author: Brian Friesen Date: Fri Aug 12 12:29:05 2016 -0700 main: add back generic SidecarInit() function Source/main.cpp commit b68c3fbc3ea5aa698cea730828fc4618c004e312 Author: Brian Friesen Date: Fri Aug 12 10:49:40 2016 -0700 Nyx_advance: put GRAVITY ifdef back in advance() Source/Nyx_advance.cpp commit 5217edbf3eddb277b05fac4a0821cbe821281041 Author: Brian Friesen Date: Fri Aug 12 10:34:25 2016 -0700 Reeber, Gimlet: change nStep()-1 back to nStep() Source/Nyx.cpp commit 8b036b9a9054f96672d2cf199e6a953b00ddf137 Author: Brian Friesen Date: Fri Aug 12 09:39:02 2016 -0700 Make.Nyx: remove restriction about supporting only 1 postprocessing workflow at a time Exec/Make.Nyx commit e30fe745bd35a5912941e035a48a952182ea6383 Author: Brian Friesen Date: Thu Aug 11 21:59:10 2016 -0700 Remove last bits of IN_SITU and IN_TRANSIT We control sidecar behavior at run time, not compile time, so we don't need these ifdefs anymore. Exec/LyA/GNUmakefile Exec/Make.Nyx Exec/MiniSB/GNUmakefile Exec/SantaBarbara/GNUmakefile Source/Make.package Source/Nyx.cpp Source/main.cpp commit d9a048001b5ef6824cff88739139a991299ea31a Author: Brian Friesen Date: Thu Aug 11 15:08:40 2016 -0700 Make nSidecarProcs a static int in the Nyx class Source/Nyx.H Source/Nyx.cpp Source/main.cpp commit acce8761cedb67f76dd9c4cc24d9a8c45db3fd26 Author: Brian Friesen Date: Thu Aug 11 14:50:17 2016 -0700 main: remove most IN_TRANSIT declarations for sidecar stuff Source/main.cpp commit 56812d9cbe2b2ec319b8d1031cee1a523c6f1f9c Merge: 40e2e39d 7b6fa368 Author: Brian Friesen Date: Wed Aug 10 07:50:07 2016 -0700 Merge branch 'tile_source_terms' into development commit 7b6fa368341f4b91a441d747a43523eb6373e55a Author: Brian Friesen Date: Wed Aug 10 07:47:51 2016 -0700 HeatCool: remove OpenMP directive from loop in integrate_state_vode() This is called within a tiled MFIter loop so this function is already called within an OpenMP parallel region. Source/HeatCool/integrate_state_vode_3d.f90 commit 7ac854d032aaec0f7d81c7e773fe677c49c6045b Author: Brian Friesen Date: Wed Aug 10 07:47:35 2016 -0700 SourceTerms: replace FillPatchIterator loop with tiled MFIter loop in Nyx::get_new_sources() Source/SourceTerms/Nyx_sources.cpp commit a5014c440853da7b89339639cc31fdad7d3a67d0 Author: Brian Friesen Date: Wed Aug 10 07:27:25 2016 -0700 SourceTerms: replace FillPatchIterator loop with tiled MFIter loop in Nyx::get_old_sources() Source/SourceTerms/Nyx_sources.cpp commit 4cc55a5c268b6022ffd857b57ee1e3a492c53329 Author: Brian Friesen Date: Mon Aug 8 16:12:55 2016 -0700 main: fix sidecar initialization so it only happens for Reeber Source/main.cpp commit 3b544dfd46b8357e7175bacca182aa8b23ffe82d Author: Brian Friesen Date: Mon Aug 8 16:12:34 2016 -0700 main: change tabs to spaces Source/main.cpp commit e0ff7481a79f86ec5b5e118b0e237c947bac34f8 Author: Brian Friesen Date: Sun Aug 7 20:00:04 2016 -0700 LyA: remove some more misc macros from GNUmakefile Exec/LyA/GNUmakefile commit 88ee056314da909aa3c76e0819d0568301f16dd0 Author: Brian Friesen Date: Sun Aug 7 19:57:15 2016 -0700 LyA: remove C++11 compile option from GNUmakefile Exec/LyA/GNUmakefile commit dbd9f44c714f34ef6647062f79583c8189bccb44 Author: Brian Friesen Date: Sun Aug 7 19:55:15 2016 -0700 inputs: update small sidecar run inputs file Exec/LyA/inputs.small.dsc commit ad16e89bf5de0be13eee119b92c7cb74790f2b03 Author: Brian Friesen Date: Sun Aug 7 19:52:25 2016 -0700 Send sidecars the nth time step as the n-1'th Source/Nyx.cpp commit 3a632f7cccd0f675a795d2447770adc0477857b3 Author: Brian Friesen Date: Sun Aug 7 19:50:43 2016 -0700 main: fixes to run (confusingly named) initInSituAnalysis() when running in-transit This actually runs in-transit; I inexplicably copied the function name from the version of Reeber that actually does run in situ. Source/main.cpp commit af8b7f4aa0ee3e1510ecf94b3670906d1f79237f Author: Brian Friesen Date: Sun Aug 7 19:50:00 2016 -0700 main: add comment label to a few #endif's Source/main.cpp commit 017bd62dcda0bcd167b4f1215f26084c84381c4e Author: Brian Friesen Date: Sun Aug 7 19:49:06 2016 -0700 inputs: change max refinement level to 0 in sidecar example inputs Exec/LyA/inputs.small.dsc commit 6c9dc56f58e6ddb0592250ed64e2df61c41ea8bb Author: Brian Friesen Date: Sun Aug 7 19:48:34 2016 -0700 Remove Vince's FAKE_REEBER since I can compile the real Reeber now Exec/LyA/GNUmakefile Exec/Make.Nyx Source/main.cpp commit 3f900ca98cd3071a93dcddedad402a52fbc4a397 Author: Brian Friesen Date: Sun Aug 7 12:52:18 2016 -0700 Minor fixes for Reeber in-transit. Source/Nyx.cpp commit 4d4c8535af03a3e0c78946d214e20ffaacaf5e0f Author: Brian Friesen Date: Sun Aug 7 11:38:18 2016 -0700 Replace hard-coded halo finding interval signal with "nyx.halo_int" parameter Source/Nyx.cpp commit 2e7032a78ca321501bd52cd5776c3cb4bef3c8fa Author: Brian Friesen Date: Sun Aug 7 11:36:02 2016 -0700 Remove old "#if 1 .. #else" code for finding halos (not Reeber) Source/Nyx.cpp commit 0f1a5501c6c92f0b284ff4282adf5a9f38c9659f Author: Brian Friesen Date: Sun Aug 7 11:27:31 2016 -0700 main: remove array of sidecar sizes that make FFTW happy (used in random resizing) FFTW sometimes segfaults when doing FFTs with certain numbers of MPI processes. I can't tell if this is a machine-specific problem or not, but trying to work around it with hard code in Nyx is not a sustainable solution. If anything, one should make a note in the docs. Source/main.cpp commit cec767d469fa052842b78f5b8166c80492851fa0 Author: Brian Friesen Date: Sun Aug 7 11:13:58 2016 -0700 main, inputs: remove logic about random sidecar sizes This was useful as a test but does not make sense to keep in a production code. Exec/LyA/inputs.small.dsc Exec/LyA/inputs_gimlet_in_transit.dsc Source/main.cpp commit eb114cf55f657531781479284d04e8c6dc5e6f95 Author: Brian Friesen Date: Sun Aug 7 11:13:29 2016 -0700 inputs: add "nyx." prefix to gimlet_int in small sidecar test inputs file Exec/LyA/inputs.small.dsc commit ee0e8c14d7d86153b4a77dd3c5ef956a01723e5e Author: Brian Friesen Date: Sun Aug 7 11:13:08 2016 -0700 inputs: add nyx.gimlet_int parameter to larger sidecar test inputs file Exec/LyA/inputs_gimlet_in_transit.dsc commit f32360065896d0db89800cae026b8cc7ea662685 Author: Brian Friesen Date: Sun Aug 7 10:56:11 2016 -0700 main: make resizeSidecar evaluation a single line of code Source/main.cpp commit 6fd85f28f9a48d6163ba1fc305cd8b1c1cd0a672 Author: Brian Friesen Date: Sun Aug 7 10:54:55 2016 -0700 main: remove print of sizeof() statements Source/main.cpp commit e5c93d62983ae4e495d8320ff72b9d1ffdd9ffef Author: Brian Friesen Date: Sun Aug 7 10:53:56 2016 -0700 main: remove unnecessary sidecar resize The resize is already done in ResizeSidecars(), which is called just before this. Source/main.cpp commit 462429bb7af0d9bde7f7e089865821f4767b0b54 Author: Brian Friesen Date: Sun Aug 7 10:51:35 2016 -0700 main: minor cleanup of initial sidecar resizing logic Source/main.cpp commit a37f9d4cabef31e1f7c63e8e1b725815e2d9b04a Author: Brian Friesen Date: Sun Aug 7 10:42:23 2016 -0700 main: clarify error message about running with Gimlet without compiling with Gimlet Source/main.cpp commit 7d196e1884232395a0ddea8ec8cf08936ae0cc19 Author: Brian Friesen Date: Sun Aug 7 10:41:54 2016 -0700 main: remove some commented-out sidecar stuff for FFTW/Gimlet Source/main.cpp commit 544fd324460a2c249942c1d7dbfbfc4a8e5b5cf3 Author: Brian Friesen Date: Sun Aug 7 10:39:25 2016 -0700 Clarify a comment about halo finding interval Source/Nyx.H commit a0dccf1d3335a0bffbfe9d8a103ddfa5008e8848 Author: Brian Friesen Date: Sun Aug 7 10:38:23 2016 -0700 main: add comment indicating that only Reeber needs to initialize Source/main.cpp commit 16d7ce3da0c47133ae3929bc806a39be015ff266 Author: Brian Friesen Date: Sun Aug 7 10:34:47 2016 -0700 main: change first resizeSidecar evaluation to a single line of code Source/main.cpp commit ea7a8360fba628a59b392ba062130091a1295324 Author: Brian Friesen Date: Sun Aug 7 10:26:56 2016 -0700 main: compute MPI_IntraGroup_Broadcast_Rank only once Source/main.cpp commit 909f19e46934330a90140767cbddff24094c8236 Author: Brian Friesen Date: Fri Aug 5 13:43:49 2016 -0700 main: add "gimlet_int" to ParmParse for setting time step interval for Gimlet analysis Exec/LyA/inputs.small.dsc Source/Nyx.H Source/Nyx.cpp commit 287ff38f3a8ae8b182cbe67f10908a625acb0b5d Author: Brian Friesen Date: Fri Aug 5 13:12:20 2016 -0700 Source: remove commented out auxDiag maps Source/Nyx.H commit d72aaae72113db3e35c84463b18ec3e75c24b78d Author: Brian Friesen Date: Fri Aug 5 13:11:41 2016 -0700 Source: remove commented out MultiFab Source/Nyx.H commit 67781b6373e8b730c6d71a80dc39a6a52a33b1bf Author: Brian Friesen Date: Fri Aug 5 13:01:29 2016 -0700 Gravity: go back to previous style of brackets with single-line if clause Source/Gravity/Gravity.cpp commit 250551108740b75aaeb612d6a5ebbd959042ae13 Author: Brian Friesen Date: Fri Aug 5 12:59:48 2016 -0700 Gravity: add comment describing purpose of AddProcsToComp() Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit 0297c03836ee8fd5905e399c06cee9187264d22f Author: Brian Friesen Date: Fri Aug 5 12:58:34 2016 -0700 MiniSB: forget about sidecars on MiniSB for now, just focus on LyA Exec/MiniSB/GNUmakefile commit d59d62b6e5b5589e02f0038dcecc453d2b91c64d Author: Brian Friesen Date: Fri Aug 5 12:56:38 2016 -0700 LyA: add comments explaining how to use sidecars in inputs files Exec/LyA/GNUmakefile Exec/LyA/inputs.small.dsc Exec/LyA/inputs_gimlet_in_transit.dsc commit b1f487cfbd29f44ebb657a7649612724e50f2cd2 Author: Brian Friesen Date: Fri Aug 5 12:50:58 2016 -0700 LyA: remove unnecessary vpath from GNUmakefile Exec/LyA/GNUmakefile commit 725309e3f3fa833d47f24d74f5c016e5cb1a2fa1 Author: Brian Friesen Date: Fri Aug 5 12:48:22 2016 -0700 LyA: add comments for new parmparse variables in sidecar example inputs files Exec/LyA/inputs.small.dsc Exec/LyA/inputs_gimlet_in_transit.dsc commit ea50abab93298dc3728ff68514a95020714966c6 Author: Brian Friesen Date: Fri Aug 5 12:38:57 2016 -0700 LyA: more fixes to GNUmakefile Exec/LyA/GNUmakefile commit 97a51e31c7f78c836463273e00bed8c40b6088bd Author: Brian Friesen Date: Fri Aug 5 12:28:30 2016 -0700 revert BOXLIB_HOME defaults in LyA GNUmakefile Exec/LyA/GNUmakefile commit d52eb6c91168e9e7d0415bef98135e0cd169d9f0 Author: Brian Friesen Date: Fri Aug 5 12:12:42 2016 -0700 Gravity: remove commented-out MFIter::validbox() call Source/Gravity/Gravity.cpp commit cda66f80e670d2e084185fe873a93ea70f052154 Author: Brian Friesen Date: Fri Aug 5 11:21:57 2016 -0700 LyA: fix FFTW directories in the GNUmakefile Exec/LyA/GNUmakefile commit 40e2e39d26391a426fed67b1afd269bf1df82126 Merge: d0e856ad ed8030a5 Author: Brian Friesen Date: Fri Aug 5 10:49:39 2016 -0700 Merge branch 'optimize_EOS_v2' into development commit 16e0064f9cd91fa7f91d2264504696d0ed04d604 Author: Brian Friesen Date: Thu Aug 4 15:39:36 2016 -0700 main: replaced deleted variable "inputs_name" Source/main.cpp commit 86af302e9c3252ff03daa7ca6a5c0ff1b0d079dc Author: Brian Friesen Date: Thu Aug 4 14:22:16 2016 -0700 from vince: small dsc inputs for 32 mpi procs. Exec/LyA/inputs.small.dsc commit 87bf8c7b8fa4915f7f6530998646842fc9571a95 Author: Brian Friesen Date: Thu Aug 4 14:21:26 2016 -0700 from vince: added inputs file to run a dsc random size problem. use 2048 total mpi procs for this example. Exec/LyA/inputs_gimlet_in_transit.dsc commit 3fc6f4daeb5356ec386cbd8eea49b70526be0861 Author: Brian Friesen Date: Thu Aug 4 14:19:14 2016 -0700 from vince: a few dsc fixes Source/main.cpp commit 5809f8651e77ab71f6c4dde86d1bb66a939e2f0e Author: Brian Friesen Date: Wed Aug 3 10:19:44 2016 -0700 minor fixes after rebasing Exec/LyA/GNUmakefile Source/main.cpp commit d1f1fa758cc7b234b148586458664cba8a4d4905 Author: vince Date: Thu Jun 9 16:35:33 2016 -0700 update for multiple sidecar support. this example only uses one sidecar currently. Source/Nyx.cpp Source/main.cpp commit d96d7424202aa005f0dad901ab62237022bebe35 Author: vince Date: Tue May 24 14:01:12 2016 -0700 update for multiple sidecars. Source/Nyx.cpp Source/main.cpp commit d15efeef674a941469cfa31f04ae4f53c5af3e03 Author: vince Date: Wed May 11 14:47:28 2016 -0700 fix for zero sidecar procs. Source/Nyx.cpp commit b4ca127ecc4009a17df23dea940aa750f2ec1578 Author: vince Date: Wed May 11 13:55:34 2016 -0700 query for random nsidecars, filter bad fftw values. Source/main.cpp commit b09a287d9bd9d6dac2512a8f84a1837bcd37510e Author: vince Date: Wed May 11 12:09:33 2016 -0700 added random fixed sidecar sizes. Source/main.cpp commit 1a39d6ce130195ecb1ecf3e27fac7544cb3fa8d4 Author: vince Date: Fri May 6 14:40:11 2016 -0700 reinstall LevelData. Source/Gravity/Gravity.cpp commit d2f0a12726bcf80dd0a5d528254bdecd715032f4 Author: vince Date: Fri May 6 14:00:13 2016 -0700 some cleanup. Source/NyxParticles.cpp commit 68c861a51dfe44cd52ecb91b606abb2601f67d9b Author: vince Date: Fri May 6 13:59:50 2016 -0700 force particle redist. Source/main.cpp commit d576e57b891e2024503f6a565cdcdb3513a20f40 Author: vince Date: Fri May 6 13:58:56 2016 -0700 added variable to allow forcing particle redist. Source/Nyx.H Source/Nyx.cpp commit 1c62fa5456217bc4c8c8c57efed9a1c5eff913cc Author: vince Date: Fri May 6 13:57:50 2016 -0700 cleanup diagnostics. Source/Gravity/Gravity.cpp commit fc2c2b72d9ed2ae22d0cf27f9df464faa76253de Author: vince Date: Thu May 5 16:59:15 2016 -0700 resolve PArrays in gravity. Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp commit 28d83b9d9288f985ee2bcfb05a02948813e0b031 Author: vince Date: Thu May 5 16:58:41 2016 -0700 resolve PArrays in gravity. Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp Source/main.cpp commit f4380be378df713260d6016f46f83a91c5926384 Author: vince Date: Tue May 3 12:28:19 2016 -0700 test dynamic resizing, not fully working yet. Source/Nyx.cpp Source/main.cpp commit 556675aa1f22da027225b6bd8a6dd07b4af6c0c2 Author: vince Date: Wed Apr 20 18:18:28 2016 -0700 dynamic sidecars for gimlet. Exec/LyA/GNUmakefile Exec/Make.Nyx Source/Make.package commit 0dd4602a33560ceaa11052d04d2459b8ab050328 Author: vince Date: Wed Apr 20 18:17:13 2016 -0700 dynamic sidecars for gimlet. Source/Nyx.cpp Source/Nyx_nd.f90 Source/main.cpp commit db64d6823707c847ec9c0323035e3cf14bf88616 Author: vince Date: Mon Apr 11 15:12:27 2016 -0700 allow non-zero initial sidecar size, meminfo init. Source/main.cpp commit 22444e725dd0fffbf5c389a7ac92e2988d40c6c7 Author: vince Date: Mon Apr 11 14:37:13 2016 -0700 added mpi checks, replaced MPI_COMM_WORLD. Source/Monitors/MemInfo.cpp commit 01d9f06c0691bc2a6b68e2ad8119294ba5ff9750 Author: vince Date: Fri Apr 8 13:58:43 2016 -0700 working version for dynamic sidecars. still a few issues. Source/Initialization/Nyx_setup.cpp Source/Nyx.cpp Source/NyxParticles.cpp Source/main.cpp commit 0edd5c06d39297973cbb0a06b0843e8157e01b04 Author: vince Date: Mon Apr 4 11:55:16 2016 -0700 added profiling. Source/Initialization/Nyx_initdata.cpp commit 8ffed28a064537874a599df57a7f98075bdf05c0 Author: vince Date: Mon Apr 4 11:54:34 2016 -0700 more dsc code. Source/main.cpp Source/sum_integrated_quantities.cpp commit d55cb11d11feb402cb3235ca2959d1d92b3ef28e Author: vince Date: Mon Apr 4 11:52:29 2016 -0700 more additions for dynamicsidecars. Source/Nyx_advance.cpp commit 026c4735f15c8efcb1920c25385f64eb49941bf2 Author: vince Date: Mon Apr 4 11:51:45 2016 -0700 added profiling and dsc code. Source/NyxParticles.cpp commit 66977301c0985ff78cd0d9677877df5391eb23e2 Author: vince Date: Mon Apr 4 11:50:13 2016 -0700 more additions for dynamicsidecars. Source/Gravity/Gravity.H Source/Gravity/Gravity.cpp Source/Nyx.H Source/Nyx.cpp commit 3785eaafbaec33b60da98986d3f7acf2b381008b Author: vince Date: Fri Mar 4 17:36:52 2016 -0800 support for sidecars. Source/Initialization/Nyx_setup.cpp Source/NyxParticles.cpp Source/main.cpp commit b921d2137160ab145b671c1eebc0ed3e595a4967 Author: vince Date: Fri Mar 4 17:35:32 2016 -0800 support for sidecars. Source/NyxBld.cpp commit db093e0a98f06a57ae7d07e78f0371feb891f547 Author: vince Date: Fri Mar 4 17:34:56 2016 -0800 AddProcsToComp function, not quite finished. Source/Nyx.H Source/Nyx.cpp commit 87883f6c7ff7ad790c262bc6282dca63ec752625 Author: vince Date: Thu Mar 3 16:27:41 2016 -0800 main with resize sidecar tests. Source/main.cpp commit edbae39f0ad47a767e467baedd8306593dce9b6c Author: vince Date: Mon Oct 26 17:39:14 2015 -0700 set halo_int in inputs. don't use the word signal. Source/Nyx.H Source/Nyx.cpp Source/main.cpp commit 335a286d5b351315a56892a1b873402015ba8eb3 Author: vince Date: Mon Oct 26 16:34:15 2015 -0700 some code cleanup. Source/main.cpp commit ed066003f48b4b3b4155faf9b322b3a40d657565 Author: vince Date: Mon Oct 26 16:16:49 2015 -0700 first cut of the dynamic sidecars. the number of sidecars can be set in the inputs. cannot yet change the number after that. also implmented a fake reeber to allow development without the real one. Exec/Make.Nyx Exec/MiniSB/GNUmakefile Source/Make.package Source/Nyx.cpp Source/main.cpp commit 1b672e5e6485cf1169592de427b1da7c70809d1a Author: Brian Friesen Date: Thu Oct 22 14:44:26 2015 -0700 WIP Source/Nyx.cpp Source/main.cpp commit da5356e37126dc9295a87126d9c1321cd47d0204 Author: Brian Friesen Date: Mon Oct 19 13:46:50 2015 -0700 WIP Exec/MiniSB/GNUmakefile Source/Make.package Source/Nyx.cpp Source/main.cpp commit e9db707cd78c1a319d29834cd28b01df3fcf511b Author: Brian Friesen Date: Thu Aug 27 09:50:36 2015 -0700 WIP Exec/Make.Nyx Exec/MiniSB/GNUmakefile Source/Initialization/Nyx_setup.cpp Source/Make.package Source/Monitors/MemInfo.cpp Source/Nyx.cpp Source/Nyx_F.H Source/Nyx_nd.f90 Source/main.cpp commit d0e856ad2fc02e94d4f6013cbe0f631135f94d3c Author: Michael Zingale Date: Thu Aug 4 16:46:53 2016 -0400 port the cpu time stuff over from Castro. now the job_info will keep track of the elapsed CPU time (in core-hours) since the simulation began Source/Initialization/Nyx_setup.cpp Source/Nyx.H Source/Nyx.cpp Source/Nyx_output.cpp commit ed8030a5c69ed6b4c07773249129a0794503a3d7 Author: Brian Friesen Date: Wed Jul 27 15:32:26 2016 -0700 EOS: change 1.0/Huge() to just Tiny() This saves us a divide in ion_n(), which already has a lot of divides and is an expensive routine in Nyx. Source/EOS/eos_hc.f90 commit c4b2fd84ea0d33f15e3ba7f84226cbd961876ea0 Author: Brian Friesen Date: Wed Jul 27 15:32:07 2016 -0700 EOS: change repeated divides to multiplies in the denominator in ion_n() Compilers may be smart enough to do this transformation automatically, but we shouldn't trust them. Writing the terms this way guarantees that we will do 3 fewer divides in ion_n(), which is already the most expensive routine in all of Nyx, thanks to all the divides and the dlog10() term. Note that changing the order of operations like this *will* change the results very slightly (especially because the EOS is called so frequently), so we may need to update the regression test results to accommodate this. Source/EOS/eos_hc.f90 commit a6d8eb0f26b4c0c54eef7b1761f36cce389e4d10 Author: Brian Friesen Date: Wed Jul 27 15:31:40 2016 -0700 EOS, HeatCool: only compute deltaT once When calculating heating/cooling terms, the parameter "deltaT" was being calculated each time one of those terms was computed. However the value is a runtime constant, so we should compute it only once and store it in atomic_rates_module. This also saves us a lot of unnecessary divides, which are expensive. Source/EOS/atomic_rates.f90 Source/EOS/eos_hc.f90 Source/HeatCool/cooling.f90 Source/HeatCool/f_rhs.f90 commit b8bd73125bfd268c5fc3f2272f3155d655bc66ea Merge: d012dedf cba28f3e Author: Brian Friesen Date: Thu Aug 4 10:51:49 2016 -0700 Merge branch 'optimize_HydroFortran' into development This series of commits improves performance of some hydro routines, in part by switching from stack arrays or allocatable arrays to bl_allocate() arrays, by improving vectorization, and by replacing some repeated divides with multiples of inverses. On my quad-core desktop, a 32^3 problem runs about 18% faster over 50 time steps. commit cba28f3e6cd4cbb29910d105ad750b9376dd5989 Author: Brian Friesen Date: Tue Aug 2 07:05:21 2016 -0700 HydroFortran: change d{x,y,z} divides into d{x,y,z}inv multiplies in ppm_type2() Source/HydroFortran/ppm_3d.f90 commit 16ddc2e7365c3efebd0880bea75f47b32baebdde Author: Brian Friesen Date: Tue Aug 2 07:04:15 2016 -0700 HydroFortran: change d{x,y,z} divides into d{x,y,z}inv multiplies in ppm_type1() Source/HydroFortran/ppm_3d.f90 commit c614a18117099bc9b5c31d971ffb513a4ecd58fa Author: Brian Friesen Date: Mon Aug 1 17:24:21 2016 -0700 HydroFortran: vectorize transz() Source/HydroFortran/trans_3d.f90 commit b5218bdb9e1d3f5532f3c3812ac5a32b4a4dae46 Author: Brian Friesen Date: Mon Aug 1 08:27:29 2016 -0700 HydroFortran: change stack arrays to bl_allocate() arrays in transz() Source/HydroFortran/trans_3d.f90 commit 77a6dd80fb4489ce176411a397bf538de8cebac8 Author: Brian Friesen Date: Mon Aug 1 08:26:29 2016 -0700 HydroFortran: change allocate() to bl_allocate() in ppm_type1() Source/HydroFortran/ppm_3d.f90 commit eb00ab7be7bc1bb9d718ab37f8f47f85260a521d Author: Brian Friesen Date: Mon Aug 1 08:25:15 2016 -0700 HydroFortran: add intent properties to arrays in ppm_type1() Source/HydroFortran/ppm_3d.f90 commit d012dedf43016d98c8d562f642ca6c87fa23e9b0 Author: Michael Zingale Date: Wed Aug 3 09:06:17 2016 -0400 forgot to add the header for inputs Source/Nyx_output.H commit bf072a91ba7836a9b3353d05e94455e251a41d63 Author: Michael Zingale Date: Tue Aug 2 19:34:10 2016 -0400 add inputs file and compiler versions to the job_info file Exec/Make.Nyx Source/Make.package Source/Nyx_output.cpp Source/main.cpp commit a18ae8557ab2f650ff983d7df5c1d9bdc3865629 Author: Ann Almgren Date: Tue Aug 2 16:04:44 2016 -0700 More tweak to refs README.md commit a8472efb9cae35624abe9397d3eab389d60bc749 Author: Ann Almgren Date: Tue Aug 2 16:02:27 2016 -0700 Fix to refs README.md commit d4d68586b5e9d7cce9b6bc3621091264d98258b3 Merge: 9c0be9bf 577eab20 Author: Ann Almgren Date: Tue Aug 2 15:26:25 2016 -0700 Merge branch 'development' Conflicts: README.md commit 9c0be9bf5d721b9ebbd691ad8732c9dc0380cdd4 Author: Zarija Date: Tue Aug 2 15:12:27 2016 -0700 References in README README.md commit 577eab200ab54e4b654f0baaa3fc9b45e2e5c884 Author: Zarija Date: Tue Aug 2 14:36:42 2016 -0700 References in README README.md commit 8f0bdc0c905f00d89d69476c98dde7f1f9c6e204 Author: Zarija Date: Tue Aug 2 14:35:26 2016 -0700 UVB rates of Onorbe et al. Exec/LyA/TREECOOL_hm_12 Exec/LyA/TREECOOL_middle Source/EOS/atomic_rates.f90 Source/HeatCool/TREECOOL_early Source/HeatCool/TREECOOL_hm_12 Source/HeatCool/TREECOOL_late Source/HeatCool/TREECOOL_middle commit 54cc8001bf4a1490453d38c88759475682b17611 Author: Ann Almgren Date: Tue Aug 2 14:21:40 2016 -0700 Change suggested directory from MiniSB to LyA UsersGuide/GettingStarted/NyxGettingStarted.tex commit 52d83add2fc34b2920c1b39d2f5ab914757618c8 Author: Ann Almgren Date: Tue Aug 2 14:16:39 2016 -0700 Update users guides now that Nyx is on github UsersGuide/GettingStarted/NyxGettingStarted.tex UsersGuide/NyxUserGuide.tex commit 63ddb3bbfcf5f470bd867689a93dfb087a7bb84b Author: Ann Almgren Date: Tue Aug 2 12:40:27 2016 -0700 Directory is UsersGuide not Docs. README.md commit f40c4985e45daea2d7533300d5c269fe83aa50ae Author: Ann Almgren Date: Tue Aug 2 12:35:40 2016 -0700 Add the nyx-help mailing list info README.md commit 004f54e8a9aadc5e7a75e3b2abfc855fe459190b Author: Ann Almgren Date: Tue Aug 2 12:34:42 2016 -0700 UC license license.txt commit 97b8843d3b97c700de1e758c89cb5580a03ac0c3 Author: Ann Almgren Date: Tue Aug 2 12:02:45 2016 -0700 Initial version for github Diagnostics/AmrDerive.cpp Diagnostics/GNUmakefile Diagnostics/Make.package Diagnostics/README Diagnostics/inputs Exec/AssignDensityTest/GNUmakefile Exec/AssignDensityTest/Make.package Exec/AssignDensityTest/Nyx_error.cpp Exec/AssignDensityTest/Prob_3d.f90 Exec/AssignDensityTest/Tagging_3d.f90 Exec/AssignDensityTest/inputs Exec/AssignDensityTest/probdata.f90 Exec/AssignDensityTest/probin Exec/GravityTests/MacLaurin/GNUmakefile Exec/GravityTests/MacLaurin/Make.package Exec/GravityTests/MacLaurin/Nyx_error.cpp Exec/GravityTests/MacLaurin/Nyx_setup.cpp Exec/GravityTests/MacLaurin/Prob_3d.f90 Exec/GravityTests/MacLaurin/Tagging_3d.f90 Exec/GravityTests/MacLaurin/inputs Exec/GravityTests/MacLaurin/probdata.f90 Exec/GravityTests/MacLaurin/probin Exec/GravityTests/MacLaurin/set_dirichlet_bcs_3d.f90 Exec/GravityTests/zeldovich_dm/README.md Exec/GravityTests/zeldovich_dm/analysis/check_ics.py Exec/GravityTests/zeldovich_dm/analysis/process_zeldovich.py Exec/GravityTests/zeldovich_dm/analysis/zeldovich.py Exec/GravityTests/zeldovich_dm/analytic.cpp Exec/GravityTests/zeldovich_dm/build/GNUmakefile Exec/GravityTests/zeldovich_dm/build/Make.package Exec/GravityTests/zeldovich_dm/build/NyxParticles.cpp Exec/GravityTests/zeldovich_dm/build/Nyx_error.cpp Exec/GravityTests/zeldovich_dm/build/Prob_3d.f90 Exec/GravityTests/zeldovich_dm/build/Tagging_3d.f90 Exec/GravityTests/zeldovich_dm/build/probdata.f90 Exec/GravityTests/zeldovich_dm/ics/generate_zeldovich_ics.cpp Exec/GravityTests/zeldovich_dm/ics/simple_zeldovich_ics.cpp Exec/GravityTests/zeldovich_dm/run/inputs Exec/GravityTests/zeldovich_dm/run/pbs_hopper Exec/GravityTests/zeldovich_dm/run/probin Exec/GravityTests/zeldovich_dm/run/probin_wmap7 Exec/GravityTests/zeldovich_dm/zeldo.cpp Exec/HydroTests/DoubleRarefaction/Figure/128/density_x Exec/HydroTests/DoubleRarefaction/Figure/128/eint_x Exec/HydroTests/DoubleRarefaction/Figure/128/pressure_x Exec/HydroTests/DoubleRarefaction/Figure/128/velocity_x Exec/HydroTests/DoubleRarefaction/Figure/512/density_x Exec/HydroTests/DoubleRarefaction/Figure/512/eint_x Exec/HydroTests/DoubleRarefaction/Figure/512/pressure_x Exec/HydroTests/DoubleRarefaction/Figure/512/velocity_x Exec/HydroTests/DoubleRarefaction/Figure/make_plots.gp Exec/HydroTests/DoubleRarefaction/GNUmakefile Exec/HydroTests/DoubleRarefaction/Make.package Exec/HydroTests/DoubleRarefaction/Nyx_error.cpp Exec/HydroTests/DoubleRarefaction/Prob_3d.f90 Exec/HydroTests/DoubleRarefaction/Tagging_3d.f90 Exec/HydroTests/DoubleRarefaction/amrvis.defaults Exec/HydroTests/DoubleRarefaction/analytic/exact.ini.test2 Exec/HydroTests/DoubleRarefaction/analytic/exact.out Exec/HydroTests/DoubleRarefaction/inputs-test2-x Exec/HydroTests/DoubleRarefaction/inputs-test2-y Exec/HydroTests/DoubleRarefaction/inputs-test2-z Exec/HydroTests/DoubleRarefaction/inputs.regtest Exec/HydroTests/DoubleRarefaction/inputs.restarttest Exec/HydroTests/DoubleRarefaction/probdata.f90 Exec/HydroTests/DoubleRarefaction/probin-test2-x Exec/HydroTests/DoubleRarefaction/probin-test2-y Exec/HydroTests/DoubleRarefaction/probin-test2-z Exec/HydroTests/Sedov/GNUmakefile Exec/HydroTests/Sedov/Make.package Exec/HydroTests/Sedov/Nyx_error.cpp Exec/HydroTests/Sedov/Prob_3d.f90 Exec/HydroTests/Sedov/Tagging_3d.f90 Exec/HydroTests/Sedov/bc_fill_3d.f90 Exec/HydroTests/Sedov/inputs.3d.sph Exec/HydroTests/Sedov/inputs.regtest Exec/HydroTests/Sedov/probdata.f90 Exec/HydroTests/Sedov/probin.3d.sph Exec/HydroTests/Sod/Figure/density_x Exec/HydroTests/Sod/Figure/density_y Exec/HydroTests/Sod/Figure/density_z Exec/HydroTests/Sod/Figure/eint_x Exec/HydroTests/Sod/Figure/eint_y Exec/HydroTests/Sod/Figure/eint_z Exec/HydroTests/Sod/Figure/make_plots.gp Exec/HydroTests/Sod/Figure/pressure_x Exec/HydroTests/Sod/Figure/pressure_y Exec/HydroTests/Sod/Figure/pressure_z Exec/HydroTests/Sod/Figure/velocity_x Exec/HydroTests/Sod/Figure/velocity_y Exec/HydroTests/Sod/Figure/velocity_z Exec/HydroTests/Sod/GNUmakefile Exec/HydroTests/Sod/Make.package Exec/HydroTests/Sod/Nyx_error.cpp Exec/HydroTests/Sod/Prob_3d.f90 Exec/HydroTests/Sod/Tagging_3d.f90 Exec/HydroTests/Sod/amrvis.defaults Exec/HydroTests/Sod/analytic/exact.ini.sod Exec/HydroTests/Sod/analytic/sod-exact.out Exec/HydroTests/Sod/inputs-sod-x Exec/HydroTests/Sod/inputs-sod-y Exec/HydroTests/Sod/inputs-sod-z Exec/HydroTests/Sod/inputs.regtest Exec/HydroTests/Sod/probdata.f90 Exec/HydroTests/Sod/probin-sod-x Exec/HydroTests/Sod/probin-sod-y Exec/HydroTests/Sod/probin-sod-z Exec/HydroTests/StrongShockTube/Figure/density_x Exec/HydroTests/StrongShockTube/Figure/density_y Exec/HydroTests/StrongShockTube/Figure/density_z Exec/HydroTests/StrongShockTube/Figure/eint_x Exec/HydroTests/StrongShockTube/Figure/eint_y Exec/HydroTests/StrongShockTube/Figure/eint_z Exec/HydroTests/StrongShockTube/Figure/make_plots.gp Exec/HydroTests/StrongShockTube/Figure/pressure_x Exec/HydroTests/StrongShockTube/Figure/pressure_y Exec/HydroTests/StrongShockTube/Figure/pressure_z Exec/HydroTests/StrongShockTube/Figure/velocity_x Exec/HydroTests/StrongShockTube/Figure/velocity_y Exec/HydroTests/StrongShockTube/Figure/velocity_z Exec/HydroTests/StrongShockTube/GNUmakefile Exec/HydroTests/StrongShockTube/Make.package Exec/HydroTests/StrongShockTube/Nyx_error.cpp Exec/HydroTests/StrongShockTube/Prob_3d.f90 Exec/HydroTests/StrongShockTube/Tagging_3d.f90 Exec/HydroTests/StrongShockTube/analytic/exact.ini.test3 Exec/HydroTests/StrongShockTube/analytic/test3-exact.out Exec/HydroTests/StrongShockTube/inputs-x Exec/HydroTests/StrongShockTube/inputs-y Exec/HydroTests/StrongShockTube/inputs-z Exec/HydroTests/StrongShockTube/inputs.regtest Exec/HydroTests/StrongShockTube/probdata.f90 Exec/HydroTests/StrongShockTube/probin-test3-x Exec/HydroTests/StrongShockTube/probin-test3-y Exec/HydroTests/StrongShockTube/probin-test3-z Exec/LyA/32.nyx Exec/LyA/GNUmakefile Exec/LyA/Make.package Exec/LyA/Nyx_error.cpp Exec/LyA/Prob_3d.f90 Exec/LyA/TREECOOL_hm_12 Exec/LyA/Tagging_3d.f90 Exec/LyA/inputs Exec/LyA/inputs.rt Exec/LyA/integrate_state_vode_3d.f90 Exec/LyA/pbs_hopper Exec/LyA/probdata.f90 Exec/LyA/probin Exec/Make.Nyx Exec/MiniSB/GNUmakefile Exec/MiniSB/Make.package Exec/MiniSB/Nyx_error.cpp Exec/MiniSB/Prob_3d.f90 Exec/MiniSB/Tagging_3d.f90 Exec/MiniSB/fixed_grids Exec/MiniSB/inputs.32 Exec/MiniSB/inputs.32.plot_z Exec/MiniSB/inputs.32.ref Exec/MiniSB/inputs.analysis Exec/MiniSB/particle_file.small Exec/MiniSB/probdata.f90 Exec/MiniSB/probin Exec/RegressionTest/GNUmakefile Exec/RegressionTest/Make.package Exec/RegressionTest/Nyx_error.cpp Exec/RegressionTest/Prob_3d.f90 Exec/RegressionTest/Tagging_3d.f90 Exec/RegressionTest/fixed_grids.mass Exec/RegressionTest/inputs.2line Exec/RegressionTest/inputs.2line.restarttest Exec/RegressionTest/inputs.mass.nosub Exec/RegressionTest/inputs.mass.sub Exec/RegressionTest/particle_file.2line Exec/RegressionTest/particle_file.mass Exec/RegressionTest/probdata.f90 Exec/RegressionTest/probin Exec/SantaBarbara/GNUmakefile Exec/SantaBarbara/Make.package Exec/SantaBarbara/Nyx_error.cpp Exec/SantaBarbara/Prob_3d.f90 Exec/SantaBarbara/Tagging_3d.f90 Exec/SantaBarbara/inputs Exec/SantaBarbara/pbs_hopper Exec/SantaBarbara/pbs_hopper_omp Exec/SantaBarbara/probdata.f90 Exec/SantaBarbara/probin README.md Source/AGN/AGN_sources.cpp Source/AGN/Make.package Source/AGN/Makefile Source/AGN/agn_geometry.f90 Source/AGN/agn_mesh.f90 Source/AGN/agn_models.f90 Source/AGN/agn_params.f90 Source/AGN/agn_random.f90 Source/AGN/agnug.f90 Source/Constants/Make.package Source/Constants/constants_cgs.f90 Source/Constants/constants_cosmo.f90 Source/DerivedQuantities/Derive_3d.f90 Source/DerivedQuantities/Derive_F.H Source/DerivedQuantities/Make.package Source/DerivedQuantities/ParticleDerive.cpp Source/EOS/Make.package Source/EOS/README Source/EOS/atomic_rates.f90 Source/EOS/eos_hc.f90 Source/EOS/eos_stuff.f90 Source/Gravity/Gravity.H Source/Gravity/Gravity.ann Source/Gravity/Gravity.cpp Source/Gravity/Gravity.tried Source/Gravity/Gravity_3d.f90 Source/Gravity/Gravity_F.H Source/Gravity/Gravity_nd.f90 Source/Gravity/Make.package Source/Gravity/prescribe_grav_3d.f90 Source/Gravity/prescribe_grav_stub.f90 Source/Gravity/set_dirichlet_bcs_3d.f90 Source/HeatCool/Make.package Source/HeatCool/TREECOOL_hm_12 Source/HeatCool/cooling.f90 Source/HeatCool/ext_src_hc_3d.f90 Source/HeatCool/f_rhs.f90 Source/HeatCool/heat_cool_stubs.f90 Source/HeatCool/integrate_state_3d.f90 Source/HeatCool/integrate_state_hc_3d.f90 Source/HeatCool/integrate_state_vode_3d.f90 Source/HeatCool/vode_aux.f90 Source/HydroFortran/Make.package Source/HydroFortran/Nyx_advection_3d.f90 Source/HydroFortran/README Source/HydroFortran/add_grav_source_3d.f90 Source/HydroFortran/analriem.f90 Source/HydroFortran/enforce_minimum_density_3d.f90 Source/HydroFortran/flatten_3d.f90 Source/HydroFortran/normalize_species_3d.f90 Source/HydroFortran/ppm_3d.f90 Source/HydroFortran/slope_3d.f90 Source/HydroFortran/trace_3d.f90 Source/HydroFortran/trace_colglaz_3d.f90 Source/HydroFortran/trace_ppm_3d.f90 Source/HydroFortran/trace_src_3d.f90 Source/HydroFortran/trans_3d.f90 Source/Initialization/Make.package Source/Initialization/Nyx_initcosmo.cpp Source/Initialization/Nyx_initdata.cpp Source/Initialization/Nyx_setup.cpp Source/Initialization/check_initial_species_3d.f90 Source/Initialization/init_e_from_rhoe_3d.f90 Source/Initialization/init_e_from_t_3d.f90 Source/Initialization/interpolate.f90 Source/Initialization/read_plotfile.cpp Source/MG/cc_smoothers.f90 Source/MG/cc_stencil_apply.f90 Source/MG/mg_tower_smoother.f90 Source/Make.package Source/Monitors/Make.package Source/Monitors/MemInfo.H Source/Monitors/MemInfo.cpp Source/Monitors/test/Makefile Source/Monitors/test/testMemInfo.cpp Source/Network/Make.package Source/Network/network.f90 Source/Network/nyx_burner.f90 Source/Nyx.H Source/Nyx.cpp Source/NyxBld.cpp Source/NyxParticles.cpp Source/Nyx_F.H Source/Nyx_advance.cpp Source/Nyx_hydro.cpp Source/Nyx_nd.f90 Source/Nyx_output.cpp Source/SourceTerms/Make.package Source/SourceTerms/Nyx_grav_sources_3d.f90 Source/SourceTerms/Nyx_sources.cpp Source/SourceTerms/Nyx_sources_3d.f90 Source/SourceTerms/ext_src_3d.f90 Source/SourceTerms/ext_src_add_3d.f90 Source/Src_3d/EstDt_3d.f90 Source/Src_3d/Make.package Source/Src_3d/Nyx_sums_3d.f90 Source/Src_3d/ang_mom_sums_3d.f90 Source/Src_3d/bc_fill_3d.f90 Source/Src_3d/compute_temp_3d.f90 Source/Src_3d/enforce_consistent_e_3d.f90 Source/Src_3d/enforce_nonnegative_species_3d.f90 Source/Src_3d/fort_avgdown_3d.f90 Source/Src_3d/reset_internal_energy_3d.f90 Source/Tagging/Make.package Source/Tagging/Nyx_error.cpp Source/Tagging/Nyx_error_F.H Source/Tagging/Tagging_3d.f90 Source/advance_particles.cpp Source/comoving.cpp Source/comoving_nd.f90 Source/comoving_params.f90 Source/eos_params.f90 Source/main.cpp Source/meth_params.f90 Source/prob_params.f90 Source/project_S.f90 Source/strang_splitting.cpp Source/sum_integrated_quantities.cpp Source/sum_utils.cpp Source/two_particle_advance.cpp Source/write_info.cpp UsersGuide/AMR/AMR.tex UsersGuide/ComovingHydro/Equations.tex UsersGuide/ComovingHydro/sgs.bib UsersGuide/EOSNetwork/EOSNetwork.tex UsersGuide/Equations/Equations.tex UsersGuide/FlowChart/FlowChart.tex UsersGuide/GNUmakefile UsersGuide/GettingStarted/NyxGettingStarted.tex UsersGuide/Gravity/NyxGravity.tex UsersGuide/Gravity/gr.bib UsersGuide/Inputs/NyxInputs.tex UsersGuide/Introduction/NyxIntroduction.tex UsersGuide/ManagingJobs/managingjobs.tex UsersGuide/NyxUserGuide.tex UsersGuide/NyxVerification/Verification.tex UsersGuide/Particles/Particles.tex UsersGuide/Scaling/Scaling.tex UsersGuide/Software/NyxSoftware.tex UsersGuide/Suggestions/Suggestions.tex UsersGuide/UnitsAndConstants/NyxUnits.tex UsersGuide/Visualization/NyxVisualization.tex Util/BLAS/GPackage.mak Util/BLAS/Make.package Util/BLAS/daxpy.f Util/BLAS/dcopy.f Util/BLAS/ddot.f Util/BLAS/dscal.f Util/BLAS/idamax.f Util/VODE/GPackage.mak Util/VODE/Make.package Util/VODE/dacopy.f Util/VODE/dewset.f Util/VODE/dgbfa.f Util/VODE/dgbsl.f Util/VODE/dgefa.f Util/VODE/dgesl.f Util/VODE/dumach.f Util/VODE/dvhin.f Util/VODE/dvindy.f Util/VODE/dvjac.f Util/VODE/dvjust.f Util/VODE/dvnlsd.f Util/VODE/dvnorm.f Util/VODE/dvode.f Util/VODE/dvset.f Util/VODE/dvsol.f Util/VODE/dvsrco.f Util/VODE/dvstep.f Util/VODE/iumach.f Util/VODE/ixsav.f Util/VODE/vode.H Util/VODE/xerrwd.f Util/VODE/xsetf.f Util/VODE/xsetun.f Util/sample_run_scripts/run_Nyx_LyA_Cori.sh