commit 745ae1e65d6c7d8bec44a90336b33f238326ca85 Author: Debojyoti Ghosh Date: Wed Jun 10 13:40:33 2026 -0700 Add 2000-vintage Bay Area, California, and US plotting shapefiles matching the 2000 census data (#157) Co-authored-by: Claude Opus 4.8 data/.gitignore data/CA_2000_Census_Tracts/tl_2000_06_tract.cpg data/CA_2000_Census_Tracts/tl_2000_06_tract.dbf data/CA_2000_Census_Tracts/tl_2000_06_tract.prj data/CA_2000_Census_Tracts/tl_2000_06_tract.shp data/San_Francisco_Bay_Region_2000_Census_Tracts/region_2000_censustract.cpg data/San_Francisco_Bay_Region_2000_Census_Tracts/region_2000_censustract.dbf data/San_Francisco_Bay_Region_2000_Census_Tracts/region_2000_censustract.prj data/San_Francisco_Bay_Region_2000_Census_Tracts/region_2000_censustract.shp data/US_2000_Counties/tl_2000_us_county.cpg data/US_2000_Counties/tl_2000_us_county.dbf data/US_2000_Counties/tl_2000_us_county.prj data/US_2000_Counties/tl_2000_us_county.shp utilities/plotMovie/generate_frames.py commit fc3e9a8a24d960037995b1437282efb493a1c7c4 Author: Andrew Myers Date: Thu Jun 4 12:19:11 2026 -0700 Don't rely on managed memory in ExaEpi (#154) * Don't rely on managed memory in ExaEpi * fix style src/InitializeInfections.cpp src/main.cpp commit c628569c6d446826735be2ca10bc5baf9e5b0e64 Author: Andrew Myers Date: Wed Jun 3 16:06:17 2026 -0700 Bump CI to use C++20 (#156) * bump CI to use C++20 * check in missing files .github/workflows/clang.yml .github/workflows/cuda.yml .github/workflows/dependencies/dependencies_gcc11.sh .github/workflows/dependencies/dependencies_gcc11_nompi.sh .github/workflows/dependencies/dependencies_gcc8.sh .github/workflows/dependencies/dependencies_gcc8_nompi.sh .github/workflows/dependencies/dependencies_nvcc12.sh .github/workflows/gcc.yml .github/workflows/hip.yml commit a3c902e647332fb71864646d05e18e943728ab11 Author: stevenhofmeyr Date: Wed Apr 8 11:15:06 2026 -1000 Compare to epicast (#152) * Added various hacks and changes to compare to Epicast: - track newly infected - disable hospital delays - hacked compliance to match the three day probabilities in Epicast - hacked hospitalization to only be checked on second day, like in Epicast - allow household transmission when individuals are hospitalized * added python script for comparing epicast and exaepi * fixed to properly use the transition probs of epicast * dump agents in debug mode. fixed some debug warnings * added household cluster and do it per community, not neighborhood * initialize hh cluster for census * hospitalize on day 2 (as per epicast), using hospital_delay to set * used some macros to simplify parallel reductions * fixed issue with dead become immune * Create a #define for enabling Epicast comparisons * converted quaryArray into a templated function * Made withdrawal compliance into arrays for days 0, 1, 2 with different probabilities for different age groups. * Removed the AgeGroups_Hosp. Confusing and potential for error * Don't allow hospital treatment on first day * Very minor tweaks * Fixed incorrect use of fields for Epicast data. Needed the ones with ctx_ prepended. * include ventilated and icu in hosp counts for comparison to epicast * Don't use epicast hack transition probabilities. Added script for estimating gamma parameters * transit actions should be commented out * cleaned up code related to neighborhoods * Assign initial infections one at a time to spread more across communities * A few changes to bring the code more in line with development * minor tweak * set defaults for several parameters to match the Epicast defaults * fixed GPU build issue * Fixed bug in plotfile writing * formatting fix * fixed some build errors that show with c++20 * default UrbanPop to inter-neighborhood definition of household clesters. * Updated NM config file * Collecting more aggregate statistics by age. Hospitalization check comes before withdrawal check. * removed unused variable * make sure to include hh_cluster fix * add more macros * a few more fixes * clang-tidy * Set hospital_random in setInfected call * Fixed incorrect number of ReduceOps * added missing initialization code * Fixed plotting script for new outputs * Updated work nborhood interactions to be more similar to home nborhoods * minor tweak to script * Added script for parsing epicast binary outputs * updated epicast comparison script * Enable plotting of multiple epicast and exaepi series for comparison. Allow splitting the output when reading the epicast events * Updated cmake to fix build issue in devcontainer * updated gitignore * added scipy stats to requirements * added exact match to disease state transition probabilities for Epicast. Added a location parameter to the gamma distribution parameters. * minor formatting * disable epicast comparison by default * Fixed issue with counting of asymptomatic and presymptomatic * updated clang format script for some edge cases * default to NTRY+10 when epicast comparison is not defined. Updated python compare to epicast script to plot multiple random runs * fixed formatting * set default parameters to match those that work for Epicast matching * Update requirements.txt Co-authored-by: Andrew Myers * Update src/InteractionModWorkNborhood.H Co-authored-by: Andrew Myers * set neborhood size default to 500 and workgroup size default to 20 to pass CI tests with ic_type census --------- Co-authored-by: Andrew Myers .gitignore CMakeLists.txt data/.gitignore requirements.txt src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/DiseaseParm.H src/DiseaseParm.cpp src/DiseaseStatus.H src/HospitalModel.H src/InitializeInfections.cpp src/InteractionModWorkNborhood.H src/main.cpp utilities/UrbanPop-scripts/plot_timeseries.py utilities/calc_epicast_trans_probs.py utilities/compare_to_epicast.py utilities/custom-clang-format.py utilities/read_epicast_events.py commit c3c470cd9cc85fc6733670b8c4e840e8c4f5994c Author: Andrew Myers Date: Tue Mar 17 14:27:15 2026 -0500 Fix Some bugs in random and air travel (#151) * Skip agents on travel in regular commute pattern * some bug fixes for air travel src/AgentContainer.cpp src/AgentDefinitions.H commit 7571206b86ceed633745ff3a1b8e8ab111e93fb8 Author: Tan Nguyen Date: Wed Feb 25 13:51:17 2026 -0800 Weather (#149) * weather data structures * weather data on gpu * support national weather data * fix index to weather data * clang format * more on clang format * silence a compiler warning * merge development into weather * clang format * clang format data/weatherData_MA.csv data/weatherData_US.csv examples/inputs.ma examples/inputs_random_us src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/CMakeLists.txt src/CensusData.cpp src/IO.cpp src/Utils.H src/Utils.cpp src/WeatherData.H src/WeatherData.cpp src/main.cpp commit c5be9c162faa00046d9ef05f81bb06f41cb4c063 Author: Debojyoti Ghosh Date: Wed Feb 18 12:59:14 2026 -0800 Fix multi-disease hospital stats bug (#146) * Fixing inconsistent statistics accumulation while leaving hospital * fixed accessing arrays * rearranging the setting of release flags * bugfix: if releasing from vent, also release from ICU and hosp, same with ICU * Tracking exit from vent/ICU/hosp independently * Improving the exit tracking logic * more corrections to the exit tracking logic * correcting the status flag * correcting the death tracking - already dead vs today * bugfix: checkHospitalization should not reset ICU and vent flags * applied clang patch * Fix multidisease case file bug - read correct component per disease Bug: Both writeFIPSData() and writeAggregatedData() were always reading component 2 (cell_data_arr(i,j,k,2)) for all diseases, which only works for disease 0. This caused all disease-specific case files to contain identical data (disease 0's data). Fix: Changed to read component 5*d+2 for disease d, which matches the documented MultiFab component structure where component 5*d+2 contains the infected count for disease d. Changes: - IO.cpp:376: writeFIPSData() now uses 5*d+2 instead of 2 - IO.cpp:455: writeAggregatedData() now uses 5*d+2 instead of 2 This ensures each disease's case file contains the correct disease- specific infection data. Co-Authored-By: Claude (claude-sonnet-4.5) * applied clang patch --------- Co-authored-by: Claude (claude-sonnet-4.5) src/DiseaseParm.H src/HospitalModel.H src/IO.cpp commit d48ea7a365f65c3810d68ed77acf1e9da2be59a4 Author: stevenhofmeyr Date: Wed Feb 18 08:55:22 2026 -1000 Optimize upop io (#144) * Write out urbanpop data in binary and read it in binary * Fixed types * Updated NM datasets for binary format * Added an early exit if there are no more infected agents * updated test to use binary file for NM UrbanPop * Added a version of the UrbanPop conversion script that uses Polars instead of Pandas and is hence much faster * Added binary printing of agents to polars UrbanPop script. * Improved efficiency and replicability for UrbanPop conversion script * More attempts to make UrbanPop polars generation script deterministic * Improved performance of teacher allocations for polars UrbanPop script * Fixed bug with zero padding * removed unecessary sort and added output of cpp header file * Set seed in polars sample for reproducibility * Optimize childcare selection * Using lazy scanning for improved performance when reading feather files * optimized writing of index * Added printing of index in binary format * Added reading of binary index in ExaEpi * Changed UrbanPop script to write a single binary file that includes the index, and read it from ExaEpi. * Added education schools data file * gzipped schools data file * deleted unzipped school file * Updated urbanpop NM file for combined binary format * Removed old urbanpop idx file * Fixed bug where whole UrbanPop binary file was read into memory and broadcasted * Don't reopen UrbanPop file * updated test file for new urbanpop file naming convention .github/workflows/tests/test_runs.sh data/EducationData/schools_with_geoids.csv.gz data/UrbanPop/urbanpop_nm.bin.gz data/UrbanPop/urbanpop_nm.idx src/AgentContainer.cpp src/InitializeInfections.cpp src/UrbanPopAgentStruct.H src/UrbanPopData.H src/UrbanPopData.cpp src/main.cpp tests/inputs.nm.urbanpop utilities/UrbanPop-scripts/upop_to_exaepi.py utilities/UrbanPop-scripts/upop_to_exaepi_polars.py utilities/compare_to_epicast.py commit fe406db3541ea8c16c772cbee50e47f536a8dd9d Author: Debojyoti Ghosh Date: Wed Feb 18 10:11:38 2026 -0800 Fix worker assignment bug causing phantom transcontinental commutes (#147) * Fix worker assignment bug causing phantom transcontinental commutes When random number falls outside cumulative distribution range, worker destination 'to' defaulted to 0, incorrectly assigning workers from any location to unit 0. Changed default from 0 to 'from' (home unit), ensuring workers stay local when edge case occurs. This eliminates unrealistic nationwide disease spread in single day. Co-Authored-By: Claude (claude-sonnet-4.5) * applied clang patch --------- Co-authored-by: Claude (claude-sonnet-4.5) src/CensusData.cpp commit b2ec5f99397dead7cb2847aff66afd18908311ee Author: Debojyoti Ghosh Date: Tue Feb 3 13:18:57 2026 -0800 Fix false failures in plotfile comparison: chkdiff.sh was matching `total` in TinyProfiler output instead of only checking comparison results. Now checks for `PLOTFILES AGREE` first and filters profiling output when scanning for differences. (#145) utilities/tests/chkdiff.sh commit e43bdeed42fe3e7bf475e8af333d0e4b2287b81b Author: stevenhofmeyr Date: Fri Jan 30 14:08:40 2026 -1000 Set NTRY in initializing infections to be 10 for faster initialization across full US (#143) src/InitializeInfections.cpp commit c898802b1c7d84dfd83db9064fe7a4fe34f2a3b4 Author: stevenhofmeyr Date: Mon Jan 26 08:10:48 2026 -1000 Bug fixes and other adjustments from comparison to Epicast (#142) * Added various hacks and changes to compare to Epicast: - track newly infected - disable hospital delays - hacked compliance to match the three day probabilities in Epicast - hacked hospitalization to only be checked on second day, like in Epicast - allow household transmission when individuals are hospitalized * added python script for comparing epicast and exaepi * fixed to properly use the transition probs of epicast * dump agents in debug mode. fixed some debug warnings * added household cluster and do it per community, not neighborhood * initialize hh cluster for census * hospitalize on day 2 (as per epicast), using hospital_delay to set * used some macros to simplify parallel reductions * fixed issue with dead become immune * Create a #define for enabling Epicast comparisons * converted quaryArray into a templated function * Made withdrawal compliance into arrays for days 0, 1, 2 with different probabilities for different age groups. * Removed the AgeGroups_Hosp. Confusing and potential for error * Don't allow hospital treatment on first day * Very minor tweaks * Fixed incorrect use of fields for Epicast data. Needed the ones with ctx_ prepended. * include ventilated and icu in hosp counts for comparison to epicast * Don't use epicast hack transition probabilities. Added script for estimating gamma parameters * transit actions should be commented out * cleaned up code related to neighborhoods * Assign initial infections one at a time to spread more across communities * A few changes to bring the code more in line with development * minor tweak * set defaults for several parameters to match the Epicast defaults * fixed GPU build issue * Fixed bug in plotfile writing * formatting fix * fixed some build errors that show with c++20 * default UrbanPop to inter-neighborhood definition of household clesters. * Updated NM config file * Collecting more aggregate statistics by age. Hospitalization check comes before withdrawal check. * removed unused variable * make sure to include hh_cluster fix * add more macros * a few more fixes * clang-tidy * Set hospital_random in setInfected call * Fixed incorrect number of ReduceOps * added missing initialization code --------- Co-authored-by: Andrew Myers docs/source/usage/how_to_run.rst examples/inputs.defaults examples/inputs.nm src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/CensusData.cpp src/DiseaseParm.H src/DiseaseParm.cpp src/DiseaseStatus.H src/HospitalModel.H src/IO.cpp src/InitializeInfections.cpp src/InteractionModHome.H src/InteractionModHomeNborhood.H src/InteractionModel.H src/UrbanPopData.cpp src/main.cpp utilities/calc_epicast_trans_probs.py utilities/compare_to_epicast.py commit 6b89e1141d752a03a07d2690d9d62fa0f29f8347 Author: Andrew Myers Date: Wed Nov 12 12:33:25 2025 -0800 Split out output for symptomatic agents based on whether or not they will be hospitalized. src/AgentContainer.cpp src/AgentDefinitions.H src/DiseaseParm.H src/DiseaseStatus.H src/IO.cpp src/main.cpp commit 0f43514e6d37406341ad2a6c564f833c0caf4029 Author: Andrew Myers Date: Wed Nov 12 12:32:50 2025 -0800 Fix age group assignment for census data (#140) src/AgentDefinitions.H src/CensusData.H src/CensusData.cpp commit 12309deb90207309334d7c7fc8d463ce13451cf4 Author: Tan Nguyen Date: Fri Sep 12 02:12:15 2025 -0700 Setup4 frontier (#137) * environment setup for Frontier * removed trailing white space * fix warning messages * clang format * clang format * void return value --------- Co-authored-by: Tan Nguyen README.md etc/frontier_environment.sh src/InteractionModel.H commit 6d4dbee20f328b38ba1522ef6afd1ad87f34eeb3 Author: Tan Nguyen Date: Sat Sep 6 14:50:23 2025 -0700 add national air traffic data (#136) data/CensusData/US_airports.dat data/US_CY20AirTraffic.dat examples/inputs_random_us src/AirTravelFlow.cpp commit 96b9debe148df854a9716b8e4097e5ba4a67cb62 Author: stevenhofmeyr Date: Wed Sep 3 10:10:04 2025 -1000 Fixed randomized hospital stays (#135) * Fixed bug where random hospital stays were never enabled. Simplified code for checking hospitalization. * Ensure days in hospital is less than hospital_offset to ensure propery treatment recovery * Added comment to clarify why the number of days in hospital needs to be less than the offset * Fixed numeric conversion error * More fixing of floating point to int conversions * Added comments to better explain how hosp_offset works. Made hosp_offset into a constant with size greater than a human lifetime, and added checks for values that exceed this. * Changed const to non-const to avoid build error on CI src/DiseaseParm.H src/DiseaseParm.cpp src/HospitalModel.H src/main.cpp commit 1f0d7227c74c6b73b4f401f10db089513b88b339 Author: stevenhofmeyr Date: Tue Aug 26 12:05:15 2025 -1000 Update UrbanPop to use LODES to generate worker and student flows (#134) * Formatted all the files with utilities/custom-clang-format.py * Added CONTRIBUTING.md with instructions on code formatting * Formatted cmake files with cmake-format, and python files with black * Added missing Utils.H header * Replaced occurrences of underscore naming of functions with camel caps * Increase penalty to prevent break before first parameter in call * Removed old comments from custom clang-format script * Added usage example to contributing.md * Updated the .clang-format config file to only include the options that differ from the default * Made .clang-format work with version 18 * updated custom clang format to show errors in underlying calls * Added `clang-format` CI test (#103) * added clang-format test More fixes to the clang-format CI test * Make the test script output the clang version number * updated formatting of main.cpp and IO.cpp * Try to force version 19 for clang-format * Use a docker image to ensure clang-format-19 version is always used for formatting * Added return code to docker call * First run docker image to ensure it gets downloaded and doesn't mess up the subsequent run * for failed clang-format test, print out patch that needs to be applied as fix --------- Co-authored-by: shofmeyr * Fixed bug where a fixed size was benig used to initialize the school xmit types * Added an implementation of writing aggregated data for urbanpop * Fixed plotting to work with UrbanPop data * Minor fixes to plotting with urbanpop * Added new plotting scripts specifically for urbanpop * Change urbpanplot geo plotting script to include four different status plots * Updated urbanpop plot geography script * formatted urbanpop plot timeseries script * Fixed census initialization family size off-by-one error * Fixed faulty merge * Reset etr/plot.py to original version * Simplified some urbanpop school extraction calculations * Minor formatting change * Added scripts for processing schools data and generating missing nt/dt data for UrbanPop * Fixed scripts for getting schools. Added schools processing to nt_dt generation script * Renamed nt_dt generation script since it uses more than just lodes data * iteratively allocate students to schools at increasing scale to minimize distance from home to school * Changed schools extraction script to add level to schools * Allocate students to schools in levels (elem, middle, etc) * Added colleges to allocations * Minor fix * Allocate agents to childcare * Make sure students that didn't get allocated are still included in the final dataset * Allocate teachers incrementally in regions, reducing number required as required slots are filled * Use only numpy sample instead of generator choice and sample mix * allocate students more accurately in python script * Updated git make file for better version * More accounting for time within fast interact home function * Fixed student allocation in python script generation of nightime/daytime urbanpop entries * Added config file for options. Cope with NaNs in the shape file lookups * Print errors and warnings in red. Abort if the work geoid is not found in the shape files * Fixed bug in school id allocations for students * Set grade levels for teachers to assign to classes * Got extract urbanpop feather script working with lodes generated worker allocations * allow for multiple lodes files in gen_nt_dt.py. Properly process file globs in config files for urbanpop scripts * Added correlation checks for workers, students and teachers * Removed old line * Added option for using NCES data for public schools. Added script (check_nt_dt.py) that compares UrbanPop nt/dt to those generated by gen_nt_dt.py * Renamed extract script to convert. Enabled config file use for get_schools.py. Added a README to the UrbanPop scripts. * Updated UrbanPopScripts README. Added file for comparing generated flows to UrbanPop nt/dt * Process UP nt/dt files in gen_nt_dt.py. Not quite working yet for allocating teachers * Fixed nt/dt generation using UP nt/dt files * Updated urbanpop conversion script to correctly process UrbanPop daytime/nighttime flows * Fixed issue in urbanpop conversion where geometry was not filtered out from shape files * Corrected option in help docs. Fixed UrbanPop types for grades to be correct. * Add missing nt/dt rows using UrbanPop values and setting dest geoids same as orig * Removed message about SoA field count * Use NAICS codes from syp files instead of nt/dt descriptions. Don't count mil as employed in generated data, per the UP nt/dt files * Correctly use raw NAICS codes in conversion script * More fixes for using raw NAICS * Finally got it working with raw NAICS * Corrected grade to school type conversion * Fix grades to school types for census data * Fixed unused function debug compilation error * Added urbanpop NM files needed for testing * The NM urbanpop index file should not be gzipped * Fixed bug where agent grade was not set but school id was * Allocate teachers from appropriate NAICS code for childcare, secondary schools and others * Handle case where the home geoid is not found in the LODES flows * Handle case where no students can be allocated at a given regional level * Added back in missing NM test files * Put test files in the correct directory * Added some extra tracking in python scripts * Fixed bugs in urbanpop initialization that only showed on some GPUs * Moved the NM upop test data * Cleaned up shadow variables * Fixed shadow again * Fixed urbanpop path in test_runs.sh * Updated upop gen nt dt workers script to use concat less frequently for faster performance * fixed several edge cases found with new datasets * Added timer ticks to long running scripts * Changed urbanpop to use an abstract grid mapping instead of longitude and latitude * Track overall work population in a community for setting the agent nborhood * choose work pop from work location for initialization * Don't output debug agents * Need to still compute lng/lat to ensure dropping of missing geoids * Tracking memory usage in urbanpop scripts and trying to reduce it for reading feather files * speed up nt/dt file processing by getting rid of stupid regex * some useful output tracking for urbanpop scripts * Fixed plotting of urbanpop results, both time series and geography * much faster way of adjusting school ids in urbanpop script * fixed exaepi reading of urbanpop files without lat/lng * More efficient reindexing of household ids and agent printing * Fixed check for US pop in urbanpop size limits. Adjusted plotting of geographic infection data * Option to set lng/lat dimensions for plot * Modified the checking script to give a more thorough comparison, and to also plot results * updated checking script * updated readme * grouped functionality in gen_nt_dt for easy use in other modules * when agents are assigned grades, only count them as employed when they are >=25 in age * Fixed upop teacher ratios to be more realistic - matching known data * some fine-tuning of teacher ratios * adjusted teacher ratios for upop and modified plotting for check script * start of new script for processing everything at once * updated format of gen script * Added processing of urbanpop nt/dt data to new script * added adjustment of indexes and printing c++ header * print agents and indexes * updated exaepi to use the newly generated urbanpop struct * fixed issue with no school being set to -1 instead of 0. set students to have -1 naics code * Added school allocations for generated data * fixed teacher allocation to work with generated nt/dt data. added debugging flag for pickling intermediates * Fixed incorrect work location settings for students and teachers. Added further correlation tests * Fixed issue with not clearing naics for students * tweaked teacher ratios for day/night * Don't use school or LODES geoids that are not also home geoids in UrbanPop * updated urbanpop_nm data * enable plotting a cloud of results in timeseries * fixed timeseries plotter * fixed plot_geo with correct frontend * Fixed assert failure when printing cases * Don't profile additional home interaction operations * cleaned up code * Fixed call to plotFile to not trigger assert in debug mode * changed plot_geo to not plot dead - not provided in plotting file now * Added some comments in writePlotFile to make it clear that the status names are per disease * Updated UrbanPop scripts README. Removed superfluous urbanpop processing scripts * Removed unneeded pickling. Changed default ic_type to urbanpop * Experimenting with multiprocessing for student allocations * simplified schools allocation in regions * implemented multithreading in student allocation * Options to use multiprocessing and multithreading in upop_to_exapi.py. Added description of upop_to_exaepi algorithms. * Added description --------- Co-authored-by: Debojyoti Ghosh .github/workflows/tests/test_runs.sh cmake/GitVersion.cmake data/.gitignore data/UrbanPop/.gitignore data/UrbanPop/NM_35/urbanpop_nm.idx data/UrbanPop/urbanpop_nm.csv.gz data/UrbanPop/urbanpop_nm.idx src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/CensusData.cpp src/HospitalModel.H src/IO.cpp src/InteractionModHome.H src/InteractionModHomeNborhood.H src/UrbanPopAgentStruct.H src/UrbanPopData.H src/UrbanPopData.cpp src/Utils.cpp src/main.cpp tests/inputs.nm.urbanpop utilities/UrbanPop-scripts/.gitignore utilities/UrbanPop-scripts/README.md utilities/UrbanPop-scripts/check_nt_dt.py utilities/UrbanPop-scripts/description_of_upop_to_exapi.txt utilities/UrbanPop-scripts/extract_urbanpop_feather.py utilities/UrbanPop-scripts/get_schools.py utilities/UrbanPop-scripts/plot_geo.py utilities/UrbanPop-scripts/plot_timeseries.py utilities/UrbanPop-scripts/upop_to_exaepi.py utilities/plotMovie/plotCases.py commit c975b889383fbf185ab040373cdac967fbbbac04 Author: Andrew Myers Date: Thu Aug 21 09:09:17 2025 -0700 Add capability to randomize length of stay in hospital (#133) docs/source/usage/how_to_run.rst src/DiseaseParm.H src/DiseaseParm.cpp commit 367323758713c2e8100fde9b6e1402103b342732 Author: Andrew Myers Date: Thu Aug 14 18:04:40 2025 -0700 Implement relative infectiousness for asymptomatic individuals (#132) docs/source/usage/how_to_run.rst examples/inputs.defaults src/InteractionModAirTravel.H src/InteractionModHome.H src/InteractionModHomeNborhood.H src/InteractionModSchool.H src/InteractionModWork.H src/InteractionModWorkNborhood.H src/InteractionModel.H commit f553e4f5f3105441424d5630c78cf6b6795db89b Author: Tan Nguyen Date: Wed Aug 13 13:32:41 2025 -0700 Sycl (#129) * support SYCL * use fast bin with SYCL (for now) because serial binning is so slow * add run instructions (with checkpoint/restart for reproducibility) for Aurora --------- Co-authored-by: Tan Nguyen Co-authored-by: Tan Nguyen Co-authored-by: Tan Nguyen Co-authored-by: Tan Nguyen Co-authored-by: Tan Nguyen README.md src/InitializeInfections.cpp src/InteractionModHome.H src/InteractionModHomeNborhood.H src/InteractionModSchool.H src/InteractionModWork.H src/InteractionModWorkNborhood.H src/InteractionModel.H commit cc9753ca2e41920bfaa9ddc4a36e675f8c233cfb Author: Andrew Myers Date: Tue Aug 12 10:06:11 2025 -0700 Add --version runtime argument (#131) src/main.cpp commit 938762011c639e09671efd7ea59f62ec8ffa9f26 Author: atmyers Date: Thu Aug 7 13:20:33 2025 -0700 worker_filename -> workerflow_filename in docs docs/source/usage/how_to_run.rst examples/inputs.defaults commit f06460f4b95058a5c443fcbd80a2b1342d247f2f Author: Andrew Myers Date: Wed Jul 30 12:24:05 2025 -0700 totalExposed -> totalInfected src/AgentDefinitions.H src/main.cpp commit a158f2d407cf2a4d2cf91951860d13d3b413b980 Author: Andrew Myers Date: Wed Jul 30 11:47:29 2025 -0700 Change format of output.dat to support GSA runs (#130) src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/main.cpp commit 62446f6b50eca0537572c29603b1265a206f66fb Author: arnav-singhal <43693924+arnav-singhal@users.noreply.github.com> Date: Mon Jun 23 16:58:35 2025 -0400 use right offset for unit_mf (#128) src/IO.cpp commit 0a3bede775f6a4b6a64491f618d4cf46e91fe34b Author: Andrew Myers Date: Tue May 20 15:15:58 2025 -0700 Checkpoint/Restart (#125) Co-authored-by: Tan Nguyen docs/source/usage/how_to_run.rst examples/inputs_random_us src/IO.H src/IO.cpp src/Utils.H src/Utils.cpp src/main.cpp commit 8480d8cc208813d84ea620fb927cfecdbecbaf96 Author: Tan Nguyen Date: Fri May 9 08:43:28 2025 -0700 Fix init case roundoff (#124) * initialize exact requested cases * remove trailing white space * remove tabs src/InitializeInfections.cpp commit 5da57705c81b599ea1fda6e3ee79e5e2d6f14206 Author: terasaki1 Date: Thu May 1 17:47:14 2025 -0700 Fix slow interaction (#94) * by commenting out define FAST_INTERACTIONS, it led to a few bug renaming variable to much naming used in FAST_INTERACTIONS * xmit_school not defined yet for playgroups! * clang-formatting * clang-formatting AMREX_GPU_DEVICE * Adults-to-adults interactions are accounted for in InteractionModWork.H, hence double counting * slow interaction fix * fix school interaction for adult * remove debugging message * fix formatting --------- Co-authored-by: Gbocho Terasaki src/InteractionModAirTravel.H src/InteractionModHome.H src/InteractionModSchool.H src/InteractionModWorkNborhood.H src/InteractionModel.H commit 66d15da8105f3faa3598cf7be488590a47262db4 Author: Debojyoti Ghosh Date: Thu May 1 11:24:45 2025 -0700 Added UrbanPop NM case to CI test (#123) * updated github runner Ubuntu version * trying to install gcc-8 on Ubuntu 24.04 * fixing g++ version * trying to fix gcc version in CUDA CI test * updated to Clang-18 * updating to CUDA 12.6 * updating NVHPC CI test based on AMReX's workflow * removed old NVHPC dependency * fix to nvhpc CI test * added urbanpop NM case to CI test * letting urbanpop case run 4 days .github/workflows/tests/test_runs.sh tests/inputs.nm.urbanpop commit 7f58e66a597ebd62899b32ce47d0017a582cd27d Author: Tan Nguyen Date: Wed Apr 30 10:38:37 2025 -0700 fix the freezing bug in case initialization (#119) * fix the freezing bug in case initialization * adding inputs.ma to CI tests * set the same tile size for particle container and multifab iterators --------- Co-authored-by: Debojyoti Ghosh src/AgentContainer.H src/main.cpp tests/inputs.ma commit ef10d6aa8b4a6d7a7b26561cf3e52f1c6bb1b6bd Author: Debojyoti Ghosh Date: Mon Apr 28 13:26:15 2025 -0700 Fixing CI tests to run on Ubuntu 24.04 (#122) * updated github runner Ubuntu version * trying to install gcc-8 on Ubuntu 24.04 * fixing g++ version * trying to fix gcc version in CUDA CI test * updated to Clang-18 * updating to CUDA 12.6 * updating NVHPC CI test based on AMReX's workflow * removed old NVHPC dependency * fix to nvhpc CI test .github/workflows/clang.yml .github/workflows/cuda.yml .github/workflows/dependencies/dependencies_clang18.sh .github/workflows/dependencies/dependencies_gcc8.sh .github/workflows/dependencies/dependencies_gcc8_nompi.sh .github/workflows/dependencies/dependencies_nvcc12.sh .github/workflows/dependencies/dependencies_nvhpc.sh .github/workflows/dependencies/dependencies_nvhpc21-11.sh .github/workflows/gcc.yml commit 4e1b90fe192bbbca4a081d0cbd013a9cd5b2d24b Author: stevenhofmeyr Date: Mon Apr 28 06:40:31 2025 -1000 Fixed bug in indexing in call to setInfected in infectRandomCommunity (#121) src/InitializeInfections.cpp commit b42abb1c57f7f52e0ecefb8795b22e9a84d9d6df Author: Debojyoti Ghosh Date: Wed Apr 2 12:55:41 2025 -0700 Adding test runs to CI tests (#117) * adding test runs to Debug build test * corrections to testing script and adding nproc & nomp as arguments * adding nproc and nomp to screen output * 2 MPI ranks for tests instead of 4 * deleting run directory after test, removing unused parameters from inputs * removing some more unnecessary parameters from test inputs * adding tests to OMP build as well * In test runs, don't use mpiexec if serial * can I do 4 OMP threads on the runner? * deleted a file created by mistake .github/workflows/gcc.yml .github/workflows/tests/test_runs.sh tests/inputs.bay tests/inputs.ca tests/inputs.ca.noair tests/inputs.ca.random tests/inputs.nm tests/inputs_2dc1c2.ca commit 10d9447dadd503615ec034120a0f25addcc6fdc4 Author: Debojyoti Ghosh Date: Fri Mar 28 12:24:41 2025 -0700 Fixed component counting in writing plotfiles (#116) * fixed the component counting in writing plotfiles * applied clang patch * added another assert to ensure sizes of varnames and output components are same src/AgentContainer.H src/AgentContainer.cpp src/IO.cpp commit d732eeacbf51618e1fa8733c3f99edd8314eead8 Author: Andrew Myers Date: Thu Mar 20 17:57:46 2025 -0700 Add "new cases" to the plotfile output (#115) * Add new cases to the diagnostic output * fix tabs * fix style src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/IO.H src/IO.cpp src/main.cpp commit c55013a3cca433e20a2a2def03d6129c6bed90f7 Author: Debojyoti Ghosh Date: Thu Mar 20 17:57:18 2025 -0700 Implemented co-immunity and co-susceptibility for multiple disease simulations (#106) * implemented a simple coimmunity/cosusceptibility model * if -> else if so that an agent doesn't enter more than one if-block * renamed isHospitalized() and flag_hosp, etc for clarity * making sure latent, incubation, & infection periods are never negative; also ensuring latent period is not greater than the incubation+infection period * simplified the condition for latent period being smaller than incubation+infectious periods * not using std::max since Clang complains! * incubation period should be less than the latent+infectious periods! * fixed the if condition for when hospitalization starts * cosusceptibility kicks in after incubation period * using consistent type in std::max * fixed the infection probability calculation such that agents that haven't been anywhere do not have non-zero probability of infection due to co-susceptibility * fixed checking for hospitalization state when if agent is already in hospital * added documentation for disease-coupling inputs * added an example input file for CA with two Covid variants * style changes based on clang-format * bugfix in checking if already hospitalized when marking for hospitalization * fixed typo Co-authored-by: Andrew Myers * switched to ASSERT from ALWAYS_ASSERT * fail if the number of elements for coimmunity/cosusceptibility matrices in input file don't match expected number of elements * clang-format fixes --------- Co-authored-by: Andrew Myers docs/source/usage/how_to_run.rst examples/inputs_2disease_covid1_covid2.ca src/AgentContainer.H src/AgentContainer.cpp src/CMakeLists.txt src/DiseaseCoupling.H src/DiseaseStatus.H commit eff799d76e44823885460288b1121c85dbcb0a5e Author: Andrew Myers Date: Mon Mar 10 11:36:44 2025 -0700 Add example set up to run US (#114) examples/inputs_random_us commit cdb17ab3aad4d4b0e879eb811c5bd21629666c87 Author: Andrew Myers Date: Tue Mar 4 22:13:39 2025 -0600 Use comms arena by default (#112) src/main.cpp commit dbb99ae8c065a63ad05644b89d0aaa562d0cc2bb Author: Andrew Myers Date: Tue Mar 4 22:13:25 2025 -0600 Census Tract IDs were not being written out correctly to plotfiles. (#113) src/IO.cpp commit e1bc31044523e77abd25edd3f320c9e34b84d351 Author: Andrew Myers Date: Tue Feb 25 14:30:00 2025 -0800 Add delay between symptom onset and hospitalization (#97) * Add delay between symptom onset and hospitalization * fix implicit cast * fix ill-formed if condition * remove debugging code * fix function name * fix trailing whitespace * clang-format docs/source/usage/how_to_run.rst docs/source/usage/utilities.rst examples/inputs.defaults src/AgentContainer.cpp src/AgentDefinitions.H src/DiseaseParm.H src/DiseaseParm.cpp src/DiseaseStatus.H src/IO.cpp src/InitializeInfections.cpp commit 94009fcdc5d2fb3030a1d78cfd4008b376632d42 Author: stevenhofmeyr Date: Tue Feb 25 11:52:15 2025 -1000 Urbanpop plotting fixes (#109) * Formatted all the files with utilities/custom-clang-format.py * Added CONTRIBUTING.md with instructions on code formatting * Formatted cmake files with cmake-format, and python files with black * Added missing Utils.H header * Replaced occurrences of underscore naming of functions with camel caps * Increase penalty to prevent break before first parameter in call * Removed old comments from custom clang-format script * Added usage example to contributing.md * Updated the .clang-format config file to only include the options that differ from the default * Made .clang-format work with version 18 * updated custom clang format to show errors in underlying calls * Added `clang-format` CI test (#103) * added clang-format test More fixes to the clang-format CI test * Make the test script output the clang version number * updated formatting of main.cpp and IO.cpp * Try to force version 19 for clang-format * Use a docker image to ensure clang-format-19 version is always used for formatting * Added return code to docker call * First run docker image to ensure it gets downloaded and doesn't mess up the subsequent run * for failed clang-format test, print out patch that needs to be applied as fix --------- Co-authored-by: shofmeyr * Fixed bug where a fixed size was benig used to initialize the school xmit types * Added an implementation of writing aggregated data for urbanpop * Fixed plotting to work with UrbanPop data * Minor fixes to plotting with urbanpop * Added new plotting scripts specifically for urbanpop * Change urbpanplot geo plotting script to include four different status plots * Updated urbanpop plot geography script * formatted urbanpop plot timeseries script * Fixed census initialization family size off-by-one error * Fixed faulty merge * Reset etr/plot.py to original version --------- Co-authored-by: Debojyoti Ghosh src/IO.H src/IO.cpp src/UrbanPopData.H src/UrbanPopData.cpp src/main.cpp utilities/UrbanPop-scripts/extract_urbanpop_feather.py utilities/UrbanPop-scripts/plot_geo.py utilities/UrbanPop-scripts/plot_timeseries.py commit 08e93a9255759eee516198c88ccbeeb6e3032d74 Author: Andrew Myers Date: Tue Feb 25 11:39:20 2025 -0800 Fix HIP CI (#111) .github/workflows/dependencies/dependencies_hip.sh .github/workflows/hip.yml commit 466d4890226f489ce8840cee32457173aeaff116 Author: stevenhofmeyr Date: Wed Feb 19 17:18:37 2025 -1000 Fixed census initialization family size off-by-one error (#108) src/CensusData.cpp commit 779e903d8263ac3df7210a6ab498e59789659cba Author: stevenhofmeyr Date: Wed Feb 19 08:08:19 2025 -1000 Format with clang (#102) * Formatted all the files with utilities/custom-clang-format.py * Added CONTRIBUTING.md with instructions on code formatting * Formatted cmake files with cmake-format, and python files with black * Added missing Utils.H header * Replaced occurrences of underscore naming of functions with camel caps * Increase penalty to prevent break before first parameter in call * Removed old comments from custom clang-format script * Added usage example to contributing.md * Updated the .clang-format config file to only include the options that differ from the default * Made .clang-format work with version 18 * updated custom clang format to show errors in underlying calls * Added `clang-format` CI test (#103) * added clang-format test More fixes to the clang-format CI test * Make the test script output the clang version number * updated formatting of main.cpp and IO.cpp * Try to force version 19 for clang-format * Use a docker image to ensure clang-format-19 version is always used for formatting * Added return code to docker call * First run docker image to ensure it gets downloaded and doesn't mess up the subsequent run * for failed clang-format test, print out patch that needs to be applied as fix --------- Co-authored-by: shofmeyr * Fixed bug where a fixed size was benig used to initialize the school xmit types --------- Co-authored-by: Debojyoti Ghosh .clang-format .github/workflows/clang-format.yml .github/workflows/dependencies/dependencies_clang_format.sh .github/workflows/tests/test_clang-format.sh .gitignore CMakeLists.txt CONTRIBUTING.md UrbanPop-scripts/extract_urbanpop_feather.py cmake/SetupAgent.cmake src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/AirTravelFlow.H src/AirTravelFlow.cpp src/CMakeLists.txt src/CaseData.H src/CaseData.cpp src/CensusData.H src/CensusData.cpp src/DemographicData.H src/DemographicData.cpp src/DiseaseParm.H src/DiseaseParm.cpp src/DiseaseStatus.H src/HospitalModel.H src/IO.H src/IO.cpp src/InitializeInfections.H src/InitializeInfections.cpp src/InteractionModAirTravel.H src/InteractionModHome.H src/InteractionModHomeNborhood.H src/InteractionModSchool.H src/InteractionModWork.H src/InteractionModWorkNborhood.H src/InteractionModel.H src/InteractionModelLibrary.H src/UrbanPopAgentStruct.H src/UrbanPopData.H src/UrbanPopData.cpp src/Utils.H src/Utils.cpp src/main.cpp src/version.h.in utilities/custom-clang-format.py commit a586b39b88700adb3d794c9ab32eed773cd72c26 Author: Debojyoti Ghosh Date: Tue Feb 11 15:51:50 2025 -0800 added autogenerated version.h to .gitignore (#105) .gitignore commit e191add2b47681946e63a08994fb3bd91688158b Author: Andrew Myers Date: Tue Feb 11 09:44:11 2025 -0800 Build against known good release of AMReX rather than development CMakeLists.txt commit d3612d40f3a686e33f13233a764cedcfeea44b9d Author: stevenhofmeyr Date: Wed Jan 29 07:28:43 2025 -1000 Expose the xmit_work option so that it can actually be set and describe it in the docs. (#100) Add the branch name to the version output cmake/GitVersion.cmake docs/source/usage/how_to_run.rst examples/inputs.defaults src/DiseaseParm.cpp commit 541d5722a71003ae9f05e7bcb20d8b85bf350f2d Author: stevenhofmeyr Date: Tue Jan 28 14:21:37 2025 -1000 Add git version (#99) * Added git version to output when running ExaEpi * Call git version in cmake and write out version when code runs cmake/GitVersion.cmake cmake/SetupAgent.cmake src/main.cpp src/version.h.in commit 3691d380ac24f1ef469ba83a4ea84646528d8458 Author: Andrew Myers Date: Tue Jan 28 11:48:54 2025 -0800 Fix default immune length alpha and beta (#98) docs/source/usage/how_to_run.rst examples/inputs.defaults src/DiseaseParm.H commit 933109a9285771a7b2773ba1216ec783ccf0f3d1 Author: Andrew Myers Date: Fri Jan 24 18:41:33 2025 -0800 Print out unused ParmParse parameters before evolution (#95) docs/source/usage/how_to_run.rst examples/inputs.bay examples/inputs.ca examples/inputs.ma examples/inputs.small_cases examples/inputs_random_ca src/main.cpp commit 309b625305370908084170b1ff2a8bb98a27a48a Author: Tan Nguyen Date: Mon Jan 6 09:50:48 2025 -0800 Update scripts (#93) * script to scale population and workerflow data * remove large example files * remove outdated files * add plot scripts back * generate workerflow from safegraph data * add more input data * update heatmap generation script * remove tabs * remove trailing white spaces data/CensusData/BayArea-wf_scaled.bin data/CensusData/BayArea_scaled.dat data/CensusData/CA-sg-wf.bin data/CensusData/CA_scaled.dat examples/inputs_sg.ca utilities/parseSafeGraph.py utilities/plotMovie/createMov.sh utilities/plotMovie/exampleCaseData/casesDay.0.csv utilities/plotMovie/exampleCaseData/casesDay.1.csv utilities/plotMovie/exampleCaseData/casesDay.10.csv utilities/plotMovie/exampleCaseData/casesDay.11.csv utilities/plotMovie/exampleCaseData/casesDay.12.csv utilities/plotMovie/exampleCaseData/casesDay.13.csv utilities/plotMovie/exampleCaseData/casesDay.2.csv utilities/plotMovie/exampleCaseData/casesDay.3.csv utilities/plotMovie/exampleCaseData/casesDay.4.csv utilities/plotMovie/exampleCaseData/casesDay.5.csv utilities/plotMovie/exampleCaseData/casesDay.6.csv utilities/plotMovie/exampleCaseData/casesDay.7.csv utilities/plotMovie/exampleCaseData/casesDay.8.csv utilities/plotMovie/exampleCaseData/casesDay.9.csv utilities/plotMovie/exampleCensusData/tl_2010_06_tract00/tl_2010_06_tract00.dbf utilities/plotMovie/exampleCensusData/tl_2010_06_tract00/tl_2010_06_tract00.prj utilities/plotMovie/exampleCensusData/tl_2010_06_tract00/tl_2010_06_tract00.shp utilities/plotMovie/exampleCensusData/tl_2010_06_tract00/tl_2010_06_tract00.shp.xml utilities/plotMovie/exampleCensusData/tl_2010_06_tract00/tl_2010_06_tract00.shx utilities/plotMovie/plotCases.py utilities/scaleCensus.py commit 70b503d62ed25c437b4dfa1b2f915b374b0f7b8b Author: shofmeyr Date: Fri Dec 20 14:50:08 2024 -1000 Updated how to run documentation to describe correct setting of disease inputs with disease. prefix. docs/source/usage/how_to_run.rst examples/inputs.defaults commit ee43392ceac1658134b8bcb454b10487a0d19e22 Author: Andrew Myers Date: Tue Dec 17 10:44:41 2024 -0800 Convert to Gamma distributions for the immune, latent, infectious, and incubation lengths. (#92) * Convert to Gamma distributions for the immune, latent, infectious, and incubation lengths. * fix conversion warnings docs/source/usage/how_to_run.rst examples/inputs.ca examples/inputs.defaults examples/inputs.ma examples/inputs.nm examples/inputs_random_ca src/DiseaseParm.H src/DiseaseParm.cpp src/DiseaseStatus.H src/HospitalModel.H commit d2aa681bca93a4dc921b7a534779ad5f501996ee Author: Andrew Myers Date: Tue Dec 10 08:57:15 2024 -0800 Follow on to #86 (#90) * Follow on to #86 * correct input files * add back the input processing code for air travel * Fixed assignment of teachers to always give the same results for the same seed when agent.fast=false * Fixed bug in age selection for workers. Use round for calculating teacher counts * cast rounded values to int --------- Co-authored-by: Tan Nguyen Co-authored-by: shofmeyr examples/inputs.bay examples/inputs.ca examples/inputs.ma examples/inputs.small_cases examples/inputs_random_ca src/AgentContainer.H src/AgentContainer.cpp src/CensusData.cpp src/IO.cpp src/InteractionModHome.H src/InteractionModHomeNborhood.H src/InteractionModSchool.H src/InteractionModWork.H src/InteractionModWorkNborhood.H src/InteractionModel.H src/Utils.cpp commit f91526e772d0f04261e07c54b9504cab36196c0c Author: arnav-singhal <43693924+arnav-singhal@users.noreply.github.com> Date: Wed Nov 20 17:01:13 2024 -0500 Fix typo in documentation code (#91) I had messed up spelling in example code causing it to break. docs/source/usage/utilities.rst commit 4206b088c87a81f6aebd7c0d5e8e01630f65914a Author: Andrew Myers Date: Mon Nov 18 13:50:52 2024 -0800 Don't specifiy cmake version in perlmutter_environment.sh etc/perlmutter_environment.sh commit 7c15756d5bbab84dbb8a5b80731c9bc9af46ab30 Author: stevenhofmeyr Date: Fri Nov 15 13:44:08 2024 -1000 UrbanPop (#86) * Removed demo ic_type. * Removed unused function * Made workgroup size and nborhood size into parameters. Call Redistribute() after moving agents (particles). Print current infections and deaths counts when running and showing the current day. Added UrbanPop ic_type and urbanpop_filename parameters. * Moved the Redistribute call to within the agentMove functions. Added workgroup_size parameter to read_workerflow * Moved function definitions from AgentContainer.H to the .cpp file, for all not setter/getter methods. * Prefixed all AgentContainer variables with m_, as per coding standards * Moved all functions and data structures that are specific to the census data ic_type into a separate CensusData class, in a separate file. All of the functions previously in Initialization.H/cpp were specific to census data and have thus been moved into the CensusData class. * Removed geom from CensusData - not needed. * Added python script for processing UrbanPop feather files. Added header file for UrbanPop data. * Fixed missing variable in auto-generated UrbanPop header file * Added UrbanPop data processing files * Added an option to produce a fixed set of initial infections to try minimize variation between runs. * Changed work interaction model to bin by workgroup as well as community, which really speeds up CPUs-only runs * Moved functionality for work interaction model into separate function to conform to same code structure as other interaction models * Added updated AgentDefinitions file for isAtWork function. Removed unused variables. * Updated InteractionModel makeBins to always make bins since agents could have been redistributed * Go through infectious first for home interactions * For the work interaction model, bin by workgroup plus community. This results in large speedups, especially for CPU only code. Also, when doing interactions, iterate through the infectious agents first, which is also faster, since most agents will be susceptible and fewer will be infectious. This requires atomic multiply for the prob_ptr for GPUs. * Updated assert calls to avoid unused variables when not in debug mode. * Changed code to use PTDType for work bins instead of PType, and removed extra AOS attribute from agents * Use particle tile data for all binning * Bin home interactions by nborhood and family cluster * Enable daytime interactions * Restructured nborhood binning - because of community interactions can't bin smaller than a community, but doing infectious then susceptible still helps performance * Cleaned up interaction models * Switched to GPU policy for building bins. Much faster on GPUs * Implemented new binner for school interactions * Trying to fix school interactions - should they be in the same nborhood? Work or home? * Better matching of school interaction model with development branch * Restructured interaction model to use a common templated function for work, home, school and nborhood. Much simpler code now. * Always rebuild the bins - needed since redistribute changes the particle locations * Fixed indentation * Removed some unused variables, and fixed reference to SOA index for non-group in nborhood interactions. * Renamed shadowed variables to avoid PR checks complaints. * Simplified interaction model template by removing the ACT typename. Switched binning policy from GPU to Serial, in order to preserve reproducibility for a given random seed. Commented out the generic interaction model, which is never used. * Moved makeBins from InteractionModel to InteractionModRandom because that is the only place it is used and it will be replaced soon. * Added a parameter for the probability of an agent going on random travel * Removed InteractionModRandom - random travel is now handled in nborhood interactions * For the interaction models, compute the max group using a parallel reduction, and only do it once. * Split nborhood interactions into separate models for work and home. Save the DenseBins for interactions to member of the interaction model. Have an option to reuse without rebuilding. This is disabled at the moment because Redistribute changes the ordering of particles. * Added command line option agent.fast to switch between fast implementation and slow. Currently this only switches between a serial and a GPU binning policy. * Removed unused variable * Fixed issue with double to Real conversion * Remove managed memory from read_workerflow * Fixed overflow when computing number of workgroups for teachers * run assignTeachersAndWorkgroup on the host for now * Added option for GPU policy binning to CensusData binning * Removed some unused code and changed a checking loop to not use managed memory. * Added a timer to the main loop output to track how long each time step takes * Fixes to prevent triggering compiler warnings. * Simplified binary interactions implementations with shared inline function. * Further cleaned up interaction probabilities. * Fixed issue where memory had to be managed * Ensure that the display of number infected currently agrees with the actual number calculated after updating agents. * Removed unused variables * Use ParticleReal to overcome atomic multiply failure in commit check. * Converted nborhood interaction models to use counting with exponents. * Modified fast interactions for nborhoods to work on GPUs * Added a function for getting the community number to reduce code duplication. Added fast interactions for work. * Added fast interactions for home * Implemented alternative fast interactions for neighborhoods, work and home (school is not yet done). These implemenations count the number of infected in each category, and so avoid the n-squared computation. * Added some comments to the fast work interactions to better explain the computation * Implemented fast interactions for schools. * Removed code for slow interactions - that is still available in the interactions-bin-by-workgroup branch. * Removed unnecessary assert. * Changed profile function names to differentiate various interaction models. * Working implementation of urbanpop init agents * Added workgroups to working agents * Only do the urbanpop agent debug output when using managed memory * Set the nborhood groups for all the urbanpop agents * Ensure that families have the same neighborhood * Added names for profiling functions in UrbanPop initialization. Allow loading of case data for UrbanPop. * Added vectors and multifabs needed for initial infections to urbanpop class. * Split infection initialization functions into separate file. Will reuse them for initial infections from urbanpop as well as census data. * Initialize all components for urbanpop agents init. Got initial infections working for UrbanPop data, although not perfectly because of community to mesh mismatch. * Added educators to schools * Removed need for unit mf from case initialization * Include NAICS field in agent data and use it to define workgroups * Removed assert that called a collective but was only called by one rank * Added some comments to better understand the columns corresponding to the counts in the output file. * Subdivide by NAICS for work interactions * For UrbanPop, use population school grades, not nt_dt_grades. Set no school to be 0, instead of -1 * Split IntIdx::school into school_grade and school_id, so that in UrbanPop students can be grouped by grade. Added another attribute, IntIdx::school_closed to represent schools that are closed. The school_id cannot just be set to -1 to indicate closure because the school id needs to be saved for when the school reopens * Separated the school transmission probabilities from the census-specific definition of school types by school id. * Allocate teachers to schools by grade. Use grades from worker data. * Add college interactions for separate transmission * Assign educators to schools * Make childcare grouping based on school id, not neighborhood. Create school transmission groups by grade (no impact on Census) * Setup educators workgroup and nborhood to be determined by school id * School grade 0 defines daycare/childcare, not the school_id. Use the neighborhood + 1 for school id, because 0 is no school. Don't do work interactions for agents at schools. * Fixed bug for work nborhood interactions where age group 0 was using home nborhoods, even if they had been moved to the work nborhoods * Use new NAICS codes from updated UrbanPop data. Draw missing educators from the county level. * Fixed bugs with new more detailed NAICS. Made family and school indexes unique only to geoid, to avoid large arrays in interaction models. * Get global max groups for home interactions to deal with CUDA effectively. Set max_grid_size to 10 for urbanpop. * Set correct pos values for x,y locations for urbanopop * Enabled daytime interactions. * Restructured urbanpop extract script and changed school ids to be unique to each geoid only, to limit max school id * Fixed problems with tiling. Now it will set tiling by default if running on CPUs, and not set it if running on GPUs. This works without requiring TilingIfNotGPU() calls to every MFI iteration. Fixed issue with UrbanPop initialization requiring managed memory - not longer required. More efficient tracking of communities in interaction models - skip empty grid points to reduce count of communities. * Fixed school allocations for census. School id of 0 means no school, and workgroups are not set for teachers because they don't interact at work as well as at school. * Allow workgroup interactions for educators - the workgroup is the school. Ensure UrbanPop work nborhood is the same as nborhood for non-workers so they can still interact during the day. * Fix unused variable * Fixed teacher allocations and some bugs. Added a print out of educator student ratios. * Moved vector allocation for infected counts in interaction models out of loop to reduce overhead of allocation. * Removed obsolete timing. * Merged in changes to terms (latent, incubation) * Cleaner implementation of lng/lat conversions to and from grid, and also use the correct lng/lat when moving to hospital locations * Added NM census data and cases * Added NM UrbanPop data * Fixed NM inputs.nm paths for data files. * Correctly initialize air travel for UrbanPop * Replace integers with AgeGroup enums where possible. * Added an additional age bracket. Restructured hospital treatment and checking for death. * Got the additional 50-64 age bracket working properly. For census data, assume 57% of previous age group 30to64 are under 50. * Remove TilingIfNotGPU calls in loops - tiling is set globally once when not using GPUs. Setting it globally ensures there are no bugs caused by tiling in some loops and not others. * Removed some commented debugging code * Fixed disease parameters to make it so that the age effect can be an explicit option * Removed redefinition of variable * Add print out of age group counts * Cleaned up options. * Cleaned up some entries in the documentation * if -> else if so that an agent doesn't enter more than one if-block * renamed isHospitalized() and flag_hosp, etc for clarity * Moved initial case settings into DiseaseParm structure since they are specific to diseases. * Renamed enum value of 'random' which was triggering a compilation error * Updated outputs: fixed switched Ventilator/ICU label and changed running program stdout details. * making sure latent, incubation, & infection periods are never negative; also ensuring latent period is not greater than the incubation+infection period * simplified the condition for latent period being smaller than incubation+infectious periods * not using std::max since Clang complains! * Removed unnecessary check for infected in hospital model * incubation period should be less than the latent+infectious periods! * Should be incubation period, not latent period. Check if agent is in hospital before assigning hospital. This can happen in multiple diseases. * Fixed error in debug build with Real check * fixed the if condition for when hospitalization starts * Created a function for setting an agent to infected, since that code is used both during updates and when initializing agents to be infected. * Made sure code is robust to having different precisions for ParticleReal and Real. * Added comments explaining every option in inputs.defaults * Formatting and some modified comments * Changed reduced_inf option to asymp_relative_inf - much clearer. Automatically set t_hosp_offset to be 3 more than highest hospitalization days, singe this was not an accessible option on the command line. * Add a stable mode and make it the default. * change default * Removed strains - this functionality is provided by multiple diseases * Changed max_grid_size to max_box_size to make it clearer to those not very familiar with amrex terminology. * Made the school ratio option used for census data into an array of values, one per school type * Fixed new bug in teacher count initialization * Default to using managed memory as that is required for the serial binning, which is required to get consistent results for a given random seed and so is set by default. --------- Co-authored-by: Andrew Myers Co-authored-by: Debojyoti Ghosh UrbanPop-scripts/extract_urbanpop_feather.py data/.gitignore data/CaseData/nm-july4.cases data/CensusData/NM_TX_2010.dat data/UrbanPop/NM_35/urbanpop_nm.csv.gz data/UrbanPop/NM_35/urbanpop_nm.idx docs/source/usage/how_to_run.rst examples/inputs.defaults examples/inputs.nm src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/CMakeLists.txt src/CensusData.H src/CensusData.cpp src/DiseaseParm.H src/DiseaseParm.cpp src/DiseaseStatus.H src/HospitalModel.H src/IO.cpp src/InitializeInfections.H src/InitializeInfections.cpp src/InteractionModAirTravel.H src/InteractionModGeneric.H src/InteractionModHome.H src/InteractionModHomeNborhood.H src/InteractionModSchool.H src/InteractionModWork.H src/InteractionModWorkNborhood.H src/InteractionModel.H src/InteractionModelLibrary.H src/UrbanPopAgentStruct.H src/UrbanPopData.H src/UrbanPopData.cpp src/Utils.H src/Utils.cpp src/main.cpp commit 81241f59895e02d7a1f70163ce99d0788a1df49e Author: Andrew Myers Date: Tue Nov 12 20:37:03 2024 -0800 Make the agent redistribution stable if agent.fast = false. (#89) * Add a stable mode and make it the default. * change default src/Utils.H src/main.cpp commit 12526c7d1fbbd63bf791931dfe3f71023701878e Author: Debojyoti Ghosh Date: Tue Nov 12 09:05:06 2024 -0800 Fix Disease Status (#88) * if -> else if so that an agent doesn't enter more than one if-block * renamed isHospitalized() and flag_hosp, etc for clarity * making sure latent, incubation, & infection periods are never negative; also ensuring latent period is not greater than the incubation+infection period * simplified the condition for latent period being smaller than incubation+infectious periods * not using std::max since Clang complains! * incubation period should be less than the latent+infectious periods! * fixed the if condition for when hospitalization starts src/AgentContainer.cpp src/AgentDefinitions.H src/DiseaseStatus.H src/HospitalModel.H src/InteractionModHome.H src/InteractionModHomeNborhood.H src/InteractionModSchool.H src/InteractionModWork.H src/InteractionModWorkNborhood.H commit 5d83e0a3c351375100bbabad9faaba2f234defc2 Author: Debojyoti Ghosh Date: Fri Nov 1 12:57:22 2024 -0700 read in name of air travel data file only if air travel is being included (#87) src/Utils.cpp commit 5101d6dec518f5500b9fe323b1b44b852ec9ca1f Author: Tan Nguyen Date: Fri Oct 4 01:15:52 2024 -0700 Air travel (#77) * add air travel model * fix compile error * move air travel statistics data to GPU * optimize the performance of the air travel implementation * remove trailing whitespaces * removed tabs * remove more tabs * remove unused variables * remove an unused variable * fix compiler warnings * address another compiler warning * fixed a type conversion error * update the code that computes the probability of travel paths * remove a tab * use the same bin for random and air travel agents * resolve conflict * add missing header * resolve conflict * remove replicated variable * update documentation * fix indentation * correct comments * fix omp bug data/CA_CY23AirTraffic.dat data/CensusData/CA_airports.dat docs/source/usage/how_to_run.rst examples/inputs.ca src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/AirTravelFlow.H src/AirTravelFlow.cpp src/CMakeLists.txt src/CensusData.cpp src/DemographicData.H src/DemographicData.cpp src/IO.cpp src/InteractionModAirTravel.H src/InteractionModHome.H src/InteractionModSchool.H src/InteractionModWork.H src/InteractionModel.H src/Utils.H src/Utils.cpp src/main.cpp commit 673646eedaca4caf28a0295684679d78ad5cc602 Author: arnav-singhal <43693924+arnav-singhal@users.noreply.github.com> Date: Thu Oct 3 15:20:44 2024 -0400 Visualization: more plotting options and handling of missing .shx file (#85) * fix handling of .shx and add command-line option to plot deaths * fix whitespace utilities/plotMovie/generate_frames.py commit 7bf437e8f59ec847181fe07e95d792a517996d99 Author: Andrew Myers Date: Thu Oct 3 09:02:59 2024 -0700 Fully rename parameters and decide hospitalization when symptoms appear (#83) * rename some output quantites * rename incubation -> latent * rename symptomdev -> incubation * also update documentation * decide hospitalization status only when symptoms appear * better formatting docs/source/usage/utilities.rst etc/plot_infected.ipynb src/AgentContainer.cpp src/AgentDefinitions.H src/CensusData.cpp src/DiseaseStatus.H src/HospitalModel.H src/IO.cpp src/InteractionModHome.H src/InteractionModSchool.H src/InteractionModWork.H src/main.cpp commit 795b384ae31a9879346a2acaa729fcba635c1560 Author: Steven Hofmeyr Date: Mon Sep 30 14:47:50 2024 -1000 Removed an assert that called a collective but may not be called by all ranks src/InteractionModHome.H commit 334a416067dd9ef6941eac158441c9f96ef0c2da Author: stevenhofmeyr Date: Fri Sep 27 09:55:25 2024 -1000 Fast interactions (#84) * For the work interaction model, bin by workgroup plus community. This results in large speedups, especially for CPU only code. Also, when doing interactions, iterate through the infectious agents first, which is also faster, since most agents will be susceptible and fewer will be infectious. This requires atomic multiply for the prob_ptr for GPUs. * Updated assert calls to avoid unused variables when not in debug mode. * Changed code to use PTDType for work bins instead of PType, and removed extra AOS attribute from agents * Use particle tile data for all binning * Bin home interactions by nborhood and family cluster * Enable daytime interactions * Restructured nborhood binning - because of community interactions can't bin smaller than a community, but doing infectious then susceptible still helps performance * Cleaned up interaction models * Switched to GPU policy for building bins. Much faster on GPUs * Implemented new binner for school interactions * Trying to fix school interactions - should they be in the same nborhood? Work or home? * Better matching of school interaction model with development branch * Restructured interaction model to use a common templated function for work, home, school and nborhood. Much simpler code now. * Always rebuild the bins - needed since redistribute changes the particle locations * Fixed indentation * Removed some unused variables, and fixed reference to SOA index for non-group in nborhood interactions. * Renamed shadowed variables to avoid PR checks complaints. * Simplified interaction model template by removing the ACT typename. Switched binning policy from GPU to Serial, in order to preserve reproducibility for a given random seed. Commented out the generic interaction model, which is never used. * Moved makeBins from InteractionModel to InteractionModRandom because that is the only place it is used and it will be replaced soon. * Added a parameter for the probability of an agent going on random travel * Removed InteractionModRandom - random travel is now handled in nborhood interactions * For the interaction models, compute the max group using a parallel reduction, and only do it once. * Split nborhood interactions into separate models for work and home. Save the DenseBins for interactions to member of the interaction model. Have an option to reuse without rebuilding. This is disabled at the moment because Redistribute changes the ordering of particles. * Added command line option agent.fast to switch between fast implementation and slow. Currently this only switches between a serial and a GPU binning policy. * Removed unused variable * Fixed issue with double to Real conversion * Remove managed memory from read_workerflow * Fixed overflow when computing number of workgroups for teachers * run assignTeachersAndWorkgroup on the host for now * Added option for GPU policy binning to CensusData binning * Removed some unused code and changed a checking loop to not use managed memory. * Implemented alternative fast interactions for neighborhoods, work and home (school is not yet done). These implemenations count the number of infected in each category, and so avoid the n-squared computation. * Added some comments to the fast work interactions to better explain the computation * Implemented fast interactions for schools. * Removed code for slow interactions - that is still available in the interactions-bin-by-workgroup branch. * Removed unnecessary assert. * Changed profile function names to differentiate various interaction models. * Added the slower binning interactions approach back, since this may be needed for contact tracing. The default is fast interactions, and the choice of implemenation is controlled by a #define. --------- Co-authored-by: Andrew Myers .gitignore CMakeLists.txt src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/CMakeLists.txt src/CensusData.H src/CensusData.cpp src/HospitalModel.H src/InteractionModHome.H src/InteractionModHomeNborhood.H src/InteractionModNborhood.H src/InteractionModRandom.H src/InteractionModSchool.H src/InteractionModWork.H src/InteractionModWorkNborhood.H src/InteractionModel.H src/InteractionModelLibrary.H src/Utils.H src/Utils.cpp src/main.cpp commit 3051145064d07c6d9a849cef89425aefb8be9768 Author: Steven Hofmeyr Date: Wed Sep 18 09:19:56 2024 -0700 Always bin because of calls to redistribute src/InteractionModel.H commit 21365029cd93866116d3115c7cc0ab1917356fa6 Author: stevenhofmeyr Date: Thu Sep 5 07:29:39 2024 -1000 Grouping census initialization data structures and functions (#79) * Removed demo ic_type. * Removed unused function * Made workgroup size and nborhood size into parameters. Call Redistribute() after moving agents (particles). Print current infections and deaths counts when running and showing the current day. Added UrbanPop ic_type and urbanpop_filename parameters. * Moved the Redistribute call to within the agentMove functions. Added workgroup_size parameter to read_workerflow * Moved function definitions from AgentContainer.H to the .cpp file, for all not setter/getter methods. * Prefixed all AgentContainer variables with m_, as per coding standards * Moved all functions and data structures that are specific to the census data ic_type into a separate CensusData class, in a separate file. All of the functions previously in Initialization.H/cpp were specific to census data and have thus been moved into the CensusData class. * Removed geom from CensusData - not needed. src/AgentContainer.H src/AgentContainer.cpp src/CMakeLists.txt src/CensusData.H src/CensusData.cpp src/DemographicData.H src/DemographicData.cpp src/IO.H src/IO.cpp src/Initialization.H src/Initialization.cpp src/Utils.H src/Utils.cpp src/main.cpp commit 0973c4cd04513dd8e18af498a37635884e89d214 Author: stevenhofmeyr Date: Fri Aug 30 19:57:24 2024 -1000 Removed demo ic_type. (#78) * Removed demo ic_type. * Removed unused function * Removed mention of demo ictype from the docs * Added a note in the utilities.rst indicating that Community data fields are specific to the census ic_type. docs/source/usage/how_to_run.rst docs/source/usage/utilities.rst src/AgentContainer.H src/AgentContainer.cpp src/Utils.H src/Utils.cpp src/main.cpp commit f7a963af35cfaa0facb37b7e7db7c34e67b134d8 Author: Andrew Myers Date: Tue Aug 27 18:05:21 2024 -0700 Fix out-of-bounds access for non-local communities in random travel (#76) * Fix out-of-bounds access for non-local communities in random travel * fix unused src/AgentContainer.cpp commit ffd8571b40f59ee91f0bb8191874266b6536ab3c Author: Andrew Myers Date: Tue Aug 27 14:03:25 2024 -0700 Fix bug introduced in PR #73 (#75) src/DiseaseParm.H commit f6546a935146f1a1fb382f91f6d3bbe83c0ecfaf Author: arnav-singhal <43693924+arnav-singhal@users.noreply.github.com> Date: Mon Aug 26 15:08:43 2024 -0400 Add script to generate population-time matrix (#74) * add cross table script * trailing whitespace utilities/travel_model_scripts.py commit 68e4fefef8bc74b7a6b0ec645d4909a825df63b3 Author: Andrew Myers Date: Wed Aug 21 12:58:12 2024 -0700 Parameter name changes for consistency with epi literature. (#73) * update meaning of vac_eff parameter * change immune time to normal rather than flat distribution * rename immunity spread parameters * rename to incubation, latent, and infectious docs/source/usage/how_to_run.rst examples/inputs.ca examples/inputs.ma examples/inputs_random_ca src/AgentContainer.cpp src/DiseaseParm.H src/DiseaseParm.cpp src/DiseaseStatus.H src/HospitalModel.H src/Initialization.cpp src/InteractionModHome.H src/InteractionModNborhood.H src/InteractionModSchool.H src/InteractionModWork.H commit e30298283635ff51f249ad00ab1bc0418320dd9d Author: Andrew Myers Date: Wed Aug 21 10:00:39 2024 -0700 Fix and update random travel (#67) * begin refactor of random travel model * don't go on random travel if withdrawn * add back onto locals * fix a couple of issues * add missing file * fix CI * more CI issues * add random_travel to IO * fix logic for random travel interaction interval * add needed overload for HospitalModel * fix some issues caught by CI * add aborts if someone uses the wrong interface for an interaction module * update comment * replace ParallelForRNG with ParallelFor src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/CMakeLists.txt src/HospitalModel.H src/IO.cpp src/InteractionModGeneric.H src/InteractionModHome.H src/InteractionModNborhood.H src/InteractionModRandom.H src/InteractionModSchool.H src/InteractionModWork.H src/InteractionModel.H src/InteractionModelLibrary.H src/main.cpp commit 5a63d17738592dfe0c679d11f1dc8b5769ca02c7 Author: Debojyoti Ghosh Date: Thu Aug 15 11:53:13 2024 -0700 Implemented unified and consistent hospitalization for multiple diseases (#65) * separating disease status update into its own object * moved the iterating over diseases to AgentContainer * moving the checking-if-hospitalized and checking-if-survived along with their age-group-wise probabilities to DiseaseParm since it is disease specific * fixing a type-mismatch error * making CHR, CIC, CVE, CVF, and number of hospitalization days user inputs with default values for Covid * bugfix: need to use device variable, not host variable, inside parallelfor * defining u50 fraction as a variable * Implemented a unified hospitalization model for multiple diseases * removed unused parameter * fixing some compiler warnings * removed some unnecessary changes * fixed double-counting of deaths/hospitalizations in the disease stats Multifabs * made the hosp/ICU/vent timer offset into a variable and making sure it's always greater than the max number of hospitalization days * consolidated the reading of disease parameters from file * minor * Using a single status array to track deaths and recovery in the hospital; using DiseaseStats enum type values for these statuses * fixed compilation errors related to -Werror,-Wsign-compare * fixed whitespaces * fixed more whitespace docs/source/usage/how_to_run.rst src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/DiseaseParm.H src/DiseaseParm.cpp src/DiseaseStatus.H src/HospitalModel.H src/IO.cpp src/InteractionModGeneric.H src/InteractionModHome.H src/InteractionModNborhood.H src/InteractionModSchool.H src/InteractionModWork.H commit 550b5a95eb0d260a4b2b5656598a539a2c71c56c Author: terasaki1 Date: Tue Aug 13 15:40:14 2024 -0700 fixing school_ptr and interaction in nborhood (#59) * proposed fix for interactions in home and nborhood * proposed fix for interactions in home and nborhood v2 * fix bug adding teachers when running on cpu * merging updated read_workerflow * removing used var * removing unused var * fixing nbordhood interaction --------- Co-authored-by: Gbocho Terasaki Co-authored-by: Gbocho Terasaki src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/Initialization.cpp src/InteractionModNborhood.H commit 2aafadb692ee2e89d033ee6567950ff763c89057 Author: Debojyoti Ghosh Date: Fri Aug 9 16:26:16 2024 -0700 Fixed whitespaces (#72) * fixed whitespaces * fixed more whitespace docs/source/usage/utilities.rst utilities/hdf5_process.py utilities/plotMovie/generate_frames.py commit 1dc1648e24d8658d6782fda99f02498a7494a406 Author: arnav-singhal <43693924+arnav-singhal@users.noreply.github.com> Date: Thu Aug 8 13:19:07 2024 -0400 Add Utilities page to readthedocs (#69) * Create utilities.rst * Update utilities.rst * add page and finish viz * clean up frames script * add hdf5 aggregation script * add info on hdf5_process to docs docs/source/index.rst docs/source/install/dependencies.rst docs/source/usage/utilities.rst utilities/hdf5_process.py utilities/plotMovie/generate_frames.py commit 42e97967a4d044bbe6b04e3ed003b46d00f9bf12 Author: Debojyoti Ghosh Date: Thu Aug 8 09:38:22 2024 -0700 Bash script for solution comparisons (#70) * added bash script to compare two sets of simulation results * fixed compilation errors related to -Werror,-Wsign-compare utilities/tests/chkdiff.sh commit 52c725c6e95d2fc17446347177115b2befd88c30 Author: Debojyoti Ghosh Date: Wed Aug 7 18:07:01 2024 -0700 fixed compilation errors related to -Werror,-Wsign-compare (#71) src/InteractionModGeneric.H src/InteractionModHome.H src/InteractionModNborhood.H src/InteractionModSchool.H src/InteractionModWork.H commit b8e8267f5433aa2f8a142966eb4a2ed7eebbca66 Author: arnav-singhal <43693924+arnav-singhal@users.noreply.github.com> Date: Tue Aug 6 16:41:38 2024 -0400 Add HDF5 documentation to readthedocs (#68) * Add HDF5 to dependencies.rst * Update cmake.rst * Fix markdown docs/source/install/cmake.rst docs/source/install/dependencies.rst commit adfb341cd9f65b87f220a61f8d22b77ab43ea476 Author: Debojyoti Ghosh Date: Wed Jul 24 11:36:51 2024 -0700 Removed unnecessary atomic ops (#66) * removing unnecessary atomic ops * switching to AMREX_ASSERT from AMREX_ALWAYS_ASSERT to skip when optimized src/InteractionModHome.H src/InteractionModNborhood.H src/InteractionModSchool.H src/InteractionModWork.H commit d67ad053ed34c623dc0213b67398ad7a0ba537d7 Author: arnav-singhal <43693924+arnav-singhal@users.noreply.github.com> Date: Fri Jul 19 18:46:06 2024 -0700 Make HDF5 optional (#64) * make hdf5 optional * mention conda env CMakeLists.txt README.md src/IO.cpp commit b1fa4ee7a8538d9d4c08169fe5446db3ef39f625 Author: arnav-singhal <43693924+arnav-singhal@users.noreply.github.com> Date: Thu Jul 18 10:14:58 2024 -0700 Write to (compressed) HDF5 (#58) * add hdf5 support * switch to level 3 compression * try adding hdf5 to CLI? * fix mpi version error * ignore unused parameters when necessary * add more unused params and try to link hdf5 .github/workflows/clang.yml .github/workflows/cuda.yml .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_clang7.sh .github/workflows/dependencies/dependencies_gcc10.sh .github/workflows/dependencies/dependencies_gcc8.sh .github/workflows/dependencies/dependencies_gcc8_nompi.sh .github/workflows/dependencies/dependencies_hip.sh .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/dependencies/dependencies_nvhpc21-11.sh .github/workflows/gcc.yml .github/workflows/hip.yml CMakeLists.txt src/IO.cpp utilities/plotMovie/generate_frames.py commit 713adfdb8bc6f633e1cf4fc2045a1e3b4f773894 Author: terasaki1 Date: Wed Jul 17 14:19:44 2024 -0700 fix bug --add_teachers (#63) * fix bug adding teachers when running on cpu * fix bug add_teachers v2 * removing used var * removing unused var --------- Co-authored-by: Gbocho Terasaki src/AgentContainer.H src/Initialization.H src/Initialization.cpp commit c0313d241c9f38eaf233941ab82e1397953892f2 Author: Debojyoti Ghosh Date: Wed Jul 17 12:02:50 2024 -0700 removing hospitalized agents from interactions (#60) src/AgentDefinitions.H src/InteractionModHome.H src/InteractionModNborhood.H src/InteractionModSchool.H src/InteractionModWork.H commit a2a473d0d94030ac10f2f6e2589b08d3fa5fc976 Author: Debojyoti Ghosh Date: Tue Jul 16 15:18:32 2024 -0700 fixed the indentation in ExaEpi::Initialization::read_workerflow() (#62) src/Initialization.cpp commit a0ebdf0b569030d9a99edd12e7b3f17bb70053e7 Author: Debojyoti Ghosh Date: Tue Jul 16 15:18:05 2024 -0700 fixed an issue with uninitialized member variable (#61) src/AgentContainer.H commit c9792c8fb4445f5f000033245bd51cb8c95a0ebc Author: Tan Nguyen Date: Thu Jul 11 14:15:40 2024 -0700 add input data for MA runs data/CensusData/MA-wf.dat data/CensusData/MA.dat examples/inputs.ma commit 056de1b30ad9bc902a2efa92164b6fb05a0795bc Author: terasaki1 Date: Thu Jul 11 12:26:08 2024 -0700 adding teachers to school interaction (#57) * adding workplace into the model, which will be further divided into workgroup * adding workgroup interaction + workplace interactions * push current code for adding teacher, but havent been able to test since no lassen acces yet, and school gpu is currently down * adding number of teachers required in each unit * working code of adding teachers - explore output.dat now * remover worker_count multifab * fixing pull request error * removing my workplace code, replacing it with original work interaction * resolving some conflicts with AMReX::EXAEPI * removing elements for workplace interaction * addressing Debos comments * addressing Debos comment v2 * fixing student_teacher_ratio * fixing errors for PR checks * Code matches when compared with dev + fixing AgentDefinitions.H typos * fixed typo Co-authored-by: Andrew Myers * documentation for input parameter -- student_teacher_ratios --------- Co-authored-by: Gbocho Terasaki Co-authored-by: Gbocho Terasaki Co-authored-by: Debojyoti Ghosh Co-authored-by: Andrew Myers docs/source/usage/how_to_run.rst src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/DiseaseParm.H src/Initialization.H src/Initialization.cpp commit 41e4f3b953ac5a40d38803ecde4a09239085e832 Author: Keilbart Date: Wed Jul 3 16:40:33 2024 -0700 The BayArea-wf.bin file was not in the correct format. Updated file has correct information. data/CensusData/BayArea-wf.bin commit 81f6b5077cb8f463fa9e5586c67ba7b5bce20b85 Author: Debojyoti Ghosh Date: Tue Jun 18 09:56:39 2024 -0700 Implemented tracking multiple diseases (#47) * adding support for multiple diseases * small change in deciding whether agent is infected but not infectious to be consistent with development branch * updated inputs documentation with the multiple diseases stuff * updated code documentation * removing disease-specific parsing for contact matrix coeffs because those are purely social attributes * fixed whitespace issue * removed more whitespaces * Update HIP install logic * updated documentation to show that only the disease parameters have the option of specifying disease-specific values * fixing a bug that caused asymptomatic agents to withdraw; also implemented an enum for symptom status to make code more readable --------- Co-authored-by: Andrew Myers docs/source/usage/how_to_run.rst src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/CaseData.H src/CaseData.cpp src/IO.H src/IO.cpp src/Initialization.H src/Initialization.cpp src/InteractionModGeneric.H src/InteractionModHome.H src/InteractionModNborhood.H src/InteractionModSchool.H src/InteractionModWork.H src/InteractionModel.H src/Utils.H src/Utils.cpp src/main.cpp commit 0f04da26a840c074a8d97ef7678393cbe3cdcdb9 Author: Andrew Myers Date: Tue Jun 11 14:20:34 2024 -0700 Fix family assignment (#55) src/AgentContainer.cpp commit a0cc1368f17d3d5ee0c2bcfe50a59810f3d7d21c Author: Tan Nguyen Date: Tue Jun 11 11:39:16 2024 -0700 remove whitespace utilities/plotMovie/generate_frames.py commit 30d8a413014becec3f1dc75fac91e30c3a3f55cd Author: arnav-singhal <43693924+arnav-singhal@users.noreply.github.com> Date: Mon Jun 10 10:52:21 2024 -0700 Add frame generation script (#53) utilities/plotMovie/generate_frames.py commit 82e7d841e0ea9f903d5613a6b07b49994891e471 Author: Andrew Myers Date: Wed May 22 14:43:35 2024 -0700 Move mean_immune_time and immune_time_spread to 'disease' rather than 'agent'. (#52) * Move mean_immune_time and immune_time_spread to 'disease' rather than 'agent' * also update docs docs/source/usage/how_to_run.rst src/AgentContainer.H src/AgentContainer.cpp src/DiseaseParm.H commit 2da247f9ce5bbe176f4e3798a0ec74a3c607b9b6 Author: Andrew Myers Date: Mon May 20 17:33:06 2024 -0700 Reset treatment timer for re-infections (#51) src/AgentContainer.cpp commit b470b245a6c70e2ff9ab0b57178de96b1bc11a51 Author: Andrew Myers Date: Fri May 17 23:27:18 2024 -0700 Add immunity waning from user-adjustable distribution. (#50) docs/source/usage/how_to_run.rst src/AgentContainer.H src/AgentContainer.cpp commit 17f79cc0789dc9d9f7ea1f27f52cfed2c604a424 Author: Andrew Myers Date: Thu May 16 11:15:25 2024 -0700 Update California_Counties.ipynb etc/California_Counties.ipynb commit e2c65e292c775bb3e14d8d2f1b57222a5f3c14ac Author: Andrew Myers Date: Thu May 16 11:14:46 2024 -0700 Update write_csv.py etc/write_csv.py commit 3ec2ae6df0925eee1dd4a759d6c7896e85b0ef9b Author: Andrew Myers Date: Thu May 16 11:13:30 2024 -0700 Update write_csv.py etc/write_csv.py commit f65e506b0af75e6315d5d35f9e76ebbe3197d157 Author: Andrew Myers Date: Tue May 14 18:03:23 2024 -0700 Compliance rate for symptomatic withdrawal. (#49) docs/source/usage/how_to_run.rst src/AgentContainer.H src/AgentContainer.cpp commit 592abe3ea5a358ae92d8c3282ca63b132bed614d Author: Debojyoti Ghosh Date: Tue May 14 12:42:21 2024 -0700 fixing a bug that caused asymptomatic agents to withdraw; also implemented an enum for symptom status to make code more readable (#48) src/AgentContainer.cpp src/AgentDefinitions.H commit 24768739f78ee58312a3390dcfe47beb57b07741 Author: Andrew Myers Date: Mon May 13 10:49:53 2024 -0700 Update HIP install logic (#46) .github/workflows/dependencies/dependencies_hip.sh commit 742211924b27cad19a90716db893fac2db45295c Author: Debojyoti Ghosh Date: Mon May 13 10:33:42 2024 -0700 Fixed whitespace (#45) utilities/plotMovie/plotCases.py commit 1c00c135c5f266243028db5fc833239e0c072ff8 Author: Tan Nguyen Date: Wed May 8 23:59:02 2024 -0700 plot movie utilities/plotMovie/createMov.sh utilities/plotMovie/exampleCaseData/casesDay.0.csv utilities/plotMovie/exampleCaseData/casesDay.1.csv utilities/plotMovie/exampleCaseData/casesDay.10.csv utilities/plotMovie/exampleCaseData/casesDay.11.csv utilities/plotMovie/exampleCaseData/casesDay.12.csv utilities/plotMovie/exampleCaseData/casesDay.13.csv utilities/plotMovie/exampleCaseData/casesDay.2.csv utilities/plotMovie/exampleCaseData/casesDay.3.csv utilities/plotMovie/exampleCaseData/casesDay.4.csv utilities/plotMovie/exampleCaseData/casesDay.5.csv utilities/plotMovie/exampleCaseData/casesDay.6.csv utilities/plotMovie/exampleCaseData/casesDay.7.csv utilities/plotMovie/exampleCaseData/casesDay.8.csv utilities/plotMovie/exampleCaseData/casesDay.9.csv utilities/plotMovie/exampleCensusData/tl_2010_06_tract00/tl_2010_06_tract00.dbf utilities/plotMovie/exampleCensusData/tl_2010_06_tract00/tl_2010_06_tract00.prj utilities/plotMovie/exampleCensusData/tl_2010_06_tract00/tl_2010_06_tract00.shp utilities/plotMovie/exampleCensusData/tl_2010_06_tract00/tl_2010_06_tract00.shp.xml utilities/plotMovie/exampleCensusData/tl_2010_06_tract00/tl_2010_06_tract00.shx utilities/plotMovie/plotCases.py commit fa821f7cfcca5ba6f6a908fd23a2ee1a531ace4a Author: Andrew Myers Date: Fri May 3 14:11:59 2024 -0700 Fix incorrect docs about time step docs/source/usage/how_to_run.rst commit 600a903d58d153f4db246093a4892f56f1462dcf Author: Andrew Myers Date: Fri May 3 14:10:39 2024 -0700 Add US-wf.bin data/CensusData/US-wf.bin commit b30006f32e9f2c7c8b4edaabf7fc45ef9412e371 Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Thu May 2 06:51:24 2024 -0700 Read output_filename (#43) * parmparse outputfilename * docs docs/source/usage/how_to_run.rst src/main.cpp commit 553e1079451319d05952d3a4a667009dc02e7a23 Author: Andrew Myers Date: Wed May 1 17:29:54 2024 -0700 only write some of the agent data after step 0 (#44) src/IO.cpp commit 5b7f27e50c03773abc0f13927d5407018ba0ad50 Author: Andrew Myers Date: Wed May 1 14:20:02 2024 -0700 Enable single precision mesh and particles by default (#42) * enable single precision mesh and particles by default * fix some conversions * more fixes * more fixes * more fixes * missing namepsace CMakeLists.txt src/AgentContainer.H src/AgentContainer.cpp src/DiseaseParm.cpp src/InteractionModHome.H src/InteractionModNborhood.H src/InteractionModSchool.H src/InteractionModWork.H src/main.cpp commit 13de11f0ded6b0263b61d165d4558502a80608fe Author: Andrew Myers Date: Wed May 1 11:32:00 2024 -0700 Fix HIP CI for rocm 6.1.0 .github/workflows/hip.yml commit ff1d11a85cee8fbf50cfddd8ab3b677c3a2bb517 Author: Andrew Myers Date: Wed May 1 10:44:21 2024 -0700 workaround for cuda 11.4 src/InteractionModHome.H src/InteractionModNborhood.H src/InteractionModSchool.H src/InteractionModWork.H commit 1fbbe4ca1c19c4f52f496ead660c0345cbe6b069 Author: Andrew Myers Date: Thu Apr 18 17:30:23 2024 -0700 Fix bug introduced in PR 39 src/AgentContainer.cpp commit 9f090e0d73904006314234be948b464613e18feb Author: Debojyoti Ghosh Date: Wed Apr 17 16:38:08 2024 -0700 Refactoring agent interactions (#30) * added doxygen comment for a new function * Separated the monolithic interactAgentHomeWork() into separate interaction classes for various locations (home, work, school, neighborhood by creating interaction location classes * moved getting the agent attribute pointers to the base class since they are used by all the inheriting interaction location classes. * added a common makeBins() function in base InteractionLocation class that is called by all inheriting interaction classes. * defined inline functions querying if agent is infectious, susceptible, not susceptible, etc and using them in all interaction functions * for each interaction type, implemented a binary (one-on-one) interaction kernel between an infectious and a susceptible agent; calling that in the main interaction function * removed/commented a unused vars * removed extraneous header files * initializing local probability to 1 instead of current value of prob_ptr * further splitting off community/nborhood interactions from home and work * removed unused vars * simplified the susceptibility and infectiousness checks * generally renaming "...location..." to "...model..." for interactions * cleaned up a lot of code by using ParticleTileData instead of handling a bunch of attrib pointers src/AgentContainer.H src/AgentContainer.cpp src/AgentDefinitions.H src/CMakeLists.txt src/DiseaseParm.cpp src/InteractionModGeneric.H src/InteractionModHome.H src/InteractionModNborhood.H src/InteractionModSchool.H src/InteractionModWork.H src/InteractionModel.H src/InteractionModelLibrary.H src/main.cpp commit 23bd4ee000a18e4afcf802aaa92413398075143a Author: Andrew Myers Date: Wed Apr 10 20:51:51 2024 -0700 Fix cpu reduction of mesh variables (#41) * fix cpu reduction of mesh variables * fix omp src/Initialization.cpp src/main.cpp commit 9822940cd1b15eea8110945a88b1aafc8d78c0ff Author: Andrew Myers Date: Fri Apr 5 17:19:20 2024 -0700 Add agent variable names to output (#40) * Add agent variable names to output * Update src/IO.cpp src/IO.cpp commit 2d406f550f42b1807a8747a783bb9216646bf278 Author: Andrew Myers Date: Fri Apr 5 16:54:32 2024 -0700 Update plot.py etc/plot.py commit df3f4a547c55c11783458373694fdf9a4650d160 Author: Andrew Myers Date: Fri Apr 5 16:54:13 2024 -0700 Update plot.py etc/plot.py commit 8aacfe45875ad59d17ca32a42107d00bfec57fc7 Author: Andrew Myers Date: Fri Apr 5 15:51:28 2024 -0700 Fix formatting and timing of the output.dat files (#39) src/AgentContainer.cpp src/main.cpp commit 0fd174ce37f45859a8c2b8b3b1785191473ab33f Author: Andrew Myers Date: Wed Apr 3 13:09:29 2024 -0700 Make the shelter compliance rate user-adjustable (#38) docs/source/usage/how_to_run.rst src/AgentContainer.H src/AgentContainer.cpp commit 931222d98ba7a5d4e53c66875769652e38e4f634 Author: Andrew Myers Date: Thu Mar 28 15:17:53 2024 -0700 More outputs for exposed but infectious, etc... (#37) * more outputs * fix problem with resetting hospitalizations and ventilations src/AgentContainer.H src/AgentContainer.cpp src/main.cpp commit a3d5c70150a5c4a4027d0671dec38019e1a5b7e1 Author: Andrew Myers Date: Thu Mar 28 08:04:07 2024 -0700 Implement start and stop for shelter-in-place (#36) * implement start and stop for shelter-in-place * remove unused * document new parameters docs/source/usage/how_to_run.rst src/AgentContainer.H src/AgentContainer.cpp src/Utils.H src/Utils.cpp src/main.cpp commit 9d3e58607813249cfd2bb1242681e15ee1dc3615 Author: Andrew Myers Date: Wed Mar 27 13:16:38 2024 -0700 Have symptomatic agents withdraw (#35) * have symptomatic agents withdraw * make the withdrawal optional src/AgentContainer.H src/AgentContainer.cpp commit 4f9dfcbb9721df119c57dc46a308dfa4a9a589ae Author: Andrew Myers Date: Tue Mar 26 16:13:17 2024 -0700 Initialize with N Random cases (#33) * Initialize with N Random cases * document new parameters docs/source/usage/how_to_run.rst examples/inputs.ca examples/inputs_random_ca src/AgentContainer.H src/Initialization.H src/Initialization.cpp src/Utils.H src/Utils.cpp src/main.cpp commit 46f56dba49fec0c363bcddee469a0c2b9faa8d76 Author: Andrew Myers Date: Tue Mar 26 14:59:31 2024 -0700 fix assertion src/main.cpp commit 0f5304439c75d4a7f7139060b662aad70f3360e0 Author: Andrew Myers Date: Tue Mar 26 11:11:59 2024 -0700 remove EpiCast particle type src/AgentContainer.H commit 85140ff92a8956de3a70f723c2f6cf38534f7d40 Merge: e7144b5 77e2dcd Author: Andrew Myers Date: Tue Mar 26 11:10:32 2024 -0700 Merge branch 'development' of github.com:AMReX-Codes/ExaEpi into development commit 77e2dcde8535817d0f4a1fe40b32ff1d1fee9f8d Author: Andrew Myers Date: Tue Mar 26 11:10:08 2024 -0700 Write summary to file rather than stdout (#32) src/AgentContainer.H src/AgentContainer.cpp src/main.cpp commit e7144b5feeec06b100a2b9be7d13472dcc48e7b4 Merge: dcb1872 61ff132 Author: Andrew Myers Date: Sun Mar 3 14:04:29 2024 -0800 Merge branch 'development' of github.com:AMReX-Codes/ExaEpi into development commit 61ff13221e9234a22e4d8d9710f4058df62392b7 Author: Andrew Myers Date: Sun Mar 3 13:33:48 2024 -0800 Add support for infectious asymptomatic window (#31) docs/source/usage/how_to_run.rst src/AgentContainer.H src/AgentContainer.cpp src/DiseaseParm.H src/Initialization.cpp commit dcb18726f140a838a9dadb0afebd67998d1f50da Merge: 32da967 e58713b Author: Andrew Myers Date: Sun Mar 3 12:22:59 2024 -0800 Merge branch 'development' of github.com:AMReX-Codes/ExaEpi into development commit e58713be5cbc39fc4123f6163c950d93bd36c52e Author: Andrew Myers Date: Thu Feb 22 19:41:43 2024 -0800 Fix double counting and data race in interactAgentsHomeWork() (#29) * make some tweaks to printing * fix important! bug in interaction loop, double-counting probs * update viz notebooks * Fix double counting and data race in main interaction loop etc/California.ipynb etc/California_Counties.ipynb src/AgentContainer.cpp src/main.cpp commit 32da9679a797b07e86c83b65539fb6d737e15091 Merge: c2381e1 2b75c8a Author: Andrew Myers Date: Wed Feb 21 14:32:51 2024 -0800 merging commit c2381e143a5b109f6a751a84bb0da85f74f911d9 Author: Andrew Myers Date: Wed Feb 21 14:31:19 2024 -0800 update viz notebooks etc/California.ipynb etc/California_Counties.ipynb commit 2b75c8ada6b6640751328355196e23d22f6149c4 Author: Debojyoti Ghosh Date: Wed Feb 21 14:00:53 2024 -0800 Bugfix in computing probability of not getting infected (#28) * initializing local probability to 1 instead of current value of prob_ptr * Apply suggestions from code review --------- Co-authored-by: Andrew Myers src/AgentContainer.cpp commit 85fda4dfe1089f9709fdca1f90714d6249817047 Author: Andrew Myers Date: Wed Feb 21 13:07:47 2024 -0800 fix important! bug in interaction loop, double-counting probs src/AgentContainer.cpp commit 3beecec7be732c7f978f5dc22b63e5050029dabf Author: Andrew Myers Date: Wed Feb 21 13:07:25 2024 -0800 make some tweaks to printing src/main.cpp commit 529b29aa6295305df65f63366c195b98f6e4fc66 Author: Debojyoti Ghosh Date: Fri Feb 9 12:08:38 2024 -0800 possible bugfixes to interactAgentHomeWork() (#27) src/AgentContainer.cpp commit af9c32f2155864b0d959d34568c96532bf6db179 Author: Debojyoti Ghosh Date: Fri Feb 9 12:07:56 2024 -0800 plotfile writes out the simulation time (in days), which is same as the step number since one step is one day. (#26) src/IO.H src/IO.cpp src/main.cpp commit 4f4c00f5cfa92c7e7274d3800ba86b99cdb8f448 Author: Andrew Myers Date: Fri Feb 2 12:29:25 2024 -0800 check in small initial cases inputs file data/CaseData/small.cases examples/inputs.small_cases src/AgentContainer.cpp commit 18b01a2d007e702d49ada163abe56ec58ac0cdd9 Author: Andrew Myers Date: Fri Feb 2 11:57:49 2024 -0800 fix the way hospitalizations, etc are tracked src/AgentContainer.cpp commit e9db71a47313c45b1bb4b1766f8b002943313783 Author: Andrew Myers Date: Fri Feb 2 11:28:29 2024 -0800 a few more checks on the agent properties in the main update loop src/AgentContainer.cpp src/Initialization.cpp commit 2a450e751c06bb47cbb01da92461f2f7ae412743 Author: Andrew Myers Date: Fri Feb 2 11:28:06 2024 -0800 adding a routine that prints the disease stats src/DiseaseParm.H src/DiseaseParm.cpp commit 2fe712954a21503e13e58dfb4c71f0929d86e17a Author: Andrew Myers Date: Fri Feb 2 11:27:36 2024 -0800 add some print statements for easy output parsing src/main.cpp commit 43dbcceabbbbf9e8484edda98bb2676968569d26 Author: Andrew Myers Date: Thu Jan 25 13:42:40 2024 -0800 make sure to use atomics in main update loop src/AgentContainer.cpp commit afffd94da834dbbd5b79a839e310e6037315e27f Author: Andrew Myers Date: Fri Jan 19 10:30:32 2024 -0800 use serial bin policy in initialization, too src/Initialization.cpp commit 4a408fede03e6c187834b9096ff1e574c9a7cd2c Author: Hubertus van Dam Date: Fri Jan 19 12:16:37 2024 -0500 Plot time series (#24) * Import from api module to avoid missing boxlib_native key error * Extract total population sizes as a function of time The time series data is stored in a CSV file that can be used for various things. The time series is also visualized so it is easy to check if the data makes sense. * Removing trailing whitespaces. etc/plot.py etc/plot_time_series.py commit b603df062df35340ada3530abd97a3cf875e3b02 Author: Debojyoti Ghosh Date: Thu Jan 18 18:06:13 2024 -0800 moving bin construction to a separate loop to avoid multi-threaded problems (#25) src/AgentContainer.cpp commit f3b0e7cea7d798b2b854436d7630af2f5b8c8b71 Author: Andrew Myers Date: Tue Jan 16 15:06:38 2024 -0800 fix bin policy for OpenMP runs to avoid race condition src/AgentContainer.cpp commit bc9242d5c32626180d1c705383ef365e0aa418ea Author: Andrew Myers Date: Tue Jan 16 11:08:04 2024 -0800 fix HIP CI .github/workflows/dependencies/dependencies_ccache.sh .github/workflows/dependencies/dependencies_hip.sh .github/workflows/hip.yml commit 712627aa9bbca6db4b25d329833f110453a9c4eb Author: Debojyoti Ghosh Date: Wed Jan 10 14:43:24 2024 -0800 Adding Documentation (#13) * added documentation to most classes/structures/functions * clarified "QDG" questions * 1) include code in documentation for easy reference; 2) improved documentation of some functions .gitignore docs/Doxyfile src/AgentContainer.H src/AgentContainer.cpp src/CaseData.H src/CaseData.cpp src/DemographicData.H src/DemographicData.cpp src/DiseaseParm.H src/DiseaseParm.cpp src/IO.H src/IO.cpp src/Initialization.H src/Initialization.cpp src/Utils.H src/Utils.cpp src/main.cpp commit 82547c95b3970bc3cdba00d565300552adba411f Author: atmyers Date: Tue Jan 9 15:04:23 2024 -0800 add lassen environment etc/lassen_environment.sh commit bea4170646ac5d0b8e9af23001a9aa55371d0b2f Merge: 8972e23 83e8a25 Author: atmyers Date: Tue Jan 9 14:18:52 2024 -0800 Merge branch 'development' of github.com:AMReX-Codes/ExaEpi into development commit 8972e23fab54c8ff7e00afbca8fee65085115d16 Author: atmyers Date: Tue Jan 9 14:17:44 2024 -0800 Add omp parallel directives to MFIter loops src/AgentContainer.cpp commit 83e8a257d30d42fd2b6a0d7e1e57bd542c7e650c Author: Andrew Myers Date: Tue Jan 9 13:22:57 2024 -0800 update bay area inputs examples/inputs.bay commit f9dd3edd95be7f65ab647b7bb3db38b48c692c1f Author: atmyers Date: Tue Jan 9 13:19:47 2024 -0800 update bay area inputs examples/inputs.bay commit 97e17fae6651f52132b05d327715a9983265b213 Author: Andrew Myers Date: Tue Jan 9 13:13:05 2024 -0800 check in a pre-made inputs file to run the bay area examples/inputs.bay examples/inputs.ca commit 97da678adc8251889296caab937ad316018b938e Author: Andrew Myers Date: Tue Jan 9 11:57:35 2024 -0800 add in bay area workerflow file data/CensusData/BayArea-wf.bin commit 619e4555d0e266dfb7722a2d523a3c8734cad623 Author: atmyers Date: Tue Jan 9 11:07:52 2024 -0800 set the initial case counts right even if taking 0 steps src/main.cpp commit 69e203408e892b89954829389df6f1d2ec0817dd Author: atmyers Date: Tue Jan 9 11:02:47 2024 -0800 also print the number of ranks src/main.cpp commit 18c70baa88f578dd7738b68fd97b3212fcd8265b Author: atmyers Date: Tue Jan 9 10:54:41 2024 -0800 print out some additional info src/main.cpp commit c10aa5f9ecb18c811d703974cc9d2c5ba9e2a94d Merge: d6e09b7 5d5c6d5 Author: atmyers Date: Tue Jan 9 10:46:09 2024 -0800 Merge branch 'development' of github.com:AMReX-Codes/ExaEpi into development commit d6e09b78dd0a32276f610a67124bb3c2b89a2090 Author: atmyers Date: Tue Jan 9 10:45:57 2024 -0800 make agent.size and agent.max_grid_size optional parameters. Remove them from the inputs. docs/source/usage/how_to_run.rst examples/inputs src/Utils.cpp commit 5d5c6d54a566fe2ebe5f5e71d1610ff7a5b9e039 Author: Andrew Myers Date: Tue Jan 9 10:02:06 2024 -0800 fix wrong command in documentation docs/source/install/cmake.rst commit 2a5bfcc5c1021868eda46d610fb3b600991ffe8e Author: Andrew Myers Date: Tue Dec 19 15:31:16 2023 -0800 don't hard-code domain size in plot.py etc/plot.py commit e33f6188b7c3c3e202e81364d24b0490354d2b57 Author: Andrew Myers Date: Mon Dec 11 18:23:45 2023 -0800 fix formatting src/Initialization.cpp commit 2fee1b054a6da86773e82711e2c2fd15b27e04ea Author: atmyers Date: Mon Dec 11 18:10:22 2023 -0800 fix DAYTIME src/AgentContainer.cpp src/main.cpp commit b9dfb2bacbd9875ebcbdce28917c16b68ee4e8c1 Author: Tan Nguyen Date: Mon Dec 11 11:35:17 2023 -0800 skip agents in the incubation period (#11) src/AgentContainer.cpp commit aafce3a6ced85e4af323462c4eb9a48d43d3e98c Author: Tan Nguyen Date: Mon Dec 4 11:10:54 2023 -0800 distribute cases to all units sharing a FIPS (#10) src/Initialization.cpp commit bac1fba9097b42961f2d2f11054a54598c211248 Author: Andrew Myers Date: Sat Dec 2 15:12:33 2023 -0800 expose the length of the incubation, infectious, and symptomatic stages docs/source/usage/how_to_run.rst src/AgentContainer.H src/AgentContainer.cpp src/DiseaseParm.H commit f14695e0aa49e133a7ed5562f31716397bcbee0d Author: Andrew Myers Date: Wed Nov 22 14:36:51 2023 -0800 fix warnings src/AgentContainer.cpp commit 8fcb201232e59b76ab5a5de793679caf8d985bc4 Author: Andrew Myers Date: Wed Nov 22 14:20:17 2023 -0800 add stats for date of peak / peak infections src/AgentContainer.H src/AgentContainer.cpp src/DiseaseParm.cpp src/main.cpp commit 87624770ad7ded426b0bdd53cad0e5e787b5787d Merge: 4130fb5 c81e09c Author: Andrew Myers Date: Wed Nov 22 13:15:50 2023 -0800 Merge branch 'development' of github.com:AMReX-Codes/ExaEpi into development commit 4130fb513e53d81794a8df4f978cef2e3556ba13 Author: Andrew Myers Date: Wed Nov 22 13:15:31 2023 -0800 remove unused docs/source/usage/how_to_run.rst commit 95a2eec6142230d58606b7c524418348c444bdd7 Author: Andrew Myers Date: Wed Nov 22 13:14:18 2023 -0800 document seed parameter docs/source/usage/how_to_run.rst commit 2da392ec6e1b7c5a31c6eb0c30ba7557dca6d686 Author: Andrew Myers Date: Wed Nov 22 13:10:21 2023 -0800 add ability to reset random seed in inputs file src/Utils.cpp commit c81e09c0015037554ff58bcbe52dd1ea15877189 Author: atmyers Date: Tue Nov 21 13:35:26 2023 -0800 update viz tools with latest stuff data/CA_2020_Census_Tracts/tl_2020_06_tract.dbf data/CA_2020_Census_Tracts/tl_2020_06_tract.prj data/CA_2020_Census_Tracts/tl_2020_06_tract.shp data/CA_2020_Counties/CA_Counties_TIGER2016.dbf data/CA_2020_Counties/CA_Counties_TIGER2016.prj data/CA_2020_Counties/CA_Counties_TIGER2016.shp etc/California.ipynb etc/California_Counties.ipynb etc/plot.py commit 6837f96f689d1723770b1c9fc763d242c90c4b26 Author: Andrew Myers Date: Tue Nov 21 13:24:09 2023 -0800 have write_csv take command-line argument etc/write_csv.py commit 8c34a843b29ce14fe6fcdbdab3de16c05b4a0127 Author: Andrew Myers Date: Tue Nov 21 12:56:28 2023 -0800 fix more warnings for CI src/AgentContainer.cpp commit 5ffc8bfbfa0e944c528943c8c83fc75714aef43c Author: Andrew Myers Date: Tue Nov 21 12:13:54 2023 -0800 fix more warnings for CI src/AgentContainer.cpp commit ef2486b899421ffd6e61c18e58fb8e7d2f2d7e7d Author: Andrew Myers Date: Tue Nov 21 12:08:03 2023 -0800 fix warnings src/AgentContainer.cpp commit 1360e99cb3a04b30f80b7965c24f5cb6248d2ca8 Author: Andrew Myers Date: Tue Nov 21 12:00:26 2023 -0800 always write plot file at end of sim src/main.cpp commit 47a8984e84ceb05f1ea84bb07d3e9170769f8e2f Author: Andrew Myers Date: Tue Nov 21 11:49:52 2023 -0800 do not remove dead agents for now (need to recompute bins after doing this) src/AgentContainer.H src/AgentContainer.cpp src/Initialization.cpp src/main.cpp commit 95978a3053e72afcd670f5f1362fcc7a61f417cb Merge: 3e4a35d 305948c Author: Andrew Myers Date: Sat Nov 4 23:01:31 2023 -0700 Merge branch 'development' of github.com:AMReX-Codes/ExaEpi into development commit 3e4a35d82acceaa3d82c4105ccf50e3f522c8803 Author: Andrew Myers Date: Sat Nov 4 23:01:02 2023 -0700 fix counter early exit src/AgentContainer.cpp commit 305948c16d8a811f114b8c429c1a2a3deb84c210 Author: atmyers Date: Fri Nov 3 23:09:48 2023 -0500 fix narrowing src/DiseaseParm.H commit 98d6a2f09a8bb35ed18a0f917470b2b536b2e40d Author: Andrew Myers Date: Tue Oct 31 14:42:49 2023 -0700 store and re-use home/work bins src/AgentContainer.H src/AgentContainer.cpp commit 3429edcec49c2af55654eeaa1b4bb21a8f39d0de Author: Andrew Myers Date: Tue Oct 31 12:13:06 2023 -0700 finish filling out transmission func src/AgentContainer.cpp commit 94d9080b99fcdd3666e489224e4b58ac3c15bf4d Author: Andrew Myers Date: Tue Oct 31 11:31:16 2023 -0700 more work on transmission func src/AgentContainer.cpp commit dc24ae516e0c4d107a4647eed90df36f62a92b80 Author: atmyers Date: Mon Oct 30 17:06:40 2023 -0700 more work on filling out transmission function src/AgentContainer.cpp src/DiseaseParm.H src/DiseaseParm.cpp commit 55c749af26bb2f0d7a6b890a255b8277f02e00ef Author: Andrew Myers Date: Tue Oct 17 10:23:44 2023 -0700 no need to use atomic for family id src/AgentContainer.cpp commit e55803b530b9e5c3c22f452666d42236104d6dfa Author: Andrew Myers Date: Tue Oct 17 08:59:12 2023 -0700 comment unused for now src/AgentContainer.cpp commit ce67df5f1b69d6f1113c3a7924746eb05850a7f5 Author: Andrew Myers Date: Tue Oct 17 08:55:32 2023 -0700 fix whitespace for CI utilities/hardware_usage/nvidiaGPU/profile_analyze.py utilities/hardware_usage/nvidiaGPU/utils.py utilities/mps/exaEPI_mps.sh commit d51b31b4b736fc6f50a35fceb96740ddf2a00243 Author: Andrew Myers Date: Tue Oct 17 08:48:23 2023 -0700 document vaccine efficacy docs/source/usage/how_to_run.rst commit 14100fa83f532242785f27e8d9e885612cbbca3f Merge: 91e98fd 9989c9a Author: Andrew Myers Date: Tue Oct 17 08:46:18 2023 -0700 Merge branch 'development' of github.com:AMReX-Codes/ExaEpi into development commit 91e98fde61ae585e3eed3925fc23183066960086 Author: Andrew Myers Date: Tue Oct 17 08:45:00 2023 -0700 set family id, requires additional prefix sum src/AgentContainer.H src/AgentContainer.cpp commit 48c20588ce76b98f33a2b0e28170663191cd4503 Author: Andrew Myers Date: Tue Oct 17 08:44:44 2023 -0700 ParmParse vaccine efficacy src/DiseaseParm.H commit 1b6cc4bc16c28d54fbf213b827f63ff90efc2974 Author: Andrew Myers Date: Tue Oct 17 08:44:14 2023 -0700 format change src/Utils.cpp commit 9989c9a6119d3b2f781efcd28e63a33f1ebbe314 Author: Tan Nguyen Date: Tue Oct 17 01:18:58 2023 -0700 perf analysis scripts utilities/hardware_usage/AMDCPU/genRoofline.sh utilities/hardware_usage/nvidiaGPU/profile_analyze.py utilities/hardware_usage/nvidiaGPU/utils.py utilities/mps/exaEPI_mps.sh commit 435036d945f11aa3efa855fec3fa784f3d70cf95 Author: atmyers Date: Fri Oct 6 16:39:35 2023 -0700 fix yml .readthedocs.yml commit 6b2ec650e313484510311026f1f8cf22b8335492 Author: atmyers Date: Fri Oct 6 16:37:28 2023 -0700 add .readthedocs.yml .readthedocs.yml commit 4c1f0fbf95549b1270d35bb52a8c777226953aa7 Author: atmyers Date: Fri Oct 6 16:09:59 2023 -0700 add documentation for inputs parameters docs/source/usage/how_to_run.rst commit 78d958302610c643fb8313e390cd178b589fc20f Author: atmyers Date: Fri Oct 6 15:36:37 2023 -0700 rename inputs.census -> inputs README.md examples/inputs commit 6de27815c99c0d745aa3bc9c09198d0ff81e3427 Author: atmyers Date: Fri Oct 6 15:35:21 2023 -0700 remove inputs.demo examples/inputs.demo commit c13b041613fcf3442a2720ea5e5d98eb7aa1e3c4 Author: Andrew Myers Date: Fri Oct 6 14:10:17 2023 -0700 updating the number of steps in census inputs examples/inputs.census commit 918fa42d004b7249c02ceda8f85b7bca72b027dd Author: Andrew Myers Date: Sat Sep 30 12:36:27 2023 -0700 add NPI multifab src/AgentContainer.H src/AgentContainer.cpp src/main.cpp commit 6d7eb686e655adbfbfc7029793878a7c2f9012ea Author: Andrew Myers Date: Sat Sep 30 12:13:44 2023 -0700 multifabs for deaths, remove dead agents src/AgentContainer.H src/AgentContainer.cpp src/main.cpp commit be7ad75d154b5b6531afb2cdf0635cd4c9bc042d Author: Andrew Myers Date: Sat Sep 30 11:40:30 2023 -0700 remove diagnostic print src/main.cpp commit 10bce142e74eb241563f0933db361d95510ce8a8 Author: Andrew Myers Date: Thu Sep 28 14:42:22 2023 -0700 refactor the main interaction loop so that it threads better when the number of people per cell varies a lot src/AgentContainer.cpp src/main.cpp commit 25be726d43c1d779d09109161d71ae0cd0601431 Author: Andrew Myers Date: Mon Sep 25 17:06:19 2023 -0700 code for tracking hospitalizations, ICUs, ventilations, and deaths src/AgentContainer.H src/AgentContainer.cpp src/Initialization.cpp commit 96ff86701793a6dbd1e5fb9681d570fb90e6dd14 Author: Andrew Myers Date: Mon Sep 25 14:34:32 2023 -0700 remove old case initialization logic src/AgentContainer.cpp src/Initialization.cpp commit b7c192a4016ddda8f561db8b0f0abe7a975e9267 Author: Andrew Myers Date: Wed Sep 20 13:42:06 2023 -0700 move the DenseBins:build out of the inner loop so it will be called fewer times src/CaseData.cpp src/Initialization.cpp src/main.cpp commit 300d0dabb669667c71449121765f7cd206e5accb Author: Andrew Myers Date: Tue Aug 1 14:29:36 2023 -0700 override managed memory default from amrex src/main.cpp commit 4e949372a05c61b422a72c0354645710b90b2f53 Author: Andrew Myers Date: Tue Aug 1 14:03:57 2023 -0700 make the setting the disease parameters and contact matrix at runtime optional examples/inputs.demo src/AgentContainer.H commit 14485cb050461bd83ef66e6d8b31857575ae6568 Author: Andrew Myers Date: Tue Aug 1 13:34:43 2023 -0700 Only read worker flow information if we are initializing from casefile src/main.cpp commit d77ef1409fd0c1defbc116aba67b2c28b4947e8c Author: Andrew Myers Date: Mon Jul 31 14:28:28 2023 -0700 update inputs.demo examples/inputs.demo commit d0af244486dc3b240dd7e091aeb84fdb4a250fbd Author: atmyers Date: Wed Jul 12 16:13:52 2023 -0700 fix more warnings src/Initialization.cpp commit 43b2ec0d6b4e9c89d550014d988f1ff148473b6a Author: atmyers Date: Wed Jul 12 13:17:26 2023 -0700 no Print() in GPU kernel src/Initialization.cpp commit 339b5a1f501c63a1acc5129087ee2342432bbb97 Author: atmyers Date: Wed Jul 12 11:06:53 2023 -0700 another unused src/Initialization.cpp commit 3bc4523ff4787d79152c64f63161a62bc23d0465 Author: atmyers Date: Wed Jul 12 10:42:41 2023 -0700 fix more warnings src/Initialization.cpp commit a389528e6c014342292ef0fedccfa66aea5491ab Author: atmyers Date: Wed Jul 12 10:19:15 2023 -0700 fix shadowing src/CaseData.cpp commit b6d18474b1e9cb0be5fd02000c75113d9efa35f4 Author: atmyers Date: Wed Jul 12 10:11:57 2023 -0700 some works towards initfromcasefile src/AgentContainer.cpp src/CaseData.H src/CaseData.cpp src/Initialization.cpp src/main.cpp commit c4109652d4fb365d026034b2a74f322e79159b92 Author: atmyers Date: Wed Jul 12 10:10:34 2023 -0700 fix path fto shape files etc/BayArea.ipynb commit d0579ae6444812c95897595aba66999598b2abf3 Author: atmyers Date: Wed Jul 12 10:07:24 2023 -0700 dat file for bay area census data data/CensusData/BayArea.dat commit a1ce315280d3ef40f5fb257b806fa168cee502c1 Author: atmyers Date: Wed Jul 12 10:06:42 2023 -0700 Python notebook for Bay Area visualization etc/BayArea.csv etc/BayArea.ipynb commit 0f2be6d28d5ea603e1c50fbf2c0105a0a4cdea5a Author: atmyers Date: Wed Jul 12 10:06:19 2023 -0700 shapefiles for Bay Area visualization data/San_Francisco_Bay_Region_2020_Census_Tracts/San_Francisco_Bay_Region_2020_Census_Tracts.xml data/San_Francisco_Bay_Region_2020_Census_Tracts/region_2020_censustract.cpg data/San_Francisco_Bay_Region_2020_Census_Tracts/region_2020_censustract.dbf data/San_Francisco_Bay_Region_2020_Census_Tracts/region_2020_censustract.prj data/San_Francisco_Bay_Region_2020_Census_Tracts/region_2020_censustract.shp data/San_Francisco_Bay_Region_2020_Census_Tracts/region_2020_censustract.shx commit 0457fd456ed73e03b86d754ae0acb55c14f80584 Author: Andrew Myers Date: Tue May 16 14:29:57 2023 -0700 ignore set but unused src/CaseData.cpp commit c4fd6216b1fd8d75cc433f73eba9a94cf8bbb059 Author: Andrew Myers Date: Tue May 16 13:32:58 2023 -0700 Fix some cuda errors in Initialization.cpp src/Initialization.cpp commit 766198010927fb6123db7a2e20d4e631f700187c Author: Andrew Myers Date: Tue May 16 12:50:58 2023 -0700 fix uninitialized src/AgentContainer.cpp src/IO.cpp commit c77175985573cc85582064a3cb276c680ae1ae85 Author: Andrew Myers Date: Tue May 16 10:25:49 2023 -0700 fix more warnings src/Initialization.cpp commit 0032734c5ba3607662701bc780084357ee600eb2 Author: Andrew Myers Date: Tue May 16 10:04:31 2023 -0700 fix more unused src/IO.cpp commit 45c2286a4f0be9bf78feed3cfc59ecf4c10f20b4 Author: Andrew Myers Date: Tue May 16 09:47:57 2023 -0700 fix signed / unsigned src/CaseData.cpp commit 7e30ffea4f545d2154a03d2fc06aab4d92a912d1 Author: Andrew Myers Date: Mon May 15 14:03:05 2023 -0700 comment out unused for now src/AgentContainer.cpp commit 36a3573a01f5d8609eeff0c5e570099990a6e962 Author: Andrew Myers Date: Mon May 15 12:40:05 2023 -0700 Fix CI src/AgentContainer.cpp commit 94a996692a0ab3d4335a70344d045b3fddebb187 Author: Andrew Myers Date: Mon May 15 12:15:37 2023 -0700 Fix CI src/AgentContainer.cpp src/DiseaseParm.H commit 0b3b05ffecaa3e8b1598d9d791a5dcc3345f8d99 Merge: e8322f0 0475872 Author: atmyers Date: Fri Apr 21 12:21:05 2023 -0700 fixing conflicts commit e8322f0ad38137ecf3e5dcad10d58986bcaa36c7 Author: atmyers Date: Fri Apr 21 12:14:16 2023 -0700 ParmParse aggregated diag stuff examples/inputs.census src/IO.H src/IO.cpp src/Utils.H src/Utils.cpp src/main.cpp commit 9d7a63da4bdf7d4c1173147acacc061cdf016657 Author: atmyers Date: Fri Apr 21 12:01:14 2023 -0700 add missing files src/DiseaseParm.H src/DiseaseParm.cpp commit edeb855fdbb79c439b35b9351db762ff9f00ee4b Author: atmyers Date: Fri Apr 21 12:00:39 2023 -0700 ParmParse additional parameters examples/inputs.census src/AgentContainer.H src/AgentContainer.cpp src/CMakeLists.txt src/Initialization.H src/Initialization.cpp commit a0f9e1ecf204d0bef4f5ae52bc5e5ca382b8eac5 Author: atmyers Date: Fri Apr 21 09:44:15 2023 -0700 remove inputs examples/inputs commit a6bf0062780d6e6bb4caf987f52c52c379faa985 Author: atmyers Date: Fri Apr 21 09:44:03 2023 -0700 also update demo inputs examples/inputs.demo commit 9935f770633a7a6f52c20aff470460c96c1f3c6e Author: atmyers Date: Fri Apr 21 09:40:50 2023 -0700 Parsing plot_int and random_travel_int examples/inputs.census src/Utils.H src/Utils.cpp src/main.cpp commit b92f58242e71a01c51c8aad0d6fc048ecbcb94d7 Author: atmyers Date: Thu Apr 20 16:56:31 2023 -0700 initial case data data/CaseData/July4.cases examples/inputs.census src/CMakeLists.txt src/CaseData.H src/CaseData.cpp src/Utils.H src/Utils.cpp src/main.cpp commit bb6faf31cf1ff73b2a88901864b0c02a6e953926 Author: atmyers Date: Thu Apr 20 13:30:48 2023 -0700 code for aggregating data by FIPS code src/AgentContainer.H src/AgentContainer.cpp src/DemographicData.H src/DemographicData.cpp src/IO.H src/IO.cpp src/main.cpp commit c096001f7218e3267ff36e55d3a57f43b7961d4b Author: atmyers Date: Thu Apr 20 13:28:34 2023 -0700 add workerflow file to inputs.census, use CA examples/inputs.census commit 4c6eec06df7446cfbe665e99629b04acd4281872 Author: atmyers Date: Wed Apr 19 16:20:58 2023 -0700 refactoring src/CMakeLists.txt src/Initialization.H src/Initialization.cpp src/main.cpp commit c5e857d415a87925c2d093682b8424adb66316dd Author: atmyers Date: Wed Apr 19 15:59:44 2023 -0700 workgroups and work nborhoods src/AgentContainer.H src/AgentContainer.cpp src/main.cpp commit fe289aa1d6bbe0c45e511f1ee91441362b5fb0e8 Author: atmyers Date: Mon Apr 17 14:45:32 2023 -0700 nborhoods and schools src/AgentContainer.H src/AgentContainer.cpp commit dff141506431e2d545599ed3492cb01fd327890d Author: atmyers Date: Fri Mar 24 13:46:40 2023 -0700 add routines for community transmittion src/AgentContainer.H src/AgentContainer.cpp src/main.cpp commit 0bcdd763126a97696c9e7537e0b7cc0abc7bb38a Author: atmyers Date: Tue Mar 14 13:41:45 2023 -0700 finish workerflow initialization src/main.cpp commit 4b41eae21ff5f608fe07f1f8d950ee1ea519a5e4 Author: Andrew Myers Date: Tue Mar 14 08:24:58 2023 -0700 ParmParse workerflow filename src/Utils.H src/Utils.cpp src/main.cpp commit f608f437aed7833ea624078a216d4baa98dc3d76 Author: atmyers Date: Tue Mar 14 06:22:13 2023 -0700 initialize worker flow matrix src/main.cpp commit 600e4d028538b8c78d1b062958bb4dc8d642a978 Author: atmyers Date: Tue Mar 14 06:21:41 2023 -0700 functions for implementing 12-hour work / home travel loop src/AgentContainer.H src/AgentContainer.cpp commit 9312978b9aa48c27b336fb63c011a657be6a1561 Author: Andrew Myers Date: Tue Jan 24 15:30:16 2023 -0800 missing ; src/IO.H src/Utils.H commit 68d3baf48b66500194e2d975ce3f85dfc52638b1 Author: Andrew Myers Date: Tue Jan 24 15:27:10 2023 -0800 missing files src/Utils.H src/Utils.cpp commit bc77f803a09a632257d472e5e88770b937186229 Author: Andrew Myers Date: Tue Jan 24 15:23:11 2023 -0800 move utility routines into their own files src/CMakeLists.txt src/main.cpp commit 92b630de1254341930cd6a6c55d2c6eee857d5a0 Author: Andrew Myers Date: Tue Jan 24 15:06:16 2023 -0800 put IO routines in their own file src/CMakeLists.txt src/IO.H src/IO.cpp src/main.cpp commit be4e22f4569e7c0814e0cff4cd8e5678c3131c94 Author: Andrew Myers Date: Mon Jan 23 11:51:33 2023 -0800 add -Wno-unused-command-line-argument to HIP CI .github/workflows/hip.yml commit 417a1c1930b9c2d1f9f81b6b464a87466e7906a2 Author: Andrew Myers Date: Mon Jan 23 11:25:10 2023 -0800 remove unused src/main.cpp commit d32bfae77b982cfb238b0302011ba0c5d6b050db Author: Andrew Myers Date: Mon Jan 23 11:18:54 2023 -0800 Add Python script for writing tract-level data in csv format etc/write_csv.py commit 9fbb7599fa7145d2069c533f1b0a82508fc91416 Author: Andrew Myers Date: Mon Jan 23 11:16:37 2023 -0800 add FIPS and tract information to plotfiles src/AgentContainer.H src/AgentContainer.cpp src/main.cpp commit 5d4a6275e1b7dcc351583683c0eb5ca2f7fe6863 Author: Andrew Myers Date: Fri Jan 13 12:03:31 2023 -0800 update inputs.census examples/inputs.census commit 1307f80a42fb52c6fa0117fc418a2f86edae2bd0 Author: Andrew Myers Date: Fri Jan 13 12:03:05 2023 -0800 specify name of census file as input param src/main.cpp commit caf169933ed59a3ca421b96d18551a17981413f1 Author: Andrew Myers Date: Fri Jan 13 12:02:32 2023 -0800 add US-level census data ascii file data/CensusData/US.dat commit 33d9fab275bbdc7aa9e9309b7c8e4d39d6a3daab Author: Andrew Myers Date: Tue Dec 20 08:35:15 2022 -0500 Add ability to track two different strains (#8) src/AgentContainer.H src/AgentContainer.cpp src/DemographicData.H src/main.cpp commit ee6d5d82c70156d37b35f40e75b472b26bba2351 Author: Andrew Myers Date: Mon Dec 19 14:53:21 2022 -0500 Realistic initial conditions from census data (#7) data/CensusData/CA-wf.bin data/CensusData/CA.dat examples/inputs examples/inputs.census examples/inputs.demo src/AgentContainer.H src/AgentContainer.cpp src/CMakeLists.txt src/DemographicData.H src/DemographicData.cpp src/main.cpp commit 04758725c4615f42e04be988789c7bf41bbc8f58 Author: Andrew Myers Date: Tue Nov 29 10:12:26 2022 -0500 Update README.md README.md commit d3c1708469d6ec61ab3b0935b1e4fe5d1a89eb85 Author: Andrew Myers Date: Fri Nov 11 10:22:02 2022 -0800 Check in the start of some sphinx documentation (#6) docs/Doxyfile docs/Makefile docs/README.md docs/doxygen/main.dox docs/requirements.txt docs/source/conf.py docs/source/index.rst docs/source/install/cmake.rst docs/source/install/dependencies.rst docs/source/usage/how_to_run.rst docs/spack.yaml pyproject.toml requirements.txt commit 9c78dc60775794d8b25d4db2d97655e4a67a2b18 Author: atmyers Date: Thu Nov 10 15:53:02 2022 -0800 typo fix in README.md README.md commit e62fb7dbb076a359cfbb5abe9e8a273cd9b8bb3e Author: Andrew Myers Date: Thu Nov 10 15:51:53 2022 -0800 Add HIP CI (#5) .github/workflows/dependencies/dependencies_hip.sh .github/workflows/hip.yml commit 73f76fa9aa94e521d7d6cec3ecc0ea983f39f4d2 Author: atmyers Date: Thu Nov 10 15:38:16 2022 -0800 Add HIP CI .github/workflows/dependencies/dependencies_hip.sh .github/workflows/hip.yml commit 531039006da391632e4976ac8cbae4bcabb7565a Author: Andrew Myers Date: Thu Nov 10 14:33:15 2022 -0800 Add CI for gcc (#4) .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_gcc10.sh .github/workflows/dependencies/dependencies_gcc8.sh .github/workflows/gcc.yml commit b52b9abd6b46e709d9b218500cf68990ad84fee1 Author: atmyers Date: Thu Nov 10 14:00:30 2022 -0800 add missing dependencies files .github/workflows/dependencies/dependencies.sh commit 4c7ad29fd47a376482adefa758bf88941078295d Author: atmyers Date: Thu Nov 10 13:59:24 2022 -0800 Add GCC CI tests .github/workflows/dependencies/dependencies_gcc10.sh .github/workflows/dependencies/dependencies_gcc8.sh .github/workflows/gcc.yml commit 7928b54562378874ba929ceb0be89c44950eb4fc Author: Andrew Myers Date: Thu Nov 10 13:51:11 2022 -0800 Turn on clang CI (and fix some issues uncovered by same) (#3) .github/workflows/clang.yml .github/workflows/dependencies/dependencies_clang7.sh src/AgentContainer.cpp commit b020230b866ee76a09434edf17daec734e8e484b Author: atmyers Date: Thu Nov 10 13:46:34 2022 -0800 turn off MPI for clang builds .github/workflows/clang.yml commit 6073dc8a467ab91c4f0a1df315f8d0f87044f9fa Author: atmyers Date: Thu Nov 10 13:42:44 2022 -0800 fix a number of warnings / bugs caught by the clang CI src/AgentContainer.cpp commit 87c862cce3581a93a6f4e8f49778eaaaab08ff51 Author: atmyers Date: Thu Nov 10 13:30:38 2022 -0800 Add workflow for clang .github/workflows/clang.yml .github/workflows/dependencies/dependencies_clang7.sh commit fb0e7926cde4e3162932889056f5bc89cc71cf94 Author: Andrew Myers Date: Thu Nov 10 13:23:08 2022 -0800 Add CI check for CUDA compilation (#2) .github/workflows/cuda.yml .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/dependencies/dependencies_nvhpc21-11.sh commit 94f3a8e8b24cc1a1605dcd0893caa06b35c270b5 Author: atmyers Date: Thu Nov 10 13:02:27 2022 -0800 remove cuda 10 check, not supported anymore since amrex requires c++17 now .github/workflows/cuda.yml .github/workflows/dependencies/dependencies_nvcc10.sh commit cf14781edb23f2e5276dfb782078170efa42a9bd Author: atmyers Date: Thu Nov 10 12:57:01 2022 -0800 specify c++14 for cuda 10 .github/workflows/cuda.yml commit da317efc7efce90b8ac6b40217016a0ea3497775 Author: atmyers Date: Thu Nov 10 12:44:40 2022 -0800 forgot dependencies .github/workflows/dependencies/dependencies_nvcc10.sh .github/workflows/dependencies/dependencies_nvcc11.sh .github/workflows/dependencies/dependencies_nvhpc21-11.sh commit b589b89278dd2dc6461d4aba26d66973b758a4f8 Author: atmyers Date: Thu Nov 10 12:41:32 2022 -0800 add workflow for CUDA compilation .github/workflows/cuda.yml commit 91883e8f3a8cb35fe7684cdd35820cf0fe95459a Merge: f6413a5 481802b Author: Andrew Myers Date: Thu Nov 10 12:14:30 2022 -0800 Merge pull request #1 from AMReX-Codes/development Add style check workflow commit 481802b3ab0e14ca4110d193a27aedf66c67865f Author: atmyers Date: Thu Nov 10 12:10:33 2022 -0800 remove trailing whitespace, as suggested by the style check src/AgentContainer.H src/AgentContainer.cpp src/main.cpp commit 276cb8e518480c438664b68e22c5ff0b4801a452 Author: atmyers Date: Thu Nov 10 12:04:17 2022 -0800 add workflow for style checks .github/workflows/style.yml .github/workflows/style/check_tabs.sh .github/workflows/style/check_trailing_whitespaces.sh commit f6413a5eed655b214652625101e8d9de9a1cffd5 Author: Andrew Myers Date: Tue Nov 8 15:41:34 2022 -0800 add perlmutter job submission script examples/perlmutter_script.sh commit 00ca1a5fcf0ae8666992d3decc29338806966bb9 Author: Andrew Myers Date: Tue Nov 8 15:41:18 2022 -0800 update perlmutter environment etc/perlmutter_environment.sh commit f2182e96bc459a822c8437e7799a4afebb094de5 Author: Andrew Myers Date: Tue Nov 8 15:41:00 2022 -0800 tweak default inputs to run a bit longer examples/inputs commit 02dcb1309f1c6ac10119e1eb8b4a015b378dfae9 Author: Andrew Myers Date: Thu Nov 3 09:53:11 2022 -0700 add LICENSE.txt LICENSE.txt commit e4b9695e31df1eceb7155ff5db34e6ba8260837e Author: Andrew Myers Date: Wed Jun 8 21:11:27 2022 -0700 Update AgentContainer.cpp src/AgentContainer.cpp commit 2d5656206ea4251b3b8695c40ef13f664c21c442 Author: Andrew Myers Date: Wed May 18 13:29:29 2022 -0700 Update inputs examples/inputs commit 6f02bfb3c10fdfa877bcc0b46fc76c016e987806 Author: Andrew Myers Date: Tue May 17 15:00:31 2022 -0700 make the init routines work with MPI parallelism. src/AgentContainer.cpp src/main.cpp commit 7a04ea1eb85ff69b2e23ad68c9675817dd5625ed Author: Andrew Myers Date: Mon May 16 14:59:06 2022 -0700 add reduction to printTotals src/AgentContainer.cpp commit f6196b9fac003b5f570b4e13fcd8da11b3c64184 Author: Andrew Myers Date: Mon May 16 14:34:48 2022 -0700 use enum for status flag src/AgentContainer.H src/AgentContainer.cpp commit 79182d0d90754a029cec580aff9f8d3795060735 Author: atmyers Date: Wed May 11 16:58:42 2022 -0700 add a couple analysis notebooks etc/plot_infected.ipynb etc/plot_initial_distribution.ipynb commit 8eedf2a17e2c166d10cbbf976436000c76846c5e Merge: bbe6fcf 5a42577 Author: Andrew Myers Date: Wed May 11 16:53:53 2022 -0700 Merge branch 'realistic_ics' into main commit 5a42577075706a7a14bb0e14eef48e11bc98266b Author: Andrew Myers Date: Wed May 11 16:53:24 2022 -0700 adjust prob again src/AgentContainer.cpp commit e39a948f5d98002e29b419cdc6241d54a8c9425d Author: Andrew Myers Date: Wed May 11 16:52:45 2022 -0700 add functions for printing num of each type; adjust probabilities src/AgentContainer.H src/AgentContainer.cpp src/main.cpp commit bbe6fcf60e15713e8dd6419b9c6ba3c0273f4547 Merge: cc161ca df3008b Author: Andrew Myers Date: Mon May 9 20:23:29 2022 -0700 Merge pull request #1 from atmyers/realistic_ics Set up a more realistic model commit df3008b9ab14930e050da0163b68c84024a66023 Author: Andrew Myers Date: Mon May 9 20:21:01 2022 -0700 update README.md README.md commit 2f70e0b432a29cc2e705c5a7ac833c4aafb1daa5 Author: Andrew Myers Date: Mon May 9 20:19:32 2022 -0700 check in new plotting script etc/Visualization.ipynb etc/plot.py commit e4edad1d5e2ce1166b1178d99fb1d87784356fe2 Author: Andrew Myers Date: Mon May 9 20:19:09 2022 -0700 set initial timer for infected people src/AgentContainer.cpp src/main.cpp commit 1992ee99965f7fd3480ca1bada07005aec4518ea Author: Andrew Myers Date: Mon May 9 19:32:03 2022 -0700 add in border thing src/AgentContainer.cpp commit 8d699a58d8165a36aa0980f6042eb3c4c3f6d7d3 Author: Andrew Myers Date: Mon May 9 18:05:23 2022 -0700 write out infected, etc... per cell to plotfiles src/AgentContainer.H src/AgentContainer.cpp src/main.cpp commit 9dbd70db35f242d8ba0e37a94c0c937cca9a1076 Author: Andrew Myers Date: Mon May 9 17:44:42 2022 -0700 implement statuses examples/inputs src/AgentContainer.H src/AgentContainer.cpp src/main.cpp commit 2e6303f5a42af98f99033657684fe475a3001307 Author: Andrew Myers Date: Mon May 9 16:51:06 2022 -0700 add TINY_PROFILE by default CMakeLists.txt commit 957015a9034d01247bb936e9a39f706c257e63ce Author: Andrew Myers Date: Mon May 9 16:50:38 2022 -0700 implement new infection model src/AgentContainer.cpp commit ab490979ef1fb53638f60d397ff8ea0708b1fb80 Author: Andrew Myers Date: Mon May 9 16:27:13 2022 -0700 add particle count to plotfile src/main.cpp commit 56de6231ed939c4f1ccae70742b05a7b00b1bac0 Author: Andrew Myers Date: Mon May 9 16:12:20 2022 -0700 initialization tweaks src/AgentContainer.H src/AgentContainer.cpp src/main.cpp commit 121ace09aa3ceea62faa4013916c855ecb31590e Author: Andrew Myers Date: Mon May 9 15:51:53 2022 -0700 tweak fill routine etc/perlmutter_environment.sh src/AgentContainer.cpp src/main.cpp commit 711a424c7fb4b32a9ac75fb3305ff266bef349af Author: Andrew Myers Date: Mon May 9 14:52:48 2022 -0700 rename perlmutter module script etc/perlmutter_environment.sh commit 0e1bd7d0f3569bf1ddf52b4444913ff81304ec63 Author: Andrew Myers Date: Mon May 9 14:52:17 2022 -0700 build instructions for perlmutter README.md commit 16b6ffe7d8993b8147d25e93be93fe334620f447 Author: Andrew Myers Date: Mon May 9 14:49:34 2022 -0700 add commands to configure perlmutter environment etc/agent_environment.sh commit 10cc91a16fb76d5c673cb1030aff293772b4bfc8 Author: Andrew Myers Date: Mon May 9 14:31:05 2022 -0700 Don't need to call the SetupCUDA cmake function CMakeLists.txt commit 8d0d5eb8a006a4e462f75b91e6f2846ea2e8d075 Author: Andrew Myers Date: Mon May 9 14:23:39 2022 -0700 realistic initial condition code src/AgentContainer.cpp commit c25dd6347e492735d6cd19da41d0c28ad42b129b Author: Andrew Myers Date: Mon May 9 14:23:24 2022 -0700 use simplified particle type for now src/AgentContainer.H commit b204c280038590754791492967916a4b0bfd7369 Author: Andrew Myers Date: Mon May 9 14:22:58 2022 -0700 tweak inputs file examples/inputs commit 1d07251977e63326c7a6273b562cffdfaf9e9083 Author: Andrew Myers Date: Mon May 9 14:22:22 2022 -0700 tweak problem size src/main.cpp commit cc161ca8682b68a09572e59cd49e2e66ad9dfc41 Author: Andrew Myers Date: Thu Apr 28 12:56:08 2022 -0700 remove tmp file cmake/SetupAgent.cmake~ commit 8e11979dc7bba13e694c72288ca3d19238b2bde4 Author: Andrew Myers Date: Thu Apr 28 12:41:13 2022 -0700 remove tmp file src/CMakeLists.txt~ commit 3774e3621bbac1761d7fe8b88554da6834014395 Author: Andrew Myers Date: Thu Apr 28 12:40:57 2022 -0700 initial commit CMakeLists.txt README.md cmake/SetupAgent.cmake cmake/SetupAgent.cmake~ etc/Visualization.ipynb examples/inputs src/AgentContainer.H src/AgentContainer.cpp src/CMakeLists.txt src/CMakeLists.txt~ src/main.cpp