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This PR will add a PopIII simulation to quokka. It will only test that the simulation starts successfully and runs for a few timesteps - it's not meant to be a _production_ simulation. --------- Co-authored-by: Piyush Sharda <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Piyush Sharda <[email protected]> Co-authored-by: Piyush Sharda <[email protected]> Co-authored-by: Ben Wibking <[email protected]> Co-authored-by: Piyush Sharda <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| if (AMReX_SPACEDIM EQUAL 3) | ||
| # Define a custom target that runs the Python script to produce the input perturbations file | ||
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| set(microphysics_network_name "primordial_chem") #this will override network_name to primordial_chem for this directory only | ||
| setup_target_for_microphysics_compilation(${microphysics_network_name} "${CMAKE_CURRENT_BINARY_DIR}/") | ||
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| #use the BEFORE keyword so that these files get priority in compilation for targets in this directory | ||
| #this is critical to ensure the correct Microphysics files are linked to primordial chem target | ||
| include_directories(BEFORE ${primordial_chem_dirs} "${CMAKE_CURRENT_BINARY_DIR}/" "includes/extern_parameters.H" "includes/network_properties.H") | ||
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| add_executable(popiii popiii.cpp ../TurbDataReader.cpp ../main.cpp "${openPMDSources}" ../GrackleDataReader.cpp ../CloudyCooling.cpp ../Chemistry.cpp ${primordial_chem_sources}) | ||
| target_compile_definitions(popiii PUBLIC PRIMORDIAL_CHEM) #this will add #define PRIMORDIAL_CHEM | ||
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| if(AMReX_GPU_BACKEND MATCHES "CUDA") | ||
| setup_target_for_cuda_compilation(popiii) | ||
| endif() | ||
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| #need h5py to run perturbations.py file below | ||
| #purpose of this code is to check whether the h5py python package is installed | ||
| execute_process( | ||
| COMMAND Python3::Interpreter -c "h5py" | ||
| RESULT_VARIABLE EXIT_CODE | ||
| OUTPUT_QUIET | ||
| ) | ||
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| #re-run cmake if this file is changed | ||
| set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS ${CMAKE_SOURCE_DIR}/tests/PopIII.in) | ||
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| # Read the 'PopIII.in' file line by line | ||
| file(READ ${CMAKE_SOURCE_DIR}/tests/PopIII.in pop_in_contents) | ||
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| # Split the file contents into lines | ||
| string(REPLACE "\n" ";" pop_in_lines "${pop_in_contents}") | ||
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| # Iterate through the lines and look for lines starting with 'amr.n_cell' | ||
| foreach(line IN LISTS pop_in_lines) | ||
| if (line MATCHES "^amr\\.n_cell.*") | ||
| set(match_line "${line}") | ||
| break() | ||
| endif() | ||
| endforeach() | ||
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| if (match_line) | ||
| message(STATUS "picked line is ${match_line}") | ||
| # Use a regular expression to find consecutive digit | ||
| string(REGEX MATCHALL "[0-9]+" digits_list "${match_line}") | ||
| # Iterate through the matched digits and extract the first one | ||
| list(GET digits_list 0 first_digits) | ||
| # Check if matched digits were found | ||
| if (first_digits) | ||
| #first_digits give the box size, but you also want box size / 2 as kmax in the script below | ||
| math(EXPR int_first_digits "${first_digits}") | ||
| # Check if the conversion was successful | ||
| if (int_first_digits) | ||
| # Divide the integer by two | ||
| math(EXPR result "${int_first_digits} / 2") | ||
| else() | ||
| message(FATAL_ERROR "Conversion to integer failed, so cannot find kmax!") | ||
| endif() | ||
| message(STATUS "Will create initial perturbations of box size ${first_digits} and kmax ${result}") | ||
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| else() | ||
| message(FATAL_ERROR "No box size found to create initial perturbations for!") | ||
| endif() | ||
| else() | ||
| message(FATAL_ERROR "No matching line found in ${CMAKE_SOURCE_DIR}/tests/PopIII.in!") | ||
| endif() | ||
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| add_test(NAME ComputePerturbations COMMAND python3 ${CMAKE_SOURCE_DIR}/src/perturbation.py --kmin=2 --kmax=${result} --size=${first_digits} --alpha=1.8 --f_solenoidal=0.66667 WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/tests) | ||
| add_test(NAME PopIII COMMAND popiii PopIII.in WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/tests) | ||
| set_tests_properties(ComputePerturbations PROPERTIES FIXTURES_SETUP PopIII_fixture) | ||
| set_tests_properties(PopIII PROPERTIES FIXTURES_REQUIRED PopIII_fixture) | ||
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| # AMR test only works on Setonix because Gadi and avatar do not have enough memory per GPU | ||
| # add_test(NAME PopIIIAMR COMMAND popiii popiii_AMR.in WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/tests) | ||
| endif() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| - | ||
| action: "add_pipelines" | ||
| pipelines: | ||
| pl1: | ||
| f2: | ||
| type: "slice" | ||
| params: | ||
| point: | ||
| x: 0. | ||
| y: 0. | ||
| z: 0. | ||
| normal: | ||
| x: 0.0 | ||
| y: 0.0 | ||
| z: 1.0 | ||
| - | ||
| action: "add_scenes" | ||
| scenes: | ||
| s1: | ||
| plots: | ||
| p1: | ||
| type: "pseudocolor" | ||
| field: "log_density" | ||
| pipeline: "pl1" | ||
| renders: | ||
| r1: | ||
| image_prefix: "dens%05d" | ||
| annotations: "true" | ||
| camera: | ||
| zoom: 1.5 |
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