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Implement ISM chemistry including metals and dust (#1642)
This PR will build on the existing primordial ISM chemistry network to include a minimal network with metals and dust. Also added are the tests that go with this PR, where the network is integrated at 7 different metallicities and the test solutions are compared against reference solutions.
1 parent 295e70b commit 3cfd7e2

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lines changed

‎.github/workflows/burn_cell_metal_chem.yml

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Original file line numberDiff line numberDiff line change
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name: burn_cell_metal_chem
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on: [pull_request]
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jobs:
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burn_cell_metal_chem:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Get AMReX
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run: |
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mkdir external
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cd external
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git clone https://github.com/AMReX-Codes/amrex.git
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cd amrex
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git checkout development
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echo 'AMREX_HOME=$(GITHUB_WORKSPACE)/external/amrex' >> $GITHUB_ENV
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echo $AMREX_HOME
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if [[ -n "${AMREX_HOME}" ]]; then exit 1; fi
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cd ../..
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- name: Install dependencies
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run: |
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sudo apt-get update -y -qq
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sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
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- name: Compile
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run: |
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cd unit_test/burn_cell_metal_chem
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make -j 2
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- name: Run and compare outputs for different Z values
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run: |
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set -e
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cd unit_test/burn_cell_metal_chem
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declare -A line_numbers_map=(
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["Z=1"]="4461 4463 4465 4467 4468 4471 4472 4475 4481 4486"
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["Z=1_z10"]="1613 1615 4456 4458 4460 4463 4470 4476 4481"
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["Z=1e-1"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463"
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["Z=1e-2"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463"
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["Z=1e-3"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463"
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["Z=1e-4"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463"
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["Z=1e-5"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463"
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["Z=1e-6"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463"
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)
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declare -A ref_map=(
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["Z=1"]="reference_solution_1.out"
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["Z=1_z10"]="reference_solution_1_z10.out"
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["Z=1e-1"]="reference_solution_1e-1.out"
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["Z=1e-2"]="reference_solution_1e-2.out"
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["Z=1e-3"]="reference_solution_1e-3.out"
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["Z=1e-4"]="reference_solution_1e-4.out"
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["Z=1e-5"]="reference_solution_1e-5.out"
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["Z=1e-6"]="reference_solution_1e-6.out"
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)
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ref_line_number_z10=(1 2 3 5 7 10 17 23 28)
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# Original input file
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original_input_file="inputs_metal_chem_1"
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modified_input_file="inputs_metal_chem_modified"
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for Z in "Z=1" "Z=1_z10" "Z=1e-1" "Z=1e-2" "Z=1e-3" "Z=1e-4" "Z=1e-5" "Z=1e-6"; do
70+
cp $original_input_file $modified_input_file
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Z_val=${Z//Z=/}
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if [[ "$Z" == "Z=1_z10" ]]; then
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# Modify the redshift line for Z=1_z10
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sed -i 's/network.redshift = 0.0/network.redshift = 10.0/g' $modified_input_file
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else
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# Replace the metallicity and dust2gas_ratio values for other Z values
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sed -i 's/network.metallicity = .*/network.metallicity = '"$Z_val"'/g' $modified_input_file
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sed -i 's/network.dust2gas_ratio = .*/network.dust2gas_ratio = '"$Z_val"'/g' $modified_input_file
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fi
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output_file="test_${Z_val}.out"
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./main1d.gnu.DEBUG.ex $modified_input_file amrex.fpe_trap_{invalid,zero,overflow}=1 > $output_file
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line_numbers="${line_numbers_map[$Z]}"
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ref_file="${ref_map[$Z]}"
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error_found=false
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index=0
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for line_number in $line_numbers; do
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value1=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH); else print 0}' $output_file)
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# Adjust the line number for the reference file
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if [[ "$Z" == "Z=1" ]]; then
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reference_line_number=$((line_number - 4460))
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elif [[ "$Z" == "Z=1_z10" ]]; then
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reference_line_number=${ref_line_number_z10[$index]}
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else
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reference_line_number=$((line_number - 4437))
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fi
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value2=$(awk 'NR=='"$reference_line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' $ref_file)
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difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }')
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if (( $(echo "$difference > 0.01" | bc -l) )); then
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echo "Z: $Z"
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echo "Line number: $line_number"
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echo "Value in $output_file: $value1"
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echo "Value in $ref_file: $value2"
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echo "Difference between test and reference value is $difference, more than allowed threshold of 0.01"
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echo
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error_found=true
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fi
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index=$((index + 1))
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done
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if [[ $error_found == true ]]; then
119+
exit 1
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fi
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done
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- name: Print backtrace if any failure
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if: ${{ failure() && hashFiles('unit_test/burn_cell_metal_chem/Backtrace.0') != '' }}
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run: cat unit_test/burn_cell_metal_chem/Backtrace.0
126+

‎.github/workflows/macos_build_cell_metal_chem.yml

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name: macos_burn_cell_metal_chem
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on: [pull_request]
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jobs:
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burn_cell:
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runs-on: macos-13
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Install dependencies
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run: |
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brew install cmake openmpi python3 || true
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brew link --overwrite [email protected]
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- name: Compile and run
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run: |
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mkdir build && cd build
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cmake .. -DBUILD_UNIT_TEST_MC=true -DBUILD_AMReX=true
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make -j2
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ctest --output-on-failure

‎.github/workflows/macos_build_cell_primordial_chem.yml

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@@ -17,6 +17,6 @@ jobs:
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- name: Compile and run
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run: |
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mkdir build && cd build
20-
cmake .. -DBUILD_UNIT_TEST=true -DBUILD_AMReX=true
20+
cmake .. -DBUILD_UNIT_TEST_PC=true -DBUILD_AMReX=true
2121
make -j2
2222
ctest --output-on-failure

‎CMakeLists.txt

+73-13
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.20)
22

33
project(Microphysics
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VERSION 1.0.0
5-
DESCRIPTION "building primordial_chemistry network in Microphysics with CMake"
5+
DESCRIPTION "building primordial_chemistry or metal_chemistry networks in Microphysics with CMake"
66
LANGUAGES CXX C)
77

88
#----------------------------------------------------------------------------------------------------------------------
@@ -23,11 +23,11 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
2323
set(integrationparamfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/_parameters")
2424
set(unittestparamfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/unit_test/_parameters")
2525

26-
set(networkpropfile "${output_dir}/network_properties.H")
2726

2827
if (${network_name} STREQUAL "gamma_law")
2928
set(EOSparamfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS/gamma_law/_parameters")
3029

30+
set(networkpropfile "${output_dir}/network_properties.H")
3131
set(networkfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/gammalaw.net")
3232
set(networkdir "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/")
3333
set(networkheadertemplatefile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/network_header.template")
@@ -44,6 +44,7 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
4444
set(gamma_law_sources ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces/eos_data.cpp
4545
${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces/network_initialization.cpp
4646
${output_dir}/extern_parameters.cpp PARENT_SCOPE)
47+
execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/write_network.py" --header_template "${networkheadertemplatefile}" --header_output "${networkpropfile}" -s "${networkfile}" WORKING_DIRECTORY ${output_dir}/)
4748

4849
elseif (${network_name} STREQUAL "primordial_chem")
4950
#need these to write extern_parameters.H
@@ -52,6 +53,7 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
5253
set(networkpcparamfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/primordial_chem/_parameters")
5354

5455
#similarly, we want network_properties.H
56+
set(networkpropfile "${output_dir}/network_properties.H")
5557
set(networkfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/primordial_chem/pynucastro.net")
5658
set(networkdir "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/primordial_chem/")
5759
set(networkheadertemplatefile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/network_header.template")
@@ -71,7 +73,7 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
7173
#so, if any of the _parameter files are changed, one needs to re-run 'cmake'
7274
#to generate updated header files
7375

74-
if(BUILD_UNIT_TEST)
76+
if(BUILD_UNIT_TEST_PC)
7577
execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${paramfile} ${EOSparamfile}
7678
${networkpcparamfile} ${networkparamfile} ${VODEparamfile} ${integrationparamfile} ${unittestparamfile}" --use_namespace WORKING_DIRECTORY ${output_dir}/)
7779
else()
@@ -88,13 +90,61 @@ function(setup_target_for_microphysics_compilation network_name output_dir)
8890

8991
#below for NAUX
9092
execute_process(COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${PYTHONPATH}:${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null" python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/get_naux.py" --net "${networkdir}" --microphysics_path "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/" WORKING_DIRECTORY ${output_dir}/)
93+
execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/write_network.py" --header_template "${networkheadertemplatefile}" --header_output "${networkpropfile}" -s "${networkfile}" WORKING_DIRECTORY ${output_dir}/)
94+
95+
elseif (${network_name} STREQUAL "metal_chem")
96+
#need these to write extern_parameters.H
97+
set(paramfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/unit_test/burn_cell_metal_chem/_parameters")
98+
set(EOSparamfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS/metal_chem/_parameters")
99+
set(networkmcparamfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/metal_chem/_parameters")
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101+
#similarly, we want network_properties.H
102+
set(networkpropfile "${output_dir}/network_properties.H")
103+
set(networkfile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/metal_chem/pynucastro.net")
104+
set(networkdir "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/metal_chem/")
105+
set(networkheadertemplatefile "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/network_header.template")
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107+
#DO NOT change the order of the directories below!
108+
set (metal_chem_dirs ${CMAKE_BINARY_DIR} ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/gcem/include
109+
${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/VODE ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration/utils
110+
${CMAKE_CURRENT_FUNCTION_LIST_DIR}/integration ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces
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${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS/metal_chem
112+
${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/metal_chem ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks
113+
${CMAKE_CURRENT_FUNCTION_LIST_DIR}/constants
114+
PARENT_SCOPE)
115+
116+
#we need to have extern_parameters.cpp be available at configure time
117+
#the script write_probin.py writes this .cpp file so we call it here
118+
#note, execute_process only works on 'cmake' and not 'make'
119+
#so, if any of the _parameter files are changed, one needs to re-run 'cmake'
120+
#to generate updated header files
121+
122+
if(BUILD_UNIT_TEST_MC)
123+
execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${paramfile} ${EOSparamfile}
124+
${networkmcparamfile} ${networkparamfile} ${VODEparamfile} ${integrationparamfile} ${unittestparamfile}" --use_namespace WORKING_DIRECTORY ${output_dir}/)
125+
else()
126+
#do not need paramfile and unittestparamfile
127+
execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/util/build_scripts/write_probin.py" --pa "${EOSparamfile} ${networkmcparamfile}
128+
${networkparamfile} ${VODEparamfile} ${integrationparamfile} " --use_namespace WORKING_DIRECTORY ${output_dir}/)
129+
endif()
130+
131+
#unlike primordial chem, we also include actual_network_data.cpp here because it is in there that we read in the Semenov opacity table
132+
set(metal_chem_sources ${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces/eos_data.cpp
133+
${CMAKE_CURRENT_FUNCTION_LIST_DIR}/interfaces/network_initialization.cpp
134+
${CMAKE_CURRENT_FUNCTION_LIST_DIR}/EOS/metal_chem/actual_eos_data.cpp
135+
${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/metal_chem/actual_network_data.cpp
136+
${output_dir}/extern_parameters.cpp PARENT_SCOPE)
137+
138+
139+
#below for NAUX
140+
execute_process(COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${PYTHONPATH}:${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null" python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/get_naux.py" --net "${networkdir}" --microphysics_path "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/" WORKING_DIRECTORY ${output_dir}/)
141+
execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/write_network.py" --header_template "${networkheadertemplatefile}" --header_output "${networkpropfile}" -s "${networkfile}" WORKING_DIRECTORY ${output_dir}/)
91142

92143
else()
93-
message(FATAL_ERROR "Given network_name " ${network_name} " currently not supported. Use either 'gamma_law' or 'primordial_chem' ")
144+
message(FATAL_ERROR "Given network_name " ${network_name} " currently not supported. Use either 'gamma_law' or 'primordial_chem' or 'metal_chem' ")
94145

95146
endif()
96147

97-
execute_process(COMMAND python3 "${CMAKE_CURRENT_FUNCTION_LIST_DIR}/networks/general_null/write_network.py" --header_template "${networkheadertemplatefile}" --header_output "${networkpropfile}" -s "${networkfile}" WORKING_DIRECTORY ${output_dir}/)
98148

99149
endfunction()
100150

@@ -126,8 +176,9 @@ endif()
126176

127177
#set a cache variable that controls whether
128178
#we want to build the unit test or not
129-
set(BUILD_UNIT_TEST false CACHE BOOL "Do you want to build the unit test? (true/false)")
130-
message("Building unit test -- ${BUILD_UNIT_TEST}")
179+
set(BUILD_UNIT_TEST_PC false CACHE BOOL "Do you want to build the primordial chem unit test? (true/false)")
180+
181+
set(BUILD_UNIT_TEST_MC false CACHE BOOL "Do you want to build the metal chem unit test? (true/false)")
131182

132183
add_compile_options(-Werror -Wall -Wextra)
133184

@@ -140,19 +191,28 @@ add_compile_options(-Werror -Wall -Wextra)
140191
#this will generate a warning but it will build successfully
141192
#do not need unit_test paramfiles when unit_test is not built
142193

143-
if(BUILD_UNIT_TEST)
144-
setup_target_for_microphysics_compilation("primordial_chem" ${CMAKE_BINARY_DIR})
194+
if(BUILD_UNIT_TEST_PC AND BUILD_UNIT_TEST_MC)
195+
message(FATAL_ERROR "Cannot build both primordial chem and metal chem tests at the same time!")
196+
endif()
145197

198+
if(BUILD_UNIT_TEST_PC)
199+
#Build primordial chem unit test
200+
setup_target_for_microphysics_compilation("primordial_chem" ${CMAKE_BINARY_DIR})
146201
include_directories(${primordial_chem_dirs})
147202

148-
#adding unit_test as subdirectories
203+
#adding unit_tests as subdirectories
149204
add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/unit_test)
150-
message("Building primordial chem unit test")
151205

152-
else()
206+
elseif(BUILD_UNIT_TEST_MC)
207+
#Build metal chem unit test
208+
setup_target_for_microphysics_compilation("metal_chem" ${CMAKE_BINARY_DIR})
209+
include_directories(${metal_chem_dirs})
210+
211+
#adding unit_tests as subdirectories
212+
add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/unit_test)
153213

154214
message("Not building primordial chem unit test")
155215
endif()
156216

157-
217+
#Sample command: cmake .. -DBUILD_UNIT_TEST_MC=True -DBUILD_AMReX=True -DAMReX_SPACEDIM=1
158218

‎EOS/metal_chem/Make.package

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@@ -0,0 +1,3 @@
1+
CEXE_headers += actual_eos.H
2+
CEXE_headers += actual_eos_data.H
3+
CEXE_sources += actual_eos_data.cpp

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