Implement ISM chemistry including metals and dust #30
Workflow file for this run
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| name: burn_cell_metal_chem | |
| on: [pull_request] | |
| jobs: | |
| burn_cell_metal_chem: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get AMReX | |
| run: | | |
| mkdir external | |
| cd external | |
| git clone https://github.com/AMReX-Codes/amrex.git | |
| cd amrex | |
| git checkout development | |
| echo 'AMREX_HOME=$(GITHUB_WORKSPACE)/external/amrex' >> $GITHUB_ENV | |
| echo $AMREX_HOME | |
| if [[ -n "${AMREX_HOME}" ]]; then exit 1; fi | |
| cd ../.. | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update -y -qq | |
| sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0 | |
| - name: Compile | |
| run: | | |
| cd unit_test/burn_cell_metal_chem | |
| make -j 2 | |
| - name: Run and compare outputs for different Z values | |
| run: | | |
| set -e | |
| cd unit_test/burn_cell_metal_chem | |
| declare -A line_numbers_map=( | |
| ["Z=1"]="4461 4463 4465 4467 4468 4471 4472 4475 4481 4486" | |
| ["Z=1_z10"]="1613 1615 4456 4458 4460 4463 4470 4476 4481" | |
| ["Z=1e-1"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463" | |
| ["Z=1e-2"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463" | |
| ["Z=1e-3"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463" | |
| ["Z=1e-4"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463" | |
| ["Z=1e-5"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463" | |
| ["Z=1e-6"]="4438 4440 4442 4444 4445 4448 4449 4452 4458 4463" | |
| ) | |
| declare -A ref_map=( | |
| ["Z=1"]="reference_solution_1.out" | |
| ["Z=1_z10"]="reference_solution_1_z10.out" | |
| ["Z=1e-1"]="reference_solution_1e-1.out" | |
| ["Z=1e-2"]="reference_solution_1e-2.out" | |
| ["Z=1e-3"]="reference_solution_1e-3.out" | |
| ["Z=1e-4"]="reference_solution_1e-4.out" | |
| ["Z=1e-5"]="reference_solution_1e-5.out" | |
| ["Z=1e-6"]="reference_solution_1e-6.out" | |
| ) | |
| ref_line_number_z10=(1 2 3 5 7 10 17 23 28) | |
| # Original input file | |
| original_input_file="inputs_metal_chem_1" | |
| modified_input_file="inputs_metal_chem_modified" | |
| 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 | |
| cp $original_input_file $modified_input_file | |
| Z_val=${Z//Z=/} | |
| if [[ "$Z" == "Z=1_z10" ]]; then | |
| # Modify the redshift line for Z=1_z10 | |
| sed -i 's/network.redshift = 0.0/network.redshift = 10.0/g' $modified_input_file | |
| else | |
| # Replace the metallicity and dust2gas_ratio values for other Z values | |
| sed -i 's/network.metallicity = .*/network.metallicity = '"$Z_val"'/g' $modified_input_file | |
| sed -i 's/network.dust2gas_ratio = .*/network.dust2gas_ratio = '"$Z_val"'/g' $modified_input_file | |
| fi | |
| output_file="test_${Z_val}.out" | |
| ./main1d.gnu.DEBUG.ex $modified_input_file amrex.fpe_trap_{invalid,zero,overflow}=1 > $output_file | |
| line_numbers="${line_numbers_map[$Z]}" | |
| ref_file="${ref_map[$Z]}" | |
| error_found=false | |
| index=0 | |
| for line_number in $line_numbers; do | |
| value1=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH); else print 0}' $output_file) | |
| # Adjust the line number for the reference file | |
| if [[ "$Z" == "Z=1" ]]; then | |
| reference_line_number=$((line_number - 4460)) | |
| elif [[ "$Z" == "Z=1_z10" ]]; then | |
| reference_line_number=${ref_line_number_z10[$index]} | |
| else | |
| reference_line_number=$((line_number - 4437)) | |
| fi | |
| value2=$(awk 'NR=='"$reference_line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' $ref_file) | |
| difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }') | |
| if (( $(echo "$difference > 0.01" | bc -l) )); then | |
| echo "Z: $Z" | |
| echo "Line number: $line_number" | |
| echo "Value in $output_file: $value1" | |
| echo "Value in $ref_file: $value2" | |
| echo "Difference between test and reference value is $difference, more than allowed threshold of 0.01" | |
| echo | |
| error_found=true | |
| fi | |
| index=$((index + 1)) | |
| done | |
| if [[ $error_found == true ]]; then | |
| exit 1 | |
| fi | |
| done | |
| - name: Print backtrace if any failure | |
| if: ${{ failure() && hashFiles('unit_test/burn_cell_metal_chem/Backtrace.0') != '' }} | |
| run: cat unit_test/burn_cell_metal_chem/Backtrace.0 | |