start of a JOSS paper #110
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 4 | |
| - name: Run and compare outputs for different Z values, also including cosmic ray ionization | |
| run: | | |
| set -e | |
| cd unit_test/burn_cell_metal_chem | |
| declare -A line_numbers_map=( | |
| ["Z=1"]="4450 4452 4454 4456 4457 4460 4461 4464 4470 4475" | |
| ["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"]="4463 4465 4467 4469 4470 4473 4474 4477 4483 4488" | |
| ["Z=1_cr"]="652 654 656 658 659 662 663 666 672 677" | |
| ["Z=1e-4_cr"]="652 654 656 658 659 662 663 666 672 677" | |
| ) | |
| 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" | |
| ["Z=1_cr"]="reference_solution_1_cr.out" | |
| ["Z=1e-4_cr"]="reference_solution_1e-4_cr.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" "Z=1_cr" "Z=1e-4_cr"; 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' $modified_input_file | |
| elif [[ "$Z" != "Z=1_cr" && "$Z" != "Z=1e-4_cr" ]]; then | |
| # Replace the metallicity and dust2gas_ratio values for other Z values | |
| sed -i 's/network.metallicity = .*/network.metallicity = '"$Z_val"'/g' $modified_input_file | |
| sed -i 's/network.dust2gas_ratio = .*/network.dust2gas_ratio = '"$Z_val"'/g' $modified_input_file | |
| fi | |
| if [[ "$Z" == "Z=1_cr" || "$Z" == "Z=1e-4_cr" ]]; then | |
| # Modify the number of steps, since CRs impact lowest densities | |
| sed -i 's/unit_test.nsteps = 100000/unit_test.nsteps = 600/g' $modified_input_file | |
| # Modify the crate line for Z=1_cr | |
| sed -i 's/network.crate = 0.0/network.crate = 3e-17/g' $modified_input_file | |
| if [[ "$Z" == "Z=1e-4_cr" ]]; then | |
| # Replace the metallicity and dust2gas_ratio values for other Z values | |
| sed -i 's/network.metallicity = 1/network.metallicity = 1e-4/g' $modified_input_file | |
| sed -i 's/network.dust2gas_ratio = 1/network.dust2gas_ratio = 1e-4/g' $modified_input_file | |
| fi | |
| fi | |
| output_file="test_${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=$((line_number - 4449)) | |
| elif [[ "$Z" == "Z=1_z10" ]]; then | |
| reference_line_number=${ref_line_number_z10[$index]} | |
| elif [[ "$Z" == "Z=1e-6" ]]; then | |
| reference_line_number=$((line_number - 4462)) | |
| elif [[ "$Z" == "Z=1_cr" || "$Z" == "Z=1e-4_cr" ]]; then | |
| reference_line_number=$((line_number - 651)) | |
| else | |
| reference_line_number=$((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 | |