Implement ISM chemistry including metals and dust #11
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 and run for Z = 1 | |
| run: | | |
| cd unit_test/burn_cell_metal_chem | |
| make -j 2 | |
| ./main1d.gnu.DEBUG.ex inputs_metal_chem_1 amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out | |
| - name: Print backtrace | |
| if: ${{ failure() && hashFiles('unit_test/burn_cell_metal_chem/Backtrace.0') != '' }} | |
| run: cat unit_test/burn_cell_metal_chem/Backtrace.0 | |
| - name: Compare to stored output for Z = 1 | |
| run: | | |
| set -e | |
| cd unit_test/burn_cell_metal_chem | |
| line_numbers=(4461 4463 4465 4467 4468 4471 4472 4475 4481 4486) | |
| threshold=0.01 | |
| error_found=false | |
| for line_number in "${line_numbers[@]}"; do | |
| value1=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH); else print 0}' test.out) | |
| # Adjust the line number for reference_solution_1.out | |
| reference_line_number=$((line_number - 24)) | |
| value2=$(awk 'NR=='"$reference_line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution_1.out) | |
| difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }') | |
| if (( $(echo "$difference > $threshold" | bc -l) )); then | |
| echo "Line number: $line_number" | |
| echo "Value in test.out: $value1" | |
| echo "Value in reference_solution_1.out: $value2" | |
| echo "Difference between test and reference value is $difference, more than allowed threshold of $threshold" | |
| echo | |
| error_found=true | |
| fi | |
| done | |
| if [[ $error_found == true ]]; then | |
| exit 1 | |
| fi | |
| - name: Run for Z = 1 at z = 10 | |
| run: | | |
| cd unit_test/burn_cell_metal_chem | |
| ./main1d.gnu.DEBUG.ex inputs_metal_chem_1_z10 amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out | |
| - name: Print backtrace | |
| if: ${{ failure() && hashFiles('unit_test/burn_cell_metal_chem/Backtrace.0') != '' }} | |
| run: cat unit_test/burn_cell_metal_chem/Backtrace.0 | |
| - name: Compare to stored output for Z = 1 at z = 10 | |
| run: | | |
| set -e | |
| cd unit_test/burn_cell_metal_chem | |
| line_numbers=(1612 1614 4479 4481 4483 4485 4486 4489 4490 4493 4499 4504) | |
| threshold=0.01 | |
| error_found=false | |
| for line_number in "${line_numbers[@]}"; do | |
| value1=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH); else print 0}' test.out) | |
| # Adjust the line number for reference_solution_1_z10.out | |
| reference_line_number=$((line_number - 24)) | |
| value2=$(awk 'NR=='"$reference_line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution_1_z10.out) | |
| difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }') | |
| if (( $(echo "$difference > $threshold" | bc -l) )); then | |
| echo "Line number: $line_number" | |
| echo "Value in test.out: $value1" | |
| echo "Value in reference_solution_1_z10.out: $value2" | |
| echo "Difference between test and reference value is $difference, more than allowed threshold of $threshold" | |
| echo | |
| error_found=true | |
| fi | |
| done | |
| if [[ $error_found == true ]]; then | |
| exit 1 | |
| fi | |
| - name: Run for Z = 1e-1 | |
| run: | | |
| cd unit_test/burn_cell_metal_chem | |
| ./main1d.gnu.DEBUG.ex inputs_metal_chem_1e-1 amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out | |
| - name: Print backtrace | |
| if: ${{ failure() && hashFiles('unit_test/burn_cell_metal_chem/Backtrace.0') != '' }} | |
| run: cat unit_test/burn_cell_metal_chem/Backtrace.0 | |
| - name: Compare to stored output for Z = 1e-1 | |
| run: | | |
| set -e | |
| cd unit_test/burn_cell_metal_chem | |
| line_numbers=(4438 4440 4442 4444 4445 4448 4449 4452 4458 4463) | |
| threshold=0.01 | |
| error_found=false | |
| for line_number in "${line_numbers[@]}"; do | |
| value1=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH); else print 0}' test.out) | |
| # Adjust the line number for reference_solution | |
| reference_line_number=$((line_number + 0)) | |
| value2=$(awk 'NR=='"$reference_line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution_1e-1.out) | |
| difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }') | |
| if (( $(echo "$difference > $threshold" | bc -l) )); then | |
| echo "Line number: $line_number" | |
| echo "Value in test.out: $value1" | |
| echo "Value in reference_solution_1e-1.out: $value2" | |
| echo "Difference between test and reference value is $difference, more than allowed threshold of $threshold" | |
| echo | |
| error_found=true | |
| fi | |
| done | |
| if [[ $error_found == true ]]; then | |
| exit 1 | |
| fi | |
| - name: Run for Z = 1e-2 | |
| run: | | |
| cd unit_test/burn_cell_metal_chem | |
| ./main1d.gnu.DEBUG.ex inputs_metal_chem_1e-2 amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out | |
| - name: Print backtrace | |
| if: ${{ failure() && hashFiles('unit_test/burn_cell_metal_chem/Backtrace.0') != '' }} | |
| run: cat unit_test/burn_cell_metal_chem/Backtrace.0 | |
| - name: Compare to stored output for Z = 1e-2 | |
| run: | | |
| set -e | |
| cd unit_test/burn_cell_metal_chem | |
| line_numbers=(4438 4440 4442 4444 4445 4448 4449 4452 4458 4463) | |
| threshold=0.01 | |
| error_found=false | |
| for line_number in "${line_numbers[@]}"; do | |
| value1=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH); else print 0}' test.out) | |
| # Adjust the line number for reference_solution | |
| reference_line_number=$((line_number + 0)) | |
| value2=$(awk 'NR=='"$reference_line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution_1e-2.out) | |
| difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }') | |
| if (( $(echo "$difference > $threshold" | bc -l) )); then | |
| echo "Line number: $line_number" | |
| echo "Value in test.out: $value1" | |
| echo "Value in reference_solution_1e-2.out: $value2" | |
| echo "Difference between test and reference value is $difference, more than allowed threshold of $threshold" | |
| echo | |
| error_found=true | |
| fi | |
| done | |
| if [[ $error_found == true ]]; then | |
| exit 1 | |
| fi | |
| - name: Run for Z = 1e-3 | |
| run: | | |
| cd unit_test/burn_cell_metal_chem | |
| ./main1d.gnu.DEBUG.ex inputs_metal_chem_1e-3 amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out | |
| - name: Print backtrace | |
| if: ${{ failure() && hashFiles('unit_test/burn_cell_metal_chem/Backtrace.0') != '' }} | |
| run: cat unit_test/burn_cell_metal_chem/Backtrace.0 | |
| - name: Compare to stored output for Z = 1e-3 | |
| run: | | |
| set -e | |
| cd unit_test/burn_cell_metal_chem | |
| line_numbers=(4438 4440 4442 4444 4445 4448 4449 4452 4458 4463) | |
| threshold=0.01 | |
| error_found=false | |
| for line_number in "${line_numbers[@]}"; do | |
| value1=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH); else print 0}' test.out) | |
| # Adjust the line number for reference_solution | |
| reference_line_number=$((line_number + 0)) | |
| value2=$(awk 'NR=='"$reference_line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution_1e-3.out) | |
| difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }') | |
| if (( $(echo "$difference > $threshold" | bc -l) )); then | |
| echo "Line number: $line_number" | |
| echo "Value in test.out: $value1" | |
| echo "Value in reference_solution_1e-3.out: $value2" | |
| echo "Difference between test and reference value is $difference, more than allowed threshold of $threshold" | |
| echo | |
| error_found=true | |
| fi | |
| done | |
| if [[ $error_found == true ]]; then | |
| exit 1 | |
| fi | |
| - name: Run for Z = 1e-4 | |
| run: | | |
| cd unit_test/burn_cell_metal_chem | |
| ./main1d.gnu.DEBUG.ex inputs_metal_chem_1e-4 amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out | |
| - name: Print backtrace | |
| if: ${{ failure() && hashFiles('unit_test/burn_cell_metal_chem/Backtrace.0') != '' }} | |
| run: cat unit_test/burn_cell_metal_chem/Backtrace.0 | |
| - name: Compare to stored output for Z = 1e-4 | |
| run: | | |
| set -e | |
| cd unit_test/burn_cell_metal_chem | |
| line_numbers=(4438 4440 4442 4444 4445 4448 4449 4452 4458 4463) | |
| threshold=0.01 | |
| error_found=false | |
| for line_number in "${line_numbers[@]}"; do | |
| value1=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH); else print 0}' test.out) | |
| # Adjust the line number for reference_solution | |
| reference_line_number=$((line_number + 0)) | |
| value2=$(awk 'NR=='"$reference_line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution_1e-4.out) | |
| difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }') | |
| if (( $(echo "$difference > $threshold" | bc -l) )); then | |
| echo "Line number: $line_number" | |
| echo "Value in test.out: $value1" | |
| echo "Value in reference_solution_1e-4.out: $value2" | |
| echo "Difference between test and reference value is $difference, more than allowed threshold of $threshold" | |
| echo | |
| error_found=true | |
| fi | |
| done | |
| if [[ $error_found == true ]]; then | |
| exit 1 | |
| fi | |
| - name: Run for Z = 1e-5 | |
| run: | | |
| cd unit_test/burn_cell_metal_chem | |
| ./main1d.gnu.DEBUG.ex inputs_metal_chem_1e-5 amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out | |
| - name: Print backtrace | |
| if: ${{ failure() && hashFiles('unit_test/burn_cell_metal_chem/Backtrace.0') != '' }} | |
| run: cat unit_test/burn_cell_metal_chem/Backtrace.0 | |
| - name: Compare to stored output for Z = 1e-5 | |
| run: | | |
| set -e | |
| cd unit_test/burn_cell_metal_chem | |
| line_numbers=(4438 4440 4442 4444 4445 4448 4449 4452 4458 4463) | |
| threshold=0.01 | |
| error_found=false | |
| for line_number in "${line_numbers[@]}"; do | |
| value1=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH); else print 0}' test.out) | |
| # Adjust the line number for reference_solution | |
| reference_line_number=$((line_number + 0)) | |
| value2=$(awk 'NR=='"$reference_line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution_1e-5.out) | |
| difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }') | |
| if (( $(echo "$difference > $threshold" | bc -l) )); then | |
| echo "Line number: $line_number" | |
| echo "Value in test.out: $value1" | |
| echo "Value in reference_solution_1e-5.out: $value2" | |
| echo "Difference between test and reference value is $difference, more than allowed threshold of $threshold" | |
| echo | |
| error_found=true | |
| fi | |
| done | |
| if [[ $error_found == true ]]; then | |
| exit 1 | |
| fi | |
| - name: Run for Z = 1e-6 | |
| run: | | |
| cd unit_test/burn_cell_metal_chem | |
| ./main1d.gnu.DEBUG.ex inputs_metal_chem_1e-6 amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out | |
| - name: Print backtrace | |
| if: ${{ failure() && hashFiles('unit_test/burn_cell_metal_chem/Backtrace.0') != '' }} | |
| run: cat unit_test/burn_cell_metal_chem/Backtrace.0 | |
| - name: Compare to stored output for Z = 1e-6 | |
| run: | | |
| set -e | |
| cd unit_test/burn_cell_metal_chem | |
| line_numbers=(4438 4440 4442 4444 4445 4448 4449 4452 4458 4463) | |
| threshold=0.01 | |
| error_found=false | |
| for line_number in "${line_numbers[@]}"; do | |
| value1=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH); else print 0}' test.out) | |
| # Adjust the line number for reference_solution | |
| reference_line_number=$((line_number + 12)) | |
| value2=$(awk 'NR=='"$reference_line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution_1e-6.out) | |
| difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }') | |
| if (( $(echo "$difference > $threshold" | bc -l) )); then | |
| echo "Line number: $line_number" | |
| echo "Value in test.out: $value1" | |
| echo "Value in reference_solution_1e-6.out: $value2" | |
| echo "Difference between test and reference value is $difference, more than allowed threshold of $threshold" | |
| echo | |
| error_found=true | |
| fi | |
| done | |
| if [[ $error_found == true ]]; then | |
| exit 1 | |
| fi | |