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smoke test for NFsim runs with bash and python3 on all platforms
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| # time O0_MT0_tot_Count O0_MT1_tot_Count O0_MT2_tot_Count O0_MT3_tot_Count O0_MT4_tot_Count s0_Count s1_Count s2_Count s3_Count s4_Count | ||
| 0.00000000e+00 6.02000000e+02 9.03000000e+02 1.20400000e+03 0.00000000e+00 0.00000000e+00 6.02000000e+02 9.03000000e+02 1.20400000e+03 0.00000000e+00 0.00000000e+00 | ||
| 1.00000000e-01 5.37000000e+02 9.68000000e+02 1.13900000e+03 0.00000000e+00 0.00000000e+00 5.37000000e+02 9.68000000e+02 1.13900000e+03 0.00000000e+00 0.00000000e+00 | ||
| 2.00000000e-01 5.24000000e+02 9.81000000e+02 1.12600000e+03 0.00000000e+00 0.00000000e+00 5.24000000e+02 9.81000000e+02 1.12600000e+03 0.00000000e+00 0.00000000e+00 | ||
| 3.00000000e-01 5.23000000e+02 9.82000000e+02 1.12500000e+03 0.00000000e+00 0.00000000e+00 5.23000000e+02 9.82000000e+02 1.12500000e+03 0.00000000e+00 0.00000000e+00 | ||
| 4.00000000e-01 5.30000000e+02 9.75000000e+02 1.13200000e+03 0.00000000e+00 0.00000000e+00 5.30000000e+02 9.75000000e+02 1.13200000e+03 0.00000000e+00 0.00000000e+00 | ||
| 5.00000000e-01 5.23000000e+02 9.82000000e+02 1.12500000e+03 0.00000000e+00 0.00000000e+00 5.23000000e+02 9.82000000e+02 1.12500000e+03 0.00000000e+00 0.00000000e+00 | ||
| 6.00000000e-01 5.21000000e+02 9.84000000e+02 1.12300000e+03 0.00000000e+00 0.00000000e+00 5.21000000e+02 9.84000000e+02 1.12300000e+03 0.00000000e+00 0.00000000e+00 | ||
| 7.00000000e-01 5.20000000e+02 9.85000000e+02 1.12200000e+03 0.00000000e+00 0.00000000e+00 5.20000000e+02 9.85000000e+02 1.12200000e+03 0.00000000e+00 0.00000000e+00 | ||
| 8.00000000e-01 5.13000000e+02 9.92000000e+02 1.11500000e+03 0.00000000e+00 0.00000000e+00 5.13000000e+02 9.92000000e+02 1.11500000e+03 0.00000000e+00 0.00000000e+00 | ||
| 9.00000000e-01 5.13000000e+02 9.92000000e+02 1.11500000e+03 0.00000000e+00 0.00000000e+00 5.13000000e+02 9.92000000e+02 1.11500000e+03 0.00000000e+00 0.00000000e+00 | ||
| 1.00000000e+00 5.33000000e+02 9.72000000e+02 1.13500000e+03 0.00000000e+00 0.00000000e+00 5.33000000e+02 9.72000000e+02 1.13500000e+03 0.00000000e+00 0.00000000e+00 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| # nfsim generated species list for system: 'nameless' | ||
| # warning! this feature is not yet fully tested! | ||
| MT0(AAA~c0,AAB~0) 532 | ||
| MT1(AAA~c0,AAB~0) 973 | ||
| MT2(AAA~c0,AAB~0) 1134 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| #!/usr/bin/env python3 | ||
|
|
||
| import os | ||
| import posixpath | ||
| import subprocess | ||
| import sys | ||
|
|
||
| # get the directory of this script | ||
| test_dir = os.path.dirname(os.path.realpath(__file__)) | ||
| # in the path replace \ with /, D:\ with /d/ | ||
| test_dir = test_dir.replace("\\", "/") | ||
| # tell os.path.join to use / as the path separator | ||
| os.path.sep = "/" | ||
| exe = sys.argv[1] | ||
|
|
||
| print(f"test_dir: {test_dir}") | ||
| print(f"exe: {exe}") | ||
|
|
||
| input_file = posixpath.join(test_dir, "SimID_273069657_0_.nfsimInput") | ||
| output = posixpath.join(test_dir, "SimID_273069657_0_.gdat") | ||
| expected_output = posixpath.join(test_dir, "SimID_273069657_0_.gdat.expected") | ||
| species = posixpath.join(test_dir, "SimID_273069657_0_.species") | ||
| expected_species = posixpath.join(test_dir, "SimID_273069657_0_.species.expected") | ||
|
|
||
| if not posixpath.exists(exe): | ||
| print(f"NFsim executable {exe} not found. Exiting...") | ||
| sys.exit(1) | ||
|
|
||
| if not posixpath.exists(input_file): | ||
| print(f"Input file {input_file} not found. Exiting...") | ||
| sys.exit(1) | ||
|
|
||
| if not posixpath.exists(expected_output): | ||
| print(f"Expected output file {expected_output} not found. Exiting...") | ||
| sys.exit(1) | ||
|
|
||
| if not posixpath.exists(expected_species): | ||
| print(f"Expected species file {expected_species} not found. Exiting...") | ||
| sys.exit(1) | ||
|
|
||
| command = [exe, "-seed", "505790288", "-vcell", "-xml", input_file, "-o", output, "-sim", "1.0", "-ss", species, "-oStep", "20", "-notf", "-utl", "1000", "-cb", "-pcmatch", "-tid", "0"] | ||
| print(" ".join(command)) | ||
|
|
||
| try: | ||
| subprocess.check_call(command) | ||
| except subprocess.CalledProcessError: | ||
| print("NFsim failed to run. Exiting...") | ||
| sys.exit(1) | ||
|
|
||
| # verify that the output files exist | ||
| if not os.path.isfile(output): | ||
| print(f"Output file {output} not found. Exiting...") | ||
| sys.exit(1) | ||
|
|
||
| if not os.path.isfile(species): | ||
| print(f"Species file {species} not found. Exiting...") | ||
| sys.exit(1) | ||
|
|
||
| # verify that the output files match the expected output files | ||
| if open(output).read() != open(expected_output).read(): | ||
| print(f"Output file {output} does not match expected output {expected_output}. Exiting...") | ||
| sys.exit(1) | ||
|
|
||
| if open(species).read() != open(expected_species).read(): | ||
| print(f"Species file {species} does not match expected species {expected_species}. Exiting...") | ||
| sys.exit(1) | ||
|
|
||
| print("NFsim solver completed and solution matched expected output. Exiting...") | ||
| sys.exit(0) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| #!/bin/bash | ||
| set -e | ||
| EXE=$1 | ||
|
|
||
| echo "Running NFsim solver with test2.sh $EXE" | ||
|
|
||
| # get the directory of this script | ||
| TEST_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" | ||
|
|
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| INPUT="${TEST_DIR}/SimID_273069657_0_.nfsimInput" | ||
| OUTPUT="${TEST_DIR}/SimID_273069657_0_.gdat" | ||
| EXPECTED_OUTPUT="${TEST_DIR}/SimID_273069657_0_.gdat.expected" | ||
| SPECIES="${TEST_DIR}/SimID_273069657_0_.species" | ||
| EXPECTED_SPECIES="${TEST_DIR}/SimID_273069657_0_.species.expected" | ||
|
|
||
| if [ ! -f $EXE ]; then | ||
| echo "NFsim executable $EXE not found. Exiting..." | ||
| exit 1 | ||
| fi | ||
| if [ ! -f $INPUT ]; then | ||
| echo "Input file $INPUT not found. Exiting..." | ||
| exit 1 | ||
| fi | ||
| if [ ! -f $EXPECTED_OUTPUT ]; then | ||
| echo "Expected output file $EXPECTED_OUTPUT not found. Exiting..." | ||
| exit 1 | ||
| fi | ||
| if [ ! -f $EXPECTED_SPECIES ]; then | ||
| echo "Expected species file $EXPECTED_SPECIES not found. Exiting..." | ||
| exit 1 | ||
| fi | ||
|
|
||
|
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| command="$EXE -seed 505790288 -vcell -xml $INPUT -o $OUTPUT -sim 1.0 -ss $SPECIES -oStep 20 -notf -utl 1000 -cb -pcmatch -tid 0" | ||
| echo $command | ||
| if ! $command; then | ||
| echo "NFsim failed to run. Exiting..." | ||
| exit 1 | ||
| fi | ||
|
|
||
| # verify that the output files exist | ||
| if [ ! -f $OUTPUT ]; then | ||
| echo "Output file $OUTPUT not found. Exiting..." | ||
| exit 1 | ||
| fi | ||
| if [ ! -f $SPECIES ]; then | ||
| echo "Species file $SPECIES not found. Exiting..." | ||
| exit 1 | ||
| fi | ||
|
|
||
| # verify that the output files match the expected output files | ||
| if ! diff $OUTPUT $EXPECTED_OUTPUT; then | ||
| echo "Output file $OUTPUT does not match expected output $EXPECTED_OUTPUT. Exiting..." | ||
| exit 1 | ||
| fi | ||
| if ! diff $SPECIES $EXPECTED_SPECIES; then | ||
| echo "Species file $SPECIES does not match expected species $EXPECTED_SPECIES. Exiting..." | ||
| exit 1 | ||
| fi | ||
|
|
||
| echo "NFsim solver complted and solution matched expected output. Exiting..." | ||
| exit 0 |
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