From 109f69b4ae599d6562e5c348ebf6383e9744e135 Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 12:55:55 +0000 Subject: [PATCH 01/16] Test python format script --- tests/python_format_test.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/python_format_test.sh b/tests/python_format_test.sh index 3b826f75..3c42291c 100755 --- a/tests/python_format_test.sh +++ b/tests/python_format_test.sh @@ -31,7 +31,7 @@ test_fail=0 find build/ tools/ -name "*.py" | { while IFS= read -r file; do test_total=$((test_total + 1)) - black --check "$file" > /dev/null 2>&1 + black --check "$file" #> /dev/null 2>&1 if [ $? -eq 0 ] ; then printf "[PASS] %s\n" "$file" else From 3ff3d605db8f1eb42450faa2ac8aedd2db8bf480 Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 13:04:20 +0000 Subject: [PATCH 02/16] Check black version --- .github/workflows/ci.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 641b163a..050c2fd2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -116,7 +116,9 @@ jobs: run: ./tools/install/install_fruit.sh $PWD - name: Install Python and Fortran formatters - run: pip install black fprettify + run: | + pip install black fprettify + black --version # ------------------------------------------------------------- # (4) Build AtChem2 using the standard compilation flags From 4ac633ce1236c0051123233f561c77577348f750 Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 14:18:26 +0000 Subject: [PATCH 03/16] Show formatting diffs --- tests/python_format_test.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/python_format_test.sh b/tests/python_format_test.sh index 3c42291c..362edeb0 100755 --- a/tests/python_format_test.sh +++ b/tests/python_format_test.sh @@ -31,7 +31,7 @@ test_fail=0 find build/ tools/ -name "*.py" | { while IFS= read -r file; do test_total=$((test_total + 1)) - black --check "$file" #> /dev/null 2>&1 + black --diff "$file" #> /dev/null 2>&1 if [ $? -eq 0 ] ; then printf "[PASS] %s\n" "$file" else From 6ecc58628f61727b722a79ee12d9265fe86db636 Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 16:01:21 +0000 Subject: [PATCH 04/16] Fix python scripts formatting --- .github/workflows/ci.yml | 4 +--- build/fix_mechanism_fac.py | 4 ---- build/kpp_conversion.py | 12 ------------ build/mech_converter.py | 23 ++++++----------------- tests/python_format_test.sh | 3 ++- 5 files changed, 9 insertions(+), 37 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 050c2fd2..641b163a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -116,9 +116,7 @@ jobs: run: ./tools/install/install_fruit.sh $PWD - name: Install Python and Fortran formatters - run: | - pip install black fprettify - black --version + run: pip install black fprettify # ------------------------------------------------------------- # (4) Build AtChem2 using the standard compilation flags diff --git a/build/fix_mechanism_fac.py b/build/fix_mechanism_fac.py index 36503ba2..33db56bf 100644 --- a/build/fix_mechanism_fac.py +++ b/build/fix_mechanism_fac.py @@ -37,10 +37,8 @@ import sys import re - # =========================== FUNCTIONS =========================== # - def fix_fac_full_contents(input_file): """ Given a .fac file, return the contents of the file, but with @@ -156,10 +154,8 @@ def fix_fac_full_contents(input_file): # Return the corrected mechanism file return fixed_file - # ------------------------------------------------------------ # - def fix_fac_full_file(input_file): """ Given a .fac file, overwrite the contents of the file with the diff --git a/build/kpp_conversion.py b/build/kpp_conversion.py index a959f949..8f9b9668 100644 --- a/build/kpp_conversion.py +++ b/build/kpp_conversion.py @@ -22,10 +22,8 @@ import sys import re - # =========================== FUNCTIONS =========================== # - def mechanism_section(input_lines, start_section, end_section): """ Parse the content of a file, provided in the form of a list @@ -60,10 +58,8 @@ def mechanism_section(input_lines, start_section, end_section): section_lines = input_lines[start_i:end_i] return section_lines - # ------------------------------------------------------------ # - def convert_ro2(kpp_lines): """ Converts the summation of organic peroxy radicals (RO2) to @@ -83,10 +79,8 @@ def convert_ro2(kpp_lines): fac_lines.append(new_line) return fac_lines - # ------------------------------------------------------------ # - def convert_rates(kpp_lines): """ Converts the generic and complex rate coefficients to @@ -130,10 +124,8 @@ def convert_rates(kpp_lines): fac_lines2.append(new_line) return fac_lines1, fac_lines2 - # ------------------------------------------------------------ # - def convert_reactions(kpp_lines): """ Converts the chemical reactions to FACSIMILE format. @@ -155,10 +147,8 @@ def convert_reactions(kpp_lines): fac_lines.append(new_line) return fac_lines - # ------------------------------------------------------------ # - def kpp_to_facsimile(input_file): """Split a .kpp file into 4 sections: the summation of organic peroxy radicals (RO2), the generic and complex rate coefficients, @@ -205,10 +195,8 @@ def kpp_to_facsimile(input_file): # Sections of the mechanism file converted to KPP format return generic_rates, complex_reactions, peroxy_radicals, reaction_definitions - # ------------------------------------------------------------ # - def write_fac_file(input_file): """ Convert a .kpp file to FACSIMILE format and save the output to a diff --git a/build/mech_converter.py b/build/mech_converter.py index 597d21f4..a43f5ad9 100644 --- a/build/mech_converter.py +++ b/build/mech_converter.py @@ -56,7 +56,6 @@ # =========================== FUNCTIONS =========================== # - def tokenise_and_process(input_string, vars_dict): """ This function takes in a single string, and a dictionary of known @@ -149,10 +148,8 @@ def tokenise_and_process(input_string, vars_dict): # Return the reconstructed string. return new_rhs - # ====================================================== - def separate_stoichiometry(input_species): """ This function takes in a string of a species from the mechanism and @@ -177,16 +174,12 @@ def separate_stoichiometry(input_species): else: # if there is no coefficient then output an assumed coefficient of 1 return (1.0, pat_match[2]) else: - raise Exception( - f"""Reaction species does not match the correct + raise Exception(f"""Reaction species does not match the correct format: '{input_species}'. Note that species names should - not begin with numerical characters.""" - ) - + not begin with numerical characters.""") # ====================================================== - def convert_to_fortran(mechFile, configDir, sharedDir, mcmV): """ This function converts a chemical mechanism file into the Fortran-compatible @@ -643,8 +636,7 @@ def convert_to_fortran(mechFile, configDir, sharedDir, mcmV): # Combine mechanism rates and RO2 sum files. with open(os.path.join(sharedDir, "mechanism.f90"), "a") as mech_rates_coeff_file: - mech_rates_coeff_file.write( - """ + mech_rates_coeff_file.write(""" module mechanism_mod use, intrinsic :: iso_c_binding implicit none @@ -657,8 +649,7 @@ def convert_to_fortran(mechFile, configDir, sharedDir, mcmV): integer, parameter :: DP = selected_real_kind( p = 15, r = 307 ) real(c_double), intent(inout) :: p(*), q(*) real(c_double), intent(in) :: t, TEMP, N2, O2, M, RH, H2O, BLHEIGHT, DEC, JFAC, DILUTE, ROOFOPEN, ASA, J(*), RO2 - """ - ) + """) # Write out 'Generic Rate Coefficients' and 'Complex reactions'. for item in mechanism_rates_coeff_list: @@ -667,12 +658,10 @@ def convert_to_fortran(mechFile, configDir, sharedDir, mcmV): # Write out 'Reaction definitions'. for r in mech_rates_list: mech_rates_coeff_file.write(r) - mech_rates_coeff_file.write( - """ + mech_rates_coeff_file.write(""" end subroutine update_p end module mechanism_mod -""" - ) +""") # ------------------------------------------------- diff --git a/tests/python_format_test.sh b/tests/python_format_test.sh index 362edeb0..c39016d7 100755 --- a/tests/python_format_test.sh +++ b/tests/python_format_test.sh @@ -31,10 +31,11 @@ test_fail=0 find build/ tools/ -name "*.py" | { while IFS= read -r file; do test_total=$((test_total + 1)) - black --diff "$file" #> /dev/null 2>&1 + black --check "$file" > /dev/null 2>&1 if [ $? -eq 0 ] ; then printf "[PASS] %s\n" "$file" else + black --diff "$file" printf "[FAIL] %s\n" "$file" test_fail=$((test_fail + 1)) fi From 0146ae4a15e111489c62ee126cda68a2b11123cd Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 16:05:48 +0000 Subject: [PATCH 05/16] Fix python scripts formatting --- build/kpp_conversion.py | 11 +++++++++++ build/mech_converter.py | 5 +++++ 2 files changed, 16 insertions(+) diff --git a/build/kpp_conversion.py b/build/kpp_conversion.py index 8f9b9668..4b5f1d5f 100644 --- a/build/kpp_conversion.py +++ b/build/kpp_conversion.py @@ -24,6 +24,7 @@ # =========================== FUNCTIONS =========================== # + def mechanism_section(input_lines, start_section, end_section): """ Parse the content of a file, provided in the form of a list @@ -58,8 +59,10 @@ def mechanism_section(input_lines, start_section, end_section): section_lines = input_lines[start_i:end_i] return section_lines + # ------------------------------------------------------------ # + def convert_ro2(kpp_lines): """ Converts the summation of organic peroxy radicals (RO2) to @@ -79,8 +82,10 @@ def convert_ro2(kpp_lines): fac_lines.append(new_line) return fac_lines + # ------------------------------------------------------------ # + def convert_rates(kpp_lines): """ Converts the generic and complex rate coefficients to @@ -124,8 +129,10 @@ def convert_rates(kpp_lines): fac_lines2.append(new_line) return fac_lines1, fac_lines2 + # ------------------------------------------------------------ # + def convert_reactions(kpp_lines): """ Converts the chemical reactions to FACSIMILE format. @@ -147,8 +154,10 @@ def convert_reactions(kpp_lines): fac_lines.append(new_line) return fac_lines + # ------------------------------------------------------------ # + def kpp_to_facsimile(input_file): """Split a .kpp file into 4 sections: the summation of organic peroxy radicals (RO2), the generic and complex rate coefficients, @@ -195,8 +204,10 @@ def kpp_to_facsimile(input_file): # Sections of the mechanism file converted to KPP format return generic_rates, complex_reactions, peroxy_radicals, reaction_definitions + # ------------------------------------------------------------ # + def write_fac_file(input_file): """ Convert a .kpp file to FACSIMILE format and save the output to a diff --git a/build/mech_converter.py b/build/mech_converter.py index a43f5ad9..1bce672c 100644 --- a/build/mech_converter.py +++ b/build/mech_converter.py @@ -56,6 +56,7 @@ # =========================== FUNCTIONS =========================== # + def tokenise_and_process(input_string, vars_dict): """ This function takes in a single string, and a dictionary of known @@ -148,8 +149,10 @@ def tokenise_and_process(input_string, vars_dict): # Return the reconstructed string. return new_rhs + # ====================================================== + def separate_stoichiometry(input_species): """ This function takes in a string of a species from the mechanism and @@ -178,8 +181,10 @@ def separate_stoichiometry(input_species): format: '{input_species}'. Note that species names should not begin with numerical characters.""") + # ====================================================== + def convert_to_fortran(mechFile, configDir, sharedDir, mcmV): """ This function converts a chemical mechanism file into the Fortran-compatible From e08a2f2150f6cff0fdb364955c266a4e6dd47cab Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 16:07:42 +0000 Subject: [PATCH 06/16] Fix python scripts formatting --- build/fix_mechanism_fac.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/build/fix_mechanism_fac.py b/build/fix_mechanism_fac.py index 33db56bf..989cea4b 100644 --- a/build/fix_mechanism_fac.py +++ b/build/fix_mechanism_fac.py @@ -39,6 +39,7 @@ # =========================== FUNCTIONS =========================== # + def fix_fac_full_contents(input_file): """ Given a .fac file, return the contents of the file, but with @@ -154,8 +155,10 @@ def fix_fac_full_contents(input_file): # Return the corrected mechanism file return fixed_file + # ------------------------------------------------------------ # + def fix_fac_full_file(input_file): """ Given a .fac file, overwrite the contents of the file with the From 671e428b376d53689856821224dcdf801b424874 Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 16:54:43 +0000 Subject: [PATCH 07/16] logfile for python tests --- tests/python_format_test.sh | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/tests/python_format_test.sh b/tests/python_format_test.sh index c39016d7..30b8f181 100755 --- a/tests/python_format_test.sh +++ b/tests/python_format_test.sh @@ -23,20 +23,24 @@ if [ $? -ne 0 ] ; then exit 1 fi -printf "\nExecuting Python format test:\n" +LOG_FILE=tests/pythontest.log + +printf "==> Executing Python format test...\n" test_total=0 test_fail=0 +printf "Python format test\n\n" > "$LOG_FILE" + find build/ tools/ -name "*.py" | { while IFS= read -r file; do test_total=$((test_total + 1)) - black --check "$file" > /dev/null 2>&1 + black -q --check "$file" if [ $? -eq 0 ] ; then - printf "[PASS] %s\n" "$file" + printf "[PASS] %s\n" "$file" >> "$LOG_FILE" else - black --diff "$file" - printf "[FAIL] %s\n" "$file" + printf "[FAIL] %s\n" "$file" >> "$LOG_FILE" + black -q --diff "$file" >> $LOG_FILE test_fail=$((test_fail + 1)) fi done @@ -50,5 +54,6 @@ find build/ tools/ -name "*.py" | { test_script_pass=1 fi + printf "==> Python format test logfile: %s\n" "$LOG_FILE" exit $test_script_pass } From 19c0a73dcc18e1ee7011a484e5036871f94c4908 Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 18:18:25 +0000 Subject: [PATCH 08/16] Move and rename the include dir --- build/build_atchem2.sh | 14 +++++++------- model/.gitignore | 4 ++-- .../{configuration/include => sharedlib}/.gitkeep | 0 tests/python_format_test.sh | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-) rename model/{configuration/include => sharedlib}/.gitkeep (100%) diff --git a/build/build_atchem2.sh b/build/build_atchem2.sh index a0d67cc4..514d436e 100755 --- a/build/build_atchem2.sh +++ b/build/build_atchem2.sh @@ -27,7 +27,7 @@ # `--shared_lib` is the shared library directory, which contains # the chemical mechanism in Fortran format (`mechanism.*`) and # the pre-compiled mechanism shared library (`mechanism.so`). -# Default value: ./model/configuration/include +# Default value: ./model/sharedlib # # `--mcm` is the MCM version of the chemical mechanism, which sets the # reference list of organic peroxy radicals (RO2) and the empirical @@ -43,7 +43,7 @@ # OR # ./build/build_atchem2.sh --mechanism=/path/to/mechanism/file # --configuration=/path/to/configuration/directory -# --shared_lib=/path/to/mechanism/directory +# --shared_lib=/path/to/shared_lib/directory # --mcm=v3.3.1 # ----------------------------------------------------------------------------- set -eu @@ -51,7 +51,7 @@ set -eu # default values for the script flags MECHF="" CONFIGD="model/configuration" -MECHD="model/configuration/include" +SHAREDLIBD="model/sharedlib" MCMV="v3.3.1" # parse the script flags @@ -64,7 +64,7 @@ while [ "$#" -gt 0 ]; do CONFIGD="${1#*=}" ;; --shared_lib=*) - MECHD="${1#*=}" + SHAREDLIBD="${1#*=}" ;; --mcm=*) MCMV="${1#*=}" @@ -100,8 +100,8 @@ if [ ! -d "$CONFIGD" ]; then fi # set the shared library directory (`--shared_lib=`) -printf "\n[*] Shared library directory: %s\n" "$MECHD" -if [ ! -d "$MECHD" ]; then +printf "\n[*] Shared library directory: %s\n" "$SHAREDLIBD" +if [ ! -d "$SHAREDLIBD" ]; then printf "\n[INPUT ERROR] The shared library directory does not exist.\n" exit 1 fi @@ -128,7 +128,7 @@ printf "\n--> Using %s\n" "$PY_BIN" # compile the chemical mechanism shared library (`mechanism.so`) printf "\n--> Compiling chemical mechanism shared library...\n\n" -make sharedlib PYTHON_BIN="$PY_BIN" MECHFILE="$MECHF" CONFIGDIR="$CONFIGD" MECHDIR="$MECHD" MCMVERS="$MCMV" +make sharedlib PYTHON_BIN="$PY_BIN" MECHFILE="$MECHF" CONFIGDIR="$CONFIGD" SHAREDLIBDIR="$SHAREDLIBD" MCMVERS="$MCMV" if [ $? -ne 0 ] ; then printf "\n[FAIL] Check error message for details.\n" exit 1 diff --git a/model/.gitignore b/model/.gitignore index c0b5ffca..472df623 100644 --- a/model/.gitignore +++ b/model/.gitignore @@ -1,10 +1,10 @@ -# Ignore auto-generated mechanism files and output files in the model/ directory +# Ignore constraint files, output files, auto-generated mechanism files in the model/ directory constraints/environment/* constraints/photolysis/* constraints/species/* -configuration/include/* output/*.output output/*.pdf output/reactionRates/* +sharedlib/* !.gitkeep diff --git a/model/configuration/include/.gitkeep b/model/sharedlib/.gitkeep similarity index 100% rename from model/configuration/include/.gitkeep rename to model/sharedlib/.gitkeep diff --git a/tests/python_format_test.sh b/tests/python_format_test.sh index 30b8f181..a0b12b90 100755 --- a/tests/python_format_test.sh +++ b/tests/python_format_test.sh @@ -16,7 +16,7 @@ # NB: the script must be run from the *Main Directory* of AtChem2. # ----------------------------------------------------------------------------- -python -c "import black" +python3 -c "import black" if [ $? -ne 0 ] ; then printf "\n[ERROR] python formatter missing -- to install it, run the command:\n" printf "pip install black\n" From ec9711b89ed977dce126cbba617c3b50c7995011 Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 18:19:57 +0000 Subject: [PATCH 09/16] Set sharedlib in model tests --- .../{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../static/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 44 files changed, 0 insertions(+), 0 deletions(-) rename tests/model_tests/env_model_1/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/model_tests/env_model_1/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/model_tests/env_model_1/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/model_tests/env_model_1/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/model_tests/env_model_2/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/model_tests/env_model_2/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/model_tests/env_model_2/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/model_tests/env_model_2/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/model_tests/env_model_3/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/model_tests/env_model_3/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/model_tests/env_model_3/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/model_tests/env_model_3/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/model_tests/env_model_4/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/model_tests/env_model_4/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/model_tests/env_model_4/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/model_tests/env_model_4/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/model_tests/firstorder/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/model_tests/firstorder/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/model_tests/firstorder/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/model_tests/firstorder/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/model_tests/secondorder/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/model_tests/secondorder/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/model_tests/secondorder/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/model_tests/secondorder/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/model_tests/spec_model_1/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/model_tests/spec_model_1/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/model_tests/spec_model_1/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/model_tests/spec_model_1/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/model_tests/spec_model_func/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/model_tests/spec_model_func/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/model_tests/spec_model_func/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/model_tests/spec_model_func/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/model_tests/spec_model_kpp/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/model_tests/spec_model_kpp/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/model_tests/spec_model_kpp/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/model_tests/spec_model_kpp/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/model_tests/spec_model_stoich/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/model_tests/spec_model_stoich/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/model_tests/spec_model_stoich/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/model_tests/spec_model_stoich/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/model_tests/static/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/model_tests/static/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/model_tests/static/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/model_tests/static/{configuration/include => sharedlib}/mechanism.species.cmp (100%) diff --git a/tests/model_tests/env_model_1/configuration/include/mechanism.prod.cmp b/tests/model_tests/env_model_1/sharedlib/mechanism.prod.cmp similarity index 100% rename from tests/model_tests/env_model_1/configuration/include/mechanism.prod.cmp rename to tests/model_tests/env_model_1/sharedlib/mechanism.prod.cmp diff --git a/tests/model_tests/env_model_1/configuration/include/mechanism.reac.cmp b/tests/model_tests/env_model_1/sharedlib/mechanism.reac.cmp similarity index 100% rename from tests/model_tests/env_model_1/configuration/include/mechanism.reac.cmp rename to tests/model_tests/env_model_1/sharedlib/mechanism.reac.cmp diff --git a/tests/model_tests/env_model_1/configuration/include/mechanism.ro2.cmp b/tests/model_tests/env_model_1/sharedlib/mechanism.ro2.cmp similarity index 100% rename from tests/model_tests/env_model_1/configuration/include/mechanism.ro2.cmp rename to tests/model_tests/env_model_1/sharedlib/mechanism.ro2.cmp diff --git a/tests/model_tests/env_model_1/configuration/include/mechanism.species.cmp b/tests/model_tests/env_model_1/sharedlib/mechanism.species.cmp similarity index 100% rename from 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from tests/model_tests/spec_model_func/configuration/include/mechanism.ro2.cmp rename to tests/model_tests/spec_model_func/sharedlib/mechanism.ro2.cmp diff --git a/tests/model_tests/spec_model_func/configuration/include/mechanism.species.cmp b/tests/model_tests/spec_model_func/sharedlib/mechanism.species.cmp similarity index 100% rename from tests/model_tests/spec_model_func/configuration/include/mechanism.species.cmp rename to tests/model_tests/spec_model_func/sharedlib/mechanism.species.cmp diff --git a/tests/model_tests/spec_model_kpp/configuration/include/mechanism.prod.cmp b/tests/model_tests/spec_model_kpp/sharedlib/mechanism.prod.cmp similarity index 100% rename from tests/model_tests/spec_model_kpp/configuration/include/mechanism.prod.cmp rename to tests/model_tests/spec_model_kpp/sharedlib/mechanism.prod.cmp diff --git a/tests/model_tests/spec_model_kpp/configuration/include/mechanism.reac.cmp b/tests/model_tests/spec_model_kpp/sharedlib/mechanism.reac.cmp similarity index 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b/tests/model_tests/spec_model_stoich/sharedlib/mechanism.species.cmp similarity index 100% rename from tests/model_tests/spec_model_stoich/configuration/include/mechanism.species.cmp rename to tests/model_tests/spec_model_stoich/sharedlib/mechanism.species.cmp diff --git a/tests/model_tests/static/configuration/include/mechanism.prod.cmp b/tests/model_tests/static/sharedlib/mechanism.prod.cmp similarity index 100% rename from tests/model_tests/static/configuration/include/mechanism.prod.cmp rename to tests/model_tests/static/sharedlib/mechanism.prod.cmp diff --git a/tests/model_tests/static/configuration/include/mechanism.reac.cmp b/tests/model_tests/static/sharedlib/mechanism.reac.cmp similarity index 100% rename from tests/model_tests/static/configuration/include/mechanism.reac.cmp rename to tests/model_tests/static/sharedlib/mechanism.reac.cmp diff --git a/tests/model_tests/static/configuration/include/mechanism.ro2.cmp b/tests/model_tests/static/sharedlib/mechanism.ro2.cmp similarity index 100% rename from tests/model_tests/static/configuration/include/mechanism.ro2.cmp rename to tests/model_tests/static/sharedlib/mechanism.ro2.cmp diff --git a/tests/model_tests/static/configuration/include/mechanism.species.cmp b/tests/model_tests/static/sharedlib/mechanism.species.cmp similarity index 100% rename from tests/model_tests/static/configuration/include/mechanism.species.cmp rename to tests/model_tests/static/sharedlib/mechanism.species.cmp From 2ef05695167254c96741eb0b7f4a76be780d8bb6 Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 18:24:53 +0000 Subject: [PATCH 10/16] Set sharedlib in old tests --- .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.prod.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.reac.cmp | 0 .../model/{configuration/include => sharedlib}/mechanism.ro2.cmp | 0 .../{configuration/include => sharedlib}/mechanism.species.cmp | 0 68 files changed, 0 insertions(+), 0 deletions(-) rename tests/tests/short/model/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/tests/short/model/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/tests/short/model/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/tests/short/model/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/tests/short_dense/model/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/tests/short_dense/model/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/tests/short_dense/model/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/tests/short_dense/model/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/tests/short_end_of_day/model/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/tests/short_end_of_day/model/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/tests/short_end_of_day/model/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/tests/short_end_of_day/model/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/tests/short_ext1/model/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/tests/short_ext1/model/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/tests/short_ext1/model/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/tests/short_ext1/model/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/tests/short_ext2/model/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/tests/short_ext2/model/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/tests/short_ext2/model/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/tests/short_ext2/model/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/tests/short_ext3/model/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/tests/short_ext3/model/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/tests/short_ext3/model/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/tests/short_ext3/model/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/tests/short_ext4/model/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/tests/short_ext4/model/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/tests/short_ext4/model/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/tests/short_ext4/model/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/tests/short_no_pre/model/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/tests/short_no_pre/model/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/tests/short_no_pre/model/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename tests/tests/short_no_pre/model/{configuration/include => sharedlib}/mechanism.species.cmp (100%) rename tests/tests/spec_no_env_yes1/model/{configuration/include => sharedlib}/mechanism.prod.cmp (100%) rename tests/tests/spec_no_env_yes1/model/{configuration/include => sharedlib}/mechanism.reac.cmp (100%) rename tests/tests/spec_no_env_yes1/model/{configuration/include => sharedlib}/mechanism.ro2.cmp (100%) rename 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rename to tests/tests/spec_yes_env_no_with_jfac_fixed/model/sharedlib/mechanism.ro2.cmp diff --git a/tests/tests/spec_yes_env_no_with_jfac_fixed/model/configuration/include/mechanism.species.cmp b/tests/tests/spec_yes_env_no_with_jfac_fixed/model/sharedlib/mechanism.species.cmp similarity index 100% rename from tests/tests/spec_yes_env_no_with_jfac_fixed/model/configuration/include/mechanism.species.cmp rename to tests/tests/spec_yes_env_no_with_jfac_fixed/model/sharedlib/mechanism.species.cmp diff --git a/tests/tests/spec_yes_env_no_with_photo/model/configuration/include/mechanism.prod.cmp b/tests/tests/spec_yes_env_no_with_photo/model/sharedlib/mechanism.prod.cmp similarity index 100% rename from tests/tests/spec_yes_env_no_with_photo/model/configuration/include/mechanism.prod.cmp rename to tests/tests/spec_yes_env_no_with_photo/model/sharedlib/mechanism.prod.cmp diff --git a/tests/tests/spec_yes_env_no_with_photo/model/configuration/include/mechanism.reac.cmp b/tests/tests/spec_yes_env_no_with_photo/model/sharedlib/mechanism.reac.cmp similarity index 100% rename from tests/tests/spec_yes_env_no_with_photo/model/configuration/include/mechanism.reac.cmp rename to tests/tests/spec_yes_env_no_with_photo/model/sharedlib/mechanism.reac.cmp diff --git a/tests/tests/spec_yes_env_no_with_photo/model/configuration/include/mechanism.ro2.cmp b/tests/tests/spec_yes_env_no_with_photo/model/sharedlib/mechanism.ro2.cmp similarity index 100% rename from tests/tests/spec_yes_env_no_with_photo/model/configuration/include/mechanism.ro2.cmp rename to tests/tests/spec_yes_env_no_with_photo/model/sharedlib/mechanism.ro2.cmp diff --git a/tests/tests/spec_yes_env_no_with_photo/model/configuration/include/mechanism.species.cmp b/tests/tests/spec_yes_env_no_with_photo/model/sharedlib/mechanism.species.cmp similarity index 100% rename from tests/tests/spec_yes_env_no_with_photo/model/configuration/include/mechanism.species.cmp rename to tests/tests/spec_yes_env_no_with_photo/model/sharedlib/mechanism.species.cmp diff --git a/tests/tests/spec_yes_env_yes/model/configuration/include/mechanism.prod.cmp b/tests/tests/spec_yes_env_yes/model/sharedlib/mechanism.prod.cmp similarity index 100% rename from tests/tests/spec_yes_env_yes/model/configuration/include/mechanism.prod.cmp rename to tests/tests/spec_yes_env_yes/model/sharedlib/mechanism.prod.cmp diff --git a/tests/tests/spec_yes_env_yes/model/configuration/include/mechanism.reac.cmp b/tests/tests/spec_yes_env_yes/model/sharedlib/mechanism.reac.cmp similarity index 100% rename from tests/tests/spec_yes_env_yes/model/configuration/include/mechanism.reac.cmp rename to tests/tests/spec_yes_env_yes/model/sharedlib/mechanism.reac.cmp diff --git a/tests/tests/spec_yes_env_yes/model/configuration/include/mechanism.ro2.cmp b/tests/tests/spec_yes_env_yes/model/sharedlib/mechanism.ro2.cmp similarity index 100% rename from tests/tests/spec_yes_env_yes/model/configuration/include/mechanism.ro2.cmp rename to tests/tests/spec_yes_env_yes/model/sharedlib/mechanism.ro2.cmp diff --git a/tests/tests/spec_yes_env_yes/model/configuration/include/mechanism.species.cmp b/tests/tests/spec_yes_env_yes/model/sharedlib/mechanism.species.cmp similarity index 100% rename from tests/tests/spec_yes_env_yes/model/configuration/include/mechanism.species.cmp rename to tests/tests/spec_yes_env_yes/model/sharedlib/mechanism.species.cmp diff --git a/tests/tests/spec_yes_plus_fixed_env_no/model/configuration/include/mechanism.prod.cmp b/tests/tests/spec_yes_plus_fixed_env_no/model/sharedlib/mechanism.prod.cmp similarity index 100% rename from tests/tests/spec_yes_plus_fixed_env_no/model/configuration/include/mechanism.prod.cmp rename to tests/tests/spec_yes_plus_fixed_env_no/model/sharedlib/mechanism.prod.cmp diff --git a/tests/tests/spec_yes_plus_fixed_env_no/model/configuration/include/mechanism.reac.cmp b/tests/tests/spec_yes_plus_fixed_env_no/model/sharedlib/mechanism.reac.cmp similarity index 100% rename from tests/tests/spec_yes_plus_fixed_env_no/model/configuration/include/mechanism.reac.cmp rename to tests/tests/spec_yes_plus_fixed_env_no/model/sharedlib/mechanism.reac.cmp diff --git a/tests/tests/spec_yes_plus_fixed_env_no/model/configuration/include/mechanism.ro2.cmp b/tests/tests/spec_yes_plus_fixed_env_no/model/sharedlib/mechanism.ro2.cmp similarity index 100% rename from tests/tests/spec_yes_plus_fixed_env_no/model/configuration/include/mechanism.ro2.cmp rename to tests/tests/spec_yes_plus_fixed_env_no/model/sharedlib/mechanism.ro2.cmp diff --git a/tests/tests/spec_yes_plus_fixed_env_no/model/configuration/include/mechanism.species.cmp b/tests/tests/spec_yes_plus_fixed_env_no/model/sharedlib/mechanism.species.cmp similarity index 100% rename from tests/tests/spec_yes_plus_fixed_env_no/model/configuration/include/mechanism.species.cmp rename to tests/tests/spec_yes_plus_fixed_env_no/model/sharedlib/mechanism.species.cmp From 45150069c3a3cdb0483851882f27df5d76ec3e4f Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 18:30:58 +0000 Subject: [PATCH 11/16] Correct paths in test scripts --- tests/run_model_tests.sh | 4 ++-- tests/run_tests.sh | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/run_model_tests.sh b/tests/run_model_tests.sh index 1d144830..f7476d5a 100755 --- a/tests/run_model_tests.sh +++ b/tests/run_model_tests.sh @@ -95,7 +95,7 @@ for test in $1; do else # by default, the chemical mechanism is in FACSIMILE format mechanism_file=$TESTS_DIR/$test/$test.fac fi - ./build/build_atchem2.sh --mechanism=$mechanism_file --shared_lib=$TESTS_DIR/$test/configuration/include --configuration=$TESTS_DIR/$test/configuration --mcm=v3.3.1 &> /dev/null + ./build/build_atchem2.sh --mechanism=$mechanism_file --shared_lib=$TESTS_DIR/$test/sharedlib --configuration=$TESTS_DIR/$test/configuration --mcm=v3.3.1 &> /dev/null exitcode=$? if [ $exitcode -ne 0 ]; then echo "Building" $test "test failed with exit code" $exitcode >> $LOG_FILE @@ -103,7 +103,7 @@ for test in $1; do fi # Run atchem2 with the argument pointing to the output directory echo "Running" $TESTS_DIR/$test "..." >> $LOG_FILE - ./atchem2 --output=$TESTS_DIR/$test/output --shared_lib=$TESTS_DIR/$test/configuration/include --configuration=$TESTS_DIR/$test/configuration --constraints=$TESTS_DIR/$test/constraints > $TESTS_DIR/$test/$test.out 2>&1 + ./atchem2 --output=$TESTS_DIR/$test/output --shared_lib=$TESTS_DIR/$test/sharedlib --configuration=$TESTS_DIR/$test/configuration --constraints=$TESTS_DIR/$test/constraints > $TESTS_DIR/$test/$test.out 2>&1 # Now begin the process of diffing the screen output file echo "Comparing" $TESTS_DIR/$test "..." >> $LOG_FILE diff --git a/tests/run_tests.sh b/tests/run_tests.sh index 52784366..b6bdc0a4 100755 --- a/tests/run_tests.sh +++ b/tests/run_tests.sh @@ -90,7 +90,7 @@ for test in $1; do test_counter=$((test_counter+1)) echo "" >> $LOG_FILE echo "Set up and make" $TESTS_DIR/$test >> $LOG_FILE - ./build/build_atchem2.sh --mechanism=$TESTS_DIR/$test/model/configuration/$test.fac --shared_lib=$TESTS_DIR/$test/model/configuration/include --configuration=$TESTS_DIR/$test/model/configuration --mcm=v3.3.1 &> /dev/null + ./build/build_atchem2.sh --mechanism=$TESTS_DIR/$test/model/configuration/$test.fac --shared_lib=$TESTS_DIR/$test/model/sharedlib --configuration=$TESTS_DIR/$test/model/configuration --mcm=v3.3.1 &> /dev/null exitcode=$? if [ $exitcode -ne 0 ]; then echo "Building" $test "test failed with exit code" $exitcode >> $LOG_FILE @@ -98,7 +98,7 @@ for test in $1; do fi # Run atchem2 with the argument pointing to the output directory echo "Running" $TESTS_DIR/$test "..." >> $LOG_FILE - ./atchem2 --output=$TESTS_DIR/$test/output --shared_lib=$TESTS_DIR/$test/model/configuration/include --configuration=$TESTS_DIR/$test/model/configuration --constraints=$TESTS_DIR/$test/model/constraints > $TESTS_DIR/$test/$test.out 2>&1 + ./atchem2 --output=$TESTS_DIR/$test/output --shared_lib=$TESTS_DIR/$test/model/sharedlib --configuration=$TESTS_DIR/$test/model/configuration --constraints=$TESTS_DIR/$test/model/constraints > $TESTS_DIR/$test/$test.out 2>&1 # Now begin the process of diffing the screen output file echo "Comparing" $TESTS_DIR/$test "..." >> $LOG_FILE From f4ef17fd2f3fa26343a2bec07beb5707febcbd52 Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 18:31:33 +0000 Subject: [PATCH 12/16] Change out files in tests --- tests/model_tests/env_model_1/env_model_1.out.cmp | 4 ++-- tests/model_tests/env_model_2/env_model_2.out.cmp | 6 +++--- tests/model_tests/env_model_3/env_model_3.out.cmp | 6 +++--- tests/model_tests/env_model_4/env_model_4.out.cmp | 6 +++--- tests/model_tests/firstorder/firstorder.out.cmp | 4 ++-- tests/model_tests/secondorder/secondorder.out.cmp | 4 ++-- tests/model_tests/spec_model_1/spec_model_1.out.cmp | 4 ++-- tests/model_tests/spec_model_func/spec_model_func.out.cmp | 4 ++-- tests/model_tests/spec_model_kpp/spec_model_kpp.out.cmp | 4 ++-- .../model_tests/spec_model_stoich/spec_model_stoich.out.cmp | 4 ++-- tests/model_tests/static/static.out.cmp | 4 ++-- tests/tests/short/short.out.cmp | 4 ++-- tests/tests/short_dense/short_dense.out.cmp | 4 ++-- tests/tests/short_end_of_day/short_end_of_day.out.cmp | 4 ++-- tests/tests/short_ext1/short_ext1.out.cmp | 4 ++-- tests/tests/short_ext2/short_ext2.out.cmp | 4 ++-- tests/tests/short_ext3/short_ext3.out.cmp | 4 ++-- tests/tests/short_ext4/short_ext4.out.cmp | 4 ++-- tests/tests/short_no_pre/short_no_pre.out.cmp | 4 ++-- tests/tests/spec_no_env_yes1/spec_no_env_yes1.out.cmp | 4 ++-- tests/tests/spec_no_env_yes2/spec_no_env_yes2.out.cmp | 4 ++-- tests/tests/spec_yes_env_no/spec_yes_env_no.out.cmp | 4 ++-- .../spec_yes_env_no_with_jfac.out.cmp | 4 ++-- .../spec_yes_env_no_with_jfac_fail1.out.cmp | 4 ++-- .../spec_yes_env_no_with_jfac_fixed.out.cmp | 6 +++--- .../spec_yes_env_no_with_photo.out.cmp | 4 ++-- tests/tests/spec_yes_env_yes/spec_yes_env_yes.out.cmp | 4 ++-- .../spec_yes_plus_fixed_env_no.out.cmp | 4 ++-- 28 files changed, 60 insertions(+), 60 deletions(-) diff --git a/tests/model_tests/env_model_1/env_model_1.out.cmp b/tests/model_tests/env_model_1/env_model_1.out.cmp index 7e6928e0..b796bbe6 100644 --- a/tests/model_tests/env_model_1/env_model_1.out.cmp +++ b/tests/model_tests/env_model_1/env_model_1.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/model_tests/env_model_1/constraints/environment Photolysis Constraints directory is: tests/model_tests/env_model_1/constraints/photolysis Species Constraints directory is: tests/model_tests/env_model_1/constraints/species - Shared Library directory is: tests/model_tests/env_model_1/configuration/include - Shared Library is: tests/model_tests/env_model_1/configuration/include/mechanism.so + Shared Library directory is: tests/model_tests/env_model_1/sharedlib + Shared Library is: tests/model_tests/env_model_1/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/model_tests/env_model_2/env_model_2.out.cmp b/tests/model_tests/env_model_2/env_model_2.out.cmp index 5cbb76e1..9d5b55e2 100644 --- a/tests/model_tests/env_model_2/env_model_2.out.cmp +++ b/tests/model_tests/env_model_2/env_model_2.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/model_tests/env_model_2/constraints/environment Photolysis Constraints directory is: tests/model_tests/env_model_2/constraints/photolysis Species Constraints directory is: tests/model_tests/env_model_2/constraints/species - Shared Library directory is: tests/model_tests/env_model_2/configuration/include - Shared Library is: tests/model_tests/env_model_2/configuration/include/mechanism.so + Shared Library directory is: tests/model_tests/env_model_2/sharedlib + Shared Library is: tests/model_tests/env_model_2/sharedlib/mechanism.so ----------------------- Species and reactions @@ -129,7 +129,7 @@ AtChem2 v1.3-dev 7 DILUTE NOTUSED 8 JFAC 1 Reading all photolysis rates from file... - 1 not found in tests/model_tests/env_model_2/configuration/include/photolysis-rates, so it will be treated as a constant. + 1 not found in tests/model_tests/env_model_2/sharedlib/photolysis-rates, so it will be treated as a constant. 9 ROOF OPEN 10 ASA NOTUSED Finished reading environment variables. diff --git a/tests/model_tests/env_model_3/env_model_3.out.cmp b/tests/model_tests/env_model_3/env_model_3.out.cmp index 9a2045f9..d997c0e3 100644 --- a/tests/model_tests/env_model_3/env_model_3.out.cmp +++ b/tests/model_tests/env_model_3/env_model_3.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/model_tests/env_model_3/constraints/environment Photolysis Constraints directory is: tests/model_tests/env_model_3/constraints/photolysis Species Constraints directory is: tests/model_tests/env_model_3/constraints/species - Shared Library directory is: tests/model_tests/env_model_3/configuration/include - Shared Library is: tests/model_tests/env_model_3/configuration/include/mechanism.so + Shared Library directory is: tests/model_tests/env_model_3/sharedlib + Shared Library is: tests/model_tests/env_model_3/sharedlib/mechanism.so ----------------------- Species and reactions @@ -129,7 +129,7 @@ AtChem2 v1.3-dev 7 DILUTE NOTUSED 8 JFAC 0 Reading all photolysis rates from file... - 0 not found in tests/model_tests/env_model_3/configuration/include/photolysis-rates, so it will be treated as a constant. + 0 not found in tests/model_tests/env_model_3/sharedlib/photolysis-rates, so it will be treated as a constant. 9 ROOF OPEN 10 ASA NOTUSED Finished reading environment variables. diff --git a/tests/model_tests/env_model_4/env_model_4.out.cmp b/tests/model_tests/env_model_4/env_model_4.out.cmp index 09d7681b..9eb6d5c0 100644 --- a/tests/model_tests/env_model_4/env_model_4.out.cmp +++ b/tests/model_tests/env_model_4/env_model_4.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/model_tests/env_model_4/constraints/environment Photolysis Constraints directory is: tests/model_tests/env_model_4/constraints/photolysis Species Constraints directory is: tests/model_tests/env_model_4/constraints/species - Shared Library directory is: tests/model_tests/env_model_4/configuration/include - Shared Library is: tests/model_tests/env_model_4/configuration/include/mechanism.so + Shared Library directory is: tests/model_tests/env_model_4/sharedlib + Shared Library is: tests/model_tests/env_model_4/sharedlib/mechanism.so ----------------------- Species and reactions @@ -129,7 +129,7 @@ AtChem2 v1.3-dev 7 DILUTE NOTUSED 8 JFAC 1 Reading all photolysis rates from file... - 1 not found in tests/model_tests/env_model_4/configuration/include/photolysis-rates, so it will be treated as a constant. + 1 not found in tests/model_tests/env_model_4/sharedlib/photolysis-rates, so it will be treated as a constant. 9 ROOF CLOSED 10 ASA NOTUSED Finished reading environment variables. diff --git a/tests/model_tests/firstorder/firstorder.out.cmp b/tests/model_tests/firstorder/firstorder.out.cmp index dc5fd78e..8c018194 100644 --- a/tests/model_tests/firstorder/firstorder.out.cmp +++ b/tests/model_tests/firstorder/firstorder.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/model_tests/firstorder/constraints/environment Photolysis Constraints directory is: tests/model_tests/firstorder/constraints/photolysis Species Constraints directory is: tests/model_tests/firstorder/constraints/species - Shared Library directory is: tests/model_tests/firstorder/configuration/include - Shared Library is: tests/model_tests/firstorder/configuration/include/mechanism.so + Shared Library directory is: tests/model_tests/firstorder/sharedlib + Shared Library is: tests/model_tests/firstorder/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/model_tests/secondorder/secondorder.out.cmp b/tests/model_tests/secondorder/secondorder.out.cmp index 2a027fae..e8016494 100644 --- a/tests/model_tests/secondorder/secondorder.out.cmp +++ b/tests/model_tests/secondorder/secondorder.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/model_tests/secondorder/constraints/environment Photolysis Constraints directory is: tests/model_tests/secondorder/constraints/photolysis Species Constraints directory is: tests/model_tests/secondorder/constraints/species - Shared Library directory is: tests/model_tests/secondorder/configuration/include - Shared Library is: tests/model_tests/secondorder/configuration/include/mechanism.so + Shared Library directory is: tests/model_tests/secondorder/sharedlib + Shared Library is: tests/model_tests/secondorder/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/model_tests/spec_model_1/spec_model_1.out.cmp b/tests/model_tests/spec_model_1/spec_model_1.out.cmp index 7b30406d..8fefcb20 100644 --- a/tests/model_tests/spec_model_1/spec_model_1.out.cmp +++ b/tests/model_tests/spec_model_1/spec_model_1.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/model_tests/spec_model_1/constraints/environment Photolysis Constraints directory is: tests/model_tests/spec_model_1/constraints/photolysis Species Constraints directory is: tests/model_tests/spec_model_1/constraints/species - Shared Library directory is: tests/model_tests/spec_model_1/configuration/include - Shared Library is: tests/model_tests/spec_model_1/configuration/include/mechanism.so + Shared Library directory is: tests/model_tests/spec_model_1/sharedlib + Shared Library is: tests/model_tests/spec_model_1/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/model_tests/spec_model_func/spec_model_func.out.cmp b/tests/model_tests/spec_model_func/spec_model_func.out.cmp index 59f9215a..879ff5cc 100644 --- a/tests/model_tests/spec_model_func/spec_model_func.out.cmp +++ b/tests/model_tests/spec_model_func/spec_model_func.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/model_tests/spec_model_func/constraints/environment Photolysis Constraints directory is: tests/model_tests/spec_model_func/constraints/photolysis Species Constraints directory is: tests/model_tests/spec_model_func/constraints/species - Shared Library directory is: tests/model_tests/spec_model_func/configuration/include - Shared Library is: tests/model_tests/spec_model_func/configuration/include/mechanism.so + Shared Library directory is: tests/model_tests/spec_model_func/sharedlib + Shared Library is: tests/model_tests/spec_model_func/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/model_tests/spec_model_kpp/spec_model_kpp.out.cmp b/tests/model_tests/spec_model_kpp/spec_model_kpp.out.cmp index 65d50ee7..bd13514e 100644 --- a/tests/model_tests/spec_model_kpp/spec_model_kpp.out.cmp +++ b/tests/model_tests/spec_model_kpp/spec_model_kpp.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/model_tests/spec_model_kpp/constraints/environment Photolysis Constraints directory is: tests/model_tests/spec_model_kpp/constraints/photolysis Species Constraints directory is: tests/model_tests/spec_model_kpp/constraints/species - Shared Library directory is: tests/model_tests/spec_model_kpp/configuration/include - Shared Library is: tests/model_tests/spec_model_kpp/configuration/include/mechanism.so + Shared Library directory is: tests/model_tests/spec_model_kpp/sharedlib + Shared Library is: tests/model_tests/spec_model_kpp/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/model_tests/spec_model_stoich/spec_model_stoich.out.cmp b/tests/model_tests/spec_model_stoich/spec_model_stoich.out.cmp index d62ee738..0e807c00 100644 --- a/tests/model_tests/spec_model_stoich/spec_model_stoich.out.cmp +++ b/tests/model_tests/spec_model_stoich/spec_model_stoich.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/model_tests/spec_model_stoich/constraints/environment Photolysis Constraints directory is: tests/model_tests/spec_model_stoich/constraints/photolysis Species Constraints directory is: tests/model_tests/spec_model_stoich/constraints/species - Shared Library directory is: tests/model_tests/spec_model_stoich/configuration/include - Shared Library is: tests/model_tests/spec_model_stoich/configuration/include/mechanism.so + Shared Library directory is: tests/model_tests/spec_model_stoich/sharedlib + Shared Library is: tests/model_tests/spec_model_stoich/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/model_tests/static/static.out.cmp b/tests/model_tests/static/static.out.cmp index fc4af145..e6f57842 100644 --- a/tests/model_tests/static/static.out.cmp +++ b/tests/model_tests/static/static.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/model_tests/static/constraints/environment Photolysis Constraints directory is: tests/model_tests/static/constraints/photolysis Species Constraints directory is: tests/model_tests/static/constraints/species - Shared Library directory is: tests/model_tests/static/configuration/include - Shared Library is: tests/model_tests/static/configuration/include/mechanism.so + Shared Library directory is: tests/model_tests/static/sharedlib + Shared Library is: tests/model_tests/static/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/short/short.out.cmp b/tests/tests/short/short.out.cmp index a34587b1..0cb0c778 100644 --- a/tests/tests/short/short.out.cmp +++ b/tests/tests/short/short.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/short/model/constraints/environment Photolysis Constraints directory is: tests/tests/short/model/constraints/photolysis Species Constraints directory is: tests/tests/short/model/constraints/species - Shared Library directory is: tests/tests/short/model/configuration/include - Shared Library is: tests/tests/short/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/short/model/sharedlib + Shared Library is: tests/tests/short/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/short_dense/short_dense.out.cmp b/tests/tests/short_dense/short_dense.out.cmp index 4d4d0489..237bf4de 100644 --- a/tests/tests/short_dense/short_dense.out.cmp +++ b/tests/tests/short_dense/short_dense.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/short_dense/model/constraints/environment Photolysis Constraints directory is: tests/tests/short_dense/model/constraints/photolysis Species Constraints directory is: tests/tests/short_dense/model/constraints/species - Shared Library directory is: tests/tests/short_dense/model/configuration/include - Shared Library is: tests/tests/short_dense/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/short_dense/model/sharedlib + Shared Library is: tests/tests/short_dense/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/short_end_of_day/short_end_of_day.out.cmp b/tests/tests/short_end_of_day/short_end_of_day.out.cmp index c50bcca3..fc2f6d39 100644 --- a/tests/tests/short_end_of_day/short_end_of_day.out.cmp +++ b/tests/tests/short_end_of_day/short_end_of_day.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/short_end_of_day/model/constraints/environment Photolysis Constraints directory is: tests/tests/short_end_of_day/model/constraints/photolysis Species Constraints directory is: tests/tests/short_end_of_day/model/constraints/species - Shared Library directory is: tests/tests/short_end_of_day/model/configuration/include - Shared Library is: tests/tests/short_end_of_day/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/short_end_of_day/model/sharedlib + Shared Library is: tests/tests/short_end_of_day/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/short_ext1/short_ext1.out.cmp b/tests/tests/short_ext1/short_ext1.out.cmp index 114f2bc7..4a649670 100644 --- a/tests/tests/short_ext1/short_ext1.out.cmp +++ b/tests/tests/short_ext1/short_ext1.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/short_ext1/model/constraints/environment Photolysis Constraints directory is: tests/tests/short_ext1/model/constraints/photolysis Species Constraints directory is: tests/tests/short_ext1/model/constraints/species - Shared Library directory is: tests/tests/short_ext1/model/configuration/include - Shared Library is: tests/tests/short_ext1/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/short_ext1/model/sharedlib + Shared Library is: tests/tests/short_ext1/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/short_ext2/short_ext2.out.cmp b/tests/tests/short_ext2/short_ext2.out.cmp index 0ad19355..945cdfd2 100644 --- a/tests/tests/short_ext2/short_ext2.out.cmp +++ b/tests/tests/short_ext2/short_ext2.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/short_ext2/model/constraints/environment Photolysis Constraints directory is: tests/tests/short_ext2/model/constraints/photolysis Species Constraints directory is: tests/tests/short_ext2/model/constraints/species - Shared Library directory is: tests/tests/short_ext2/model/configuration/include - Shared Library is: tests/tests/short_ext2/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/short_ext2/model/sharedlib + Shared Library is: tests/tests/short_ext2/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/short_ext3/short_ext3.out.cmp b/tests/tests/short_ext3/short_ext3.out.cmp index e7bcfca6..5782a05f 100644 --- a/tests/tests/short_ext3/short_ext3.out.cmp +++ b/tests/tests/short_ext3/short_ext3.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/short_ext3/model/constraints/environment Photolysis Constraints directory is: tests/tests/short_ext3/model/constraints/photolysis Species Constraints directory is: tests/tests/short_ext3/model/constraints/species - Shared Library directory is: tests/tests/short_ext3/model/configuration/include - Shared Library is: tests/tests/short_ext3/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/short_ext3/model/sharedlib + Shared Library is: tests/tests/short_ext3/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/short_ext4/short_ext4.out.cmp b/tests/tests/short_ext4/short_ext4.out.cmp index ba1c3a81..42ce283d 100644 --- a/tests/tests/short_ext4/short_ext4.out.cmp +++ b/tests/tests/short_ext4/short_ext4.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/short_ext4/model/constraints/environment Photolysis Constraints directory is: tests/tests/short_ext4/model/constraints/photolysis Species Constraints directory is: tests/tests/short_ext4/model/constraints/species - Shared Library directory is: tests/tests/short_ext4/model/configuration/include - Shared Library is: tests/tests/short_ext4/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/short_ext4/model/sharedlib + Shared Library is: tests/tests/short_ext4/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/short_no_pre/short_no_pre.out.cmp b/tests/tests/short_no_pre/short_no_pre.out.cmp index 6a069a36..5b2a8791 100644 --- a/tests/tests/short_no_pre/short_no_pre.out.cmp +++ b/tests/tests/short_no_pre/short_no_pre.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/short_no_pre/model/constraints/environment Photolysis Constraints directory is: tests/tests/short_no_pre/model/constraints/photolysis Species Constraints directory is: tests/tests/short_no_pre/model/constraints/species - Shared Library directory is: tests/tests/short_no_pre/model/configuration/include - Shared Library is: tests/tests/short_no_pre/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/short_no_pre/model/sharedlib + Shared Library is: tests/tests/short_no_pre/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/spec_no_env_yes1/spec_no_env_yes1.out.cmp b/tests/tests/spec_no_env_yes1/spec_no_env_yes1.out.cmp index 45bf4e31..91fe84bb 100644 --- a/tests/tests/spec_no_env_yes1/spec_no_env_yes1.out.cmp +++ b/tests/tests/spec_no_env_yes1/spec_no_env_yes1.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/spec_no_env_yes1/model/constraints/environment Photolysis Constraints directory is: tests/tests/spec_no_env_yes1/model/constraints/photolysis Species Constraints directory is: tests/tests/spec_no_env_yes1/model/constraints/species - Shared Library directory is: tests/tests/spec_no_env_yes1/model/configuration/include - Shared Library is: tests/tests/spec_no_env_yes1/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/spec_no_env_yes1/model/sharedlib + Shared Library is: tests/tests/spec_no_env_yes1/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/spec_no_env_yes2/spec_no_env_yes2.out.cmp b/tests/tests/spec_no_env_yes2/spec_no_env_yes2.out.cmp index e4d31ffb..33b7c15b 100644 --- a/tests/tests/spec_no_env_yes2/spec_no_env_yes2.out.cmp +++ b/tests/tests/spec_no_env_yes2/spec_no_env_yes2.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/spec_no_env_yes2/model/constraints/environment Photolysis Constraints directory is: tests/tests/spec_no_env_yes2/model/constraints/photolysis Species Constraints directory is: tests/tests/spec_no_env_yes2/model/constraints/species - Shared Library directory is: tests/tests/spec_no_env_yes2/model/configuration/include - Shared Library is: tests/tests/spec_no_env_yes2/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/spec_no_env_yes2/model/sharedlib + Shared Library is: tests/tests/spec_no_env_yes2/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/spec_yes_env_no/spec_yes_env_no.out.cmp b/tests/tests/spec_yes_env_no/spec_yes_env_no.out.cmp index e533e7e2..4dbb4c9e 100644 --- a/tests/tests/spec_yes_env_no/spec_yes_env_no.out.cmp +++ b/tests/tests/spec_yes_env_no/spec_yes_env_no.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/spec_yes_env_no/model/constraints/environment Photolysis Constraints directory is: tests/tests/spec_yes_env_no/model/constraints/photolysis Species Constraints directory is: tests/tests/spec_yes_env_no/model/constraints/species - Shared Library directory is: tests/tests/spec_yes_env_no/model/configuration/include - Shared Library is: tests/tests/spec_yes_env_no/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/spec_yes_env_no/model/sharedlib + Shared Library is: tests/tests/spec_yes_env_no/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/spec_yes_env_no_with_jfac/spec_yes_env_no_with_jfac.out.cmp b/tests/tests/spec_yes_env_no_with_jfac/spec_yes_env_no_with_jfac.out.cmp index 16b035e4..bf70bc72 100644 --- a/tests/tests/spec_yes_env_no_with_jfac/spec_yes_env_no_with_jfac.out.cmp +++ b/tests/tests/spec_yes_env_no_with_jfac/spec_yes_env_no_with_jfac.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/spec_yes_env_no_with_jfac/model/constraints/environment Photolysis Constraints directory is: tests/tests/spec_yes_env_no_with_jfac/model/constraints/photolysis Species Constraints directory is: tests/tests/spec_yes_env_no_with_jfac/model/constraints/species - Shared Library directory is: tests/tests/spec_yes_env_no_with_jfac/model/configuration/include - Shared Library is: tests/tests/spec_yes_env_no_with_jfac/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/spec_yes_env_no_with_jfac/model/sharedlib + Shared Library is: tests/tests/spec_yes_env_no_with_jfac/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/spec_yes_env_no_with_jfac_fail1/spec_yes_env_no_with_jfac_fail1.out.cmp b/tests/tests/spec_yes_env_no_with_jfac_fail1/spec_yes_env_no_with_jfac_fail1.out.cmp index b701cf9c..8c95d122 100644 --- a/tests/tests/spec_yes_env_no_with_jfac_fail1/spec_yes_env_no_with_jfac_fail1.out.cmp +++ b/tests/tests/spec_yes_env_no_with_jfac_fail1/spec_yes_env_no_with_jfac_fail1.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/spec_yes_env_no_with_jfac_fail1/model/constraints/environment Photolysis Constraints directory is: tests/tests/spec_yes_env_no_with_jfac_fail1/model/constraints/photolysis Species Constraints directory is: tests/tests/spec_yes_env_no_with_jfac_fail1/model/constraints/species - Shared Library directory is: tests/tests/spec_yes_env_no_with_jfac_fail1/model/configuration/include - Shared Library is: tests/tests/spec_yes_env_no_with_jfac_fail1/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/spec_yes_env_no_with_jfac_fail1/model/sharedlib + Shared Library is: tests/tests/spec_yes_env_no_with_jfac_fail1/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/spec_yes_env_no_with_jfac_fixed/spec_yes_env_no_with_jfac_fixed.out.cmp b/tests/tests/spec_yes_env_no_with_jfac_fixed/spec_yes_env_no_with_jfac_fixed.out.cmp index bb1079c1..52bf4184 100644 --- a/tests/tests/spec_yes_env_no_with_jfac_fixed/spec_yes_env_no_with_jfac_fixed.out.cmp +++ b/tests/tests/spec_yes_env_no_with_jfac_fixed/spec_yes_env_no_with_jfac_fixed.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/spec_yes_env_no_with_jfac_fixed/model/constraints/environment Photolysis Constraints directory is: tests/tests/spec_yes_env_no_with_jfac_fixed/model/constraints/photolysis Species Constraints directory is: tests/tests/spec_yes_env_no_with_jfac_fixed/model/constraints/species - Shared Library directory is: tests/tests/spec_yes_env_no_with_jfac_fixed/model/configuration/include - Shared Library is: tests/tests/spec_yes_env_no_with_jfac_fixed/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/spec_yes_env_no_with_jfac_fixed/model/sharedlib + Shared Library is: tests/tests/spec_yes_env_no_with_jfac_fixed/model/sharedlib/mechanism.so ----------------------- Species and reactions @@ -129,7 +129,7 @@ AtChem2 v1.3-dev 7 DILUTE NOTUSED 8 JFAC 0.9 Reading all photolysis rates from file... - 0.9 not found in tests/tests/spec_yes_env_no_with_jfac_fixed/model/configuration/include/photolysis-rates, so it will be treated as a constant. + 0.9 not found in tests/tests/spec_yes_env_no_with_jfac_fixed/model/sharedlib/photolysis-rates, so it will be treated as a constant. 9 ROOF OPEN 10 ASA NOTUSED Finished reading environment variables. diff --git a/tests/tests/spec_yes_env_no_with_photo/spec_yes_env_no_with_photo.out.cmp b/tests/tests/spec_yes_env_no_with_photo/spec_yes_env_no_with_photo.out.cmp index 6a19441b..f4b9d473 100644 --- a/tests/tests/spec_yes_env_no_with_photo/spec_yes_env_no_with_photo.out.cmp +++ b/tests/tests/spec_yes_env_no_with_photo/spec_yes_env_no_with_photo.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/spec_yes_env_no_with_photo/model/constraints/environment Photolysis Constraints directory is: tests/tests/spec_yes_env_no_with_photo/model/constraints/photolysis Species Constraints directory is: tests/tests/spec_yes_env_no_with_photo/model/constraints/species - Shared Library directory is: tests/tests/spec_yes_env_no_with_photo/model/configuration/include - Shared Library is: tests/tests/spec_yes_env_no_with_photo/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/spec_yes_env_no_with_photo/model/sharedlib + Shared Library is: tests/tests/spec_yes_env_no_with_photo/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/spec_yes_env_yes/spec_yes_env_yes.out.cmp b/tests/tests/spec_yes_env_yes/spec_yes_env_yes.out.cmp index 67f07c07..c80a9285 100644 --- a/tests/tests/spec_yes_env_yes/spec_yes_env_yes.out.cmp +++ b/tests/tests/spec_yes_env_yes/spec_yes_env_yes.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/spec_yes_env_yes/model/constraints/environment Photolysis Constraints directory is: tests/tests/spec_yes_env_yes/model/constraints/photolysis Species Constraints directory is: tests/tests/spec_yes_env_yes/model/constraints/species - Shared Library directory is: tests/tests/spec_yes_env_yes/model/configuration/include - Shared Library is: tests/tests/spec_yes_env_yes/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/spec_yes_env_yes/model/sharedlib + Shared Library is: tests/tests/spec_yes_env_yes/model/sharedlib/mechanism.so ----------------------- Species and reactions diff --git a/tests/tests/spec_yes_plus_fixed_env_no/spec_yes_plus_fixed_env_no.out.cmp b/tests/tests/spec_yes_plus_fixed_env_no/spec_yes_plus_fixed_env_no.out.cmp index adcecce3..eea9ab3d 100644 --- a/tests/tests/spec_yes_plus_fixed_env_no/spec_yes_plus_fixed_env_no.out.cmp +++ b/tests/tests/spec_yes_plus_fixed_env_no/spec_yes_plus_fixed_env_no.out.cmp @@ -11,8 +11,8 @@ AtChem2 v1.3-dev Environment Constraints directory is: tests/tests/spec_yes_plus_fixed_env_no/model/constraints/environment Photolysis Constraints directory is: tests/tests/spec_yes_plus_fixed_env_no/model/constraints/photolysis Species Constraints directory is: tests/tests/spec_yes_plus_fixed_env_no/model/constraints/species - Shared Library directory is: tests/tests/spec_yes_plus_fixed_env_no/model/configuration/include - Shared Library is: tests/tests/spec_yes_plus_fixed_env_no/model/configuration/include/mechanism.so + Shared Library directory is: tests/tests/spec_yes_plus_fixed_env_no/model/sharedlib + Shared Library is: tests/tests/spec_yes_plus_fixed_env_no/model/sharedlib/mechanism.so ----------------------- Species and reactions From 68e219e39f473bb1df55c2faf38fe4a6c65abbc1 Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 18:35:17 +0000 Subject: [PATCH 13/16] Correct paths for GH actions --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 641b163a..ad4f7db3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -126,7 +126,7 @@ jobs: FORT_VERSION: ${{ matrix.fortran }} run: | cp tools/install/Makefile.skel Makefile - ./build/build_atchem2.sh --mechanism=./model/mechanism.fac --shared_lib=./model/configuration/include --configuration=./model/configuration --mcm=v3.3.1 + ./build/build_atchem2.sh --mechanism=./model/mechanism.fac --shared_lib=./model/sharedlib --configuration=./model/configuration --mcm=v3.3.1 # macos only if [ $RUNNER_OS != "Linux" ] ; then From cac6110f1e519431eb7648a32b9a3fb2363b1826 Mon Sep 17 00:00:00 2001 From: rs028 Date: Mon, 19 Jan 2026 18:46:19 +0000 Subject: [PATCH 14/16] Correct paths in src and Makefile --- build/mech_converter.py | 4 ++-- src/argparse.f90 | 2 +- tools/install/Makefile.skel | 24 ++++++++++++------------ 3 files changed, 15 insertions(+), 15 deletions(-) diff --git a/build/mech_converter.py b/build/mech_converter.py index 1bce672c..9f6b2bba 100644 --- a/build/mech_converter.py +++ b/build/mech_converter.py @@ -715,9 +715,9 @@ def main(): config_dir = "model/configuration" else: config_dir = sys.argv[2] - # `shared_dir` defaults to `model/configuration/include`, if not given as argument + # `shared_dir` defaults to `model/sharedlib`, if not given as argument if len(sys.argv) <= 3: - shared_dir = "model/configuration/include" + shared_dir = "model/sharedlib" else: shared_dir = sys.argv[3] # `mcm_vers` defaults to `v3.3.1`, if not given as argument diff --git a/src/argparse.f90 b/src/argparse.f90 index 94bc2787..76ead650 100644 --- a/src/argparse.f90 +++ b/src/argparse.f90 @@ -281,7 +281,7 @@ subroutine get_and_set_directories_from_command_arguments() spec_constraints_dir = read_value_or_default( valid_flags(8)%flag_switch, & trim(constraints_dir)//'/species', names, values ) shared_lib_dir = read_value_or_default( valid_flags(9)%flag_switch, & - trim(model_dir)//'/configuration/include', names, values ) + trim(model_dir)//'/sharedlib', names, values ) shared_library = trim(shared_lib_dir)//'/mechanism.so' write (*, '(2A)') ' Model directory is: ', trim( model_dir ) diff --git a/tools/install/Makefile.skel b/tools/install/Makefile.skel index 0a145eac..926549d7 100644 --- a/tools/install/Makefile.skel +++ b/tools/install/Makefile.skel @@ -124,29 +124,29 @@ include tests/makefile.tests # - the MCM version is: v3.3.1 MECHFILE = model/mechanism.fac CONFIGDIR = model/configuration -MECHDIR = $(CONFIGDIR)/include -SHAREDLIB = $(MECHDIR)/mechanism.so +SHAREDLIBDIR = model/sharedlib +SHAREDLIB = $(SHAREDLIBDIR)/mechanism.so MCMVERS = v3.3.1 # mechanism conversion MECH_CONVERTER = build/mech_converter.py -MECH_GEN = $(MECHDIR)/mechanism.f90 $(MECHDIR)/mechanism.species \ - $(MECHDIR)/mechanism.reac $(MECHDIR)/mechanism.prod \ - $(MECHDIR)/mechanism.ro2 +MECH_GEN = $(SHAREDLIBDIR)/mechanism.f90 $(SHAREDLIBDIR)/mechanism.species \ + $(SHAREDLIBDIR)/mechanism.reac $(SHAREDLIBDIR)/mechanism.prod \ + $(SHAREDLIBDIR)/mechanism.ro2 # the mechanism conversion script is run every time the mechanism file ($MECHFILE) # is modified PYTHON_BIN = python $(MECH_GEN): $(MECHFILE) $(MECH_CONVERTER) - $(PYTHON_BIN) $(MECH_CONVERTER) $(MECHFILE) $(CONFIGDIR) $(MECHDIR) $(MCMVERS) + $(PYTHON_BIN) $(MECH_CONVERTER) $(MECHFILE) $(CONFIGDIR) $(SHAREDLIBDIR) $(MCMVERS) # the mechanism shared library is rebuilt if the fortran files (`mechanism.*`) -# in $MECHDIR or the `customRateFuncs.f90` file in $CONFIGDIR are modified +# in $SHAREDLIBDIR or the `customRateFuncs.f90` file in $CONFIGDIR are modified $(SHAREDLIB): $(MECH_GEN) - $(FORT_COMP) -c $(SRC)/dataStructures.f90 $(FSHAREDFLAGS) -o $(MECHDIR)/dataStructures.o -J$(MECHDIR) -I$(MECHDIR) - $(FORT_COMP) -c $(CONFIGDIR)/customRateFuncs.f90 $(FSHAREDFLAGS) -o $(MECHDIR)/customRateFuncs.o -J$(MECHDIR) -I$(MECHDIR) - $(FORT_COMP) -c $(MECHDIR)/mechanism.f90 $(FSHAREDFLAGS) -o $(MECHDIR)/mechanism.o -J$(MECHDIR) -I$(MECHDIR) - $(FORT_COMP) -shared -o $(SHAREDLIB) $(MECHDIR)/dataStructures.o $(MECHDIR)/customRateFuncs.o $(MECHDIR)/mechanism.o + $(FORT_COMP) -c $(SRC)/dataStructures.f90 $(FSHAREDFLAGS) -o $(SHAREDLIBDIR)/dataStructures.o -J$(SHAREDLIBDIR) -I$(SHAREDLIBDIR) + $(FORT_COMP) -c $(CONFIGDIR)/customRateFuncs.f90 $(FSHAREDFLAGS) -o $(SHAREDLIBDIR)/customRateFuncs.o -J$(SHAREDLIBDIR) -I$(SHAREDLIBDIR) + $(FORT_COMP) -c $(SHAREDLIBDIR)/mechanism.f90 $(FSHAREDFLAGS) -o $(SHAREDLIBDIR)/mechanism.o -J$(SHAREDLIBDIR) -I$(SHAREDLIBDIR) + $(FORT_COMP) -shared -o $(SHAREDLIB) $(SHAREDLIBDIR)/dataStructures.o $(SHAREDLIBDIR)/customRateFuncs.o $(SHAREDLIBDIR)/mechanism.o # ====================== Makefile rules ====================== # @@ -160,7 +160,7 @@ clean: rm -rf build/__pycache__ rm -f *.{gcda,gcno,xml} build/*.pyc tests/*.log rm -f doc/figures/*.png doc/latex/*.{aux,bbl,blg,log,out,toc} - rm -f $(MECHDIR)/mechanism.{f90,prod,reac,ro2,species} $(MECHDIR)/*.{o,mod,so} \ + rm -f $(SHAREDLIBDIR)/mechanism.{f90,prod,reac,ro2,species} $(SHAREDLIBDIR)/*.{o,mod,so} \ model/output/*.{output,pdf} model/output/reactionRates/*[0-9] rm -f tests/tests/*/*.out tests/tests/*/model/configuration/include/mechanism.{f90,prod,reac,ro2,species} \ tests/tests/*/model/configuration/include/*.{o,mod,so} \ From b703b734fee930c1e0b59468e194cb9391680570 Mon Sep 17 00:00:00 2001 From: rs028 Date: Tue, 20 Jan 2026 12:47:34 +0000 Subject: [PATCH 15/16] Correct info --- CHANGELOG.md | 8 ++++++-- src/inputFunctions.f90 | 4 ++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 601d2141..7cd29546 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,8 +5,12 @@ AtChem2 -- CHANGELOG post v1.2.3 ----------- -- make install scripts more robust, and update to **openlibm v0.8.6** -- add option to use time in user-defined Fortran functions +- implement named arguments (flags) for the `build_atchem2.sh` script +- remove the `mcm` argument from the executable, and redefine it in the build script to indicate the version of the MCM used +- make shell scripts more robust, and update to **openlibm v0.8.6** +- reformat python scripts using **black**, and add a python format test to the Testsuite +- add option to use time in user-defined custom Fortran functions +- update copyright notes v1.2.3 (May 2025) diff --git a/src/inputFunctions.f90 b/src/inputFunctions.f90 index 766f711e..673d3569 100644 --- a/src/inputFunctions.f90 +++ b/src/inputFunctions.f90 @@ -262,7 +262,7 @@ end subroutine setConcentrations ! ----------------------------------------------------------------- ! This is called from readPhotoRates(). It reads photolysisNumbers - ! from the first column of `model/configuration/include/photolysis-rates` so that we know + ! from the first column of `model/sharedlib/photolysis-rates` so that we know ! the ID numbers of all photolysis rates and how many there are. subroutine readPhotolysisNumbers() use, intrinsic :: iso_fortran_env, only : stderr => error_unit @@ -604,7 +604,7 @@ end subroutine readUnconstrainedPhotolysisRates ! This is called from readPhotoRates() if ! model/configuration/photolysisConstant.config doesn't exist/is ! empty. It reads ck, cl, cmm, cnn, unconstrainedPhotoNames and - ! transmissionFactor from `model/configuration/include/photolysis-rates`. It uses + ! transmissionFactor from `model/sharedlib/photolysis-rates`. It uses ! numUnconstrainedPhotoRates to allocate accordingly. subroutine readAllPhotolysisRates() use, intrinsic :: iso_fortran_env, only : stderr => error_unit From 45372fb2ac0f73eef8fdca4223a7c57364b7bbac Mon Sep 17 00:00:00 2001 From: rs028 Date: Tue, 3 Feb 2026 14:45:55 +0000 Subject: [PATCH 16/16] Mechanism file flag is optional --- build/build_atchem2.sh | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/build/build_atchem2.sh b/build/build_atchem2.sh index 514d436e..ccd38423 100755 --- a/build/build_atchem2.sh +++ b/build/build_atchem2.sh @@ -69,10 +69,14 @@ while [ "$#" -gt 0 ]; do --mcm=*) MCMV="${1#*=}" ;; - *) + -*) printf "\n[INPUT ERROR] Invalid argument: %s\n" "$1" >&2 exit 1 ;; + *) # if the script flag is not specified assume the argument is the + # chemical mechanism file (`$MECHF`) + MECHF="$1" + ;; esac shift done