Set shared library directory

.github/workflows/ci.yml

@@ -93,8 +93,9 @@ jobs:
       # -------------------------------------------------------------
       # (3) Install the AtChem2 dependencies: CVODE, openlibm, numdiff, FRUIT
       #
-      # NB: Ruby v3.2 does not work with the current version of FRUIT,
-      #     so v3.0 is used here as a temporary fix
+      # NB: the current version of FRUIT (v3.4.3) does not work with the most
+      #     recent versions of Ruby; as a temporary fix, Ruby v3.0 is used for
+      #     all unit tests in this workflow
       #
       # ACTION: https://github.com/marketplace/actions/setup-ruby-jruby-and-truffleruby
 
@@ -134,8 +135,10 @@ jobs:
           fi
 
       # -------------------------------------------------------------
-      # (5) Run the Testsuite using the standard compilation flags and
-      #     the default model settings
+      # (5) Run the Testsuite using the standard compilation flags and the
+      #     default model settings, then upload the log files as artifacts
+      #
+      # ACTION: https://github.com/marketplace/actions/upload-a-build-artifact
 
       - name: Indent and Style tests
         run: |
@@ -145,12 +148,19 @@ jobs:
       - name: Unit and Model tests
         env:
           FORT_VERSION: ${{ matrix.fortran }}
+        # continue-on-error: true
         run: |
           export PATH=$PATH:$PWD/numdiff/bin
           make unittests
           make oldtests   # NB: oldtests will eventually be merged into modeltests
           make modeltests
 
+      - name: Save log files
+        uses: actions/upload-artifact@v4
+        with:
+          name: testsuite_${{ matrix.os }}_fortran-${{ matrix.fortran }}.log
+          path: tests/*.log
+
       # -------------------------------------------------------------
       # (6) Recompile AtChem2 using the code coverage compilation flags,
       #     run the Testsuite and upload the gcov files to Codecov

build/build_atchem2.sh

@@ -11,55 +11,77 @@
 # -----------------------------------------------------------------------------
 
 # -----------------------------------------------------------------------------
-# Script to process the mechanism file (*.fac) and convert it to the
-# correct format for AtChem2.
+# Script to build and compile AtChem2.
 #
-# $1 is the location of the chemical mechanism file in FACSIMILE
-#    format. Argument $1 is NOT optional, and there is no default.
+# `$1` is the chemical mechanism file in FACSIMILE or KPP format.
+#      Argument `$1` is NOT optional, and there is no default.
 #
-# $2 is the directory for the chemical mechanism in Fortran format:
-#    - mechanism.species
-#    - mechanism.reac
-#    - mechanism.prod
-#    - mechanism.ro2
-#    - mechanism.f90
-#    By default, argument $2 is: ./model/configuration/
+# `$2` is the model comfiguration directory, which contanins:
+#        - the model configuration files (`*.config` and `*.parameters`)
+#        - the subdirectory `include/` for the chemical mechanism in Fortran
+#          format (`mechanism.*`) and the pre-compiled mechanism shared
+#          library (`mechanism.so`).
+#      By default, argument `$2` is: ./model/configuration/
 #
-# $3 is the directory of the MCM data files:
-#    - list of organic peroxy radicals (RO2)
-#    - parameters to calculate photolysis rates
-#    By default, argument $3 is: ./mcm/
+# `$3` is the directory of the MCM data files, which contains:
+#        - the reference list of organic peroxy radicals (RO2)
+#        - the empirical parameters to calculate photolysis rates
+#      By default, argument `$3` is: ./mcm/
 #
 # Usage:
 #   ./build/build_atchem2.sh /path/to/mechanism/file
+#   OR
 #   ./build/build_atchem2.sh /path/to/mechanism/file /path/to/mechanism/directory
 # -----------------------------------------------------------------------------
+set -eu
 
-echo ""
-echo "     AtChem2 v1.3-dev"
-echo ""
+printf "\n--> Building AtChem2...\n"
 
-echo "* Chemical mechanism file:" $1
-echo "* Fortran mechanism directory [ default = ./model/configuration/ ]:" $2
-echo "* MCM data files directory [ default = ./mcm/ ]:" $3
+# set chemical mechanism file (argument `$1`)
+if [ -z "$1" ] ; then
+    printf "\n[INPUT ERROR] Missing argument: chemical mechanism file (.fac/.kpp).\n"
+    exit 1
+else
+    MECHF="$1"
+    if [ ! -f "$MECHF" ]; then
+        printf "\n[INPUT ERROR] The chemical mechanism file does not exist.\n"
+        exit 1
+    else
+        printf "\n[*] Chemical mechanism file: %s\n" "$MECHF"
+    fi
+fi
 
-echo ""
-echo "-> Call mech_converter.py"
-python ./build/mech_converter.py $1 $2 $3
+# set model configuration directory (argument `$2`)
+CONFIGD="${2:-./model/configuration/}"
+printf "\n[*] Model configuration directory: %s\n" "$CONFIGD"
+if [ ! -d "$CONFIGD" ]; then
+    printf "\n[INPUT ERROR] The model configuration directory does not exist.\n"
+    exit 1
+fi
 
-echo ""
-echo "-> Create shared library"
-if [ -z $2 ]; then
-  make sharedlib
-  echo "=> shared library created in: ./model/configuration/"
-else
-  make sharedlib SHAREDLIBDIR=$2
-  echo "=> shared library created in:" $2
+# set MCM data directory (argument `$3`)
+MCMV="${3:-./mcm/}"
+printf "\n[*] MCM data directory: %s\n" "$MCMV"
+if [ ! -d "$MCMV" ]; then
+    printf "\n[INPUT ERROR] The MCM data directory does not exist.\n"
+    exit 1
 fi
 
-echo ""
-echo "-> Create atchem2 executable"
-make
-echo ""
+# compile chemical mechanism shared library (`mechanism.so`)
+printf "\n--> Compiling shared library...\n"
+make sharedlib MECHFILE="$MECHF" CONFIGDIR="$CONFIGD" MCMDIR="$MCMV"
+if [ $? -ne 0 ] ; then
+    printf "\n[FAIL] Check output above for details.\n"
+    exit 1
+fi
+
+# compile atchem executable
+printf "\n--> Compiling atchem executable...\n"
+make -j
+if [ $? -ne 0 ] ; then
+    printf "\n[FAIL] Check output above for details.\n"
+    exit 1
+fi
 
+printf "\n--> AtChem2 build process successfully completed!\n"
 exit 0

build/mech_converter.py

@@ -16,7 +16,7 @@
 # This script converts a chemical mechanism file -- in FACSIMILE (.fac)
 # or KPP (.kpp) format -- into the Fortran-compatible format used by
 # AtChem2.  The script generates 5 files in the model configuration
-# directory:
+# `include/` directory:
 #
 # - mechanism.species
 # - mechanism.reac
@@ -149,7 +149,7 @@ def separate_stoichiometry(input_species):
                         format: '{input_species}'. Note that species names should
                         not begin with numerical characters.""")
 
-def convert_to_fortran(input_file, mech_dir, mcm_vers):
+def convert_to_fortran(input_file, conf_dir, mcm_vers):
     """
     This function converts a chemical mechanism file into the
     Fortran-compatible format used by the AtChem2 ODE solver. The
@@ -161,36 +161,37 @@ def convert_to_fortran(input_file, mech_dir, mcm_vers):
       an ID number.
 
     * The equations defined in sections 'Generic Rate Coefficients'
-      and 'Complex reactions' go to the mechanism.f90 file with little
+      and 'Complex reactions' go to the `mechanism.f90` file with little
       more than formatting changes -- each line is replicated in full,
       with each named rate converted to an element in vector q.
 
     * The reaction rates defined in section 'Reaction definitions' go
-      to the mechanism.f90 file as elements of vector p.
+      to the `mechanism.f90` file as elements of vector p.
 
     * The species involved as reactants (respectively products) in the
       reactions in section 'Reaction definitions' are split up into
       individual species, and the species and reactions ID numbers go
-      to mechanism.reac (respectively mechanism.prod). Combining
-      mechanism.reac, mechanism.prod and the last section of
-      mechanism.f90 gives the original information contained in
+      to `mechanism.reac` (respectively `mechanism.prod`). Combining
+      `mechanism.reac`, `mechanism.prod` and the last section of
+      `mechanism.f90` gives the original information contained in
       section 'Reaction definitions' of the .fac file, but in a
       format that AtChem2 can parse.
 
     * The ID numbers and names of all species in the chemical
-      mechanism go to the mechanism.species file.
+      mechanism go to the `mechanism.species` file.
 
     * The ID numbers and names of all RO2 species in section 'Peroxy
-      radicals' go to the mechanism.ro2 file.
+      radicals' go to the `mechanism.ro2` file.
 
     Args:
         input_file (str): relative or absolute reference to the .fac file
-        mech_dir (str): relative or absolute reference to the directory where
-                        the mechanism.* files will be created, and where
-                        the environmentVariables.config file should be read from
+        conf_dir (str): relative or absolute reference to the configuration
+                        directory where the mechanism.* files will be created
+                        (inside the `include/` subdirectory), and where the
+                        `environmentVariables.config` file should be read from
                         By default it is: model/configuration/
         mcm_vers (str): relative or absolute reference to the directory containing
-                        the reference list of RO2 species (peroxy-radicals_v*)
+                        the reference list of RO2 species (`peroxy-radicals_v*`)
                         By default it is: mcm/
     """
 
@@ -203,6 +204,8 @@ def convert_to_fortran(input_file, mech_dir, mcm_vers):
         'The input file ' + str(input_path) + ' does not exist.'
     print('Chemical mechanism file in:', input_directory)
 
+    mech_dir = os.path.join(conf_dir, 'include/')
+
     # Check if the chemical mechanism file is in KPP format, in which case convert it
     # to FACSIMILE format (see documentation of `kpp_conversion.py` for more info)
     if input_filename.split('.')[-1] == 'kpp':
@@ -290,7 +293,7 @@ def convert_to_fortran(input_file, mech_dir, mcm_vers):
 
     # Check the DILUTE environment variable to identify whether dilution should be applied.
     dilute = False
-    with open(mech_dir + '/environmentVariables.config') as env_var_file:
+    with open(conf_dir + '/environmentVariables.config') as env_var_file:
         environmentVariables = env_var_file.readlines()
         for x in environmentVariables:
             x = x.split()
@@ -304,7 +307,7 @@ def convert_to_fortran(input_file, mech_dir, mcm_vers):
     # Read in the names of user-defined custom rate functions and add them
     # to the list of reserved names so that they will be carried through the
     # rate definitions (in a similar manner to LOG10)
-    with open(mech_dir + '/customRateFuncs.f90') as custom_func_file:
+    with open(conf_dir + '/customRateFuncs.f90') as custom_func_file:
         func_def_pat = r'function +([a-zA-Z0-9_]*) *\('
         custom_func_names = re.findall(func_def_pat, custom_func_file.read(), re.I)
 

model/.gitignore

@@ -1,5 +1,10 @@
 # Ignore auto-generated mechanism files and output files in the model/ directory
-configuration/mechanism.*
-configuration/customRateFuncs.o
+constraints/environment/*
+constraints/photolysis/*
+constraints/species/*
+configuration/include/*
 output/*.output
 output/*.pdf
+output/reactionRates/*
+
+!.gitkeep

obj/.gitignore

@@ -1,2 +1,3 @@
-# Ignore fortran module files in the obj/ directory
+# Ignore fortran object and module files in the obj/ directory
+*.o
 *.mod

src/argparse.f90

@@ -26,19 +26,19 @@ module argparse_mod
   end type flag
 
   ! Arguments for the atchem2 executable
-  type(flag), parameter :: valid_flags(10) = &
-              [ flag('--help', 'Displays this help message.'), &
+  type(flag), parameter :: valid_flags(9) = &
+              [ flag('--help', 'Displays the help message.'), &
                 flag('--model', 'The base directory of the model.'), &
-                flag('--output', 'The destination directory for output.'), &
-                flag('--configuration', 'The directory of the model configuration.'), &
-                flag('--constraints', 'The base directory of constraints. ' // &
-                                      'This typically contains 3 subdirectories: environment, photolysis, and species.'), &
-                flag('--env_constraints', 'The directory containing environment constraints data.'), &
-                flag('--photo_constraints', 'The directory containing photolysis constraints data.'), &
-                flag('--spec_constraints', 'The directory containing species constraints data.'), &
-                flag('--mcm', 'The directory containing the MCM data files.'), &
-                flag('--shared_lib', 'The full path to the mechanism.so shared library ' // &
-                                     '(generated by ./build/build_atchem2.sh).') ]
+                flag('--output', 'The destination directory for output. ' // &
+                                 'Contains one subdirectory: reactionRates.'), &
+                flag('--configuration', 'The directory for the model configuration. ' // &
+                                        'Contains the shared library: mechanism.so.'), &
+                flag('--constraints', 'The base directory of the model constraints. ' // &
+                                      'Contains 3 subdirectories: environment, photolysis, and species.'), &
+                flag('--env_constraints', 'The directory containing the environment constraints data.'), &
+                flag('--photo_constraints', 'The directory containing the photolysis constraints data.'), &
+                flag('--spec_constraints', 'The directory containing the species constraints data.'), &
+                flag('--mcm', 'The directory containing the MCM data files.') ]
 
 contains
 
@@ -67,13 +67,13 @@ subroutine print_help()
     write(*,*) 'In essence, the directories default to sit in the following tree.'
     write(*,*) 'Modification via the input parameters cascades to lower directories, but is overwritten by explicit input.'
     write(*,*)
-    write(*,*) '                                      +--------------------+--------------------+'
-    write(*,*) '                                      |                    |                    |'
-    write(*,*) '                                  model_dir             mcm_dir         shared_lib_dir'
+    write(*,*) '                                      +--------------------+'
+    write(*,*) '                                      |                    |'
+    write(*,*) '                                  model_dir             mcm_dir'
     write(*,*) '                                      | '
     write(*,*) '     +--------------------------------+--------------------------------+'
     write(*,*) '     |                                |                                |'
-    write(*,*) ' output_dir                    constraints_dir                 configuration_dir' 
+    write(*,*) ' output_dir                    constraints_dir                 configuration_dir'
     write(*,*) '                                      |'
     write(*,*) '             +------------------------+------------------------+'
     write(*,*) '             |                        |                        |'
@@ -270,16 +270,25 @@ subroutine get_and_set_directories_from_command_arguments()
 
     ! set each of the directory locations from the command-line, following the
     ! defined logic for defaults if some are not supplied
-    model_dir             = read_value_or_default( valid_flags(2)%flag_switch, 'model', names, values )
-    output_dir            = read_value_or_default( valid_flags(3)%flag_switch, trim(model_dir)//'/output', names, values )
+    model_dir             = read_value_or_default( valid_flags(2)%flag_switch, &
+                                                   'model', names, values )
+    output_dir            = read_value_or_default( valid_flags(3)%flag_switch, &
+                                                   trim(model_dir)//'/output', names, values )
     reactionRates_dir     = trim(output_dir)//'/reactionRates'
-    configuration_dir     = read_value_or_default( valid_flags(4)%flag_switch, trim(model_dir)//'/configuration', names, values )
-    constraints_dir       = read_value_or_default( valid_flags(5)%flag_switch, trim(model_dir)//'/constraints', names, values )
-    env_constraints_dir  = read_value_or_default( valid_flags(6)%flag_switch, trim(constraints_dir)//'/environment', names, values )
-    photo_constraints_dir = read_value_or_default( valid_flags(7)%flag_switch, trim(constraints_dir)//'/photolysis', names, values )
-    spec_constraints_dir  = read_value_or_default( valid_flags(8)%flag_switch, trim(constraints_dir)//'/species', names, values )
-    mcm_dir               = read_value_or_default( valid_flags(9)%flag_switch, 'mcm', names, values )
-    shared_library        = read_value_or_default( valid_flags(10)%flag_switch, 'model/configuration/mechanism.so', names, values )
+    configuration_dir     = read_value_or_default( valid_flags(4)%flag_switch, &
+                                                   trim(model_dir)//'/configuration', names, values )
+    constraints_dir       = read_value_or_default( valid_flags(5)%flag_switch, &
+                                                   trim(model_dir)//'/constraints', names, values )
+    env_constraints_dir   = read_value_or_default( valid_flags(6)%flag_switch, &
+                                                   trim(constraints_dir)//'/environment', names, values )
+    photo_constraints_dir = read_value_or_default( valid_flags(7)%flag_switch, &
+                                                   trim(constraints_dir)//'/photolysis', names, values )
+    spec_constraints_dir  = read_value_or_default( valid_flags(8)%flag_switch, &
+                                                   trim(constraints_dir)//'/species', names, values )
+    mcm_dir               = read_value_or_default( valid_flags(9)%flag_switch, &
+                                                   'mcm', names, values )
+    mechanism_dir         = trim(configuration_dir)//'/include'
+    shared_library        = trim(mechanism_dir)//'/mechanism.so'
 
     write (*, '(2A)') ' Model directory is: ', trim( model_dir )
     write (*, '(2A)') ' Output directory is: ', trim( output_dir )
@@ -290,6 +299,7 @@ subroutine get_and_set_directories_from_command_arguments()
     write (*, '(2A)') ' Photolysis Constraints directory is: ', trim( photo_constraints_dir )
     write (*, '(2A)') ' Species Constraints directory is: ', trim( spec_constraints_dir )
     write (*, '(2A)') ' MCM directory is: ', trim( mcm_dir )
+    write (*, '(2A)') ' Mechanism directory is: ', trim( mechanism_dir )
     write (*, '(2A)') ' Shared library is: ', trim( shared_library )
 
   end subroutine get_and_set_directories_from_command_arguments

src/dataStructures.f90

@@ -95,7 +95,8 @@ module directories_mod
   character(len=maxFilepathLength) :: model_dir, output_dir, reactionRates_dir, &
                                       configuration_dir, mcm_dir, shared_library, &
                                       constraints_dir, spec_constraints_dir, &
-                                      env_constraints_dir, photo_constraints_dir
+                                      env_constraints_dir, photo_constraints_dir, &
+                                      mechanism_dir
 
 end module directories_mod