Move a bunch of directories around

.github/workflows/ci.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Check formatting
         uses: DoozyX/[email protected]
         with:
-          source: './Eos ./Transport ./Reactions ./Source ./Utility ./Testing ./Support/Mechanism/Models'
+          source: './Source ./Testing ./Mechanisms'
           exclude: '.'
           extensions: 'H,h,cpp'
           clangFormatVersion: 16
@@ -75,9 +75,9 @@ jobs:
       - name: Run tests
         run: poetry run pytest
       - name: Convert air mechanism
-        run: poetry run convert -f ${{github.workspace}}/Support/Mechanism/Models/air/mechanism.yaml
+        run: poetry run convert -f ${{github.workspace}}/Mechanisms/air/mechanism.yaml
       - name: Convert LiDryer mechanism
-        run: poetry run convert -f ${{github.workspace}}/Support/Mechanism/Models/LiDryer/mechanism.yaml
+        run: poetry run convert -f ${{github.workspace}}/Mechanisms/LiDryer/mechanism.yaml
 
   Transport-EOS-Reactions:
     needs: Formatting
@@ -275,8 +275,8 @@ jobs:
           if [ "${{matrix.comp}}" == 'gnu' ] || [ "${{matrix.comp}}" == 'llvm' ]; then \
               ccache -z
               cd ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/ceptr
-              poetry run qssa -f ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/Mechanism/Models/dodecane_lu_qss/skeletal.yaml -n ${{github.workspace}}/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml
-              poetry run convert -f ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/Mechanism/Models/dodecane_lu_qss/qssa.yaml --qss_format_input ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/Mechanism/Models/dodecane_lu_qss/qssa_input_non_optimized.toml --qss_symbolic_jacobian
+              poetry run qssa -f ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Mechanisms/dodecane_lu_qss/skeletal.yaml -n ${{github.workspace}}/Mechanisms/dodecane_lu_qss/non_qssa_list.yaml
+              poetry run convert -f ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Mechanisms/dodecane_lu_qss/qssa.yaml --qss_format_input ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Mechanisms/dodecane_lu_qss/qssa_input_non_optimized.toml --qss_symbolic_jacobian
               cd ${{env.JAC_WORKING_DIRECTORY}}
               make -j ${{env.NPROCS}} Eos_Model=Fuego Chemistry_Model=dodecane_lu_qss DEBUG=TRUE TINY_PROFILE=TRUE USE_CCACHE=TRUE ${{matrix.amrex_build_args}}
               ./Pele3d.${{matrix.comp}}.DEBUG.TPROF.ex; \

Docs/sphinx/Ceptr.rst

@@ -30,15 +30,15 @@ There are three ways to use CEPTR to generate C++ mechanism files for a given ch
 1. Using CEPTR directly::
 
      $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-     $ poetry run convert -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/LiDryer/mechanism.yaml
+     $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/LiDryer/mechanism.yaml
 
 2. Using a helper script in the directory containing the ``mechanism.yaml`` file::
 
      $ ./convert.sh
 
 3. Using a helper script in the ``Models`` directory::
 
-     $ bash ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/converter.sh -f ./LiDryer/mechanism.yaml
+     $ bash ${PELE_PHYSICS_HOME}/Mechanisms/converter.sh -f ./LiDryer/mechanism.yaml
 
 
 Batched generation
@@ -52,23 +52,23 @@ Batched generation
 For non-reduced chemistries, CEPTR can take a file with a list of ``mechanism.yaml`` files to convert::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run convert -l ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_mech
+  $ poetry run convert -l ${PELE_PHYSICS_HOME}/Mechanisms/list_mech
 
 For reduced chemistries, CEPTR can take a file with a list of ``qssa.yaml`` and ``qssa_input.toml`` to convert::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_qss_mech
+  $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
 
 For generating ``qssa.yaml`` for reduced chemistries, CEPTR can take a file with a list of ``skeletal.yaml`` and ``non_qssa_list.yaml``::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_qss_mech
+  $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
 
 To generate all mechanisms::
 
-  $ poetry run convert -l ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_mech
-  $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_qss_mech
-  $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_qss_mech
+  $ poetry run convert -l ${PELE_PHYSICS_HOME}/Mechanisms/list_mech
+  $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
+  $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
 
 
 Converting CHEMKIN files

Docs/sphinx/Tutorials.rst

@@ -18,21 +18,21 @@ Update ``poetry``::
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
   $ poetry update  
 
-Make sure the list of non-QSS species is correct in ``${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml``
+Make sure the list of non-QSS species is correct in ``${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/non_qssa_list.yaml``
 
 
-In the next step, ``skeletal.yaml`` is the ``mechanism.yaml`` of the skeletal version of the mechanism (here available under ``${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu``).
+In the next step, ``skeletal.yaml`` is the ``mechanism.yaml`` of the skeletal version of the mechanism (here available under ``${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu``).
 If only CHEMKIN files are available for the skeletal mechanism, see :ref:`Converting CHEMKIN files <sec_convertCK>` for generating ``skeletal.yaml``.
 
 Generate ``qssa.yaml`` from ``skeletal.yaml`` and ``non_qssa_list.yaml``::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run qssa -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml
+  $ poetry run qssa -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/non_qssa_list.yaml
 
 Generate ``mechanism.H`` and ``mechanism.cpp`` from ``qssa.yaml``::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run convert -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/qssa.yaml --qss_format_input ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/qssa_input.toml --qss_symbolic_jacobian
+  $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/qssa.yaml --qss_format_input ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/qssa_input.toml --qss_symbolic_jacobian
 
 We recommend using the following ``qssa_input.toml``::
 
@@ -67,20 +67,20 @@ Update ``poetry``::
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
   $ poetry update  
 
-Make sure the list of non-QSS species is correct in ``Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml``
+Make sure the list of non-QSS species is correct in ``Mechanisms/dodecane_lu_qss/non_qssa_list.yaml``
 
-In the next step, ``skeletal.yaml`` is the ``mechanism.yaml`` of the skeletal version of the mechanism (here available under ``${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu``).
+In the next step, ``skeletal.yaml`` is the ``mechanism.yaml`` of the skeletal version of the mechanism (here available under ``${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu``).
 If only CHEMKIN files are available for the skeletal mechanism, see :ref:`Converting CHEMKIN files <sec_convertCK>` for generating ``skeletal.yaml``.
 
 Generate ``qssa.yaml`` from ``skeletal.yaml`` and ``non_qssa_list.yaml``::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run qssa -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml
+  $ poetry run qssa -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/non_qssa_list.yaml
 
 Generate ``mechanism.H`` and ``mechanism.cpp`` from ``qssa.yaml``::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run convert -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/qssa.yaml
+  $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/qssa.yaml
 
 Tutorial 3 - Generating NC12H26 Skeletal mechanism
 --------------------------------------------------
@@ -97,5 +97,5 @@ If only CHEMKIN files are available, see :ref:`Converting CHEMKIN files <sec_con
 Generate ``mechanism.H`` and ``mechanism.cpp`` from ``mechanism.yaml``::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run convert -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu/mechanism.yaml
+  $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu/mechanism.yaml
 

Support/Mechanism/Models/converter.sh → Mechanisms/converter.sh

@@ -50,7 +50,7 @@ while getopts ":hf:" option; do
 done
 
 if [ -z "${PELE_PHYSICS_HOME+xxx}" ]; then
-    remove="Support/Mechanism/Models"
+    remove="Mechanisms"
     script_dir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
     PELE_PHYSICS_HOME=${script_dir%%"${remove}"}
     echo "Using PELE_PHYSICS_HOME: ${PELE_PHYSICS_HOME}. Set PELE_PHYSICS_HOME you want a different one."

Support/Mechanism/Models/H2-CO-CO2-3spec/Make.package → Mechanisms/drm19/Make.package

@@ -1,6 +1,7 @@
-CEXE_sources+=mechanism.cpp
 CEXE_headers+=mechanism.H
 
+CEXE_sources+=mechanism.cpp
+
 LIBRARIES +=
 
 INCLUDE_LOCATIONS += $(CHEM_DIR)

Support/Mechanism/Models/IonizedAir/Make.package → Mechanisms/ethylene_af/Make.package

@@ -1,4 +1,5 @@
 CEXE_headers+=mechanism.H
+
 CEXE_sources+=mechanism.cpp
 
 LIBRARIES +=

Support/Mechanism/Models/LiDryer/Make.package → Mechanisms/grimech12/Make.package

@@ -1,6 +1,7 @@
-CEXE_sources+=mechanism.cpp
 CEXE_headers+=mechanism.H
 
+CEXE_sources+=mechanism.cpp
+
 LIBRARIES +=
 
 INCLUDE_LOCATIONS += $(CHEM_DIR)

Support/Mechanism/Models/Null/Make.package → Mechanisms/grimech30-noArN/Make.package

@@ -1,6 +1,7 @@
-CEXE_sources+=mechanism.cpp
 CEXE_headers+=mechanism.H
 
+CEXE_sources+=mechanism.cpp
+
 LIBRARIES +=
 
 INCLUDE_LOCATIONS += $(CHEM_DIR)

Mechanisms/grimech30/Make.package

@@ -0,0 +1,9 @@
+CEXE_headers+=mechanism.H
+
+CEXE_sources+=mechanism.cpp
+
+LIBRARIES +=
+
+INCLUDE_LOCATIONS += $(CHEM_DIR)
+
+VPATH_LOCATIONS +=  $(CHEM_DIR)/PMFs