diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d159dc0cb..cc08a8096 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -20,7 +20,7 @@ jobs: - name: Check formatting uses: DoozyX/clang-format-lint-action@v0.16.2 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; \ diff --git a/Docs/sphinx/Ceptr.rst b/Docs/sphinx/Ceptr.rst index c7d77b682..49c99d061 100644 --- a/Docs/sphinx/Ceptr.rst +++ b/Docs/sphinx/Ceptr.rst @@ -30,7 +30,7 @@ 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:: @@ -38,7 +38,7 @@ There are three ways to use CEPTR to generate C++ mechanism files for a given ch 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 diff --git a/Docs/sphinx/Tutorials.rst b/Docs/sphinx/Tutorials.rst index 6a14c2370..7bba5e199 100644 --- a/Docs/sphinx/Tutorials.rst +++ b/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 ` 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 ` 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 ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/qssa.yaml Tutorial 3 - Generating NC12H26 Skeletal mechanism -------------------------------------------------- @@ -97,5 +97,5 @@ If only CHEMKIN files are available, see :ref:`Converting CHEMKIN files /dev/null && pwd ) PELE_PHYSICS_HOME=${script_dir%%"${remove}"} echo "Using PELE_PHYSICS_HOME: ${PELE_PHYSICS_HOME}. Set PELE_PHYSICS_HOME you want a different one." diff --git a/Support/Mechanism/Models/heptane_fc/Make.package b/Mechanisms/decane_3sp/Make.package similarity index 100% rename from Support/Mechanism/Models/heptane_fc/Make.package rename to Mechanisms/decane_3sp/Make.package diff --git a/Support/Mechanism/Models/decane_3sp/convert.sh b/Mechanisms/decane_3sp/convert.sh similarity index 100% rename from Support/Mechanism/Models/decane_3sp/convert.sh rename to Mechanisms/decane_3sp/convert.sh diff --git a/Support/Mechanism/Models/decane_3sp/mechanism.H b/Mechanisms/decane_3sp/mechanism.H similarity index 100% rename from Support/Mechanism/Models/decane_3sp/mechanism.H rename to Mechanisms/decane_3sp/mechanism.H diff --git a/Support/Mechanism/Models/decane_3sp/mechanism.cpp b/Mechanisms/decane_3sp/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/decane_3sp/mechanism.cpp rename to Mechanisms/decane_3sp/mechanism.cpp diff --git a/Support/Mechanism/Models/decane_3sp/mechanism.inp b/Mechanisms/decane_3sp/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/decane_3sp/mechanism.inp rename to Mechanisms/decane_3sp/mechanism.inp diff --git a/Support/Mechanism/Models/decane_3sp/mechanism.yaml b/Mechanisms/decane_3sp/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/decane_3sp/mechanism.yaml rename to Mechanisms/decane_3sp/mechanism.yaml diff --git a/Support/Mechanism/Models/decane_3sp/therm.dat b/Mechanisms/decane_3sp/therm.dat similarity index 100% rename from Support/Mechanism/Models/decane_3sp/therm.dat rename to Mechanisms/decane_3sp/therm.dat diff --git a/Support/Mechanism/Models/decane_3sp/tran.dat b/Mechanisms/decane_3sp/tran.dat similarity index 100% rename from Support/Mechanism/Models/decane_3sp/tran.dat rename to Mechanisms/decane_3sp/tran.dat diff --git a/Support/Mechanism/Models/dodecane_lu/ARC/ckwyp.f b/Mechanisms/dodecane_lu/ARC/ckwyp.f similarity index 100% rename from Support/Mechanism/Models/dodecane_lu/ARC/ckwyp.f rename to Mechanisms/dodecane_lu/ARC/ckwyp.f diff --git a/Support/Mechanism/Models/heptane_lu_qss/Make.package b/Mechanisms/dodecane_lu/Make.package similarity index 100% rename from Support/Mechanism/Models/heptane_lu_qss/Make.package rename to Mechanisms/dodecane_lu/Make.package diff --git a/Support/Mechanism/Models/dodecane_lu/README.md b/Mechanisms/dodecane_lu/README.md similarity index 100% rename from Support/Mechanism/Models/dodecane_lu/README.md rename to Mechanisms/dodecane_lu/README.md diff --git a/Support/Mechanism/Models/dodecane_lu/convert.sh b/Mechanisms/dodecane_lu/convert.sh similarity index 100% rename from Support/Mechanism/Models/dodecane_lu/convert.sh rename to Mechanisms/dodecane_lu/convert.sh diff --git a/Support/Mechanism/Models/dodecane_lu/mechanism.H b/Mechanisms/dodecane_lu/mechanism.H similarity index 100% rename from Support/Mechanism/Models/dodecane_lu/mechanism.H rename to Mechanisms/dodecane_lu/mechanism.H diff --git a/Support/Mechanism/Models/dodecane_lu/mechanism.cpp b/Mechanisms/dodecane_lu/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/dodecane_lu/mechanism.cpp rename to Mechanisms/dodecane_lu/mechanism.cpp diff --git a/Support/Mechanism/Models/dodecane_lu/mechanism.inp b/Mechanisms/dodecane_lu/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/dodecane_lu/mechanism.inp rename to Mechanisms/dodecane_lu/mechanism.inp diff --git a/Support/Mechanism/Models/dodecane_lu/mechanism.yaml b/Mechanisms/dodecane_lu/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/dodecane_lu/mechanism.yaml rename to Mechanisms/dodecane_lu/mechanism.yaml diff --git a/Support/Mechanism/Models/dodecane_lu/therm.dat b/Mechanisms/dodecane_lu/therm.dat similarity index 100% rename from Support/Mechanism/Models/dodecane_lu/therm.dat rename to Mechanisms/dodecane_lu/therm.dat diff --git a/Support/Mechanism/Models/dodecane_lu/tran.dat b/Mechanisms/dodecane_lu/tran.dat similarity index 100% rename from Support/Mechanism/Models/dodecane_lu/tran.dat rename to Mechanisms/dodecane_lu/tran.dat diff --git a/Support/Mechanism/Models/isooctane_lu/Make.package b/Mechanisms/dodecane_lu_qss/Make.package similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/Make.package rename to Mechanisms/dodecane_lu_qss/Make.package diff --git a/Support/Mechanism/Models/dodecane_lu_qss/README.md b/Mechanisms/dodecane_lu_qss/README.md similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/README.md rename to Mechanisms/dodecane_lu_qss/README.md diff --git a/Support/Mechanism/Models/dodecane_lu_qss/clean.sh b/Mechanisms/dodecane_lu_qss/clean.sh similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/clean.sh rename to Mechanisms/dodecane_lu_qss/clean.sh diff --git a/Support/Mechanism/Models/dodecane_lu_qss/mechanism.H b/Mechanisms/dodecane_lu_qss/mechanism.H similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/mechanism.H rename to Mechanisms/dodecane_lu_qss/mechanism.H diff --git a/Support/Mechanism/Models/dodecane_lu_qss/mechanism.cpp b/Mechanisms/dodecane_lu_qss/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/mechanism.cpp rename to Mechanisms/dodecane_lu_qss/mechanism.cpp diff --git a/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.txt b/Mechanisms/dodecane_lu_qss/non_qssa_list.txt similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.txt rename to Mechanisms/dodecane_lu_qss/non_qssa_list.txt diff --git a/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml b/Mechanisms/dodecane_lu_qss/non_qssa_list.yaml similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml rename to Mechanisms/dodecane_lu_qss/non_qssa_list.yaml diff --git a/Support/Mechanism/Models/dodecane_lu_qss/qssa.yaml b/Mechanisms/dodecane_lu_qss/qssa.yaml similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/qssa.yaml rename to Mechanisms/dodecane_lu_qss/qssa.yaml diff --git a/Support/Mechanism/Models/dodecane_lu_qss/qssa_input.toml b/Mechanisms/dodecane_lu_qss/qssa_input.toml similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/qssa_input.toml rename to Mechanisms/dodecane_lu_qss/qssa_input.toml diff --git a/Support/Mechanism/Models/dodecane_lu_qss/qssa_input_non_optimized.toml b/Mechanisms/dodecane_lu_qss/qssa_input_non_optimized.toml similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/qssa_input_non_optimized.toml rename to Mechanisms/dodecane_lu_qss/qssa_input_non_optimized.toml diff --git a/Support/Mechanism/Models/dodecane_lu_qss/skeletal.inp b/Mechanisms/dodecane_lu_qss/skeletal.inp similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/skeletal.inp rename to Mechanisms/dodecane_lu_qss/skeletal.inp diff --git a/Support/Mechanism/Models/dodecane_lu_qss/skeletal.yaml b/Mechanisms/dodecane_lu_qss/skeletal.yaml similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/skeletal.yaml rename to Mechanisms/dodecane_lu_qss/skeletal.yaml diff --git a/Support/Mechanism/Models/dodecane_lu_qss/therm.dat b/Mechanisms/dodecane_lu_qss/therm.dat similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/therm.dat rename to Mechanisms/dodecane_lu_qss/therm.dat diff --git a/Support/Mechanism/Models/dodecane_lu_qss/tran.dat b/Mechanisms/dodecane_lu_qss/tran.dat similarity index 100% rename from Support/Mechanism/Models/dodecane_lu_qss/tran.dat rename to Mechanisms/dodecane_lu_qss/tran.dat diff --git a/Support/Mechanism/Models/propane_fc/Make.package b/Mechanisms/dodecane_wang/Make.package similarity index 100% rename from Support/Mechanism/Models/propane_fc/Make.package rename to Mechanisms/dodecane_wang/Make.package diff --git a/Support/Mechanism/Models/dodecane_wang/convert.sh b/Mechanisms/dodecane_wang/convert.sh similarity index 100% rename from Support/Mechanism/Models/dodecane_wang/convert.sh rename to Mechanisms/dodecane_wang/convert.sh diff --git a/Support/Mechanism/Models/dodecane_wang/mechanism.H b/Mechanisms/dodecane_wang/mechanism.H similarity index 100% rename from Support/Mechanism/Models/dodecane_wang/mechanism.H rename to Mechanisms/dodecane_wang/mechanism.H diff --git a/Support/Mechanism/Models/dodecane_wang/mechanism.cpp b/Mechanisms/dodecane_wang/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/dodecane_wang/mechanism.cpp rename to Mechanisms/dodecane_wang/mechanism.cpp diff --git a/Support/Mechanism/Models/dodecane_wang/mechanism.inp b/Mechanisms/dodecane_wang/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/dodecane_wang/mechanism.inp rename to Mechanisms/dodecane_wang/mechanism.inp diff --git a/Support/Mechanism/Models/dodecane_wang/mechanism.yaml b/Mechanisms/dodecane_wang/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/dodecane_wang/mechanism.yaml rename to Mechanisms/dodecane_wang/mechanism.yaml diff --git a/Support/Mechanism/Models/dodecane_wang/therm.dat b/Mechanisms/dodecane_wang/therm.dat similarity index 100% rename from Support/Mechanism/Models/dodecane_wang/therm.dat rename to Mechanisms/dodecane_wang/therm.dat diff --git a/Support/Mechanism/Models/dodecane_wang/tran.dat b/Mechanisms/dodecane_wang/tran.dat similarity index 100% rename from Support/Mechanism/Models/dodecane_wang/tran.dat rename to Mechanisms/dodecane_wang/tran.dat diff --git a/Support/Mechanism/Models/sCO2/Make.package b/Mechanisms/dodmethair_4sp/Make.package similarity index 100% rename from Support/Mechanism/Models/sCO2/Make.package rename to Mechanisms/dodmethair_4sp/Make.package diff --git a/Support/Mechanism/Models/dodmethair_4sp/convert.sh b/Mechanisms/dodmethair_4sp/convert.sh similarity index 100% rename from Support/Mechanism/Models/dodmethair_4sp/convert.sh rename to Mechanisms/dodmethair_4sp/convert.sh diff --git a/Support/Mechanism/Models/dodmethair_4sp/mechanism.H b/Mechanisms/dodmethair_4sp/mechanism.H similarity index 100% rename from Support/Mechanism/Models/dodmethair_4sp/mechanism.H rename to Mechanisms/dodmethair_4sp/mechanism.H diff --git a/Support/Mechanism/Models/dodmethair_4sp/mechanism.cpp b/Mechanisms/dodmethair_4sp/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/dodmethair_4sp/mechanism.cpp rename to Mechanisms/dodmethair_4sp/mechanism.cpp diff --git a/Support/Mechanism/Models/dodmethair_4sp/mechanism.inp b/Mechanisms/dodmethair_4sp/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/dodmethair_4sp/mechanism.inp rename to Mechanisms/dodmethair_4sp/mechanism.inp diff --git a/Support/Mechanism/Models/dodmethair_4sp/mechanism.yaml b/Mechanisms/dodmethair_4sp/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/dodmethair_4sp/mechanism.yaml rename to Mechanisms/dodmethair_4sp/mechanism.yaml diff --git a/Support/Mechanism/Models/dodmethair_4sp/therm.dat b/Mechanisms/dodmethair_4sp/therm.dat similarity index 100% rename from Support/Mechanism/Models/dodmethair_4sp/therm.dat rename to Mechanisms/dodmethair_4sp/therm.dat diff --git a/Support/Mechanism/Models/dodmethair_4sp/tran.dat b/Mechanisms/dodmethair_4sp/tran.dat similarity index 100% rename from Support/Mechanism/Models/dodmethair_4sp/tran.dat rename to Mechanisms/dodmethair_4sp/tran.dat diff --git a/Support/Mechanism/Models/H2-CO-CO2-3spec/Make.package b/Mechanisms/drm19/Make.package similarity index 99% rename from Support/Mechanism/Models/H2-CO-CO2-3spec/Make.package rename to Mechanisms/drm19/Make.package index 8a2397e5f..24c663c9a 100644 --- a/Support/Mechanism/Models/H2-CO-CO2-3spec/Make.package +++ b/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) diff --git a/Support/Mechanism/Models/drm19/convert.sh b/Mechanisms/drm19/convert.sh similarity index 100% rename from Support/Mechanism/Models/drm19/convert.sh rename to Mechanisms/drm19/convert.sh diff --git a/Support/Mechanism/Models/drm19/mechanism.H b/Mechanisms/drm19/mechanism.H similarity index 100% rename from Support/Mechanism/Models/drm19/mechanism.H rename to Mechanisms/drm19/mechanism.H diff --git a/Support/Mechanism/Models/drm19/mechanism.cpp b/Mechanisms/drm19/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/drm19/mechanism.cpp rename to Mechanisms/drm19/mechanism.cpp diff --git a/Support/Mechanism/Models/drm19/mechanism.inp b/Mechanisms/drm19/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/drm19/mechanism.inp rename to Mechanisms/drm19/mechanism.inp diff --git a/Support/Mechanism/Models/drm19/mechanism.yaml b/Mechanisms/drm19/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/drm19/mechanism.yaml rename to Mechanisms/drm19/mechanism.yaml diff --git a/Support/Mechanism/Models/drm19/therm.dat b/Mechanisms/drm19/therm.dat similarity index 100% rename from Support/Mechanism/Models/drm19/therm.dat rename to Mechanisms/drm19/therm.dat diff --git a/Support/Mechanism/Models/drm19/tran.dat b/Mechanisms/drm19/tran.dat similarity index 100% rename from Support/Mechanism/Models/drm19/tran.dat rename to Mechanisms/drm19/tran.dat diff --git a/Support/Mechanism/Models/ethylene_af/CANTERA/ARC.cti b/Mechanisms/ethylene_af/CANTERA/ARC.cti similarity index 100% rename from Support/Mechanism/Models/ethylene_af/CANTERA/ARC.cti rename to Mechanisms/ethylene_af/CANTERA/ARC.cti diff --git a/Support/Mechanism/Models/ethylene_af/CANTERA/C2H4DET_T298_P1_Phi0.8_Y.csv b/Mechanisms/ethylene_af/CANTERA/C2H4DET_T298_P1_Phi0.8_Y.csv similarity index 100% rename from Support/Mechanism/Models/ethylene_af/CANTERA/C2H4DET_T298_P1_Phi0.8_Y.csv rename to Mechanisms/ethylene_af/CANTERA/C2H4DET_T298_P1_Phi0.8_Y.csv diff --git a/Support/Mechanism/Models/ethylene_af/CANTERA/C2H4SK_T298_P1_Phi0.8_Y.csv b/Mechanisms/ethylene_af/CANTERA/C2H4SK_T298_P1_Phi0.8_Y.csv similarity index 100% rename from Support/Mechanism/Models/ethylene_af/CANTERA/C2H4SK_T298_P1_Phi0.8_Y.csv rename to Mechanisms/ethylene_af/CANTERA/C2H4SK_T298_P1_Phi0.8_Y.csv diff --git a/Support/Mechanism/Models/ethylene_af/CANTERA/Cantera_UPF_Global.py b/Mechanisms/ethylene_af/CANTERA/Cantera_UPF_Global.py similarity index 100% rename from Support/Mechanism/Models/ethylene_af/CANTERA/Cantera_UPF_Global.py rename to Mechanisms/ethylene_af/CANTERA/Cantera_UPF_Global.py diff --git a/Support/Mechanism/Models/ethylene_af/CANTERA/DET.cti b/Mechanisms/ethylene_af/CANTERA/DET.cti similarity index 100% rename from Support/Mechanism/Models/ethylene_af/CANTERA/DET.cti rename to Mechanisms/ethylene_af/CANTERA/DET.cti diff --git a/Support/Mechanism/Models/ethylene_af/CANTERA/adiabatic_flame.py b/Mechanisms/ethylene_af/CANTERA/adiabatic_flame.py similarity index 100% rename from Support/Mechanism/Models/ethylene_af/CANTERA/adiabatic_flame.py rename to Mechanisms/ethylene_af/CANTERA/adiabatic_flame.py diff --git a/Support/Mechanism/Models/ethylene_af/CANTERA/c2h4-T298-P1_ARC.csv b/Mechanisms/ethylene_af/CANTERA/c2h4-T298-P1_ARC.csv similarity index 100% rename from Support/Mechanism/Models/ethylene_af/CANTERA/c2h4-T298-P1_ARC.csv rename to Mechanisms/ethylene_af/CANTERA/c2h4-T298-P1_ARC.csv diff --git a/Support/Mechanism/Models/ethylene_af/CANTERA/c2h4-T298-P1_SK.csv b/Mechanisms/ethylene_af/CANTERA/c2h4-T298-P1_SK.csv similarity index 100% rename from Support/Mechanism/Models/ethylene_af/CANTERA/c2h4-T298-P1_SK.csv rename to Mechanisms/ethylene_af/CANTERA/c2h4-T298-P1_SK.csv diff --git a/Support/Mechanism/Models/ethylene_af/CANTERA/skeletal.cti b/Mechanisms/ethylene_af/CANTERA/skeletal.cti similarity index 100% rename from Support/Mechanism/Models/ethylene_af/CANTERA/skeletal.cti rename to Mechanisms/ethylene_af/CANTERA/skeletal.cti diff --git a/Support/Mechanism/Models/ethylene_af/CANTERA/skeletal.inp b/Mechanisms/ethylene_af/CANTERA/skeletal.inp similarity index 100% rename from Support/Mechanism/Models/ethylene_af/CANTERA/skeletal.inp rename to Mechanisms/ethylene_af/CANTERA/skeletal.inp diff --git a/Support/Mechanism/Models/ethylene_af/CANTERA/skeletal.thermo b/Mechanisms/ethylene_af/CANTERA/skeletal.thermo similarity index 100% rename from Support/Mechanism/Models/ethylene_af/CANTERA/skeletal.thermo rename to Mechanisms/ethylene_af/CANTERA/skeletal.thermo diff --git a/Support/Mechanism/Models/ethylene_af/CANTERA/skeletal.tran b/Mechanisms/ethylene_af/CANTERA/skeletal.tran similarity index 100% rename from Support/Mechanism/Models/ethylene_af/CANTERA/skeletal.tran rename to Mechanisms/ethylene_af/CANTERA/skeletal.tran diff --git a/Support/Mechanism/Models/IonizedAir/Make.package b/Mechanisms/ethylene_af/Make.package similarity index 99% rename from Support/Mechanism/Models/IonizedAir/Make.package rename to Mechanisms/ethylene_af/Make.package index 6b0fa8de5..24c663c9a 100644 --- a/Support/Mechanism/Models/IonizedAir/Make.package +++ b/Mechanisms/ethylene_af/Make.package @@ -1,4 +1,5 @@ CEXE_headers+=mechanism.H + CEXE_sources+=mechanism.cpp LIBRARIES += diff --git a/Support/Mechanism/Models/ethylene_af/convert.sh b/Mechanisms/ethylene_af/convert.sh similarity index 100% rename from Support/Mechanism/Models/ethylene_af/convert.sh rename to Mechanisms/ethylene_af/convert.sh diff --git a/Support/Mechanism/Models/ethylene_af/mechanism.H b/Mechanisms/ethylene_af/mechanism.H similarity index 100% rename from Support/Mechanism/Models/ethylene_af/mechanism.H rename to Mechanisms/ethylene_af/mechanism.H diff --git a/Support/Mechanism/Models/ethylene_af/mechanism.cpp b/Mechanisms/ethylene_af/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/ethylene_af/mechanism.cpp rename to Mechanisms/ethylene_af/mechanism.cpp diff --git a/Support/Mechanism/Models/ethylene_af/mechanism.inp b/Mechanisms/ethylene_af/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/ethylene_af/mechanism.inp rename to Mechanisms/ethylene_af/mechanism.inp diff --git a/Support/Mechanism/Models/ethylene_af/mechanism.yaml b/Mechanisms/ethylene_af/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/ethylene_af/mechanism.yaml rename to Mechanisms/ethylene_af/mechanism.yaml diff --git a/Support/Mechanism/Models/ethylene_af/therm.dat b/Mechanisms/ethylene_af/therm.dat similarity index 100% rename from Support/Mechanism/Models/ethylene_af/therm.dat rename to Mechanisms/ethylene_af/therm.dat diff --git a/Support/Mechanism/Models/ethylene_af/tran.dat b/Mechanisms/ethylene_af/tran.dat similarity index 100% rename from Support/Mechanism/Models/ethylene_af/tran.dat rename to Mechanisms/ethylene_af/tran.dat diff --git a/Support/Mechanism/Models/LiDryer/Make.package b/Mechanisms/grimech12/Make.package similarity index 99% rename from Support/Mechanism/Models/LiDryer/Make.package rename to Mechanisms/grimech12/Make.package index 8a2397e5f..24c663c9a 100644 --- a/Support/Mechanism/Models/LiDryer/Make.package +++ b/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) diff --git a/Support/Mechanism/Models/grimech12/convert.sh b/Mechanisms/grimech12/convert.sh similarity index 100% rename from Support/Mechanism/Models/grimech12/convert.sh rename to Mechanisms/grimech12/convert.sh diff --git a/Support/Mechanism/Models/grimech12/mechanism.H b/Mechanisms/grimech12/mechanism.H similarity index 100% rename from Support/Mechanism/Models/grimech12/mechanism.H rename to Mechanisms/grimech12/mechanism.H diff --git a/Support/Mechanism/Models/grimech12/mechanism.cpp b/Mechanisms/grimech12/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/grimech12/mechanism.cpp rename to Mechanisms/grimech12/mechanism.cpp diff --git a/Support/Mechanism/Models/grimech12/mechanism.inp b/Mechanisms/grimech12/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/grimech12/mechanism.inp rename to Mechanisms/grimech12/mechanism.inp diff --git a/Support/Mechanism/Models/grimech12/mechanism.yaml b/Mechanisms/grimech12/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/grimech12/mechanism.yaml rename to Mechanisms/grimech12/mechanism.yaml diff --git a/Support/Mechanism/Models/grimech12/therm.dat b/Mechanisms/grimech12/therm.dat similarity index 100% rename from Support/Mechanism/Models/grimech12/therm.dat rename to Mechanisms/grimech12/therm.dat diff --git a/Support/Mechanism/Models/grimech12/tran.dat b/Mechanisms/grimech12/tran.dat similarity index 100% rename from Support/Mechanism/Models/grimech12/tran.dat rename to Mechanisms/grimech12/tran.dat diff --git a/Support/Mechanism/Models/Null/Make.package b/Mechanisms/grimech30-noArN/Make.package similarity index 99% rename from Support/Mechanism/Models/Null/Make.package rename to Mechanisms/grimech30-noArN/Make.package index 8a2397e5f..24c663c9a 100644 --- a/Support/Mechanism/Models/Null/Make.package +++ b/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) diff --git a/Support/Mechanism/Models/grimech30-noArN/convert.sh b/Mechanisms/grimech30-noArN/convert.sh similarity index 100% rename from Support/Mechanism/Models/grimech30-noArN/convert.sh rename to Mechanisms/grimech30-noArN/convert.sh diff --git a/Support/Mechanism/Models/grimech30-noArN/mechanism.H b/Mechanisms/grimech30-noArN/mechanism.H similarity index 100% rename from Support/Mechanism/Models/grimech30-noArN/mechanism.H rename to Mechanisms/grimech30-noArN/mechanism.H diff --git a/Support/Mechanism/Models/grimech30-noArN/mechanism.cpp b/Mechanisms/grimech30-noArN/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/grimech30-noArN/mechanism.cpp rename to Mechanisms/grimech30-noArN/mechanism.cpp diff --git a/Support/Mechanism/Models/grimech30-noArN/mechanism.inp b/Mechanisms/grimech30-noArN/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/grimech30-noArN/mechanism.inp rename to Mechanisms/grimech30-noArN/mechanism.inp diff --git a/Support/Mechanism/Models/grimech30-noArN/mechanism.yaml b/Mechanisms/grimech30-noArN/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/grimech30-noArN/mechanism.yaml rename to Mechanisms/grimech30-noArN/mechanism.yaml diff --git a/Support/Mechanism/Models/grimech30-noArN/therm.dat b/Mechanisms/grimech30-noArN/therm.dat similarity index 100% rename from Support/Mechanism/Models/grimech30-noArN/therm.dat rename to Mechanisms/grimech30-noArN/therm.dat diff --git a/Support/Mechanism/Models/grimech30-noArN/tran.dat b/Mechanisms/grimech30-noArN/tran.dat similarity index 100% rename from Support/Mechanism/Models/grimech30-noArN/tran.dat rename to Mechanisms/grimech30-noArN/tran.dat diff --git a/Mechanisms/grimech30/Make.package b/Mechanisms/grimech30/Make.package new file mode 100644 index 000000000..24c663c9a --- /dev/null +++ b/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 diff --git a/Support/Mechanism/Models/grimech30/convert.sh b/Mechanisms/grimech30/convert.sh similarity index 100% rename from Support/Mechanism/Models/grimech30/convert.sh rename to Mechanisms/grimech30/convert.sh diff --git a/Support/Mechanism/Models/grimech30/mechanism.H b/Mechanisms/grimech30/mechanism.H similarity index 100% rename from Support/Mechanism/Models/grimech30/mechanism.H rename to Mechanisms/grimech30/mechanism.H diff --git a/Support/Mechanism/Models/grimech30/mechanism.cpp b/Mechanisms/grimech30/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/grimech30/mechanism.cpp rename to Mechanisms/grimech30/mechanism.cpp diff --git a/Support/Mechanism/Models/grimech30/mechanism.inp b/Mechanisms/grimech30/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/grimech30/mechanism.inp rename to Mechanisms/grimech30/mechanism.inp diff --git a/Support/Mechanism/Models/grimech30/mechanism.yaml b/Mechanisms/grimech30/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/grimech30/mechanism.yaml rename to Mechanisms/grimech30/mechanism.yaml diff --git a/Support/Mechanism/Models/grimech30/therm.dat b/Mechanisms/grimech30/therm.dat similarity index 100% rename from Support/Mechanism/Models/grimech30/therm.dat rename to Mechanisms/grimech30/therm.dat diff --git a/Support/Mechanism/Models/grimech30/tran.dat b/Mechanisms/grimech30/tran.dat similarity index 100% rename from Support/Mechanism/Models/grimech30/tran.dat rename to Mechanisms/grimech30/tran.dat diff --git a/Mechanisms/heptane_3sp/Make.package b/Mechanisms/heptane_3sp/Make.package new file mode 100644 index 000000000..24c663c9a --- /dev/null +++ b/Mechanisms/heptane_3sp/Make.package @@ -0,0 +1,9 @@ +CEXE_headers+=mechanism.H + +CEXE_sources+=mechanism.cpp + +LIBRARIES += + +INCLUDE_LOCATIONS += $(CHEM_DIR) + +VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/heptane_3sp/convert.sh b/Mechanisms/heptane_3sp/convert.sh similarity index 100% rename from Support/Mechanism/Models/heptane_3sp/convert.sh rename to Mechanisms/heptane_3sp/convert.sh diff --git a/Support/Mechanism/Models/heptane_3sp/mechanism.H b/Mechanisms/heptane_3sp/mechanism.H similarity index 100% rename from Support/Mechanism/Models/heptane_3sp/mechanism.H rename to Mechanisms/heptane_3sp/mechanism.H diff --git a/Support/Mechanism/Models/heptane_3sp/mechanism.cpp b/Mechanisms/heptane_3sp/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/heptane_3sp/mechanism.cpp rename to Mechanisms/heptane_3sp/mechanism.cpp diff --git a/Support/Mechanism/Models/heptane_3sp/mechanism.inp b/Mechanisms/heptane_3sp/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/heptane_3sp/mechanism.inp rename to Mechanisms/heptane_3sp/mechanism.inp diff --git a/Support/Mechanism/Models/heptane_3sp/mechanism.yaml b/Mechanisms/heptane_3sp/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/heptane_3sp/mechanism.yaml rename to Mechanisms/heptane_3sp/mechanism.yaml diff --git a/Support/Mechanism/Models/heptane_3sp/therm.dat b/Mechanisms/heptane_3sp/therm.dat similarity index 100% rename from Support/Mechanism/Models/heptane_3sp/therm.dat rename to Mechanisms/heptane_3sp/therm.dat diff --git a/Support/Mechanism/Models/heptane_3sp/tran.dat b/Mechanisms/heptane_3sp/tran.dat similarity index 100% rename from Support/Mechanism/Models/heptane_3sp/tran.dat rename to Mechanisms/heptane_3sp/tran.dat diff --git a/Mechanisms/heptane_fc/Make.package b/Mechanisms/heptane_fc/Make.package new file mode 100644 index 000000000..24c663c9a --- /dev/null +++ b/Mechanisms/heptane_fc/Make.package @@ -0,0 +1,9 @@ +CEXE_headers+=mechanism.H + +CEXE_sources+=mechanism.cpp + +LIBRARIES += + +INCLUDE_LOCATIONS += $(CHEM_DIR) + +VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/heptane_fc/convert.sh b/Mechanisms/heptane_fc/convert.sh similarity index 100% rename from Support/Mechanism/Models/heptane_fc/convert.sh rename to Mechanisms/heptane_fc/convert.sh diff --git a/Support/Mechanism/Models/heptane_fc/mechanism.H b/Mechanisms/heptane_fc/mechanism.H similarity index 100% rename from Support/Mechanism/Models/heptane_fc/mechanism.H rename to Mechanisms/heptane_fc/mechanism.H diff --git a/Support/Mechanism/Models/heptane_fc/mechanism.cpp b/Mechanisms/heptane_fc/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/heptane_fc/mechanism.cpp rename to Mechanisms/heptane_fc/mechanism.cpp diff --git a/Support/Mechanism/Models/heptane_fc/mechanism.inp b/Mechanisms/heptane_fc/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/heptane_fc/mechanism.inp rename to Mechanisms/heptane_fc/mechanism.inp diff --git a/Support/Mechanism/Models/heptane_fc/mechanism.yaml b/Mechanisms/heptane_fc/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/heptane_fc/mechanism.yaml rename to Mechanisms/heptane_fc/mechanism.yaml diff --git a/Support/Mechanism/Models/heptane_fc/therm.dat b/Mechanisms/heptane_fc/therm.dat similarity index 100% rename from Support/Mechanism/Models/heptane_fc/therm.dat rename to Mechanisms/heptane_fc/therm.dat diff --git a/Support/Mechanism/Models/heptane_fc/tran.dat b/Mechanisms/heptane_fc/tran.dat similarity index 100% rename from Support/Mechanism/Models/heptane_fc/tran.dat rename to Mechanisms/heptane_fc/tran.dat diff --git a/Mechanisms/heptane_lu_88sk/Make.package b/Mechanisms/heptane_lu_88sk/Make.package new file mode 100644 index 000000000..24c663c9a --- /dev/null +++ b/Mechanisms/heptane_lu_88sk/Make.package @@ -0,0 +1,9 @@ +CEXE_headers+=mechanism.H + +CEXE_sources+=mechanism.cpp + +LIBRARIES += + +INCLUDE_LOCATIONS += $(CHEM_DIR) + +VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/heptane_lu_88sk/TRANFILE_APPEND.txt b/Mechanisms/heptane_lu_88sk/TRANFILE_APPEND.txt similarity index 100% rename from Support/Mechanism/Models/heptane_lu_88sk/TRANFILE_APPEND.txt rename to Mechanisms/heptane_lu_88sk/TRANFILE_APPEND.txt diff --git a/Support/Mechanism/Models/heptane_lu_88sk/TRANFILE_APPEND_upper.txt b/Mechanisms/heptane_lu_88sk/TRANFILE_APPEND_upper.txt similarity index 100% rename from Support/Mechanism/Models/heptane_lu_88sk/TRANFILE_APPEND_upper.txt rename to Mechanisms/heptane_lu_88sk/TRANFILE_APPEND_upper.txt diff --git a/Support/Mechanism/Models/heptane_lu_88sk/chem.inp b/Mechanisms/heptane_lu_88sk/chem.inp similarity index 100% rename from Support/Mechanism/Models/heptane_lu_88sk/chem.inp rename to Mechanisms/heptane_lu_88sk/chem.inp diff --git a/Support/Mechanism/Models/heptane_lu_88sk/chem_upper.inp b/Mechanisms/heptane_lu_88sk/chem_upper.inp similarity index 100% rename from Support/Mechanism/Models/heptane_lu_88sk/chem_upper.inp rename to Mechanisms/heptane_lu_88sk/chem_upper.inp diff --git a/Support/Mechanism/Models/heptane_lu_88sk/mechanism.H b/Mechanisms/heptane_lu_88sk/mechanism.H similarity index 100% rename from Support/Mechanism/Models/heptane_lu_88sk/mechanism.H rename to Mechanisms/heptane_lu_88sk/mechanism.H diff --git a/Support/Mechanism/Models/heptane_lu_88sk/mechanism.cpp b/Mechanisms/heptane_lu_88sk/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/heptane_lu_88sk/mechanism.cpp rename to Mechanisms/heptane_lu_88sk/mechanism.cpp diff --git a/Support/Mechanism/Models/heptane_lu_88sk/mechanism.yaml b/Mechanisms/heptane_lu_88sk/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/heptane_lu_88sk/mechanism.yaml rename to Mechanisms/heptane_lu_88sk/mechanism.yaml diff --git a/Support/Mechanism/Models/heptane_lu_88sk/therm.dat b/Mechanisms/heptane_lu_88sk/therm.dat similarity index 100% rename from Support/Mechanism/Models/heptane_lu_88sk/therm.dat rename to Mechanisms/heptane_lu_88sk/therm.dat diff --git a/Support/Mechanism/Models/heptane_lu_88sk/therm_upper.dat b/Mechanisms/heptane_lu_88sk/therm_upper.dat similarity index 100% rename from Support/Mechanism/Models/heptane_lu_88sk/therm_upper.dat rename to Mechanisms/heptane_lu_88sk/therm_upper.dat diff --git a/Support/Mechanism/Models/heptane_lu_88sk/tran.dat b/Mechanisms/heptane_lu_88sk/tran.dat similarity index 100% rename from Support/Mechanism/Models/heptane_lu_88sk/tran.dat rename to Mechanisms/heptane_lu_88sk/tran.dat diff --git a/Support/Mechanism/Models/heptane_lu_88sk/tran_upper.dat b/Mechanisms/heptane_lu_88sk/tran_upper.dat similarity index 100% rename from Support/Mechanism/Models/heptane_lu_88sk/tran_upper.dat rename to Mechanisms/heptane_lu_88sk/tran_upper.dat diff --git a/Mechanisms/heptane_lu_qss/Make.package b/Mechanisms/heptane_lu_qss/Make.package new file mode 100644 index 000000000..24c663c9a --- /dev/null +++ b/Mechanisms/heptane_lu_qss/Make.package @@ -0,0 +1,9 @@ +CEXE_headers+=mechanism.H + +CEXE_sources+=mechanism.cpp + +LIBRARIES += + +INCLUDE_LOCATIONS += $(CHEM_DIR) + +VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/heptane_lu_qss/mechanism.H b/Mechanisms/heptane_lu_qss/mechanism.H similarity index 100% rename from Support/Mechanism/Models/heptane_lu_qss/mechanism.H rename to Mechanisms/heptane_lu_qss/mechanism.H diff --git a/Support/Mechanism/Models/heptane_lu_qss/mechanism.cpp b/Mechanisms/heptane_lu_qss/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/heptane_lu_qss/mechanism.cpp rename to Mechanisms/heptane_lu_qss/mechanism.cpp diff --git a/Support/Mechanism/Models/heptane_lu_qss/non_qssa_list.yaml b/Mechanisms/heptane_lu_qss/non_qssa_list.yaml similarity index 100% rename from Support/Mechanism/Models/heptane_lu_qss/non_qssa_list.yaml rename to Mechanisms/heptane_lu_qss/non_qssa_list.yaml diff --git a/Support/Mechanism/Models/heptane_lu_qss/qssa.yaml b/Mechanisms/heptane_lu_qss/qssa.yaml similarity index 100% rename from Support/Mechanism/Models/heptane_lu_qss/qssa.yaml rename to Mechanisms/heptane_lu_qss/qssa.yaml diff --git a/Support/Mechanism/Models/heptane_lu_qss/qssa_input.toml b/Mechanisms/heptane_lu_qss/qssa_input.toml similarity index 100% rename from Support/Mechanism/Models/heptane_lu_qss/qssa_input.toml rename to Mechanisms/heptane_lu_qss/qssa_input.toml diff --git a/Support/Mechanism/Models/heptane_lu_qss/skeletal.yaml b/Mechanisms/heptane_lu_qss/skeletal.yaml similarity index 100% rename from Support/Mechanism/Models/heptane_lu_qss/skeletal.yaml rename to Mechanisms/heptane_lu_qss/skeletal.yaml diff --git a/Support/Mechanism/Models/heptane_lu_qss/therm.dat b/Mechanisms/heptane_lu_qss/therm.dat similarity index 100% rename from Support/Mechanism/Models/heptane_lu_qss/therm.dat rename to Mechanisms/heptane_lu_qss/therm.dat diff --git a/Support/Mechanism/Models/heptane_lu_qss/tran.dat b/Mechanisms/heptane_lu_qss/tran.dat similarity index 100% rename from Support/Mechanism/Models/heptane_lu_qss/tran.dat rename to Mechanisms/heptane_lu_qss/tran.dat diff --git a/Mechanisms/isooctane_lu/Make.package b/Mechanisms/isooctane_lu/Make.package new file mode 100644 index 000000000..24c663c9a --- /dev/null +++ b/Mechanisms/isooctane_lu/Make.package @@ -0,0 +1,9 @@ +CEXE_headers+=mechanism.H + +CEXE_sources+=mechanism.cpp + +LIBRARIES += + +INCLUDE_LOCATIONS += $(CHEM_DIR) + +VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/isooctane_lu/convert.sh b/Mechanisms/isooctane_lu/convert.sh similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/convert.sh rename to Mechanisms/isooctane_lu/convert.sh diff --git a/Support/Mechanism/Models/isooctane_lu/iso140/chem.inp b/Mechanisms/isooctane_lu/iso140/chem.inp similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/iso140/chem.inp rename to Mechanisms/isooctane_lu/iso140/chem.inp diff --git a/Support/Mechanism/Models/isooctane_lu/iso140/therm.dat b/Mechanisms/isooctane_lu/iso140/therm.dat similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/iso140/therm.dat rename to Mechanisms/isooctane_lu/iso140/therm.dat diff --git a/Support/Mechanism/Models/isooctane_lu/iso140/tran.dat b/Mechanisms/isooctane_lu/iso140/tran.dat similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/iso140/tran.dat rename to Mechanisms/isooctane_lu/iso140/tran.dat diff --git a/Support/Mechanism/Models/isooctane_lu/mechanism.H b/Mechanisms/isooctane_lu/mechanism.H similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/mechanism.H rename to Mechanisms/isooctane_lu/mechanism.H diff --git a/Support/Mechanism/Models/isooctane_lu/mechanism.cpp b/Mechanisms/isooctane_lu/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/mechanism.cpp rename to Mechanisms/isooctane_lu/mechanism.cpp diff --git a/Support/Mechanism/Models/isooctane_lu/mechanism.inp b/Mechanisms/isooctane_lu/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/mechanism.inp rename to Mechanisms/isooctane_lu/mechanism.inp diff --git a/Support/Mechanism/Models/isooctane_lu/mechanism.yaml b/Mechanisms/isooctane_lu/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/mechanism.yaml rename to Mechanisms/isooctane_lu/mechanism.yaml diff --git a/Support/Mechanism/Models/isooctane_lu/red99/chem.inp b/Mechanisms/isooctane_lu/red99/chem.inp similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/red99/chem.inp rename to Mechanisms/isooctane_lu/red99/chem.inp diff --git a/Support/Mechanism/Models/isooctane_lu/red99/ckwyp.f b/Mechanisms/isooctane_lu/red99/ckwyp.f similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/red99/ckwyp.f rename to Mechanisms/isooctane_lu/red99/ckwyp.f diff --git a/Support/Mechanism/Models/isooctane_lu/red99/mcadif.f b/Mechanisms/isooctane_lu/red99/mcadif.f similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/red99/mcadif.f rename to Mechanisms/isooctane_lu/red99/mcadif.f diff --git a/Support/Mechanism/Models/isooctane_lu/red99/therm.dat b/Mechanisms/isooctane_lu/red99/therm.dat similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/red99/therm.dat rename to Mechanisms/isooctane_lu/red99/therm.dat diff --git a/Support/Mechanism/Models/isooctane_lu/red99/tran.dat b/Mechanisms/isooctane_lu/red99/tran.dat similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/red99/tran.dat rename to Mechanisms/isooctane_lu/red99/tran.dat diff --git a/Support/Mechanism/Models/isooctane_lu/sk143/chem.inp b/Mechanisms/isooctane_lu/sk143/chem.inp similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/sk143/chem.inp rename to Mechanisms/isooctane_lu/sk143/chem.inp diff --git a/Support/Mechanism/Models/isooctane_lu/sk143/therm.dat b/Mechanisms/isooctane_lu/sk143/therm.dat similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/sk143/therm.dat rename to Mechanisms/isooctane_lu/sk143/therm.dat diff --git a/Support/Mechanism/Models/isooctane_lu/sk143/tran.dat b/Mechanisms/isooctane_lu/sk143/tran.dat similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/sk143/tran.dat rename to Mechanisms/isooctane_lu/sk143/tran.dat diff --git a/Support/Mechanism/Models/isooctane_lu/therm.dat b/Mechanisms/isooctane_lu/therm.dat similarity index 100% rename from Support/Mechanism/Models/isooctane_lu/therm.dat rename to Mechanisms/isooctane_lu/therm.dat diff --git a/Support/Mechanism/Models/list_mech b/Mechanisms/list_mech similarity index 100% rename from Support/Mechanism/Models/list_mech rename to Mechanisms/list_mech diff --git a/Support/Mechanism/Models/list_qss_mech b/Mechanisms/list_qss_mech similarity index 100% rename from Support/Mechanism/Models/list_qss_mech rename to Mechanisms/list_qss_mech diff --git a/Mechanisms/methaneIons_diRenzo/Make.package b/Mechanisms/methaneIons_diRenzo/Make.package new file mode 100644 index 000000000..24c663c9a --- /dev/null +++ b/Mechanisms/methaneIons_diRenzo/Make.package @@ -0,0 +1,9 @@ +CEXE_headers+=mechanism.H + +CEXE_sources+=mechanism.cpp + +LIBRARIES += + +INCLUDE_LOCATIONS += $(CHEM_DIR) + +VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/methaneIons_diRenzo/mechanism.H b/Mechanisms/methaneIons_diRenzo/mechanism.H similarity index 100% rename from Support/Mechanism/Models/methaneIons_diRenzo/mechanism.H rename to Mechanisms/methaneIons_diRenzo/mechanism.H diff --git a/Support/Mechanism/Models/methaneIons_diRenzo/mechanism.cpp b/Mechanisms/methaneIons_diRenzo/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/methaneIons_diRenzo/mechanism.cpp rename to Mechanisms/methaneIons_diRenzo/mechanism.cpp diff --git a/Support/Mechanism/Models/methaneIons_diRenzo/reducedS26R134_0.yaml b/Mechanisms/methaneIons_diRenzo/reducedS26R134_0.yaml similarity index 100% rename from Support/Mechanism/Models/methaneIons_diRenzo/reducedS26R134_0.yaml rename to Mechanisms/methaneIons_diRenzo/reducedS26R134_0.yaml diff --git a/Support/Mechanism/Models/methaneIons_diRenzo/reducedS26R134_0.yaml_presDep b/Mechanisms/methaneIons_diRenzo/reducedS26R134_0.yaml_presDep similarity index 100% rename from Support/Mechanism/Models/methaneIons_diRenzo/reducedS26R134_0.yaml_presDep rename to Mechanisms/methaneIons_diRenzo/reducedS26R134_0.yaml_presDep diff --git a/Mechanisms/ndodecane_35/Make.package b/Mechanisms/ndodecane_35/Make.package new file mode 100644 index 000000000..24c663c9a --- /dev/null +++ b/Mechanisms/ndodecane_35/Make.package @@ -0,0 +1,9 @@ +CEXE_headers+=mechanism.H + +CEXE_sources+=mechanism.cpp + +LIBRARIES += + +INCLUDE_LOCATIONS += $(CHEM_DIR) + +VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/ndodecane_35/ckwc.f b/Mechanisms/ndodecane_35/ckwc.f similarity index 100% rename from Support/Mechanism/Models/ndodecane_35/ckwc.f rename to Mechanisms/ndodecane_35/ckwc.f diff --git a/Support/Mechanism/Models/ndodecane_35/convert.sh b/Mechanisms/ndodecane_35/convert.sh similarity index 100% rename from Support/Mechanism/Models/ndodecane_35/convert.sh rename to Mechanisms/ndodecane_35/convert.sh diff --git a/Support/Mechanism/Models/ndodecane_35/mechanism.H b/Mechanisms/ndodecane_35/mechanism.H similarity index 100% rename from Support/Mechanism/Models/ndodecane_35/mechanism.H rename to Mechanisms/ndodecane_35/mechanism.H diff --git a/Support/Mechanism/Models/ndodecane_35/mechanism.cpp b/Mechanisms/ndodecane_35/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/ndodecane_35/mechanism.cpp rename to Mechanisms/ndodecane_35/mechanism.cpp diff --git a/Support/Mechanism/Models/ndodecane_35/mechanism.inp b/Mechanisms/ndodecane_35/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/ndodecane_35/mechanism.inp rename to Mechanisms/ndodecane_35/mechanism.inp diff --git a/Support/Mechanism/Models/ndodecane_35/mechanism.yaml b/Mechanisms/ndodecane_35/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/ndodecane_35/mechanism.yaml rename to Mechanisms/ndodecane_35/mechanism.yaml diff --git a/Support/Mechanism/Models/ndodecane_35/therm.dat b/Mechanisms/ndodecane_35/therm.dat similarity index 100% rename from Support/Mechanism/Models/ndodecane_35/therm.dat rename to Mechanisms/ndodecane_35/therm.dat diff --git a/Support/Mechanism/Models/ndodecane_35/tran.dat b/Mechanisms/ndodecane_35/tran.dat similarity index 100% rename from Support/Mechanism/Models/ndodecane_35/tran.dat rename to Mechanisms/ndodecane_35/tran.dat diff --git a/Mechanisms/nitrogens/Make.package b/Mechanisms/nitrogens/Make.package new file mode 100644 index 000000000..24c663c9a --- /dev/null +++ b/Mechanisms/nitrogens/Make.package @@ -0,0 +1,9 @@ +CEXE_headers+=mechanism.H + +CEXE_sources+=mechanism.cpp + +LIBRARIES += + +INCLUDE_LOCATIONS += $(CHEM_DIR) + +VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/nitrogens/README b/Mechanisms/nitrogens/README similarity index 100% rename from Support/Mechanism/Models/nitrogens/README rename to Mechanisms/nitrogens/README diff --git a/Support/Mechanism/Models/nitrogens/convert.sh b/Mechanisms/nitrogens/convert.sh similarity index 100% rename from Support/Mechanism/Models/nitrogens/convert.sh rename to Mechanisms/nitrogens/convert.sh diff --git a/Support/Mechanism/Models/nitrogens/mechanism.H b/Mechanisms/nitrogens/mechanism.H similarity index 100% rename from Support/Mechanism/Models/nitrogens/mechanism.H rename to Mechanisms/nitrogens/mechanism.H diff --git a/Support/Mechanism/Models/nitrogens/mechanism.cpp b/Mechanisms/nitrogens/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/nitrogens/mechanism.cpp rename to Mechanisms/nitrogens/mechanism.cpp diff --git a/Support/Mechanism/Models/nitrogens/mechanism.inp b/Mechanisms/nitrogens/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/nitrogens/mechanism.inp rename to Mechanisms/nitrogens/mechanism.inp diff --git a/Support/Mechanism/Models/nitrogens/mechanism.yaml b/Mechanisms/nitrogens/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/nitrogens/mechanism.yaml rename to Mechanisms/nitrogens/mechanism.yaml diff --git a/Support/Mechanism/Models/nitrogens/therm.dat b/Mechanisms/nitrogens/therm.dat similarity index 100% rename from Support/Mechanism/Models/nitrogens/therm.dat rename to Mechanisms/nitrogens/therm.dat diff --git a/Support/Mechanism/Models/nitrogens/tran.dat b/Mechanisms/nitrogens/tran.dat similarity index 100% rename from Support/Mechanism/Models/nitrogens/tran.dat rename to Mechanisms/nitrogens/tran.dat diff --git a/Mechanisms/propane_fc/Make.package b/Mechanisms/propane_fc/Make.package new file mode 100644 index 000000000..24c663c9a --- /dev/null +++ b/Mechanisms/propane_fc/Make.package @@ -0,0 +1,9 @@ +CEXE_headers+=mechanism.H + +CEXE_sources+=mechanism.cpp + +LIBRARIES += + +INCLUDE_LOCATIONS += $(CHEM_DIR) + +VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/propane_fc/convert.sh b/Mechanisms/propane_fc/convert.sh similarity index 100% rename from Support/Mechanism/Models/propane_fc/convert.sh rename to Mechanisms/propane_fc/convert.sh diff --git a/Support/Mechanism/Models/propane_fc/mechanism.H b/Mechanisms/propane_fc/mechanism.H similarity index 100% rename from Support/Mechanism/Models/propane_fc/mechanism.H rename to Mechanisms/propane_fc/mechanism.H diff --git a/Support/Mechanism/Models/propane_fc/mechanism.cpp b/Mechanisms/propane_fc/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/propane_fc/mechanism.cpp rename to Mechanisms/propane_fc/mechanism.cpp diff --git a/Support/Mechanism/Models/propane_fc/mechanism.inp b/Mechanisms/propane_fc/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/propane_fc/mechanism.inp rename to Mechanisms/propane_fc/mechanism.inp diff --git a/Support/Mechanism/Models/propane_fc/mechanism.yaml b/Mechanisms/propane_fc/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/propane_fc/mechanism.yaml rename to Mechanisms/propane_fc/mechanism.yaml diff --git a/Support/Mechanism/Models/propane_fc/therm.dat b/Mechanisms/propane_fc/therm.dat similarity index 100% rename from Support/Mechanism/Models/propane_fc/therm.dat rename to Mechanisms/propane_fc/therm.dat diff --git a/Mechanisms/sCO2/Make.package b/Mechanisms/sCO2/Make.package new file mode 100644 index 000000000..24c663c9a --- /dev/null +++ b/Mechanisms/sCO2/Make.package @@ -0,0 +1,9 @@ +CEXE_headers+=mechanism.H + +CEXE_sources+=mechanism.cpp + +LIBRARIES += + +INCLUDE_LOCATIONS += $(CHEM_DIR) + +VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/sCO2/convert.sh b/Mechanisms/sCO2/convert.sh similarity index 100% rename from Support/Mechanism/Models/sCO2/convert.sh rename to Mechanisms/sCO2/convert.sh diff --git a/Support/Mechanism/Models/sCO2/mechanism.H b/Mechanisms/sCO2/mechanism.H similarity index 100% rename from Support/Mechanism/Models/sCO2/mechanism.H rename to Mechanisms/sCO2/mechanism.H diff --git a/Support/Mechanism/Models/sCO2/mechanism.cpp b/Mechanisms/sCO2/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/sCO2/mechanism.cpp rename to Mechanisms/sCO2/mechanism.cpp diff --git a/Support/Mechanism/Models/sCO2/mechanism.inp b/Mechanisms/sCO2/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/sCO2/mechanism.inp rename to Mechanisms/sCO2/mechanism.inp diff --git a/Support/Mechanism/Models/sCO2/mechanism.yaml b/Mechanisms/sCO2/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/sCO2/mechanism.yaml rename to Mechanisms/sCO2/mechanism.yaml diff --git a/Support/Mechanism/Models/sCO2/therm.dat b/Mechanisms/sCO2/therm.dat similarity index 100% rename from Support/Mechanism/Models/sCO2/therm.dat rename to Mechanisms/sCO2/therm.dat diff --git a/Support/Mechanism/Models/sCO2/transport.txt b/Mechanisms/sCO2/transport.txt similarity index 100% rename from Support/Mechanism/Models/sCO2/transport.txt rename to Mechanisms/sCO2/transport.txt diff --git a/README.md b/README.md index b379d2c88..d85409ec2 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ This information is read by the CEPTR tool, and source code files are generated * Mixture-averaged thermal diffusion coefficients are also available using the transport.use_soret flag (see PeleLMeX implementation for more information) * Utilization of auxiliary source files (C++) that follow the Cantera species production rate function interface (e.g., QSS approximations) -If the `Pele` codes are built with `Eos_dir = Fuego`, the make system variable `Chemistry_Model` must be set to one of the models (subfolders) that exist in the `${PELE_PHYSICS_HOME}/Support/Mechanism/Models` folder. The repository currently provides (multiple) models for each of the following mixtures: +If the `Pele` codes are built with `Eos_Model = Fuego`, the make system variable `Chemistry_Model` must be set to one of the models (subfolders) that exist in the `${PELE_PHYSICS_HOME}/Mechanisms` folder. The repository currently provides (multiple) models for each of the following mixtures: * air * hydrogen * methane @@ -32,7 +32,7 @@ If the `Pele` codes are built with `Eos_dir = Fuego`, the make system variable ` ### NOTE: Non-ideal equations of state -`PelePhysics` currently supports a cubic EOS model: `Soave-Redlich-Kwong`. It is built on top of the ideal gas models, and is selected by specifying its name as the `Eos_dir` during the build (the make system requires that both `Eos_dir` and `Chemistry_Model` be specified). Any additional parameters required for the EOS (e.g., attractions, repulsions, critical states) are either included in the underlying CEPTR database used to generate the source file model implementation, or else are inferred from the input model data. +`PelePhysics` currently supports a cubic EOS model: `Soave-Redlich-Kwong`. It is built on top of the ideal gas models, and is selected by specifying its name as the `Eos_Model` during the build (the make system requires that both `Eos_Model` and `Chemistry_Model` be specified). Any additional parameters required for the EOS (e.g., attractions, repulsions, critical states) are either included in the underlying CEPTR database used to generate the source file model implementation, or else are inferred from the input model data. ## Model generation procedures -This repository provides the tools necessary for generating new Pele-compatible combustion mechanisms. Please refer to the `CEPTR documentation `_ for instructions on generating mechanism models. Make sure that you edit the `GNUmakefile` where you want to use this (in, e.g., `PeleC/Exec`) so that `Chemistry_Model` is `XXX`. In `PeleC/Exec/Make.PeleC`, the model is expected to be in the folder `${PELE_PHYSICS_HOME}/Support/Mechanism/Models/$(Chemistry_Model)`, and it is expected that the folder contains a `Make.package` file to include, so make sure things are where they need to be. Refer to other mechanisms for additional guidance. +This repository provides the tools necessary for generating new Pele-compatible combustion mechanisms. Please refer to the `CEPTR documentation `_ for instructions on generating mechanism models. Make sure that you edit the `GNUmakefile` where you want to use this (in, e.g., `PeleC/Exec`) so that `Chemistry_Model` is `XXX`. In `PeleC/Exec/Make.PeleC`, the model is expected to be in the folder `${PELE_PHYSICS_HOME}/Mechanisms/$(Chemistry_Model)`, and it is expected that the folder contains a `Make.package` file to include, so make sure things are where they need to be. Refer to other mechanisms for additional guidance. diff --git a/Eos/EOS.H b/Source/Eos/EOS.H similarity index 100% rename from Eos/EOS.H rename to Source/Eos/EOS.H diff --git a/Eos/EOS.cpp b/Source/Eos/EOS.cpp similarity index 100% rename from Eos/EOS.cpp rename to Source/Eos/EOS.cpp diff --git a/Eos/Fuego.H b/Source/Eos/Fuego.H similarity index 100% rename from Eos/Fuego.H rename to Source/Eos/Fuego.H diff --git a/Eos/GammaLaw.H b/Source/Eos/GammaLaw.H similarity index 100% rename from Eos/GammaLaw.H rename to Source/Eos/GammaLaw.H diff --git a/Source/Eos/Make.package b/Source/Eos/Make.package new file mode 100644 index 000000000..34456518e --- /dev/null +++ b/Source/Eos/Make.package @@ -0,0 +1,5 @@ +CEXE_headers += EOS.H GammaLaw.H Fuego.H SRK.H +CEXE_sources += EOS.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Eos +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Eos \ No newline at end of file diff --git a/Eos/README b/Source/Eos/README similarity index 96% rename from Eos/README rename to Source/Eos/README index 92231a9bd..44ae23a4c 100644 --- a/Eos/README +++ b/Source/Eos/README @@ -14,7 +14,7 @@ Fuego: A mixture of ideal gases, computed using CEPTR-generated codes. The specific model is selected at compile time from the list in - ../Support/Mechanism/Models + ../Mechanisms Soave-Redlich-Kwong: diff --git a/Eos/SRK.H b/Source/Eos/SRK.H similarity index 100% rename from Eos/SRK.H rename to Source/Eos/SRK.H diff --git a/Reactions/Make.package b/Source/Reactions/Make.package similarity index 80% rename from Reactions/Make.package rename to Source/Reactions/Make.package index bcaee2f9e..78ff85528 100644 --- a/Reactions/Make.package +++ b/Source/Reactions/Make.package @@ -1,2 +1,5 @@ CEXE_headers += ReactorUtils.H ReactorTypes.H ReactorBase.H ReactorBDF.H ReactorBDFsolver.H ReactorRK64.H ReactorArkode.H ReactorNull.H ReactorCvode.H ReactorCvodeUtils.H ReactorCvodePreconditioner.H ReactorCvodeJacobian.H ReactorCvodeCustomLinSolver.H CEXE_sources += ReactorUtils.cpp ReactorBase.cpp ReactorBDF.cpp ReactorRK64.cpp ReactorArkode.cpp ReactorNull.cpp ReactorCvode.cpp ReactorCvodeUtils.cpp ReactorCvodePreconditioner.cpp ReactorCvodeJacobian.cpp ReactorCvodeCustomLinSolver.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Reactions +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Reactions \ No newline at end of file diff --git a/Reactions/ReactorArkode.H b/Source/Reactions/ReactorArkode.H similarity index 100% rename from Reactions/ReactorArkode.H rename to Source/Reactions/ReactorArkode.H diff --git a/Reactions/ReactorArkode.cpp b/Source/Reactions/ReactorArkode.cpp similarity index 100% rename from Reactions/ReactorArkode.cpp rename to Source/Reactions/ReactorArkode.cpp diff --git a/Reactions/ReactorBDF.H b/Source/Reactions/ReactorBDF.H similarity index 100% rename from Reactions/ReactorBDF.H rename to Source/Reactions/ReactorBDF.H diff --git a/Reactions/ReactorBDF.cpp b/Source/Reactions/ReactorBDF.cpp similarity index 100% rename from Reactions/ReactorBDF.cpp rename to Source/Reactions/ReactorBDF.cpp diff --git a/Reactions/ReactorBDFsolver.H b/Source/Reactions/ReactorBDFsolver.H similarity index 100% rename from Reactions/ReactorBDFsolver.H rename to Source/Reactions/ReactorBDFsolver.H diff --git a/Reactions/ReactorBase.H b/Source/Reactions/ReactorBase.H similarity index 100% rename from Reactions/ReactorBase.H rename to Source/Reactions/ReactorBase.H diff --git a/Reactions/ReactorBase.cpp b/Source/Reactions/ReactorBase.cpp similarity index 100% rename from Reactions/ReactorBase.cpp rename to Source/Reactions/ReactorBase.cpp diff --git a/Reactions/ReactorCvode.H b/Source/Reactions/ReactorCvode.H similarity index 100% rename from Reactions/ReactorCvode.H rename to Source/Reactions/ReactorCvode.H diff --git a/Reactions/ReactorCvode.cpp b/Source/Reactions/ReactorCvode.cpp similarity index 100% rename from Reactions/ReactorCvode.cpp rename to Source/Reactions/ReactorCvode.cpp diff --git a/Reactions/ReactorCvodeCustomLinSolver.H b/Source/Reactions/ReactorCvodeCustomLinSolver.H similarity index 100% rename from Reactions/ReactorCvodeCustomLinSolver.H rename to Source/Reactions/ReactorCvodeCustomLinSolver.H diff --git a/Reactions/ReactorCvodeCustomLinSolver.cpp b/Source/Reactions/ReactorCvodeCustomLinSolver.cpp similarity index 100% rename from Reactions/ReactorCvodeCustomLinSolver.cpp rename to Source/Reactions/ReactorCvodeCustomLinSolver.cpp diff --git a/Reactions/ReactorCvodeJacobian.H b/Source/Reactions/ReactorCvodeJacobian.H similarity index 100% rename from Reactions/ReactorCvodeJacobian.H rename to Source/Reactions/ReactorCvodeJacobian.H diff --git a/Reactions/ReactorCvodeJacobian.cpp b/Source/Reactions/ReactorCvodeJacobian.cpp similarity index 100% rename from Reactions/ReactorCvodeJacobian.cpp rename to Source/Reactions/ReactorCvodeJacobian.cpp diff --git a/Reactions/ReactorCvodePreconditioner.H b/Source/Reactions/ReactorCvodePreconditioner.H similarity index 100% rename from Reactions/ReactorCvodePreconditioner.H rename to Source/Reactions/ReactorCvodePreconditioner.H diff --git a/Reactions/ReactorCvodePreconditioner.cpp b/Source/Reactions/ReactorCvodePreconditioner.cpp similarity index 100% rename from Reactions/ReactorCvodePreconditioner.cpp rename to Source/Reactions/ReactorCvodePreconditioner.cpp diff --git a/Reactions/ReactorCvodeUtils.H b/Source/Reactions/ReactorCvodeUtils.H similarity index 100% rename from Reactions/ReactorCvodeUtils.H rename to Source/Reactions/ReactorCvodeUtils.H diff --git a/Reactions/ReactorCvodeUtils.cpp b/Source/Reactions/ReactorCvodeUtils.cpp similarity index 100% rename from Reactions/ReactorCvodeUtils.cpp rename to Source/Reactions/ReactorCvodeUtils.cpp diff --git a/Reactions/ReactorNull.H b/Source/Reactions/ReactorNull.H similarity index 100% rename from Reactions/ReactorNull.H rename to Source/Reactions/ReactorNull.H diff --git a/Reactions/ReactorNull.cpp b/Source/Reactions/ReactorNull.cpp similarity index 100% rename from Reactions/ReactorNull.cpp rename to Source/Reactions/ReactorNull.cpp diff --git a/Reactions/ReactorRK64.H b/Source/Reactions/ReactorRK64.H similarity index 100% rename from Reactions/ReactorRK64.H rename to Source/Reactions/ReactorRK64.H diff --git a/Reactions/ReactorRK64.cpp b/Source/Reactions/ReactorRK64.cpp similarity index 100% rename from Reactions/ReactorRK64.cpp rename to Source/Reactions/ReactorRK64.cpp diff --git a/Reactions/ReactorTypes.H b/Source/Reactions/ReactorTypes.H similarity index 100% rename from Reactions/ReactorTypes.H rename to Source/Reactions/ReactorTypes.H diff --git a/Reactions/ReactorUtils.H b/Source/Reactions/ReactorUtils.H similarity index 100% rename from Reactions/ReactorUtils.H rename to Source/Reactions/ReactorUtils.H diff --git a/Reactions/ReactorUtils.cpp b/Source/Reactions/ReactorUtils.cpp similarity index 100% rename from Reactions/ReactorUtils.cpp rename to Source/Reactions/ReactorUtils.cpp diff --git a/Source/Soot/Make.package b/Source/Soot/Make.package index e030770b8..e43311df6 100644 --- a/Source/Soot/Make.package +++ b/Source/Soot/Make.package @@ -1,3 +1,6 @@ CEXE_headers += Constants_Soot.H SootData.H SootReactions.H SootModel.H SootModel_derive.H CEXE_sources += SootModel.cpp SootModel_react.cpp SootModel_derive.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Soot +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Soot \ No newline at end of file diff --git a/Source/Soot/SootModel.H b/Source/Soot/SootModel.H index ddc668e1d..9b83e66e2 100644 --- a/Source/Soot/SootModel.H +++ b/Source/Soot/SootModel.H @@ -5,7 +5,7 @@ // AMReX include statements #include -// PeleMP include statements +// Soot include statements #include "Constants_Soot.H" #include "SootData.H" #include "SootReactions.H" diff --git a/Source/Soot/SootModel.cpp b/Source/Soot/SootModel.cpp index 4b063cb20..6806618cf 100644 --- a/Source/Soot/SootModel.cpp +++ b/Source/Soot/SootModel.cpp @@ -5,7 +5,7 @@ // PelePhysics include statements #include "PelePhysics.H" -// PeleMP include statements +// Soot include statements #include "SootModel.H" using namespace amrex; diff --git a/Source/Soot/SootModel_react.cpp b/Source/Soot/SootModel_react.cpp index 36dc6c589..8a8396319 100644 --- a/Source/Soot/SootModel_react.cpp +++ b/Source/Soot/SootModel_react.cpp @@ -1,5 +1,5 @@ -// PeleMP include statements +// Soot include statements #include "SootModel.H" // PelePhysics include statements diff --git a/Source/Spray/BreakupSplash/AhamedSplash.H b/Source/Spray/BreakupSplash/AhamedSplash.H index 2487a69af..88abf21ce 100644 --- a/Source/Spray/BreakupSplash/AhamedSplash.H +++ b/Source/Spray/BreakupSplash/AhamedSplash.H @@ -203,8 +203,8 @@ void droplet_splashing( SprayParticleContainer::ParticleType& p, int pid, - const amrex::RealVect& dx, - const amrex::RealVect& plo, + const amrex::RealVect& /*dx*/, + const amrex::RealVect& /*plo*/, const SprayData& fdat, const amrex::Real p_gas, const amrex::RealVect& vel_part, diff --git a/Source/Spray/BreakupSplash/Make.package b/Source/Spray/BreakupSplash/Make.package index d313c208a..c425ecdeb 100644 --- a/Source/Spray/BreakupSplash/Make.package +++ b/Source/Spray/BreakupSplash/Make.package @@ -1,6 +1,8 @@ - CEXE_headers += AhamedSplash.H CEXE_headers += TABBreakup.H CEXE_headers += ReitzKHRT.H CEXE_headers += SBData.H CEXE_headers += WallFilm.H + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Spray/BreakupSplash +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Spray/BreakupSplash \ No newline at end of file diff --git a/Source/Spray/BreakupSplash/WallFilm.H b/Source/Spray/BreakupSplash/WallFilm.H index 9d547cf15..83238f9d4 100644 --- a/Source/Spray/BreakupSplash/WallFilm.H +++ b/Source/Spray/BreakupSplash/WallFilm.H @@ -136,7 +136,7 @@ calculateFilmSource( // Species index const int fspec = fdat.indx[spf]; // Gas species index, might be the same - const int fdspec = fdat.dep_indx[spf]; + // const int fdspec = fdat.dep_indx[spf]; // Convert mass diffusion coefficient from mixture average // to binary for fuel only, not concerned with other species Ddiag[fspec] *= mw_skin / gpv.mw[fspec] * SPU.rhod_conv; diff --git a/Source/Spray/Distribution/Make.package b/Source/Spray/Distribution/Make.package index b66e67f25..870e1be22 100644 --- a/Source/Spray/Distribution/Make.package +++ b/Source/Spray/Distribution/Make.package @@ -1,3 +1,6 @@ CEXE_headers += DistBase.H CEXE_headers += Distributions.H CEXE_sources += Distributions.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Spray/Distribution +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Spray/Distribution \ No newline at end of file diff --git a/Source/Spray/Make.package b/Source/Spray/Make.package index ba442c540..074d89f7b 100644 --- a/Source/Spray/Make.package +++ b/Source/Spray/Make.package @@ -15,3 +15,6 @@ CEXE_sources += SprayIO.cpp CEXE_headers += Drag.H CEXE_headers += WallFunctions.H + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Spray +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Spray \ No newline at end of file diff --git a/Source/Spray/SprayInjection.H b/Source/Spray/SprayInjection.H index 37e05336b..aeb2cb6dd 100644 --- a/Source/Spray/SprayInjection.H +++ b/Source/Spray/SprayInjection.H @@ -226,6 +226,9 @@ SprayParticleContainer::uniformSprayInit( } part_vals[SprayComps::pstateT] = T_part; part_vals[SprayComps::pstateDia] = dia_part; + for (int spf = 0; spf < SPRAY_FUEL_NUM; ++spf) { + part_vals[SprayComps::pstateY + spf] = Y_part[spf]; + } const SprayData* fdat = m_sprayData; amrex::Real initial_bm2 = 0.; if (fdat->do_breakup == 2) { diff --git a/Source/Spray/SprayParticles.H b/Source/Spray/SprayParticles.H index 679b05137..704b4bda0 100644 --- a/Source/Spray/SprayParticles.H +++ b/Source/Spray/SprayParticles.H @@ -20,7 +20,7 @@ #define NAI_SPR 0 // Forward declarations -class SBPtrs; +struct SBPtrs; class MyParIter : public amrex::ParIter { diff --git a/Source/Spray/SprayParticles.cpp b/Source/Spray/SprayParticles.cpp index b3a5e5156..36c366377 100644 --- a/Source/Spray/SprayParticles.cpp +++ b/Source/Spray/SprayParticles.cpp @@ -439,7 +439,7 @@ SprayParticleContainer::updateParticles( } Gpu::Atomic::Add( &engSrcarr(cur_indx), cur_coef * gpv.fluid_eng_src); - Real new_time = static_cast(cur_iter + 1) * sub_dt; + // Real new_time = static_cast(cur_iter + 1) * sub_dt; // Modify particle position by whole time step if (do_move && !fdat->fixed_parts && p.id() > 0 && !is_film) { for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) { diff --git a/Source/Spray/SpraySB.cpp b/Source/Spray/SpraySB.cpp index 93d0d5412..8db55ea17 100644 --- a/Source/Spray/SpraySB.cpp +++ b/Source/Spray/SpraySB.cpp @@ -60,10 +60,10 @@ SprayParticleContainer::CreateSBDroplets( rho_part = 1. / rho_part; #else Real rho_part = fdat->rhoL(T0, 0); - Real mu_part = fdat->muL(T0, 0); + // Real mu_part = fdat->muL(T0, 0); Y0[0] = 1.; #endif - Real pmass = M_PI / 6. * rho_part * std::pow(ref_dia, 3); + // Real pmass = M_PI / 6. * rho_part * std::pow(ref_dia, 3); Real U0mag = vel0.vectorLength(); // Splashing @@ -78,7 +78,7 @@ SprayParticleContainer::CreateSBDroplets( Real U0norm = normal.dotProduct(vel0); Real alpha = amrex::max(M_PI / 6., std::asin(amrex::Math::abs(U0norm) / U0mag)); - Real alpha_d = alpha * 180. / M_PI; + // Real alpha_d = alpha * 180. / M_PI; Real U0tan = std::sqrt(U0mag * U0mag - U0norm * U0norm); Real uBeta_0, uBeta_half, uBeta_pi, uPsi_coeff, usNorm; get_splash_vels( @@ -90,7 +90,6 @@ SprayParticleContainer::CreateSBDroplets( get_ms_theta(alpha, ms, del_film, ms_thetas); // Note: Must be -pi/2 < psi < pi, not 0 < psi < pi for symmetry for (int new_parts = 0; new_parts < Nsint; ++new_parts) { - Real psi = 0.5 * M_PI * (static_cast(new_parts) - 1.); ParticleType p; p.id() = ParticleType::NextID(); p.cpu() = ParallelDescriptor::MyProc(); @@ -103,7 +102,9 @@ SprayParticleContainer::CreateSBDroplets( } else if (new_parts == 3) { utBeta = uBeta_pi; } - Real utPsi = uPsi_coeff * std::sin(psi); + AMREX_D_PICK( + , , Real psi = 0.5 * M_PI * (static_cast(new_parts) - 1.); + Real utPsi = uPsi_coeff * std::sin(psi);) for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) { Real pvel = AMREX_D_TERM( usNorm * normal[dir], +utBeta * tanBeta[dir], @@ -136,7 +137,7 @@ SprayParticleContainer::CreateSBDroplets( Real N_s = std::pow(num_dens0, m_breakupPPPFact); int N_d = amrex::max(1, static_cast(num_dens0 / N_s)); N_s = num_dens0 / static_cast(N_d); - Real new_mass = M_PI / 6. * rho_part * std::pow(dmean, 3); + // Real new_mass = M_PI / 6. * rho_part * std::pow(dmean, 3); #if AMREX_SPACEDIM == 3 RealVect testvec(1., 0., 0.); if (testvec.crossProduct(normal).vectorLength() < 1.E-5) { diff --git a/Source/Spray/WallFunctions.H b/Source/Spray/WallFunctions.H index ccb198675..c2499e1bd 100644 --- a/Source/Spray/WallFunctions.H +++ b/Source/Spray/WallFunctions.H @@ -96,7 +96,7 @@ check_wall( const amrex::IntVect& ijkc, #ifdef AMREX_USE_EB const amrex::IntVect& ijkc_prev, - const amrex::RealVect& vel_part, + const amrex::RealVect& /*vel_part*/, const bool use_EB, amrex::Array4 const& flags, amrex::Array4 const& bcent, @@ -185,7 +185,7 @@ impose_wall( const SprayData& fdat, const amrex::RealVect& dx, const amrex::RealVect& plo, - const amrex::RealVect& phi, + const amrex::RealVect& /*phi*/, amrex::IntVect& bflags, const amrex::Real* cBoilT, const amrex::Real p_fluid, @@ -215,8 +215,8 @@ impose_wall( ijkc_prev, vel_part, use_EB, flags, bcent, bnorm, #endif par_dot, normal); - amrex::IntVect refl_prev = ijkc; - bool do_deposit = false; + // amrex::IntVect refl_prev = ijkc; + // bool do_deposit = false; if (do_refl) { amrex::Real Nw_Vp = normal.dotProduct(vel_part); if (do_splash) { diff --git a/Transport/Constant.H b/Source/Transport/Constant.H similarity index 100% rename from Transport/Constant.H rename to Source/Transport/Constant.H diff --git a/Source/Transport/Make.package b/Source/Transport/Make.package new file mode 100644 index 000000000..4af749035 --- /dev/null +++ b/Source/Transport/Make.package @@ -0,0 +1,5 @@ +CEXE_headers += Transport.H TransportTypes.H TransportParams.H Constant.H Simple.H Sutherland.H +CEXE_sources += Transport.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Transport +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Transport \ No newline at end of file diff --git a/Transport/Simple.H b/Source/Transport/Simple.H similarity index 100% rename from Transport/Simple.H rename to Source/Transport/Simple.H diff --git a/Transport/Sutherland.H b/Source/Transport/Sutherland.H similarity index 100% rename from Transport/Sutherland.H rename to Source/Transport/Sutherland.H diff --git a/Transport/Transport.H b/Source/Transport/Transport.H similarity index 100% rename from Transport/Transport.H rename to Source/Transport/Transport.H diff --git a/Transport/Transport.cpp b/Source/Transport/Transport.cpp similarity index 100% rename from Transport/Transport.cpp rename to Source/Transport/Transport.cpp diff --git a/Transport/TransportParams.H b/Source/Transport/TransportParams.H similarity index 100% rename from Transport/TransportParams.H rename to Source/Transport/TransportParams.H diff --git a/Transport/TransportTypes.H b/Source/Transport/TransportTypes.H similarity index 100% rename from Transport/TransportTypes.H rename to Source/Transport/TransportTypes.H diff --git a/Utility/Diagnostics/DiagBase.H b/Source/Utility/Diagnostics/DiagBase.H similarity index 100% rename from Utility/Diagnostics/DiagBase.H rename to Source/Utility/Diagnostics/DiagBase.H diff --git a/Utility/Diagnostics/DiagBase.cpp b/Source/Utility/Diagnostics/DiagBase.cpp similarity index 100% rename from Utility/Diagnostics/DiagBase.cpp rename to Source/Utility/Diagnostics/DiagBase.cpp diff --git a/Utility/Diagnostics/DiagConditional.H b/Source/Utility/Diagnostics/DiagConditional.H similarity index 100% rename from Utility/Diagnostics/DiagConditional.H rename to Source/Utility/Diagnostics/DiagConditional.H diff --git a/Utility/Diagnostics/DiagConditional.cpp b/Source/Utility/Diagnostics/DiagConditional.cpp similarity index 100% rename from Utility/Diagnostics/DiagConditional.cpp rename to Source/Utility/Diagnostics/DiagConditional.cpp diff --git a/Utility/Diagnostics/DiagFilter.H b/Source/Utility/Diagnostics/DiagFilter.H similarity index 100% rename from Utility/Diagnostics/DiagFilter.H rename to Source/Utility/Diagnostics/DiagFilter.H diff --git a/Utility/Diagnostics/DiagFilter.cpp b/Source/Utility/Diagnostics/DiagFilter.cpp similarity index 100% rename from Utility/Diagnostics/DiagFilter.cpp rename to Source/Utility/Diagnostics/DiagFilter.cpp diff --git a/Utility/Diagnostics/DiagFramePlane.H b/Source/Utility/Diagnostics/DiagFramePlane.H similarity index 100% rename from Utility/Diagnostics/DiagFramePlane.H rename to Source/Utility/Diagnostics/DiagFramePlane.H diff --git a/Utility/Diagnostics/DiagFramePlane.cpp b/Source/Utility/Diagnostics/DiagFramePlane.cpp similarity index 100% rename from Utility/Diagnostics/DiagFramePlane.cpp rename to Source/Utility/Diagnostics/DiagFramePlane.cpp diff --git a/Utility/Diagnostics/DiagPDF.H b/Source/Utility/Diagnostics/DiagPDF.H similarity index 100% rename from Utility/Diagnostics/DiagPDF.H rename to Source/Utility/Diagnostics/DiagPDF.H diff --git a/Utility/Diagnostics/DiagPDF.cpp b/Source/Utility/Diagnostics/DiagPDF.cpp similarity index 100% rename from Utility/Diagnostics/DiagPDF.cpp rename to Source/Utility/Diagnostics/DiagPDF.cpp diff --git a/Utility/Diagnostics/Make.package b/Source/Utility/Diagnostics/Make.package similarity index 69% rename from Utility/Diagnostics/Make.package rename to Source/Utility/Diagnostics/Make.package index e29bd45eb..7e642da98 100644 --- a/Utility/Diagnostics/Make.package +++ b/Source/Utility/Diagnostics/Make.package @@ -9,3 +9,6 @@ CEXE_sources += DiagBase.cpp CEXE_sources += DiagFramePlane.cpp CEXE_sources += DiagPDF.cpp CEXE_sources += DiagConditional.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/Diagnostics +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/Diagnostics diff --git a/Utility/Filter/Filter.H b/Source/Utility/Filter/Filter.H similarity index 100% rename from Utility/Filter/Filter.H rename to Source/Utility/Filter/Filter.H diff --git a/Utility/Filter/Filter.cpp b/Source/Utility/Filter/Filter.cpp similarity index 100% rename from Utility/Filter/Filter.cpp rename to Source/Utility/Filter/Filter.cpp diff --git a/Source/Utility/Filter/Make.package b/Source/Utility/Filter/Make.package new file mode 100644 index 000000000..0571d37b4 --- /dev/null +++ b/Source/Utility/Filter/Make.package @@ -0,0 +1,5 @@ +CEXE_sources += Filter.cpp +CEXE_headers += Filter.H + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/Filter +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/Filter diff --git a/Source/Utility/PMF/Make.package b/Source/Utility/PMF/Make.package new file mode 100644 index 000000000..a94e2e6f4 --- /dev/null +++ b/Source/Utility/PMF/Make.package @@ -0,0 +1,5 @@ +CEXE_sources += PMFData.cpp +CEXE_headers += PMF.H PMFData.H + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/PMF +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/PMF diff --git a/Utility/PMF/PMF.H b/Source/Utility/PMF/PMF.H similarity index 100% rename from Utility/PMF/PMF.H rename to Source/Utility/PMF/PMF.H diff --git a/Utility/PMF/PMFData.H b/Source/Utility/PMF/PMFData.H similarity index 100% rename from Utility/PMF/PMFData.H rename to Source/Utility/PMF/PMFData.H diff --git a/Utility/PMF/PMFData.cpp b/Source/Utility/PMF/PMFData.cpp similarity index 100% rename from Utility/PMF/PMFData.cpp rename to Source/Utility/PMF/PMFData.cpp diff --git a/Utility/PMF/cantera_pmf_generator.py b/Source/Utility/PMF/cantera_pmf_generator.py similarity index 97% rename from Utility/PMF/cantera_pmf_generator.py rename to Source/Utility/PMF/cantera_pmf_generator.py index 1c2553a20..2677dc5fb 100644 --- a/Utility/PMF/cantera_pmf_generator.py +++ b/Source/Utility/PMF/cantera_pmf_generator.py @@ -28,7 +28,7 @@ "-m", "--mechanism", default="drm19", - help="Name of PelePhysics mechanism from Support/Mechanism/Models", + help="Name of PelePhysics mechanism from Mechanisms", ) parser.add_argument( "-pp", "--pp_home", default="../../", help="Path to PelePhysics directory" @@ -60,7 +60,7 @@ "--output", default=None, help=( - "Path to directory where flames will be saved, if not specified files are saved to PelePhysics/Support/Mechanism/Models//PMFs/" + "Path to directory where flames will be saved, if not specified files are saved to PelePhysics/Mechanisms//PMFs/" ), ) args = parser.parse_args() @@ -99,7 +99,7 @@ ################# # Find mechanism in PelePhysics -pp_path = os.path.join(args.pp_home, "Support/Mechanism/Models") +pp_path = os.path.join(args.pp_home, "Mechanisms") if args.output is None: outdir = os.path.join(pp_path, mechanism, "PMFs") else: diff --git a/Utility/PMF/plotPMF.py b/Source/Utility/PMF/plotPMF.py similarity index 100% rename from Utility/PMF/plotPMF.py rename to Source/Utility/PMF/plotPMF.py diff --git a/Source/Utility/PltFileManager/Make.package b/Source/Utility/PltFileManager/Make.package new file mode 100644 index 000000000..4d3d87edb --- /dev/null +++ b/Source/Utility/PltFileManager/Make.package @@ -0,0 +1,5 @@ +CEXE_sources += PltFileManager.cpp +CEXE_headers += PltFileManager.H PltFileManagerBCfill.H + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/PltFileManager +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/PltFileManager diff --git a/Utility/PltFileManager/PltFileManager.H b/Source/Utility/PltFileManager/PltFileManager.H similarity index 100% rename from Utility/PltFileManager/PltFileManager.H rename to Source/Utility/PltFileManager/PltFileManager.H diff --git a/Utility/PltFileManager/PltFileManager.cpp b/Source/Utility/PltFileManager/PltFileManager.cpp similarity index 100% rename from Utility/PltFileManager/PltFileManager.cpp rename to Source/Utility/PltFileManager/PltFileManager.cpp diff --git a/Utility/PltFileManager/PltFileManagerBCFill.H b/Source/Utility/PltFileManager/PltFileManagerBCFill.H similarity index 100% rename from Utility/PltFileManager/PltFileManagerBCFill.H rename to Source/Utility/PltFileManager/PltFileManagerBCFill.H diff --git a/Source/Utility/TurbInflow/Make.package b/Source/Utility/TurbInflow/Make.package new file mode 100644 index 000000000..09f78bb0f --- /dev/null +++ b/Source/Utility/TurbInflow/Make.package @@ -0,0 +1,5 @@ +CEXE_headers += turbinflow.H +CEXE_sources += turbinflow.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/TurbInflow +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/TurbInflow diff --git a/Utility/TurbInflow/turbinflow.H b/Source/Utility/TurbInflow/turbinflow.H similarity index 100% rename from Utility/TurbInflow/turbinflow.H rename to Source/Utility/TurbInflow/turbinflow.H diff --git a/Utility/TurbInflow/turbinflow.cpp b/Source/Utility/TurbInflow/turbinflow.cpp similarity index 100% rename from Utility/TurbInflow/turbinflow.cpp rename to Source/Utility/TurbInflow/turbinflow.cpp diff --git a/Support/Mechanism/Models/Aromatic_KrNara/Make.package b/Support/Mechanism/Models/Aromatic_KrNara/Make.package deleted file mode 100644 index ddcc0b6a2..000000000 --- a/Support/Mechanism/Models/Aromatic_KrNara/Make.package +++ /dev/null @@ -1,10 +0,0 @@ -CEXE_headers+=chemistry_file.H - -CEXE_sources+=mechanism.cpp mechanism_1.cpp mechanism_2.cpp - -LIBRARIES += - -INCLUDE_LOCATIONS += $(CHEM_DIR) - -VPATH_LOCATIONS += $(CHEM_DIR)/PMFs - diff --git a/Support/Mechanism/Models/FFCM1_Red/Make.package b/Support/Mechanism/Models/FFCM1_Red/Make.package deleted file mode 100644 index 2154d7164..000000000 --- a/Support/Mechanism/Models/FFCM1_Red/Make.package +++ /dev/null @@ -1,10 +0,0 @@ -CEXE_headers+=mechanism.H - -CEXE_sources+=mechanism.cpp - -LIBRARIES += - -INCLUDE_LOCATIONS += $(CHEM_DIR) - -VPATH_LOCATIONS += $(CHEM_DIR)/PMFs - diff --git a/Support/Mechanism/Models/HP_DME/Make.package b/Support/Mechanism/Models/HP_DME/Make.package deleted file mode 100644 index e4168f09c..000000000 --- a/Support/Mechanism/Models/HP_DME/Make.package +++ /dev/null @@ -1,2 +0,0 @@ -CEXE_headers+=mechanism.H -CEXE_sources+=mechanism.cpp diff --git a/Support/Mechanism/Models/SootReaction/Make.package b/Support/Mechanism/Models/SootReaction/Make.package deleted file mode 100644 index 0c7558a78..000000000 --- a/Support/Mechanism/Models/SootReaction/Make.package +++ /dev/null @@ -1,4 +0,0 @@ -CEXE_sources+=mechanism.cpp - -#VPATH_LOCATIONS += $(CHEM_DIR)/PMFs - diff --git a/Support/Mechanism/Models/air/Make.package b/Support/Mechanism/Models/air/Make.package deleted file mode 100644 index 8a2397e5f..000000000 --- a/Support/Mechanism/Models/air/Make.package +++ /dev/null @@ -1,8 +0,0 @@ -CEXE_sources+=mechanism.cpp -CEXE_headers+=mechanism.H - -LIBRARIES += - -INCLUDE_LOCATIONS += $(CHEM_DIR) - -VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/dodecane_wang/Make.package b/Support/Mechanism/Models/dodecane_wang/Make.package deleted file mode 100644 index 909eb2264..000000000 --- a/Support/Mechanism/Models/dodecane_wang/Make.package +++ /dev/null @@ -1,9 +0,0 @@ -CEXE_headers+=mechanism.H - -CEXE_sources+=mechanism.cpp solver.cpp solver_simplified.cpp - -LIBRARIES += - -INCLUDE_LOCATIONS += $(CHEM_DIR) - -VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/grimech30-noArN/Make.package b/Support/Mechanism/Models/grimech30-noArN/Make.package deleted file mode 100644 index 6b0fa8de5..000000000 --- a/Support/Mechanism/Models/grimech30-noArN/Make.package +++ /dev/null @@ -1,8 +0,0 @@ -CEXE_headers+=mechanism.H -CEXE_sources+=mechanism.cpp - -LIBRARIES += - -INCLUDE_LOCATIONS += $(CHEM_DIR) - -VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/header/header.end b/Support/Mechanism/Models/header/header.end deleted file mode 100644 index ddd5dae0d..000000000 --- a/Support/Mechanism/Models/header/header.end +++ /dev/null @@ -1,2 +0,0 @@ - -#endif diff --git a/Support/Mechanism/Models/header/header.mec b/Support/Mechanism/Models/header/header.mec deleted file mode 100644 index f2a227abf..000000000 --- a/Support/Mechanism/Models/header/header.mec +++ /dev/null @@ -1,6 +0,0 @@ - -\\ -\\ -\\ This is the mechanism file -\\ -\\ diff --git a/Support/Mechanism/Models/header/header.start b/Support/Mechanism/Models/header/header.start deleted file mode 100644 index 64b14978b..000000000 --- a/Support/Mechanism/Models/header/header.start +++ /dev/null @@ -1,8 +0,0 @@ - - - - -#if 0 - - - diff --git a/Support/Mechanism/Models/header/header.therm b/Support/Mechanism/Models/header/header.therm deleted file mode 100644 index 038e3ef28..000000000 --- a/Support/Mechanism/Models/header/header.therm +++ /dev/null @@ -1,6 +0,0 @@ - -\\ -\\ -\\ This is the therm file -\\ -\\ diff --git a/Support/Mechanism/Models/header/header.trans b/Support/Mechanism/Models/header/header.trans deleted file mode 100644 index a694754cf..000000000 --- a/Support/Mechanism/Models/header/header.trans +++ /dev/null @@ -1,6 +0,0 @@ - -\\ -\\ -\\ This is the tran file -\\ -\\ diff --git a/Support/Mechanism/Models/heptane_lu_88sk/Make.package b/Support/Mechanism/Models/heptane_lu_88sk/Make.package deleted file mode 100644 index 1ed6a7046..000000000 --- a/Support/Mechanism/Models/heptane_lu_88sk/Make.package +++ /dev/null @@ -1,9 +0,0 @@ -CEXE_headers+=chemistry_file.H - -CEXE_sources+=mechanism.cpp - -LIBRARIES += - -INCLUDE_LOCATIONS += $(CHEM_DIR) - -VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/methaneIons_diRenzo/Make.package b/Support/Mechanism/Models/methaneIons_diRenzo/Make.package deleted file mode 100644 index 6b0fa8de5..000000000 --- a/Support/Mechanism/Models/methaneIons_diRenzo/Make.package +++ /dev/null @@ -1,8 +0,0 @@ -CEXE_headers+=mechanism.H -CEXE_sources+=mechanism.cpp - -LIBRARIES += - -INCLUDE_LOCATIONS += $(CHEM_DIR) - -VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/ndodecane_35/Make.package b/Support/Mechanism/Models/ndodecane_35/Make.package deleted file mode 100644 index 1ed6a7046..000000000 --- a/Support/Mechanism/Models/ndodecane_35/Make.package +++ /dev/null @@ -1,9 +0,0 @@ -CEXE_headers+=chemistry_file.H - -CEXE_sources+=mechanism.cpp - -LIBRARIES += - -INCLUDE_LOCATIONS += $(CHEM_DIR) - -VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/nitrogens/Make.package b/Support/Mechanism/Models/nitrogens/Make.package deleted file mode 100644 index 8a2397e5f..000000000 --- a/Support/Mechanism/Models/nitrogens/Make.package +++ /dev/null @@ -1,8 +0,0 @@ -CEXE_sources+=mechanism.cpp -CEXE_headers+=mechanism.H - -LIBRARIES += - -INCLUDE_LOCATIONS += $(CHEM_DIR) - -VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/ceptr/ceptr/qssa.py b/Support/ceptr/ceptr/qssa.py index b1d821187..fdd0febc1 100644 --- a/Support/ceptr/ceptr/qssa.py +++ b/Support/ceptr/ceptr/qssa.py @@ -72,9 +72,9 @@ def process_qss(fname, nqssa, visualize, method): raise ValueError("Failure to generate QSSA mechanism.") qssa.update_user_header({"description": f"QSSA of {mechanism.name}"}) - qssa.update_user_data({ - "qssa_species": qssa_species, "n_qssa_species": len(qssa_species) - }) + qssa.update_user_data( + {"qssa_species": qssa_species, "n_qssa_species": len(qssa_species)} + ) forward_to_remove_idx = [] if forward_to_remove: for fr in forward_to_remove: diff --git a/Support/ceptr/ceptr/symbolic_math.py b/Support/ceptr/ceptr/symbolic_math.py index 740f12151..9c6d768b0 100644 --- a/Support/ceptr/ceptr/symbolic_math.py +++ b/Support/ceptr/ceptr/symbolic_math.py @@ -196,30 +196,22 @@ def convert_to_cpp(self, sym_smp): if self.remove_pow: # Positive exponents - user_functions["Pow"].append( - ( - lambda b, e: (e.is_Integer or e.is_Float) - and ( - abs(e - 1) < 1e-16 or abs(e - 2) < 1e-16 or abs(e - 3) < 1e-16 - ), - lambda b, e: "(" + "*".join(["(" + b + ")"] * int(float(e))) + ")", - ) - ) + user_functions["Pow"].append(( + lambda b, e: (e.is_Integer or e.is_Float) + and (abs(e - 1) < 1e-16 or abs(e - 2) < 1e-16 or abs(e - 3) < 1e-16), + lambda b, e: "(" + "*".join(["(" + b + ")"] * int(float(e))) + ")", + )) # Negative exponents - user_functions["Pow"].append( - ( - lambda b, e: (e.is_Integer or e.is_Float) - and ( - abs(e + 1) < 1e-16 or abs(e + 2) < 1e-16 or abs(e + 3) < 1e-16 - ), - lambda b, e: "(" - + "1.0/" - + "(" - + "*".join(["(" + b + ")"] * int(-float(e))) - + ")" - + ")", - ) - ) + user_functions["Pow"].append(( + lambda b, e: (e.is_Integer or e.is_Float) + and (abs(e + 1) < 1e-16 or abs(e + 2) < 1e-16 or abs(e + 3) < 1e-16), + lambda b, e: "(" + + "1.0/" + + "(" + + "*".join(["(" + b + ")"] * int(-float(e))) + + ")" + + ")", + )) if self.remove_pow10: user_functions["Pow"].append( diff --git a/Support/ceptr/ceptr/utilities.py b/Support/ceptr/ceptr/utilities.py index 829c93dd7..555dfab75 100644 --- a/Support/ceptr/ceptr/utilities.py +++ b/Support/ceptr/ceptr/utilities.py @@ -215,9 +215,9 @@ def fkc_conv_inv(self, mechanism, reaction, syms=None): if record_symbolic_operations: conversion_smp *= syms.refCinv_smp * syms.refCinv_smp else: - conversion = "*".join([ - f"pow(std::max(refCinv, {sc_cutoff(dim)}), {dim:f})" - ]) + conversion = "*".join( + [f"pow(std::max(refCinv, {sc_cutoff(dim)}), {dim:f})"] + ) if record_symbolic_operations: conversion_smp *= syms.refCinv_smp**dim else: @@ -229,9 +229,9 @@ def fkc_conv_inv(self, mechanism, reaction, syms=None): if dim.is_integer(): conversion = "*".join(["refC"] * int(dim)) else: - conversion = "*".join([ - f"pow(std::max(refC, {sc_cutoff(abs(dim))}), {abs(dim):f})" - ]) + conversion = "*".join( + [f"pow(std::max(refC, {sc_cutoff(abs(dim))}), {abs(dim):f})"] + ) if record_symbolic_operations: conversion_smp *= syms.refC_smp**dim @@ -263,9 +263,9 @@ def kc_conv(mechanism, reaction): if dim.is_integer(): conversion = "*".join(["refC"] * int(dim)) else: - conversion = "*".join([ - f"pow(std::max(refC, {sc_cutoff(dim)}),{dim:f})" - ]) + conversion = "*".join( + [f"pow(std::max(refC, {sc_cutoff(dim)}),{dim:f})"] + ) else: if dim == -1.0: conversion = "*".join(["refCinv"]) @@ -273,9 +273,9 @@ def kc_conv(mechanism, reaction): if dim.is_integer(): conversion = "*".join(["refCinv"] * int(dim)) else: - conversion = "*".join([ - f"pow(std::max(refCinv, {sc_cutoff(abs(dim))}),{abs(dim):f})" - ]) + conversion = "*".join( + [f"pow(std::max(refCinv, {sc_cutoff(abs(dim))}),{abs(dim):f})"] + ) return conversion diff --git a/Support/ceptr/tests/test_ceptr.py b/Support/ceptr/tests/test_ceptr.py index 2c93c196a..c005b6c73 100644 --- a/Support/ceptr/tests/test_ceptr.py +++ b/Support/ceptr/tests/test_ceptr.py @@ -11,8 +11,8 @@ def mechanism_path(mname): """Determine mechanism path.""" this_file_dir = pathlib.Path(__file__).parent.resolve() - model_path = "Mechanism/Models" - return this_file_dir.parents[1] / model_path / mname + model_path = "Mechanisms" + return this_file_dir.parents[2] / model_path / mname def test_version(): diff --git a/Testing/Exec/Make.PelePhysics b/Testing/Exec/Make.PelePhysics index 85ed2ae5d..777e8bd12 100644 --- a/Testing/Exec/Make.PelePhysics +++ b/Testing/Exec/Make.PelePhysics @@ -3,9 +3,10 @@ PELE_PHYSICS_HOME ?= $(abspath $(lastword $(PELE_HOME)/Submodules/PelePhysics)) AMREX_HOME ?= $(abspath $(lastword $(PELE_PHYSICS_HOME)/Submodules/amrex)) SUNDIALS_HOME ?= $(abspath $(lastword $(PELE_PHYSICS_HOME)/Submodules/sundials)) -EOS_HOME ?= $(PELE_PHYSICS_HOME)/Eos -REACTIONS_HOME ?= $(PELE_PHYSICS_HOME)/Reactions -TRAN_HOME ?= $(PELE_PHYSICS_HOME)/Transport +EOS_HOME ?= $(PELE_PHYSICS_HOME)/Source/Eos +REACTIONS_HOME ?= $(PELE_PHYSICS_HOME)/Source/Reactions +TRAN_HOME ?= $(PELE_PHYSICS_HOME)/Source/Transport +UTILITY_HOME ?= $(PELE_PHYSICS_HOME)/Source/Utility EBASE = Pele BL_NO_FORT = TRUE @@ -76,13 +77,12 @@ ifeq ($(Eos_Model), GammaLaw) $(error Chemistry_Model definition not compatible with Eos_Model=GammaLaw) endif endif -CHEM_HOME = $(PELE_PHYSICS_HOME)/Support/Mechanism/Models/$(Chemistry_Model) -CHEM_ALL = $(PELE_PHYSICS_HOME)/Support/Mechanism/Models +CHEM_HOME = $(PELE_PHYSICS_HOME)/Mechanisms/$(Chemistry_Model) +CHEM_ALL = $(PELE_PHYSICS_HOME)/Mechanisms VPATH_LOCATIONS += $(CHEM_HOME) $(CHEM_ALL) Bpack += $(CHEM_HOME)/Make.package \ $(CHEM_ALL)/Make.package Blocs += $(CHEM_HOME) $(CHEM_ALL) -Blocs += $(PELE_PHYSICS_HOME)/Support/Evaluation # Transport include $(TRAN_HOME)/Make.package @@ -90,8 +90,6 @@ INCLUDE_LOCATIONS += $(TRAN_HOME) VPATH_LOCATIONS += $(TRAN_HOME) USE_FUEGO = FALSE -Blocs += $(PELE_PHYSICS_HOME)/Support/Mechanism - ifeq ($(Transport_Model), Simple) DEFINES += -DUSE_SIMPLE_TRANSPORT endif @@ -107,9 +105,13 @@ ifeq ($(Transport_Model), Sutherland) endif # Utilities -include $(PELE_PHYSICS_HOME)/Utility/PMF/Make.package -include $(PELE_PHYSICS_HOME)/Utility/PltFileManager/Make.package - +INCLUDE_LOCATIONS += $(UTILITY_HOME) +VPATH_LOCATIONS += $(UTILITY_HOME) +include $(UTILITY_HOME)/Diagnostics/Make.package +include $(UTILITY_HOME)/Filter/Make.package +include $(UTILITY_HOME)/PMF/Make.package +include $(UTILITY_HOME)/PltFileManager/Make.package +include $(UTILITY_HOME)/TurbInflow/Make.package Pdirs := Base Boundary AmrCore diff --git a/Transport/Make.package b/Transport/Make.package deleted file mode 100644 index 8e346880c..000000000 --- a/Transport/Make.package +++ /dev/null @@ -1,2 +0,0 @@ -CEXE_headers += Transport.H TransportTypes.H TransportParams.H Constant.H Simple.H Sutherland.H -CEXE_sources += Transport.cpp \ No newline at end of file diff --git a/Utility/Filter/Make.package b/Utility/Filter/Make.package deleted file mode 100644 index 147f76e85..000000000 --- a/Utility/Filter/Make.package +++ /dev/null @@ -1,5 +0,0 @@ -CEXE_sources += Filter.cpp -CEXE_headers += Filter.H - -VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Utility/Filter -INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Utility/Filter diff --git a/Utility/PMF/Make.package b/Utility/PMF/Make.package deleted file mode 100644 index 0c9f1a2f3..000000000 --- a/Utility/PMF/Make.package +++ /dev/null @@ -1,5 +0,0 @@ -CEXE_sources += PMFData.cpp -CEXE_headers += PMF.H PMFData.H - -VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Utility/PMF -INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Utility/PMF diff --git a/Utility/PltFileManager/Make.package b/Utility/PltFileManager/Make.package deleted file mode 100644 index f0584a4fe..000000000 --- a/Utility/PltFileManager/Make.package +++ /dev/null @@ -1,5 +0,0 @@ -CEXE_sources += PltFileManager.cpp -CEXE_headers += PltFileManager.H PltFileManagerBCfill.H - -VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Utility/PltFileManager -INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Utility/PltFileManager diff --git a/Utility/TurbInflow/Make.package b/Utility/TurbInflow/Make.package deleted file mode 100644 index 2ca9e782d..000000000 --- a/Utility/TurbInflow/Make.package +++ /dev/null @@ -1,3 +0,0 @@ -CEXE_headers += turbinflow.H -CEXE_sources += turbinflow.cpp -