Moved directories around (#452)

Moving files around --------- Co-authored-by: Bruce Perry <bruce.perry@nrel.gov>
AMReX-Combustion · Dec 12, 2023 · ab2c54a · ab2c54a
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diff --git 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
@@ -30,15 +30,15 @@ There are three ways to use CEPTR to generate C++ mechanism files for a given ch
 1. Using CEPTR directly::
 
      $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-     $ poetry run convert -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/LiDryer/mechanism.yaml
+     $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/LiDryer/mechanism.yaml
 
 2. Using a helper script in the directory containing the ``mechanism.yaml`` file::
 
      $ ./convert.sh
 
 3. Using a helper script in the ``Models`` directory::
 
-     $ bash ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/converter.sh -f ./LiDryer/mechanism.yaml
+     $ bash ${PELE_PHYSICS_HOME}/Mechanisms/converter.sh -f ./LiDryer/mechanism.yaml
 
 
 Batched generation
@@ -52,23 +52,23 @@ Batched generation
 For non-reduced chemistries, CEPTR can take a file with a list of ``mechanism.yaml`` files to convert::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run convert -l ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_mech
+  $ poetry run convert -l ${PELE_PHYSICS_HOME}/Mechanisms/list_mech
 
 For reduced chemistries, CEPTR can take a file with a list of ``qssa.yaml`` and ``qssa_input.toml`` to convert::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_qss_mech
+  $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
 
 For generating ``qssa.yaml`` for reduced chemistries, CEPTR can take a file with a list of ``skeletal.yaml`` and ``non_qssa_list.yaml``::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_qss_mech
+  $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
 
 To generate all mechanisms::
 
-  $ poetry run convert -l ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_mech
-  $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_qss_mech
-  $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_qss_mech
+  $ poetry run convert -l ${PELE_PHYSICS_HOME}/Mechanisms/list_mech
+  $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
+  $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech
 
 
 Converting CHEMKIN files

diff --git 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 <sec_convertCK>` for generating ``skeletal.yaml``.
 
 Generate ``qssa.yaml`` from ``skeletal.yaml`` and ``non_qssa_list.yaml``::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run qssa -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml
+  $ poetry run qssa -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/non_qssa_list.yaml
 
 Generate ``mechanism.H`` and ``mechanism.cpp`` from ``qssa.yaml``::
   
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run convert -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/qssa.yaml --qss_format_input ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/qssa_input.toml --qss_symbolic_jacobian
+  $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/qssa.yaml --qss_format_input ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/qssa_input.toml --qss_symbolic_jacobian
 
 We recommend using the following ``qssa_input.toml``::
  
@@ -67,20 +67,20 @@ Update ``poetry``::
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
   $ poetry update  
 
-Make sure the list of non-QSS species is correct in ``Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml``
+Make sure the list of non-QSS species is correct in ``Mechanisms/dodecane_lu_qss/non_qssa_list.yaml``
 
-In the next step, ``skeletal.yaml`` is the ``mechanism.yaml`` of the skeletal version of the mechanism (here available under ``${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu``).
+In the next step, ``skeletal.yaml`` is the ``mechanism.yaml`` of the skeletal version of the mechanism (here available under ``${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu``).
 If only CHEMKIN files are available for the skeletal mechanism, see :ref:`Converting CHEMKIN files <sec_convertCK>` for generating ``skeletal.yaml``.
 
 Generate ``qssa.yaml`` from ``skeletal.yaml`` and ``non_qssa_list.yaml``::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run qssa -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml
+  $ poetry run qssa -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/non_qssa_list.yaml
 
 Generate ``mechanism.H`` and ``mechanism.cpp`` from ``qssa.yaml``::
   
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run convert -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/qssa.yaml
+  $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/qssa.yaml
 
 Tutorial 3 - Generating NC12H26 Skeletal mechanism
 --------------------------------------------------
@@ -97,5 +97,5 @@ If only CHEMKIN files are available, see :ref:`Converting CHEMKIN files <sec_con
 Generate ``mechanism.H`` and ``mechanism.cpp`` from ``mechanism.yaml``::
 
   $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
-  $ poetry run convert -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu/mechanism.yaml
+  $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu/mechanism.yaml
 
diff --git a/Eos/Make.package b/Eos/Make.package
diff --git a/...Mechanism/Models/Aromatic_KrNara/COFD.dat → Mechanisms/Aromatic_KrNara/COFD.dat b/...Mechanism/Models/Aromatic_KrNara/COFD.dat → Mechanisms/Aromatic_KrNara/COFD.dat
diff --git a/...chanism/Models/Aromatic_KrNara/COFETA.dat → Mechanisms/Aromatic_KrNara/COFETA.dat b/...chanism/Models/Aromatic_KrNara/COFETA.dat → Mechanisms/Aromatic_KrNara/COFETA.dat
diff --git a/...chanism/Models/Aromatic_KrNara/COFLAM.dat → Mechanisms/Aromatic_KrNara/COFLAM.dat b/...chanism/Models/Aromatic_KrNara/COFLAM.dat → Mechanisms/Aromatic_KrNara/COFLAM.dat
diff --git a/...echanism/Models/Aromatic_KrNara/COFTD.dat → Mechanisms/Aromatic_KrNara/COFTD.dat b/...echanism/Models/Aromatic_KrNara/COFTD.dat → Mechanisms/Aromatic_KrNara/COFTD.dat
diff --git a/.../Mechanism/Models/BurkeDryer/Make.package → Mechanisms/Aromatic_KrNara/Make.package b/.../Mechanism/Models/BurkeDryer/Make.package → Mechanisms/Aromatic_KrNara/Make.package
diff --git a/.../Models/Aromatic_KrNara/README_bigMech.md → Mechanisms/Aromatic_KrNara/README_bigMech.md b/.../Models/Aromatic_KrNara/README_bigMech.md → Mechanisms/Aromatic_KrNara/README_bigMech.md
diff --git a/...chanism/Models/Aromatic_KrNara/convert.sh → Mechanisms/Aromatic_KrNara/convert.sh b/...chanism/Models/Aromatic_KrNara/convert.sh → Mechanisms/Aromatic_KrNara/convert.sh
diff --git a/...hanism/Models/Aromatic_KrNara/mechanism.H → Mechanisms/Aromatic_KrNara/mechanism.H b/...hanism/Models/Aromatic_KrNara/mechanism.H → Mechanisms/Aromatic_KrNara/mechanism.H
diff --git a/...nism/Models/Aromatic_KrNara/mechanism.cpp → Mechanisms/Aromatic_KrNara/mechanism.cpp b/...nism/Models/Aromatic_KrNara/mechanism.cpp → Mechanisms/Aromatic_KrNara/mechanism.cpp
diff --git a/...nism/Models/Aromatic_KrNara/mechanism.inp → Mechanisms/Aromatic_KrNara/mechanism.inp b/...nism/Models/Aromatic_KrNara/mechanism.inp → Mechanisms/Aromatic_KrNara/mechanism.inp
diff --git a/...ism/Models/Aromatic_KrNara/mechanism.yaml → Mechanisms/Aromatic_KrNara/mechanism.yaml b/...ism/Models/Aromatic_KrNara/mechanism.yaml → Mechanisms/Aromatic_KrNara/mechanism.yaml
diff --git a/...echanism/Models/Aromatic_KrNara/therm.dat → Mechanisms/Aromatic_KrNara/therm.dat b/...echanism/Models/Aromatic_KrNara/therm.dat → Mechanisms/Aromatic_KrNara/therm.dat
diff --git a/...Mechanism/Models/Aromatic_KrNara/tran.dat → Mechanisms/Aromatic_KrNara/tran.dat b/...Mechanism/Models/Aromatic_KrNara/tran.dat → Mechanisms/Aromatic_KrNara/tran.dat
diff --git a/...rt/Mechanism/Models/C1-C2-NO/Make.package → Mechanisms/BurkeDryer/Make.package b/...rt/Mechanism/Models/C1-C2-NO/Make.package → Mechanisms/BurkeDryer/Make.package
diff --git a/...rt/Mechanism/Models/BurkeDryer/convert.sh → Mechanisms/BurkeDryer/convert.sh b/...rt/Mechanism/Models/BurkeDryer/convert.sh → Mechanisms/BurkeDryer/convert.sh
diff --git a/...t/Mechanism/Models/BurkeDryer/mechanism.H → Mechanisms/BurkeDryer/mechanism.H b/...t/Mechanism/Models/BurkeDryer/mechanism.H → Mechanisms/BurkeDryer/mechanism.H
diff --git a/...Mechanism/Models/BurkeDryer/mechanism.cpp → Mechanisms/BurkeDryer/mechanism.cpp b/...Mechanism/Models/BurkeDryer/mechanism.cpp → Mechanisms/BurkeDryer/mechanism.cpp
diff --git a/...Mechanism/Models/BurkeDryer/mechanism.inp → Mechanisms/BurkeDryer/mechanism.inp b/...Mechanism/Models/BurkeDryer/mechanism.inp → Mechanisms/BurkeDryer/mechanism.inp
diff --git a/...echanism/Models/BurkeDryer/mechanism.yaml → Mechanisms/BurkeDryer/mechanism.yaml b/...echanism/Models/BurkeDryer/mechanism.yaml → Mechanisms/BurkeDryer/mechanism.yaml
diff --git a/...ort/Mechanism/Models/BurkeDryer/therm.dat → Mechanisms/BurkeDryer/therm.dat b/...ort/Mechanism/Models/BurkeDryer/therm.dat → Mechanisms/BurkeDryer/therm.dat
diff --git a/Support/Mechanism/Models/BurkeDryer/tran.dat → Mechanisms/BurkeDryer/tran.dat b/Support/Mechanism/Models/BurkeDryer/tran.dat → Mechanisms/BurkeDryer/tran.dat
diff --git a/...echanism/Models/C1-C2-NO_qss/Make.package → Mechanisms/C1-C2-NO/Make.package b/...echanism/Models/C1-C2-NO_qss/Make.package → Mechanisms/C1-C2-NO/Make.package
diff --git a/...ort/Mechanism/Models/C1-C2-NO/mechanism.H → Mechanisms/C1-C2-NO/mechanism.H b/...ort/Mechanism/Models/C1-C2-NO/mechanism.H → Mechanisms/C1-C2-NO/mechanism.H
diff --git a/...t/Mechanism/Models/C1-C2-NO/mechanism.cpp → Mechanisms/C1-C2-NO/mechanism.cpp b/...t/Mechanism/Models/C1-C2-NO/mechanism.cpp → Mechanisms/C1-C2-NO/mechanism.cpp
diff --git a/...t/Mechanism/Models/C1-C2-NO/mechanism.inp → Mechanisms/C1-C2-NO/mechanism.inp b/...t/Mechanism/Models/C1-C2-NO/mechanism.inp → Mechanisms/C1-C2-NO/mechanism.inp
diff --git a/.../Mechanism/Models/C1-C2-NO/mechanism.yaml → Mechanisms/C1-C2-NO/mechanism.yaml b/.../Mechanism/Models/C1-C2-NO/mechanism.yaml → Mechanisms/C1-C2-NO/mechanism.yaml
diff --git a/Support/Mechanism/Models/C1-C2-NO/therm.dat → Mechanisms/C1-C2-NO/therm.dat b/Support/Mechanism/Models/C1-C2-NO/therm.dat → Mechanisms/C1-C2-NO/therm.dat
diff --git a/Support/Mechanism/Models/C1-C2-NO/tran.dat → Mechanisms/C1-C2-NO/tran.dat b/Support/Mechanism/Models/C1-C2-NO/tran.dat → Mechanisms/C1-C2-NO/tran.dat
diff --git a/...rt/Mechanism/Models/CH4_lean/Make.package → Mechanisms/C1-C2-NO_qss/Make.package b/...rt/Mechanism/Models/CH4_lean/Make.package → Mechanisms/C1-C2-NO_qss/Make.package
diff --git a/...Mechanism/Models/C1-C2-NO_qss/mechanism.H → Mechanisms/C1-C2-NO_qss/mechanism.H b/...Mechanism/Models/C1-C2-NO_qss/mechanism.H → Mechanisms/C1-C2-NO_qss/mechanism.H
diff --git a/...chanism/Models/C1-C2-NO_qss/mechanism.cpp → Mechanisms/C1-C2-NO_qss/mechanism.cpp b/...chanism/Models/C1-C2-NO_qss/mechanism.cpp → Mechanisms/C1-C2-NO_qss/mechanism.cpp
diff --git a/...sm/Models/C1-C2-NO_qss/non_qssa_list.yaml → Mechanisms/C1-C2-NO_qss/non_qssa_list.yaml b/...sm/Models/C1-C2-NO_qss/non_qssa_list.yaml → Mechanisms/C1-C2-NO_qss/non_qssa_list.yaml
diff --git a/...t/Mechanism/Models/C1-C2-NO_qss/qssa.yaml → Mechanisms/C1-C2-NO_qss/qssa.yaml b/...t/Mechanism/Models/C1-C2-NO_qss/qssa.yaml → Mechanisms/C1-C2-NO_qss/qssa.yaml
diff --git a/...anism/Models/C1-C2-NO_qss/qssa_input.toml → Mechanisms/C1-C2-NO_qss/qssa_input.toml b/...anism/Models/C1-C2-NO_qss/qssa_input.toml → Mechanisms/C1-C2-NO_qss/qssa_input.toml
diff --git a/...echanism/Models/C1-C2-NO_qss/skeletal.inp → Mechanisms/C1-C2-NO_qss/skeletal.inp b/...echanism/Models/C1-C2-NO_qss/skeletal.inp → Mechanisms/C1-C2-NO_qss/skeletal.inp
diff --git a/...chanism/Models/C1-C2-NO_qss/skeletal.yaml → Mechanisms/C1-C2-NO_qss/skeletal.yaml b/...chanism/Models/C1-C2-NO_qss/skeletal.yaml → Mechanisms/C1-C2-NO_qss/skeletal.yaml
diff --git a/...t/Mechanism/Models/C1-C2-NO_qss/therm.dat → Mechanisms/C1-C2-NO_qss/therm.dat b/...t/Mechanism/Models/C1-C2-NO_qss/therm.dat → Mechanisms/C1-C2-NO_qss/therm.dat
diff --git a/...rt/Mechanism/Models/C1-C2-NO_qss/tran.dat → Mechanisms/C1-C2-NO_qss/tran.dat b/...rt/Mechanism/Models/C1-C2-NO_qss/tran.dat → Mechanisms/C1-C2-NO_qss/tran.dat
diff --git a/...echanism/Models/CH4_lean_qss/Make.package → Mechanisms/CH4_lean/Make.package b/...echanism/Models/CH4_lean_qss/Make.package → Mechanisms/CH4_lean/Make.package
diff --git a/...ort/Mechanism/Models/CH4_lean/mechanism.H → Mechanisms/CH4_lean/mechanism.H b/...ort/Mechanism/Models/CH4_lean/mechanism.H → Mechanisms/CH4_lean/mechanism.H
diff --git a/...t/Mechanism/Models/CH4_lean/mechanism.cpp → Mechanisms/CH4_lean/mechanism.cpp b/...t/Mechanism/Models/CH4_lean/mechanism.cpp → Mechanisms/CH4_lean/mechanism.cpp
diff --git a/...t/Mechanism/Models/CH4_lean/mechanism.inp → Mechanisms/CH4_lean/mechanism.inp b/...t/Mechanism/Models/CH4_lean/mechanism.inp → Mechanisms/CH4_lean/mechanism.inp
diff --git a/.../Mechanism/Models/CH4_lean/mechanism.yaml → Mechanisms/CH4_lean/mechanism.yaml b/.../Mechanism/Models/CH4_lean/mechanism.yaml → Mechanisms/CH4_lean/mechanism.yaml
diff --git a/Support/Mechanism/Models/CH4_lean/therm.dat → Mechanisms/CH4_lean/therm.dat b/Support/Mechanism/Models/CH4_lean/therm.dat → Mechanisms/CH4_lean/therm.dat
diff --git a/Support/Mechanism/Models/CH4_lean/tran.dat → Mechanisms/CH4_lean/tran.dat b/Support/Mechanism/Models/CH4_lean/tran.dat → Mechanisms/CH4_lean/tran.dat
diff --git a/Support/Mechanism/Models/Davis/Make.package → Mechanisms/CH4_lean_qss/Make.package b/Support/Mechanism/Models/Davis/Make.package → Mechanisms/CH4_lean_qss/Make.package
diff --git a/...Mechanism/Models/CH4_lean_qss/mechanism.H → Mechanisms/CH4_lean_qss/mechanism.H b/...Mechanism/Models/CH4_lean_qss/mechanism.H → Mechanisms/CH4_lean_qss/mechanism.H
diff --git a/...chanism/Models/CH4_lean_qss/mechanism.cpp → Mechanisms/CH4_lean_qss/mechanism.cpp b/...chanism/Models/CH4_lean_qss/mechanism.cpp → Mechanisms/CH4_lean_qss/mechanism.cpp
diff --git a/...sm/Models/CH4_lean_qss/non_qssa_list.yaml → Mechanisms/CH4_lean_qss/non_qssa_list.yaml b/...sm/Models/CH4_lean_qss/non_qssa_list.yaml → Mechanisms/CH4_lean_qss/non_qssa_list.yaml
diff --git a/...t/Mechanism/Models/CH4_lean_qss/qssa.yaml → Mechanisms/CH4_lean_qss/qssa.yaml b/...t/Mechanism/Models/CH4_lean_qss/qssa.yaml → Mechanisms/CH4_lean_qss/qssa.yaml
diff --git a/...anism/Models/CH4_lean_qss/qssa_input.toml → Mechanisms/CH4_lean_qss/qssa_input.toml b/...anism/Models/CH4_lean_qss/qssa_input.toml → Mechanisms/CH4_lean_qss/qssa_input.toml
diff --git a/...chanism/Models/CH4_lean_qss/skeletal.yaml → Mechanisms/CH4_lean_qss/skeletal.yaml b/...chanism/Models/CH4_lean_qss/skeletal.yaml → Mechanisms/CH4_lean_qss/skeletal.yaml
diff --git a/...t/Mechanism/Models/CH4_lean_qss/therm.dat → Mechanisms/CH4_lean_qss/therm.dat b/...t/Mechanism/Models/CH4_lean_qss/therm.dat → Mechanisms/CH4_lean_qss/therm.dat
diff --git a/...rt/Mechanism/Models/CH4_lean_qss/tran.dat → Mechanisms/CH4_lean_qss/tran.dat b/...rt/Mechanism/Models/CH4_lean_qss/tran.dat → Mechanisms/CH4_lean_qss/tran.dat
diff --git a/Support/Mechanism/Models/JL4/Make.package → Mechanisms/Davis/Make.package b/Support/Mechanism/Models/JL4/Make.package → Mechanisms/Davis/Make.package
diff --git a/Support/Mechanism/Models/Davis/convert.sh → Mechanisms/Davis/convert.sh b/Support/Mechanism/Models/Davis/convert.sh → Mechanisms/Davis/convert.sh
diff --git a/Support/Mechanism/Models/Davis/mechanism.H → Mechanisms/Davis/mechanism.H b/Support/Mechanism/Models/Davis/mechanism.H → Mechanisms/Davis/mechanism.H
diff --git a/Support/Mechanism/Models/Davis/mechanism.cpp → Mechanisms/Davis/mechanism.cpp b/Support/Mechanism/Models/Davis/mechanism.cpp → Mechanisms/Davis/mechanism.cpp
diff --git a/Support/Mechanism/Models/Davis/mechanism.inp → Mechanisms/Davis/mechanism.inp b/Support/Mechanism/Models/Davis/mechanism.inp → Mechanisms/Davis/mechanism.inp
diff --git a/...ort/Mechanism/Models/Davis/mechanism.yaml → Mechanisms/Davis/mechanism.yaml b/...ort/Mechanism/Models/Davis/mechanism.yaml → Mechanisms/Davis/mechanism.yaml
diff --git a/Support/Mechanism/Models/Davis/therm.dat → Mechanisms/Davis/therm.dat b/Support/Mechanism/Models/Davis/therm.dat → Mechanisms/Davis/therm.dat
diff --git a/Support/Mechanism/Models/Davis/tran.dat → Mechanisms/Davis/tran.dat b/Support/Mechanism/Models/Davis/tran.dat → Mechanisms/Davis/tran.dat
diff --git a/Support/Mechanism/Models/Kolla/Make.package → Mechanisms/FFCM1_Red/Make.package b/Support/Mechanism/Models/Kolla/Make.package → Mechanisms/FFCM1_Red/Make.package
diff --git a/...ort/Mechanism/Models/FFCM1_Red/convert.sh → Mechanisms/FFCM1_Red/convert.sh b/...ort/Mechanism/Models/FFCM1_Red/convert.sh → Mechanisms/FFCM1_Red/convert.sh
diff --git a/...rt/Mechanism/Models/FFCM1_Red/mechanism.H → Mechanisms/FFCM1_Red/mechanism.H b/...rt/Mechanism/Models/FFCM1_Red/mechanism.H → Mechanisms/FFCM1_Red/mechanism.H
diff --git a/.../Mechanism/Models/FFCM1_Red/mechanism.cpp → Mechanisms/FFCM1_Red/mechanism.cpp b/.../Mechanism/Models/FFCM1_Red/mechanism.cpp → Mechanisms/FFCM1_Red/mechanism.cpp
diff --git a/.../Mechanism/Models/FFCM1_Red/mechanism.inp → Mechanisms/FFCM1_Red/mechanism.inp b/.../Mechanism/Models/FFCM1_Red/mechanism.inp → Mechanisms/FFCM1_Red/mechanism.inp
diff --git a/...Mechanism/Models/FFCM1_Red/mechanism.yaml → Mechanisms/FFCM1_Red/mechanism.yaml b/...Mechanism/Models/FFCM1_Red/mechanism.yaml → Mechanisms/FFCM1_Red/mechanism.yaml
diff --git a/Support/Mechanism/Models/FFCM1_Red/therm.dat → Mechanisms/FFCM1_Red/therm.dat b/Support/Mechanism/Models/FFCM1_Red/therm.dat → Mechanisms/FFCM1_Red/therm.dat
diff --git a/Support/Mechanism/Models/FFCM1_Red/tran.dat → Mechanisms/FFCM1_Red/tran.dat b/Support/Mechanism/Models/FFCM1_Red/tran.dat → Mechanisms/FFCM1_Red/tran.dat
diff --git a/Support/Mechanism/Models/LuDME/Make.package → Mechanisms/H2-CO-CO2-3spec/Make.package b/Support/Mechanism/Models/LuDME/Make.package → Mechanisms/H2-CO-CO2-3spec/Make.package
diff --git a/...hanism/Models/H2-CO-CO2-3spec/mechanism.H → Mechanisms/H2-CO-CO2-3spec/mechanism.H b/...hanism/Models/H2-CO-CO2-3spec/mechanism.H → Mechanisms/H2-CO-CO2-3spec/mechanism.H
diff --git a/...nism/Models/H2-CO-CO2-3spec/mechanism.cpp → Mechanisms/H2-CO-CO2-3spec/mechanism.cpp b/...nism/Models/H2-CO-CO2-3spec/mechanism.cpp → Mechanisms/H2-CO-CO2-3spec/mechanism.cpp
diff --git a/...nism/Models/H2-CO-CO2-3spec/mechanism.inp → Mechanisms/H2-CO-CO2-3spec/mechanism.inp b/...nism/Models/H2-CO-CO2-3spec/mechanism.inp → Mechanisms/H2-CO-CO2-3spec/mechanism.inp
diff --git a/...ism/Models/H2-CO-CO2-3spec/mechanism.yaml → Mechanisms/H2-CO-CO2-3spec/mechanism.yaml b/...ism/Models/H2-CO-CO2-3spec/mechanism.yaml → Mechanisms/H2-CO-CO2-3spec/mechanism.yaml
diff --git a/...Mechanism/Models/H2-CO-CO2-3spec/tran.dat → Mechanisms/H2-CO-CO2-3spec/tran.dat b/...Mechanism/Models/H2-CO-CO2-3spec/tran.dat → Mechanisms/H2-CO-CO2-3spec/tran.dat
diff --git a/.../Mechanism/Models/LuEthylene/Make.package → Mechanisms/HP_DME/Make.package b/.../Mechanism/Models/LuEthylene/Make.package → Mechanisms/HP_DME/Make.package
diff --git a/Support/Mechanism/Models/HP_DME/convert.sh → Mechanisms/HP_DME/convert.sh b/Support/Mechanism/Models/HP_DME/convert.sh → Mechanisms/HP_DME/convert.sh
diff --git a/Support/Mechanism/Models/HP_DME/mechanism.H → Mechanisms/HP_DME/mechanism.H b/Support/Mechanism/Models/HP_DME/mechanism.H → Mechanisms/HP_DME/mechanism.H
diff --git a/...ort/Mechanism/Models/HP_DME/mechanism.cpp → Mechanisms/HP_DME/mechanism.cpp b/...ort/Mechanism/Models/HP_DME/mechanism.cpp → Mechanisms/HP_DME/mechanism.cpp
diff --git a/...ort/Mechanism/Models/HP_DME/mechanism.inp → Mechanisms/HP_DME/mechanism.inp b/...ort/Mechanism/Models/HP_DME/mechanism.inp → Mechanisms/HP_DME/mechanism.inp
diff --git a/...rt/Mechanism/Models/HP_DME/mechanism.yaml → Mechanisms/HP_DME/mechanism.yaml b/...rt/Mechanism/Models/HP_DME/mechanism.yaml → Mechanisms/HP_DME/mechanism.yaml
diff --git a/Support/Mechanism/Models/HP_DME/therm.dat → Mechanisms/HP_DME/therm.dat b/Support/Mechanism/Models/HP_DME/therm.dat → Mechanisms/HP_DME/therm.dat
diff --git a/Support/Mechanism/Models/HP_DME/tran.dat → Mechanisms/HP_DME/tran.dat b/Support/Mechanism/Models/HP_DME/tran.dat → Mechanisms/HP_DME/tran.dat
diff --git a/...hanism/Models/LuEthylene_qss/Make.package → Mechanisms/IonizedAir/Make.package b/...hanism/Models/LuEthylene_qss/Make.package → Mechanisms/IonizedAir/Make.package
diff --git a/...rt/Mechanism/Models/IonizedAir/convert.sh → Mechanisms/IonizedAir/convert.sh b/...rt/Mechanism/Models/IonizedAir/convert.sh → Mechanisms/IonizedAir/convert.sh
diff --git a/...t/Mechanism/Models/IonizedAir/mechanism.H → Mechanisms/IonizedAir/mechanism.H b/...t/Mechanism/Models/IonizedAir/mechanism.H → Mechanisms/IonizedAir/mechanism.H
diff --git a/...Mechanism/Models/IonizedAir/mechanism.cpp → Mechanisms/IonizedAir/mechanism.cpp b/...Mechanism/Models/IonizedAir/mechanism.cpp → Mechanisms/IonizedAir/mechanism.cpp
diff --git a/...Mechanism/Models/IonizedAir/mechanism.inp → Mechanisms/IonizedAir/mechanism.inp b/...Mechanism/Models/IonizedAir/mechanism.inp → Mechanisms/IonizedAir/mechanism.inp
diff --git a/...echanism/Models/IonizedAir/mechanism.yaml → Mechanisms/IonizedAir/mechanism.yaml b/...echanism/Models/IonizedAir/mechanism.yaml → Mechanisms/IonizedAir/mechanism.yaml
diff --git a/...ort/Mechanism/Models/IonizedAir/therm.dat → Mechanisms/IonizedAir/therm.dat b/...ort/Mechanism/Models/IonizedAir/therm.dat → Mechanisms/IonizedAir/therm.dat
diff --git a/Support/Mechanism/Models/IonizedAir/tran.dat → Mechanisms/IonizedAir/tran.dat b/Support/Mechanism/Models/IonizedAir/tran.dat → Mechanisms/IonizedAir/tran.dat
diff --git a/...t/Mechanism/Models/NUIGalway/Make.package → Mechanisms/JL4/Make.package b/...t/Mechanism/Models/NUIGalway/Make.package → Mechanisms/JL4/Make.package
diff --git a/Support/Mechanism/Models/JL4/convert.sh → Mechanisms/JL4/convert.sh b/Support/Mechanism/Models/JL4/convert.sh → Mechanisms/JL4/convert.sh
diff --git a/Support/Mechanism/Models/JL4/mechanism.H → Mechanisms/JL4/mechanism.H b/Support/Mechanism/Models/JL4/mechanism.H → Mechanisms/JL4/mechanism.H
diff --git a/Support/Mechanism/Models/JL4/mechanism.cpp → Mechanisms/JL4/mechanism.cpp b/Support/Mechanism/Models/JL4/mechanism.cpp → Mechanisms/JL4/mechanism.cpp
diff --git a/Support/Mechanism/Models/JL4/mechanism.inp → Mechanisms/JL4/mechanism.inp b/Support/Mechanism/Models/JL4/mechanism.inp → Mechanisms/JL4/mechanism.inp
diff --git a/Support/Mechanism/Models/JL4/mechanism.yaml → Mechanisms/JL4/mechanism.yaml b/Support/Mechanism/Models/JL4/mechanism.yaml → Mechanisms/JL4/mechanism.yaml
diff --git a/Support/Mechanism/Models/JL4/therm.dat → Mechanisms/JL4/therm.dat b/Support/Mechanism/Models/JL4/therm.dat → Mechanisms/JL4/therm.dat
diff --git a/Support/Mechanism/Models/JL4/tran.dat → Mechanisms/JL4/tran.dat b/Support/Mechanism/Models/JL4/tran.dat → Mechanisms/JL4/tran.dat
diff --git a/...ort/Mechanism/Models/Kolla/ARC/getrates.f → Mechanisms/Kolla/ARC/getrates.f b/...ort/Mechanism/Models/Kolla/ARC/getrates.f → Mechanisms/Kolla/ARC/getrates.f
diff --git a/Support/Mechanism/Models/alzeta/Make.package → Mechanisms/Kolla/Make.package b/Support/Mechanism/Models/alzeta/Make.package → Mechanisms/Kolla/Make.package
diff --git a/Support/Mechanism/Models/Kolla/README.md → Mechanisms/Kolla/README.md b/Support/Mechanism/Models/Kolla/README.md → Mechanisms/Kolla/README.md
diff --git a/Support/Mechanism/Models/Kolla/chem.cti → Mechanisms/Kolla/chem.cti b/Support/Mechanism/Models/Kolla/chem.cti → Mechanisms/Kolla/chem.cti
diff --git a/Support/Mechanism/Models/Kolla/convert.sh → Mechanisms/Kolla/convert.sh b/Support/Mechanism/Models/Kolla/convert.sh → Mechanisms/Kolla/convert.sh
diff --git a/Support/Mechanism/Models/Kolla/mechanism.H → Mechanisms/Kolla/mechanism.H b/Support/Mechanism/Models/Kolla/mechanism.H → Mechanisms/Kolla/mechanism.H
diff --git a/Support/Mechanism/Models/Kolla/mechanism.cpp → Mechanisms/Kolla/mechanism.cpp b/Support/Mechanism/Models/Kolla/mechanism.cpp → Mechanisms/Kolla/mechanism.cpp
diff --git a/Support/Mechanism/Models/Kolla/mechanism.inp → Mechanisms/Kolla/mechanism.inp b/Support/Mechanism/Models/Kolla/mechanism.inp → Mechanisms/Kolla/mechanism.inp
diff --git a/...ort/Mechanism/Models/Kolla/mechanism.yaml → Mechanisms/Kolla/mechanism.yaml b/...ort/Mechanism/Models/Kolla/mechanism.yaml → Mechanisms/Kolla/mechanism.yaml
diff --git a/Support/Mechanism/Models/Kolla/therm.dat → Mechanisms/Kolla/therm.dat b/Support/Mechanism/Models/Kolla/therm.dat → Mechanisms/Kolla/therm.dat
diff --git a/Support/Mechanism/Models/Kolla/tran.dat → Mechanisms/Kolla/tran.dat b/Support/Mechanism/Models/Kolla/tran.dat → Mechanisms/Kolla/tran.dat
diff --git a/...hanism/Models/chem-CH4-2step/Make.package → Mechanisms/LiDryer/Make.package b/...hanism/Models/chem-CH4-2step/Make.package → Mechanisms/LiDryer/Make.package
diff --git a/Support/Mechanism/Models/LiDryer/convert.sh → Mechanisms/LiDryer/convert.sh b/Support/Mechanism/Models/LiDryer/convert.sh → Mechanisms/LiDryer/convert.sh
diff --git a/Support/Mechanism/Models/LiDryer/mechanism.H → Mechanisms/LiDryer/mechanism.H b/Support/Mechanism/Models/LiDryer/mechanism.H → Mechanisms/LiDryer/mechanism.H
diff --git a/...rt/Mechanism/Models/LiDryer/mechanism.cpp → Mechanisms/LiDryer/mechanism.cpp b/...rt/Mechanism/Models/LiDryer/mechanism.cpp → Mechanisms/LiDryer/mechanism.cpp
diff --git a/...rt/Mechanism/Models/LiDryer/mechanism.inp → Mechanisms/LiDryer/mechanism.inp b/...rt/Mechanism/Models/LiDryer/mechanism.inp → Mechanisms/LiDryer/mechanism.inp
diff --git a/...t/Mechanism/Models/LiDryer/mechanism.yaml → Mechanisms/LiDryer/mechanism.yaml b/...t/Mechanism/Models/LiDryer/mechanism.yaml → Mechanisms/LiDryer/mechanism.yaml
diff --git a/Support/Mechanism/Models/LiDryer/therm.dat → Mechanisms/LiDryer/therm.dat b/Support/Mechanism/Models/LiDryer/therm.dat → Mechanisms/LiDryer/therm.dat
diff --git a/Support/Mechanism/Models/LiDryer/tran.dat → Mechanisms/LiDryer/tran.dat b/Support/Mechanism/Models/LiDryer/tran.dat → Mechanisms/LiDryer/tran.dat
diff --git a/...anism/Models/LuDME/LuDME_typVals_0700.dat → Mechanisms/LuDME/LuDME_typVals_0700.dat b/...anism/Models/LuDME/LuDME_typVals_0700.dat → Mechanisms/LuDME/LuDME_typVals_0700.dat
diff --git a/Support/Mechanism/Models/chem-H/Make.package → Mechanisms/LuDME/Make.package b/Support/Mechanism/Models/chem-H/Make.package → Mechanisms/LuDME/Make.package
diff --git a/Support/Mechanism/Models/LuDME/convert.sh → Mechanisms/LuDME/convert.sh b/Support/Mechanism/Models/LuDME/convert.sh → Mechanisms/LuDME/convert.sh
diff --git a/Support/Mechanism/Models/LuDME/mechanism.H → Mechanisms/LuDME/mechanism.H b/Support/Mechanism/Models/LuDME/mechanism.H → Mechanisms/LuDME/mechanism.H
diff --git a/Support/Mechanism/Models/LuDME/mechanism.cpp → Mechanisms/LuDME/mechanism.cpp b/Support/Mechanism/Models/LuDME/mechanism.cpp → Mechanisms/LuDME/mechanism.cpp
diff --git a/Support/Mechanism/Models/LuDME/mechanism.inp → Mechanisms/LuDME/mechanism.inp b/Support/Mechanism/Models/LuDME/mechanism.inp → Mechanisms/LuDME/mechanism.inp
diff --git a/...ort/Mechanism/Models/LuDME/mechanism.yaml → Mechanisms/LuDME/mechanism.yaml b/...ort/Mechanism/Models/LuDME/mechanism.yaml → Mechanisms/LuDME/mechanism.yaml
diff --git a/Support/Mechanism/Models/LuDME/therm.dat → Mechanisms/LuDME/therm.dat b/Support/Mechanism/Models/LuDME/therm.dat → Mechanisms/LuDME/therm.dat
diff --git a/Support/Mechanism/Models/LuDME/tran.dat → Mechanisms/LuDME/tran.dat b/Support/Mechanism/Models/LuDME/tran.dat → Mechanisms/LuDME/tran.dat
diff --git a/...hanism/Models/LuEthylene/ARC/LuEthylene.f → Mechanisms/LuEthylene/ARC/LuEthylene.f b/...hanism/Models/LuEthylene/ARC/LuEthylene.f → Mechanisms/LuEthylene/ARC/LuEthylene.f
diff --git a/.../Mechanism/Models/decane_3sp/Make.package → Mechanisms/LuEthylene/Make.package b/.../Mechanism/Models/decane_3sp/Make.package → Mechanisms/LuEthylene/Make.package
diff --git a/...ort/Mechanism/Models/LuEthylene/README.md → Mechanisms/LuEthylene/README.md b/...ort/Mechanism/Models/LuEthylene/README.md → Mechanisms/LuEthylene/README.md
diff --git a/...rt/Mechanism/Models/LuEthylene/convert.sh → Mechanisms/LuEthylene/convert.sh b/...rt/Mechanism/Models/LuEthylene/convert.sh → Mechanisms/LuEthylene/convert.sh
diff --git a/...t/Mechanism/Models/LuEthylene/mechanism.H → Mechanisms/LuEthylene/mechanism.H b/...t/Mechanism/Models/LuEthylene/mechanism.H → Mechanisms/LuEthylene/mechanism.H
diff --git a/...Mechanism/Models/LuEthylene/mechanism.cpp → Mechanisms/LuEthylene/mechanism.cpp b/...Mechanism/Models/LuEthylene/mechanism.cpp → Mechanisms/LuEthylene/mechanism.cpp
diff --git a/...Mechanism/Models/LuEthylene/mechanism.inp → Mechanisms/LuEthylene/mechanism.inp b/...Mechanism/Models/LuEthylene/mechanism.inp → Mechanisms/LuEthylene/mechanism.inp
diff --git a/...echanism/Models/LuEthylene/mechanism.yaml → Mechanisms/LuEthylene/mechanism.yaml b/...echanism/Models/LuEthylene/mechanism.yaml → Mechanisms/LuEthylene/mechanism.yaml
diff --git a/...ort/Mechanism/Models/LuEthylene/therm.dat → Mechanisms/LuEthylene/therm.dat b/...ort/Mechanism/Models/LuEthylene/therm.dat → Mechanisms/LuEthylene/therm.dat
diff --git a/Support/Mechanism/Models/LuEthylene/tran.dat → Mechanisms/LuEthylene/tran.dat b/Support/Mechanism/Models/LuEthylene/tran.dat → Mechanisms/LuEthylene/tran.dat
diff --git a/...Mechanism/Models/dodecane_lu/Make.package → Mechanisms/LuEthylene_qss/Make.package b/...Mechanism/Models/dodecane_lu/Make.package → Mechanisms/LuEthylene_qss/Make.package
diff --git a/...chanism/Models/LuEthylene_qss/mechanism.H → Mechanisms/LuEthylene_qss/mechanism.H b/...chanism/Models/LuEthylene_qss/mechanism.H → Mechanisms/LuEthylene_qss/mechanism.H
diff --git a/...anism/Models/LuEthylene_qss/mechanism.cpp → Mechanisms/LuEthylene_qss/mechanism.cpp b/...anism/Models/LuEthylene_qss/mechanism.cpp → Mechanisms/LuEthylene_qss/mechanism.cpp
diff --git a/.../Models/LuEthylene_qss/non_qssa_list.yaml → Mechanisms/LuEthylene_qss/non_qssa_list.yaml b/.../Models/LuEthylene_qss/non_qssa_list.yaml → Mechanisms/LuEthylene_qss/non_qssa_list.yaml
diff --git a/...Mechanism/Models/LuEthylene_qss/qssa.yaml → Mechanisms/LuEthylene_qss/qssa.yaml b/...Mechanism/Models/LuEthylene_qss/qssa.yaml → Mechanisms/LuEthylene_qss/qssa.yaml
diff --git a/...ism/Models/LuEthylene_qss/qssa_input.toml → Mechanisms/LuEthylene_qss/qssa_input.toml b/...ism/Models/LuEthylene_qss/qssa_input.toml → Mechanisms/LuEthylene_qss/qssa_input.toml
diff --git a/...anism/Models/LuEthylene_qss/skeletal.yaml → Mechanisms/LuEthylene_qss/skeletal.yaml b/...anism/Models/LuEthylene_qss/skeletal.yaml → Mechanisms/LuEthylene_qss/skeletal.yaml
diff --git a/...Mechanism/Models/LuEthylene_qss/therm.dat → Mechanisms/LuEthylene_qss/therm.dat b/...Mechanism/Models/LuEthylene_qss/therm.dat → Mechanisms/LuEthylene_qss/therm.dat
diff --git a/.../Mechanism/Models/LuEthylene_qss/tran.dat → Mechanisms/LuEthylene_qss/tran.dat b/.../Mechanism/Models/LuEthylene_qss/tran.dat → Mechanisms/LuEthylene_qss/tran.dat
diff --git a/Support/Mechanism/Models/Make.package → Mechanisms/Make.package b/Support/Mechanism/Models/Make.package → Mechanisms/Make.package
diff --git a/...anism/Models/dodecane_lu_qss/Make.package → Mechanisms/NUIGalway/Make.package b/...anism/Models/dodecane_lu_qss/Make.package → Mechanisms/NUIGalway/Make.package
diff --git a/...ort/Mechanism/Models/NUIGalway/convert.sh → Mechanisms/NUIGalway/convert.sh b/...ort/Mechanism/Models/NUIGalway/convert.sh → Mechanisms/NUIGalway/convert.sh
diff --git a/...rt/Mechanism/Models/NUIGalway/mechanism.H → Mechanisms/NUIGalway/mechanism.H b/...rt/Mechanism/Models/NUIGalway/mechanism.H → Mechanisms/NUIGalway/mechanism.H
diff --git a/.../Mechanism/Models/NUIGalway/mechanism.cpp → Mechanisms/NUIGalway/mechanism.cpp b/.../Mechanism/Models/NUIGalway/mechanism.cpp → Mechanisms/NUIGalway/mechanism.cpp
diff --git a/.../Mechanism/Models/NUIGalway/mechanism.inp → Mechanisms/NUIGalway/mechanism.inp b/.../Mechanism/Models/NUIGalway/mechanism.inp → Mechanisms/NUIGalway/mechanism.inp
diff --git a/...Mechanism/Models/NUIGalway/mechanism.yaml → Mechanisms/NUIGalway/mechanism.yaml b/...Mechanism/Models/NUIGalway/mechanism.yaml → Mechanisms/NUIGalway/mechanism.yaml
diff --git a/Support/Mechanism/Models/NUIGalway/therm.dat → Mechanisms/NUIGalway/therm.dat b/Support/Mechanism/Models/NUIGalway/therm.dat → Mechanisms/NUIGalway/therm.dat
diff --git a/Support/Mechanism/Models/NUIGalway/tran.dat → Mechanisms/NUIGalway/tran.dat b/Support/Mechanism/Models/NUIGalway/tran.dat → Mechanisms/NUIGalway/tran.dat
diff --git a/...hanism/Models/dodmethair_4sp/Make.package → Mechanisms/Null/Make.package b/...hanism/Models/dodmethair_4sp/Make.package → Mechanisms/Null/Make.package
diff --git a/Support/Mechanism/Models/Null/mechanism.H → Mechanisms/Null/mechanism.H b/Support/Mechanism/Models/Null/mechanism.H → Mechanisms/Null/mechanism.H
diff --git a/Support/Mechanism/Models/Null/mechanism.cpp → Mechanisms/Null/mechanism.cpp b/Support/Mechanism/Models/Null/mechanism.cpp → Mechanisms/Null/mechanism.cpp
diff --git a/Support/Mechanism/Models/PPHYS_CONSTANTS.H → Mechanisms/PPHYS_CONSTANTS.H b/Support/Mechanism/Models/PPHYS_CONSTANTS.H → Mechanisms/PPHYS_CONSTANTS.H
diff --git a/Support/Mechanism/Models/drm19/Make.package → Mechanisms/SootReaction/Make.package b/Support/Mechanism/Models/drm19/Make.package → Mechanisms/SootReaction/Make.package
diff --git a/...t/Mechanism/Models/SootReaction/README.md → Mechanisms/SootReaction/README.md b/...t/Mechanism/Models/SootReaction/README.md → Mechanisms/SootReaction/README.md
diff --git a/.../Mechanism/Models/SootReaction/convert.sh → Mechanisms/SootReaction/convert.sh b/.../Mechanism/Models/SootReaction/convert.sh → Mechanisms/SootReaction/convert.sh
diff --git a/...Mechanism/Models/SootReaction/mechanism.H → Mechanisms/SootReaction/mechanism.H b/...Mechanism/Models/SootReaction/mechanism.H → Mechanisms/SootReaction/mechanism.H
diff --git a/...chanism/Models/SootReaction/mechanism.cpp → Mechanisms/SootReaction/mechanism.cpp b/...chanism/Models/SootReaction/mechanism.cpp → Mechanisms/SootReaction/mechanism.cpp
diff --git a/...chanism/Models/SootReaction/mechanism.inp → Mechanisms/SootReaction/mechanism.inp b/...chanism/Models/SootReaction/mechanism.inp → Mechanisms/SootReaction/mechanism.inp
diff --git a/...hanism/Models/SootReaction/mechanism.yaml → Mechanisms/SootReaction/mechanism.yaml b/...hanism/Models/SootReaction/mechanism.yaml → Mechanisms/SootReaction/mechanism.yaml
diff --git a/...t/Mechanism/Models/SootReaction/therm.dat → Mechanisms/SootReaction/therm.dat b/...t/Mechanism/Models/SootReaction/therm.dat → Mechanisms/SootReaction/therm.dat
diff --git a/...Mechanism/Models/ethylene_af/Make.package → Mechanisms/air/Make.package b/...Mechanism/Models/ethylene_af/Make.package → Mechanisms/air/Make.package
diff --git a/Support/Mechanism/Models/air/convert.sh → Mechanisms/air/convert.sh b/Support/Mechanism/Models/air/convert.sh → Mechanisms/air/convert.sh
diff --git a/Support/Mechanism/Models/air/mechanism.H → Mechanisms/air/mechanism.H b/Support/Mechanism/Models/air/mechanism.H → Mechanisms/air/mechanism.H
diff --git a/Support/Mechanism/Models/air/mechanism.cpp → Mechanisms/air/mechanism.cpp b/Support/Mechanism/Models/air/mechanism.cpp → Mechanisms/air/mechanism.cpp
diff --git a/Support/Mechanism/Models/air/mechanism.inp → Mechanisms/air/mechanism.inp b/Support/Mechanism/Models/air/mechanism.inp → Mechanisms/air/mechanism.inp
diff --git a/Support/Mechanism/Models/air/mechanism.yaml → Mechanisms/air/mechanism.yaml b/Support/Mechanism/Models/air/mechanism.yaml → Mechanisms/air/mechanism.yaml
diff --git a/Support/Mechanism/Models/air/therm.dat → Mechanisms/air/therm.dat b/Support/Mechanism/Models/air/therm.dat → Mechanisms/air/therm.dat
diff --git a/Support/Mechanism/Models/air/tran.dat → Mechanisms/air/tran.dat b/Support/Mechanism/Models/air/tran.dat → Mechanisms/air/tran.dat
diff --git a/...t/Mechanism/Models/alzeta/ALZ_F-MechC.cti → Mechanisms/alzeta/ALZ_F-MechC.cti b/...t/Mechanism/Models/alzeta/ALZ_F-MechC.cti → Mechanisms/alzeta/ALZ_F-MechC.cti
diff --git a/...ism/Models/alzeta/ALZ_F-MechC_ck.dat-orig → Mechanisms/alzeta/ALZ_F-MechC_ck.dat-orig b/...ism/Models/alzeta/ALZ_F-MechC_ck.dat-orig → Mechanisms/alzeta/ALZ_F-MechC_ck.dat-orig
diff --git a/...t/Mechanism/Models/grimech12/Make.package → Mechanisms/alzeta/Make.package b/...t/Mechanism/Models/grimech12/Make.package → Mechanisms/alzeta/Make.package
diff --git a/Support/Mechanism/Models/alzeta/convert.sh → Mechanisms/alzeta/convert.sh b/Support/Mechanism/Models/alzeta/convert.sh → Mechanisms/alzeta/convert.sh
diff --git a/Support/Mechanism/Models/alzeta/mechanism.H → Mechanisms/alzeta/mechanism.H b/Support/Mechanism/Models/alzeta/mechanism.H → Mechanisms/alzeta/mechanism.H
diff --git a/...ort/Mechanism/Models/alzeta/mechanism.cpp → Mechanisms/alzeta/mechanism.cpp b/...ort/Mechanism/Models/alzeta/mechanism.cpp → Mechanisms/alzeta/mechanism.cpp
diff --git a/...ort/Mechanism/Models/alzeta/mechanism.inp → Mechanisms/alzeta/mechanism.inp b/...ort/Mechanism/Models/alzeta/mechanism.inp → Mechanisms/alzeta/mechanism.inp
diff --git a/...rt/Mechanism/Models/alzeta/mechanism.yaml → Mechanisms/alzeta/mechanism.yaml b/...rt/Mechanism/Models/alzeta/mechanism.yaml → Mechanisms/alzeta/mechanism.yaml
diff --git a/Support/Mechanism/Models/alzeta/therm.dat → Mechanisms/alzeta/therm.dat b/Support/Mechanism/Models/alzeta/therm.dat → Mechanisms/alzeta/therm.dat
diff --git a/Support/Mechanism/Models/alzeta/tran.dat → Mechanisms/alzeta/tran.dat b/Support/Mechanism/Models/alzeta/tran.dat → Mechanisms/alzeta/tran.dat
diff --git a/...t/Mechanism/Models/grimech30/Make.package → Mechanisms/chem-CH4-2step/Make.package b/...t/Mechanism/Models/grimech30/Make.package → Mechanisms/chem-CH4-2step/Make.package
diff --git a/...echanism/Models/chem-CH4-2step/convert.sh → Mechanisms/chem-CH4-2step/convert.sh b/...echanism/Models/chem-CH4-2step/convert.sh → Mechanisms/chem-CH4-2step/convert.sh
diff --git a/...chanism/Models/chem-CH4-2step/mechanism.H → Mechanisms/chem-CH4-2step/mechanism.H b/...chanism/Models/chem-CH4-2step/mechanism.H → Mechanisms/chem-CH4-2step/mechanism.H
diff --git a/...anism/Models/chem-CH4-2step/mechanism.cpp → Mechanisms/chem-CH4-2step/mechanism.cpp b/...anism/Models/chem-CH4-2step/mechanism.cpp → Mechanisms/chem-CH4-2step/mechanism.cpp
diff --git a/...anism/Models/chem-CH4-2step/mechanism.inp → Mechanisms/chem-CH4-2step/mechanism.inp b/...anism/Models/chem-CH4-2step/mechanism.inp → Mechanisms/chem-CH4-2step/mechanism.inp
diff --git a/...nism/Models/chem-CH4-2step/mechanism.yaml → Mechanisms/chem-CH4-2step/mechanism.yaml b/...nism/Models/chem-CH4-2step/mechanism.yaml → Mechanisms/chem-CH4-2step/mechanism.yaml
diff --git a/...Mechanism/Models/chem-CH4-2step/therm.dat → Mechanisms/chem-CH4-2step/therm.dat b/...Mechanism/Models/chem-CH4-2step/therm.dat → Mechanisms/chem-CH4-2step/therm.dat
diff --git a/.../Mechanism/Models/chem-CH4-2step/tran.dat → Mechanisms/chem-CH4-2step/tran.dat b/.../Mechanism/Models/chem-CH4-2step/tran.dat → Mechanisms/chem-CH4-2step/tran.dat
diff --git a/...Mechanism/Models/heptane_3sp/Make.package → Mechanisms/chem-H/Make.package b/...Mechanism/Models/heptane_3sp/Make.package → Mechanisms/chem-H/Make.package
diff --git a/Support/Mechanism/Models/chem-H/convert.sh → Mechanisms/chem-H/convert.sh b/Support/Mechanism/Models/chem-H/convert.sh → Mechanisms/chem-H/convert.sh
diff --git a/Support/Mechanism/Models/chem-H/mechanism.H → Mechanisms/chem-H/mechanism.H b/Support/Mechanism/Models/chem-H/mechanism.H → Mechanisms/chem-H/mechanism.H
diff --git a/...ort/Mechanism/Models/chem-H/mechanism.cpp → Mechanisms/chem-H/mechanism.cpp b/...ort/Mechanism/Models/chem-H/mechanism.cpp → Mechanisms/chem-H/mechanism.cpp
diff --git a/...ort/Mechanism/Models/chem-H/mechanism.inp → Mechanisms/chem-H/mechanism.inp b/...ort/Mechanism/Models/chem-H/mechanism.inp → Mechanisms/chem-H/mechanism.inp
diff --git a/...rt/Mechanism/Models/chem-H/mechanism.yaml → Mechanisms/chem-H/mechanism.yaml b/...rt/Mechanism/Models/chem-H/mechanism.yaml → Mechanisms/chem-H/mechanism.yaml
diff --git a/Support/Mechanism/Models/chem-H/therm.dat → Mechanisms/chem-H/therm.dat b/Support/Mechanism/Models/chem-H/therm.dat → Mechanisms/chem-H/therm.dat
diff --git a/Support/Mechanism/Models/chem-H/tran.dat → Mechanisms/chem-H/tran.dat b/Support/Mechanism/Models/chem-H/tran.dat → Mechanisms/chem-H/tran.dat
diff --git a/Support/Mechanism/Models/converter.sh → Mechanisms/converter.sh b/Support/Mechanism/Models/converter.sh → Mechanisms/converter.sh
@@ -50,7 +50,7 @@ while getopts ":hf:" option; do
 done
 
 if [ -z "${PELE_PHYSICS_HOME+xxx}" ]; then
-    remove="Support/Mechanism/Models"
+    remove="Mechanisms"
     script_dir=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
     PELE_PHYSICS_HOME=${script_dir%%"${remove}"}
     echo "Using PELE_PHYSICS_HOME: ${PELE_PHYSICS_HOME}. Set PELE_PHYSICS_HOME you want a different one."

diff --git a/.../Mechanism/Models/heptane_fc/Make.package → Mechanisms/decane_3sp/Make.package b/.../Mechanism/Models/heptane_fc/Make.package → Mechanisms/decane_3sp/Make.package
diff --git a/...rt/Mechanism/Models/decane_3sp/convert.sh → Mechanisms/decane_3sp/convert.sh b/...rt/Mechanism/Models/decane_3sp/convert.sh → Mechanisms/decane_3sp/convert.sh
diff --git a/...t/Mechanism/Models/decane_3sp/mechanism.H → Mechanisms/decane_3sp/mechanism.H b/...t/Mechanism/Models/decane_3sp/mechanism.H → Mechanisms/decane_3sp/mechanism.H
diff --git a/...Mechanism/Models/decane_3sp/mechanism.cpp → Mechanisms/decane_3sp/mechanism.cpp b/...Mechanism/Models/decane_3sp/mechanism.cpp → Mechanisms/decane_3sp/mechanism.cpp
diff --git a/...Mechanism/Models/decane_3sp/mechanism.inp → Mechanisms/decane_3sp/mechanism.inp b/...Mechanism/Models/decane_3sp/mechanism.inp → Mechanisms/decane_3sp/mechanism.inp
diff --git a/...echanism/Models/decane_3sp/mechanism.yaml → Mechanisms/decane_3sp/mechanism.yaml b/...echanism/Models/decane_3sp/mechanism.yaml → Mechanisms/decane_3sp/mechanism.yaml
diff --git a/...ort/Mechanism/Models/decane_3sp/therm.dat → Mechanisms/decane_3sp/therm.dat b/...ort/Mechanism/Models/decane_3sp/therm.dat → Mechanisms/decane_3sp/therm.dat
diff --git a/Support/Mechanism/Models/decane_3sp/tran.dat → Mechanisms/decane_3sp/tran.dat b/Support/Mechanism/Models/decane_3sp/tran.dat → Mechanisms/decane_3sp/tran.dat
diff --git a/.../Mechanism/Models/dodecane_lu/ARC/ckwyp.f → Mechanisms/dodecane_lu/ARC/ckwyp.f b/.../Mechanism/Models/dodecane_lu/ARC/ckwyp.f → Mechanisms/dodecane_lu/ARC/ckwyp.f
diff --git a/...hanism/Models/heptane_lu_qss/Make.package → Mechanisms/dodecane_lu/Make.package b/...hanism/Models/heptane_lu_qss/Make.package → Mechanisms/dodecane_lu/Make.package
diff --git a/...rt/Mechanism/Models/dodecane_lu/README.md → Mechanisms/dodecane_lu/README.md b/...rt/Mechanism/Models/dodecane_lu/README.md → Mechanisms/dodecane_lu/README.md
diff --git a/...t/Mechanism/Models/dodecane_lu/convert.sh → Mechanisms/dodecane_lu/convert.sh b/...t/Mechanism/Models/dodecane_lu/convert.sh → Mechanisms/dodecane_lu/convert.sh
diff --git a/.../Mechanism/Models/dodecane_lu/mechanism.H → Mechanisms/dodecane_lu/mechanism.H b/.../Mechanism/Models/dodecane_lu/mechanism.H → Mechanisms/dodecane_lu/mechanism.H
diff --git a/...echanism/Models/dodecane_lu/mechanism.cpp → Mechanisms/dodecane_lu/mechanism.cpp b/...echanism/Models/dodecane_lu/mechanism.cpp → Mechanisms/dodecane_lu/mechanism.cpp
diff --git a/...echanism/Models/dodecane_lu/mechanism.inp → Mechanisms/dodecane_lu/mechanism.inp b/...echanism/Models/dodecane_lu/mechanism.inp → Mechanisms/dodecane_lu/mechanism.inp
diff --git a/...chanism/Models/dodecane_lu/mechanism.yaml → Mechanisms/dodecane_lu/mechanism.yaml b/...chanism/Models/dodecane_lu/mechanism.yaml → Mechanisms/dodecane_lu/mechanism.yaml
diff --git a/...rt/Mechanism/Models/dodecane_lu/therm.dat → Mechanisms/dodecane_lu/therm.dat b/...rt/Mechanism/Models/dodecane_lu/therm.dat → Mechanisms/dodecane_lu/therm.dat
diff --git a/...ort/Mechanism/Models/dodecane_lu/tran.dat → Mechanisms/dodecane_lu/tran.dat b/...ort/Mechanism/Models/dodecane_lu/tran.dat → Mechanisms/dodecane_lu/tran.dat
diff --git a/...echanism/Models/isooctane_lu/Make.package → Mechanisms/dodecane_lu_qss/Make.package b/...echanism/Models/isooctane_lu/Make.package → Mechanisms/dodecane_lu_qss/Make.package
diff --git a/...echanism/Models/dodecane_lu_qss/README.md → Mechanisms/dodecane_lu_qss/README.md b/...echanism/Models/dodecane_lu_qss/README.md → Mechanisms/dodecane_lu_qss/README.md
diff --git a/...Mechanism/Models/dodecane_lu_qss/clean.sh → Mechanisms/dodecane_lu_qss/clean.sh b/...Mechanism/Models/dodecane_lu_qss/clean.sh → Mechanisms/dodecane_lu_qss/clean.sh
diff --git a/...hanism/Models/dodecane_lu_qss/mechanism.H → Mechanisms/dodecane_lu_qss/mechanism.H b/...hanism/Models/dodecane_lu_qss/mechanism.H → Mechanisms/dodecane_lu_qss/mechanism.H
diff --git a/...nism/Models/dodecane_lu_qss/mechanism.cpp → Mechanisms/dodecane_lu_qss/mechanism.cpp b/...nism/Models/dodecane_lu_qss/mechanism.cpp → Mechanisms/dodecane_lu_qss/mechanism.cpp
diff --git a/.../Models/dodecane_lu_qss/non_qssa_list.txt → Mechanisms/dodecane_lu_qss/non_qssa_list.txt b/.../Models/dodecane_lu_qss/non_qssa_list.txt → Mechanisms/dodecane_lu_qss/non_qssa_list.txt
diff --git a/...Models/dodecane_lu_qss/non_qssa_list.yaml → ...anisms/dodecane_lu_qss/non_qssa_list.yaml b/...Models/dodecane_lu_qss/non_qssa_list.yaml → ...anisms/dodecane_lu_qss/non_qssa_list.yaml
diff --git a/...echanism/Models/dodecane_lu_qss/qssa.yaml → Mechanisms/dodecane_lu_qss/qssa.yaml b/...echanism/Models/dodecane_lu_qss/qssa.yaml → Mechanisms/dodecane_lu_qss/qssa.yaml
diff --git a/...sm/Models/dodecane_lu_qss/qssa_input.toml → Mechanisms/dodecane_lu_qss/qssa_input.toml b/...sm/Models/dodecane_lu_qss/qssa_input.toml → Mechanisms/dodecane_lu_qss/qssa_input.toml
diff --git a/...cane_lu_qss/qssa_input_non_optimized.toml → ...cane_lu_qss/qssa_input_non_optimized.toml b/...cane_lu_qss/qssa_input_non_optimized.toml → ...cane_lu_qss/qssa_input_non_optimized.toml
diff --git a/...anism/Models/dodecane_lu_qss/skeletal.inp → Mechanisms/dodecane_lu_qss/skeletal.inp b/...anism/Models/dodecane_lu_qss/skeletal.inp → Mechanisms/dodecane_lu_qss/skeletal.inp
diff --git a/...nism/Models/dodecane_lu_qss/skeletal.yaml → Mechanisms/dodecane_lu_qss/skeletal.yaml b/...nism/Models/dodecane_lu_qss/skeletal.yaml → Mechanisms/dodecane_lu_qss/skeletal.yaml
diff --git a/...echanism/Models/dodecane_lu_qss/therm.dat → Mechanisms/dodecane_lu_qss/therm.dat b/...echanism/Models/dodecane_lu_qss/therm.dat → Mechanisms/dodecane_lu_qss/therm.dat
diff --git a/...Mechanism/Models/dodecane_lu_qss/tran.dat → Mechanisms/dodecane_lu_qss/tran.dat b/...Mechanism/Models/dodecane_lu_qss/tran.dat → Mechanisms/dodecane_lu_qss/tran.dat
diff --git a/.../Mechanism/Models/propane_fc/Make.package → Mechanisms/dodecane_wang/Make.package b/.../Mechanism/Models/propane_fc/Make.package → Mechanisms/dodecane_wang/Make.package
diff --git a/...Mechanism/Models/dodecane_wang/convert.sh → Mechanisms/dodecane_wang/convert.sh b/...Mechanism/Models/dodecane_wang/convert.sh → Mechanisms/dodecane_wang/convert.sh
diff --git a/...echanism/Models/dodecane_wang/mechanism.H → Mechanisms/dodecane_wang/mechanism.H b/...echanism/Models/dodecane_wang/mechanism.H → Mechanisms/dodecane_wang/mechanism.H
diff --git a/...hanism/Models/dodecane_wang/mechanism.cpp → Mechanisms/dodecane_wang/mechanism.cpp b/...hanism/Models/dodecane_wang/mechanism.cpp → Mechanisms/dodecane_wang/mechanism.cpp
diff --git a/...hanism/Models/dodecane_wang/mechanism.inp → Mechanisms/dodecane_wang/mechanism.inp b/...hanism/Models/dodecane_wang/mechanism.inp → Mechanisms/dodecane_wang/mechanism.inp
diff --git a/...anism/Models/dodecane_wang/mechanism.yaml → Mechanisms/dodecane_wang/mechanism.yaml b/...anism/Models/dodecane_wang/mechanism.yaml → Mechanisms/dodecane_wang/mechanism.yaml
diff --git a/.../Mechanism/Models/dodecane_wang/therm.dat → Mechanisms/dodecane_wang/therm.dat b/.../Mechanism/Models/dodecane_wang/therm.dat → Mechanisms/dodecane_wang/therm.dat
diff --git a/...t/Mechanism/Models/dodecane_wang/tran.dat → Mechanisms/dodecane_wang/tran.dat b/...t/Mechanism/Models/dodecane_wang/tran.dat → Mechanisms/dodecane_wang/tran.dat
diff --git a/Support/Mechanism/Models/sCO2/Make.package → Mechanisms/dodmethair_4sp/Make.package b/Support/Mechanism/Models/sCO2/Make.package → Mechanisms/dodmethair_4sp/Make.package
diff --git a/...echanism/Models/dodmethair_4sp/convert.sh → Mechanisms/dodmethair_4sp/convert.sh b/...echanism/Models/dodmethair_4sp/convert.sh → Mechanisms/dodmethair_4sp/convert.sh
diff --git a/...chanism/Models/dodmethair_4sp/mechanism.H → Mechanisms/dodmethair_4sp/mechanism.H b/...chanism/Models/dodmethair_4sp/mechanism.H → Mechanisms/dodmethair_4sp/mechanism.H
diff --git a/...anism/Models/dodmethair_4sp/mechanism.cpp → Mechanisms/dodmethair_4sp/mechanism.cpp b/...anism/Models/dodmethair_4sp/mechanism.cpp → Mechanisms/dodmethair_4sp/mechanism.cpp
diff --git a/...anism/Models/dodmethair_4sp/mechanism.inp → Mechanisms/dodmethair_4sp/mechanism.inp b/...anism/Models/dodmethair_4sp/mechanism.inp → Mechanisms/dodmethair_4sp/mechanism.inp
diff --git a/...nism/Models/dodmethair_4sp/mechanism.yaml → Mechanisms/dodmethair_4sp/mechanism.yaml b/...nism/Models/dodmethair_4sp/mechanism.yaml → Mechanisms/dodmethair_4sp/mechanism.yaml
diff --git a/...Mechanism/Models/dodmethair_4sp/therm.dat → Mechanisms/dodmethair_4sp/therm.dat b/...Mechanism/Models/dodmethair_4sp/therm.dat → Mechanisms/dodmethair_4sp/therm.dat
diff --git a/.../Mechanism/Models/dodmethair_4sp/tran.dat → Mechanisms/dodmethair_4sp/tran.dat b/.../Mechanism/Models/dodmethair_4sp/tran.dat → Mechanisms/dodmethair_4sp/tran.dat
diff --git a/...anism/Models/H2-CO-CO2-3spec/Make.package → Mechanisms/drm19/Make.package b/...anism/Models/H2-CO-CO2-3spec/Make.package → Mechanisms/drm19/Make.package
@@ -1,6 +1,7 @@
-CEXE_sources+=mechanism.cpp
 CEXE_headers+=mechanism.H
 
+CEXE_sources+=mechanism.cpp
+
 LIBRARIES +=
 
 INCLUDE_LOCATIONS += $(CHEM_DIR)

diff --git a/Support/Mechanism/Models/drm19/convert.sh → Mechanisms/drm19/convert.sh b/Support/Mechanism/Models/drm19/convert.sh → Mechanisms/drm19/convert.sh
diff --git a/Support/Mechanism/Models/drm19/mechanism.H → Mechanisms/drm19/mechanism.H b/Support/Mechanism/Models/drm19/mechanism.H → Mechanisms/drm19/mechanism.H
diff --git a/Support/Mechanism/Models/drm19/mechanism.cpp → Mechanisms/drm19/mechanism.cpp b/Support/Mechanism/Models/drm19/mechanism.cpp → Mechanisms/drm19/mechanism.cpp
diff --git a/Support/Mechanism/Models/drm19/mechanism.inp → Mechanisms/drm19/mechanism.inp b/Support/Mechanism/Models/drm19/mechanism.inp → Mechanisms/drm19/mechanism.inp
diff --git a/...ort/Mechanism/Models/drm19/mechanism.yaml → Mechanisms/drm19/mechanism.yaml b/...ort/Mechanism/Models/drm19/mechanism.yaml → Mechanisms/drm19/mechanism.yaml
diff --git a/Support/Mechanism/Models/drm19/therm.dat → Mechanisms/drm19/therm.dat b/Support/Mechanism/Models/drm19/therm.dat → Mechanisms/drm19/therm.dat
diff --git a/Support/Mechanism/Models/drm19/tran.dat → Mechanisms/drm19/tran.dat b/Support/Mechanism/Models/drm19/tran.dat → Mechanisms/drm19/tran.dat
diff --git a/...hanism/Models/ethylene_af/CANTERA/ARC.cti → Mechanisms/ethylene_af/CANTERA/ARC.cti b/...hanism/Models/ethylene_af/CANTERA/ARC.cti → Mechanisms/ethylene_af/CANTERA/ARC.cti
diff --git a/...e_af/CANTERA/C2H4DET_T298_P1_Phi0.8_Y.csv → ...e_af/CANTERA/C2H4DET_T298_P1_Phi0.8_Y.csv b/...e_af/CANTERA/C2H4DET_T298_P1_Phi0.8_Y.csv → ...e_af/CANTERA/C2H4DET_T298_P1_Phi0.8_Y.csv
diff --git a/...ne_af/CANTERA/C2H4SK_T298_P1_Phi0.8_Y.csv → ...ne_af/CANTERA/C2H4SK_T298_P1_Phi0.8_Y.csv b/...ne_af/CANTERA/C2H4SK_T298_P1_Phi0.8_Y.csv → ...ne_af/CANTERA/C2H4SK_T298_P1_Phi0.8_Y.csv
diff --git a/...ethylene_af/CANTERA/Cantera_UPF_Global.py → ...ethylene_af/CANTERA/Cantera_UPF_Global.py b/...ethylene_af/CANTERA/Cantera_UPF_Global.py → ...ethylene_af/CANTERA/Cantera_UPF_Global.py
diff --git a/...hanism/Models/ethylene_af/CANTERA/DET.cti → Mechanisms/ethylene_af/CANTERA/DET.cti b/...hanism/Models/ethylene_af/CANTERA/DET.cti → Mechanisms/ethylene_af/CANTERA/DET.cti
diff --git a/...ls/ethylene_af/CANTERA/adiabatic_flame.py → ...ms/ethylene_af/CANTERA/adiabatic_flame.py b/...ls/ethylene_af/CANTERA/adiabatic_flame.py → ...ms/ethylene_af/CANTERA/adiabatic_flame.py
diff --git a/.../ethylene_af/CANTERA/c2h4-T298-P1_ARC.csv → .../ethylene_af/CANTERA/c2h4-T298-P1_ARC.csv b/.../ethylene_af/CANTERA/c2h4-T298-P1_ARC.csv → .../ethylene_af/CANTERA/c2h4-T298-P1_ARC.csv
diff --git a/...s/ethylene_af/CANTERA/c2h4-T298-P1_SK.csv → ...s/ethylene_af/CANTERA/c2h4-T298-P1_SK.csv b/...s/ethylene_af/CANTERA/c2h4-T298-P1_SK.csv → ...s/ethylene_af/CANTERA/c2h4-T298-P1_SK.csv
diff --git a/...m/Models/ethylene_af/CANTERA/skeletal.cti → Mechanisms/ethylene_af/CANTERA/skeletal.cti b/...m/Models/ethylene_af/CANTERA/skeletal.cti → Mechanisms/ethylene_af/CANTERA/skeletal.cti
diff --git a/...m/Models/ethylene_af/CANTERA/skeletal.inp → Mechanisms/ethylene_af/CANTERA/skeletal.inp b/...m/Models/ethylene_af/CANTERA/skeletal.inp → Mechanisms/ethylene_af/CANTERA/skeletal.inp
diff --git a/...odels/ethylene_af/CANTERA/skeletal.thermo → ...nisms/ethylene_af/CANTERA/skeletal.thermo b/...odels/ethylene_af/CANTERA/skeletal.thermo → ...nisms/ethylene_af/CANTERA/skeletal.thermo
diff --git a/.../Models/ethylene_af/CANTERA/skeletal.tran → Mechanisms/ethylene_af/CANTERA/skeletal.tran b/.../Models/ethylene_af/CANTERA/skeletal.tran → Mechanisms/ethylene_af/CANTERA/skeletal.tran
diff --git a/.../Mechanism/Models/IonizedAir/Make.package → Mechanisms/ethylene_af/Make.package b/.../Mechanism/Models/IonizedAir/Make.package → Mechanisms/ethylene_af/Make.package
@@ -1,4 +1,5 @@
 CEXE_headers+=mechanism.H
+
 CEXE_sources+=mechanism.cpp
 
 LIBRARIES +=

diff --git a/...t/Mechanism/Models/ethylene_af/convert.sh → Mechanisms/ethylene_af/convert.sh b/...t/Mechanism/Models/ethylene_af/convert.sh → Mechanisms/ethylene_af/convert.sh
diff --git a/.../Mechanism/Models/ethylene_af/mechanism.H → Mechanisms/ethylene_af/mechanism.H b/.../Mechanism/Models/ethylene_af/mechanism.H → Mechanisms/ethylene_af/mechanism.H
diff --git a/...echanism/Models/ethylene_af/mechanism.cpp → Mechanisms/ethylene_af/mechanism.cpp b/...echanism/Models/ethylene_af/mechanism.cpp → Mechanisms/ethylene_af/mechanism.cpp
diff --git a/...echanism/Models/ethylene_af/mechanism.inp → Mechanisms/ethylene_af/mechanism.inp b/...echanism/Models/ethylene_af/mechanism.inp → Mechanisms/ethylene_af/mechanism.inp
diff --git a/...chanism/Models/ethylene_af/mechanism.yaml → Mechanisms/ethylene_af/mechanism.yaml b/...chanism/Models/ethylene_af/mechanism.yaml → Mechanisms/ethylene_af/mechanism.yaml
diff --git a/...rt/Mechanism/Models/ethylene_af/therm.dat → Mechanisms/ethylene_af/therm.dat b/...rt/Mechanism/Models/ethylene_af/therm.dat → Mechanisms/ethylene_af/therm.dat
diff --git a/...ort/Mechanism/Models/ethylene_af/tran.dat → Mechanisms/ethylene_af/tran.dat b/...ort/Mechanism/Models/ethylene_af/tran.dat → Mechanisms/ethylene_af/tran.dat
diff --git a/...ort/Mechanism/Models/LiDryer/Make.package → Mechanisms/grimech12/Make.package b/...ort/Mechanism/Models/LiDryer/Make.package → Mechanisms/grimech12/Make.package
@@ -1,6 +1,7 @@
-CEXE_sources+=mechanism.cpp
 CEXE_headers+=mechanism.H
 
+CEXE_sources+=mechanism.cpp
+
 LIBRARIES +=
 
 INCLUDE_LOCATIONS += $(CHEM_DIR)

diff --git a/...ort/Mechanism/Models/grimech12/convert.sh → Mechanisms/grimech12/convert.sh b/...ort/Mechanism/Models/grimech12/convert.sh → Mechanisms/grimech12/convert.sh
diff --git a/...rt/Mechanism/Models/grimech12/mechanism.H → Mechanisms/grimech12/mechanism.H b/...rt/Mechanism/Models/grimech12/mechanism.H → Mechanisms/grimech12/mechanism.H
diff --git a/.../Mechanism/Models/grimech12/mechanism.cpp → Mechanisms/grimech12/mechanism.cpp b/.../Mechanism/Models/grimech12/mechanism.cpp → Mechanisms/grimech12/mechanism.cpp
diff --git a/.../Mechanism/Models/grimech12/mechanism.inp → Mechanisms/grimech12/mechanism.inp b/.../Mechanism/Models/grimech12/mechanism.inp → Mechanisms/grimech12/mechanism.inp
diff --git a/...Mechanism/Models/grimech12/mechanism.yaml → Mechanisms/grimech12/mechanism.yaml b/...Mechanism/Models/grimech12/mechanism.yaml → Mechanisms/grimech12/mechanism.yaml
diff --git a/Support/Mechanism/Models/grimech12/therm.dat → Mechanisms/grimech12/therm.dat b/Support/Mechanism/Models/grimech12/therm.dat → Mechanisms/grimech12/therm.dat
diff --git a/Support/Mechanism/Models/grimech12/tran.dat → Mechanisms/grimech12/tran.dat b/Support/Mechanism/Models/grimech12/tran.dat → Mechanisms/grimech12/tran.dat
diff --git a/Support/Mechanism/Models/Null/Make.package → Mechanisms/grimech30-noArN/Make.package b/Support/Mechanism/Models/Null/Make.package → Mechanisms/grimech30-noArN/Make.package
@@ -1,6 +1,7 @@
-CEXE_sources+=mechanism.cpp
 CEXE_headers+=mechanism.H
 
+CEXE_sources+=mechanism.cpp
+
 LIBRARIES +=
 
 INCLUDE_LOCATIONS += $(CHEM_DIR)

diff --git a/...chanism/Models/grimech30-noArN/convert.sh → Mechanisms/grimech30-noArN/convert.sh b/...chanism/Models/grimech30-noArN/convert.sh → Mechanisms/grimech30-noArN/convert.sh
diff --git a/...hanism/Models/grimech30-noArN/mechanism.H → Mechanisms/grimech30-noArN/mechanism.H b/...hanism/Models/grimech30-noArN/mechanism.H → Mechanisms/grimech30-noArN/mechanism.H
diff --git a/...nism/Models/grimech30-noArN/mechanism.cpp → Mechanisms/grimech30-noArN/mechanism.cpp b/...nism/Models/grimech30-noArN/mechanism.cpp → Mechanisms/grimech30-noArN/mechanism.cpp
diff --git a/...nism/Models/grimech30-noArN/mechanism.inp → Mechanisms/grimech30-noArN/mechanism.inp b/...nism/Models/grimech30-noArN/mechanism.inp → Mechanisms/grimech30-noArN/mechanism.inp
diff --git a/...ism/Models/grimech30-noArN/mechanism.yaml → Mechanisms/grimech30-noArN/mechanism.yaml b/...ism/Models/grimech30-noArN/mechanism.yaml → Mechanisms/grimech30-noArN/mechanism.yaml
diff --git a/...echanism/Models/grimech30-noArN/therm.dat → Mechanisms/grimech30-noArN/therm.dat b/...echanism/Models/grimech30-noArN/therm.dat → Mechanisms/grimech30-noArN/therm.dat
diff --git a/...Mechanism/Models/grimech30-noArN/tran.dat → Mechanisms/grimech30-noArN/tran.dat b/...Mechanism/Models/grimech30-noArN/tran.dat → Mechanisms/grimech30-noArN/tran.dat
diff --git a/Mechanisms/grimech30/Make.package 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