in CI, regen all mechanisms and check if there are diffs

.github/workflows/ci.yml

@@ -74,10 +74,38 @@ jobs:
         run: poetry run flake8 .
       - name: Run tests
         run: poetry run pytest
-      - name: Convert air mechanism
-        run: poetry run convert -f ${{github.workspace}}/Mechanisms/air/mechanism.yaml
-      - name: Convert LiDryer mechanism
-        run: poetry run convert -f ${{github.workspace}}/Mechanisms/LiDryer/mechanism.yaml
+      - name: Convert regular mechanisms
+        continue-on-error: true
+        run: |
+          if [ "${{matrix.python-version}}" == '3.10' ]; then
+            poetry run convert -l ${{github.workspace}}/Mechanisms/list_mech
+            # Fail if there are diffs to the committed mechanisms
+            git diff --exit-code
+            # Also fail if there are any uncommitted or untracked changes
+            if [ -n "$(git status --porcelain=v1)" ]; then
+              echo "Uncommitted changes (including untracked files) detected after mechanism conversion:"
+              git status
+              exit 1
+            fi
+          else
+            poetry run convert -f ${{github.workspace}}/Mechanisms/air/mechanism.yaml
+            poetry run convert -f ${{github.workspace}}/Mechanisms/LiDryer/mechanism.yaml
+          fi
+      - name: Convert QSS mechanisms
+        continue-on-error: true
+        run: |
+          if [ "${{matrix.python-version}}" == '3.10' ]; then
+            poetry run qssa -lq ${{github.workspace}}/Mechanisms/list_qss_mech
+            poetry run convert -lq ${{github.workspace}}/Mechanisms/list_qss_mech
+            # Fail if there are diffs to the committed mechanisms
+            git diff --exit-code
+            # Also fail if there are any uncommitted or untracked changes
+            if [ -n "$(git status --porcelain=v1)" ]; then
+              echo "Uncommitted changes (including untracked files) detected after mechanism conversion:"
+              git status
+              exit 1
+            fi
+          fi
 
   Transport-EOS-Reactions:
     needs: Formatting

.gitignore

@@ -21,6 +21,7 @@ dodecane_wang.cpp_opt3
 drm19.cpp_OK
 callgrind.out*
 .ccls-cache
+poetry.lock
 
 # AMReX build directories
 d/

Mechanisms/C3MechLite/1_000atm/mechanism.H

@@ -95,11 +95,7 @@
 #define NUM_FIT 4
 
 //  ALWAYS on CPU stuff -- can have different def depending on if we are CPU or
-//  GPU based. Defined in mechanism.cpp
-void atomicWeight(amrex::Real* awt);
-//  MISC
-void CKAWT(amrex::Real* awt);
-void CKNCF(int* ncf);
+//  GPU based. Defined in mechanism.cpp MISC
 void CKSYME_STR(amrex::Vector<std::string>& ename);
 void CKSYMS_STR(amrex::Vector<std::string>& kname);
 void GET_RMAP(int* _rmap);
@@ -137,6 +133,299 @@ CKINDX(int& mm, int& kk, int& ii, int& nfit)
   nfit = -1; // Why do you need this anyway ?
 }
 
+// save atomic weights into array
+AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE void
+atomicWeight(amrex::Real* awt)
+{
+  awt[0] = 12.011000; // C
+  awt[1] = 1.008000;  // H
+  awt[2] = 14.007000; // N
+  awt[3] = 15.999000; // O
+  awt[4] = 39.950000; // Ar
+  awt[5] = 4.002602;  // He
+}
+
+// get atomic weight for all elements
+AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE void
+CKAWT(amrex::Real* awt)
+{
+  atomicWeight(awt);
+}
+
+// Returns the elemental composition
+// of the speciesi (mdim is num of elements)
+AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE void
+CKNCF(int* ncf)
+{
+  int kd = 6;
+  // Zero ncf
+  for (int id = 0; id < kd * 61; ++id) {
+    ncf[id] = 0;
+  }
+
+  // HE
+  ncf[0 * kd + 5] = 1; // He
+
+  // H2
+  ncf[1 * kd + 1] = 2; // H
+
+  // H
+  ncf[2 * kd + 1] = 1; // H
+
+  // O
+  ncf[3 * kd + 3] = 1; // O
+
+  // OH
+  ncf[4 * kd + 1] = 1; // H
+  ncf[4 * kd + 3] = 1; // O
+
+  // H2O
+  ncf[5 * kd + 1] = 2; // H
+  ncf[5 * kd + 3] = 1; // O
+
+  // O2
+  ncf[6 * kd + 3] = 2; // O
+
+  // N2
+  ncf[7 * kd + 2] = 2; // N
+
+  // AR
+  ncf[8 * kd + 4] = 1; // Ar
+
+  // H2O2
+  ncf[9 * kd + 1] = 2; // H
+  ncf[9 * kd + 3] = 2; // O
+
+  // HO2
+  ncf[10 * kd + 1] = 1; // H
+  ncf[10 * kd + 3] = 2; // O
+
+  // NH3
+  ncf[11 * kd + 1] = 3; // H
+  ncf[11 * kd + 2] = 1; // N
+
+  // NH2
+  ncf[12 * kd + 1] = 2; // H
+  ncf[12 * kd + 2] = 1; // N
+
+  // NO2
+  ncf[13 * kd + 2] = 1; // N
+  ncf[13 * kd + 3] = 2; // O
+
+  // HONO
+  ncf[14 * kd + 1] = 1; // H
+  ncf[14 * kd + 2] = 1; // N
+  ncf[14 * kd + 3] = 2; // O
+
+  // NH
+  ncf[15 * kd + 1] = 1; // H
+  ncf[15 * kd + 2] = 1; // N
+
+  // N
+  ncf[16 * kd + 2] = 1; // N
+
+  // HNO
+  ncf[17 * kd + 1] = 1; // H
+  ncf[17 * kd + 2] = 1; // N
+  ncf[17 * kd + 3] = 1; // O
+
+  // NO
+  ncf[18 * kd + 2] = 1; // N
+  ncf[18 * kd + 3] = 1; // O
+
+  // H2NO
+  ncf[19 * kd + 1] = 2; // H
+  ncf[19 * kd + 2] = 1; // N
+  ncf[19 * kd + 3] = 1; // O
+
+  // NNH
+  ncf[20 * kd + 1] = 1; // H
+  ncf[20 * kd + 2] = 2; // N
+
+  // N2O
+  ncf[21 * kd + 2] = 2; // N
+  ncf[21 * kd + 3] = 1; // O
+
+  // N2H2
+  ncf[22 * kd + 1] = 2; // H
+  ncf[22 * kd + 2] = 2; // N
+
+  // N2H3
+  ncf[23 * kd + 1] = 3; // H
+  ncf[23 * kd + 2] = 2; // N
+
+  // N2H4
+  ncf[24 * kd + 1] = 4; // H
+  ncf[24 * kd + 2] = 2; // N
+
+  // CO2
+  ncf[25 * kd + 0] = 1; // C
+  ncf[25 * kd + 3] = 2; // O
+
+  // CO
+  ncf[26 * kd + 0] = 1; // C
+  ncf[26 * kd + 3] = 1; // O
+
+  // CH4
+  ncf[27 * kd + 0] = 1; // C
+  ncf[27 * kd + 1] = 4; // H
+
+  // CH3
+  ncf[28 * kd + 0] = 1; // C
+  ncf[28 * kd + 1] = 3; // H
+
+  // CH3O2
+  ncf[29 * kd + 0] = 1; // C
+  ncf[29 * kd + 1] = 3; // H
+  ncf[29 * kd + 3] = 2; // O
+
+  // CH3O2H
+  ncf[30 * kd + 0] = 1; // C
+  ncf[30 * kd + 1] = 4; // H
+  ncf[30 * kd + 3] = 2; // O
+
+  // CH2
+  ncf[31 * kd + 0] = 1; // C
+  ncf[31 * kd + 1] = 2; // H
+
+  // HCO
+  ncf[32 * kd + 0] = 1; // C
+  ncf[32 * kd + 1] = 1; // H
+  ncf[32 * kd + 3] = 1; // O
+
+  // CH2O
+  ncf[33 * kd + 0] = 1; // C
+  ncf[33 * kd + 1] = 2; // H
+  ncf[33 * kd + 3] = 1; // O
+
+  // C2H4
+  ncf[34 * kd + 0] = 2; // C
+  ncf[34 * kd + 1] = 4; // H
+
+  // CH3O
+  ncf[35 * kd + 0] = 1; // C
+  ncf[35 * kd + 1] = 3; // H
+  ncf[35 * kd + 3] = 1; // O
+
+  // CH2O2H
+  ncf[36 * kd + 0] = 1; // C
+  ncf[36 * kd + 1] = 3; // H
+  ncf[36 * kd + 3] = 2; // O
+
+  // CH3OH
+  ncf[37 * kd + 0] = 1; // C
+  ncf[37 * kd + 1] = 4; // H
+  ncf[37 * kd + 3] = 1; // O
+
+  // C2H5
+  ncf[38 * kd + 0] = 2; // C
+  ncf[38 * kd + 1] = 5; // H
+
+  // C2H6
+  ncf[39 * kd + 0] = 2; // C
+  ncf[39 * kd + 1] = 6; // H
+
+  // C2H3
+  ncf[40 * kd + 0] = 2; // C
+  ncf[40 * kd + 1] = 3; // H
+
+  // CH2CHO
+  ncf[41 * kd + 0] = 2; // C
+  ncf[41 * kd + 1] = 3; // H
+  ncf[41 * kd + 3] = 1; // O
+
+  // CH2CO
+  ncf[42 * kd + 0] = 2; // C
+  ncf[42 * kd + 1] = 2; // H
+  ncf[42 * kd + 3] = 1; // O
+
+  // C2H2
+  ncf[43 * kd + 0] = 2; // C
+  ncf[43 * kd + 1] = 2; // H
+
+  // CH2OH
+  ncf[44 * kd + 0] = 1; // C
+  ncf[44 * kd + 1] = 3; // H
+  ncf[44 * kd + 3] = 1; // O
+
+  // C2H5O2
+  ncf[45 * kd + 0] = 2; // C
+  ncf[45 * kd + 1] = 5; // H
+  ncf[45 * kd + 3] = 2; // O
+
+  // C2H5O2H
+  ncf[46 * kd + 0] = 2; // C
+  ncf[46 * kd + 1] = 6; // H
+  ncf[46 * kd + 3] = 2; // O
+
+  // C2H5O
+  ncf[47 * kd + 0] = 2; // C
+  ncf[47 * kd + 1] = 5; // H
+  ncf[47 * kd + 3] = 1; // O
+
+  // CH3CHO
+  ncf[48 * kd + 0] = 2; // C
+  ncf[48 * kd + 1] = 4; // H
+  ncf[48 * kd + 3] = 1; // O
+
+  // HCCO
+  ncf[49 * kd + 0] = 2; // C
+  ncf[49 * kd + 1] = 1; // H
+  ncf[49 * kd + 3] = 1; // O
+
+  // C3H8
+  ncf[50 * kd + 0] = 3; // C
+  ncf[50 * kd + 1] = 8; // H
+
+  // NC3H7
+  ncf[51 * kd + 0] = 3; // C
+  ncf[51 * kd + 1] = 7; // H
+
+  // H2CN
+  ncf[52 * kd + 0] = 1; // C
+  ncf[52 * kd + 1] = 2; // H
+  ncf[52 * kd + 2] = 1; // N
+
+  // CH3NO2
+  ncf[53 * kd + 0] = 1; // C
+  ncf[53 * kd + 1] = 3; // H
+  ncf[53 * kd + 2] = 1; // N
+  ncf[53 * kd + 3] = 2; // O
+
+  // NC3H7O2
+  ncf[54 * kd + 0] = 3; // C
+  ncf[54 * kd + 1] = 7; // H
+  ncf[54 * kd + 3] = 2; // O
+
+  // IC3H7
+  ncf[55 * kd + 0] = 3; // C
+  ncf[55 * kd + 1] = 7; // H
+
+  // C3H6
+  ncf[56 * kd + 0] = 3; // C
+  ncf[56 * kd + 1] = 6; // H
+
+  // C3H6OOH1-3
+  ncf[57 * kd + 0] = 3; // C
+  ncf[57 * kd + 1] = 7; // H
+  ncf[57 * kd + 3] = 2; // O
+
+  // C3H6OOH1-3O2
+  ncf[58 * kd + 0] = 3; // C
+  ncf[58 * kd + 1] = 7; // H
+  ncf[58 * kd + 3] = 4; // O
+
+  // OCHCH2CH2O
+  ncf[59 * kd + 0] = 3; // C
+  ncf[59 * kd + 1] = 5; // H
+  ncf[59 * kd + 3] = 2; // O
+
+  // C3KET13
+  ncf[60 * kd + 0] = 3; // C
+  ncf[60 * kd + 1] = 6; // H
+  ncf[60 * kd + 3] = 3; // O
+}
+
 //  inverse molecular weights
 #ifdef AMREX_USE_GPU
 AMREX_GPU_CONSTANT const amrex::Real global_imw[61] = {