Surface Chemistry - Modified mechanism.H preprocessor directives & me…

…chanism.cpp reaction maps (#473) #### This work was performed at the [FLAME](https://flamelab-iisc.github.io/) Lab headed by [Dr. Konduri Aditya](http://cds.iisc.ac.in/faculty/konduriadi/) at [CDS, IISc Bengaluru](https://cds.iisc.ac.in/) with funding from Shell India Markets Pvt. Ltd. and periodic reviews from the Fluid Flow and Reaction Engineering Group at Shell Technology Center Bengaluru. Co-authored-by: Marc Henry de Frahan <[email protected]>
AMReX-Combustion · Feb 9, 2024 · de505b3 · de505b3
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diff --git a/Docs/sphinx/Ceptr.rst b/Docs/sphinx/Ceptr.rst
@@ -27,11 +27,28 @@ Generating for a single chemistry
 
 There are three ways to use CEPTR to generate C++ mechanism files for a given chemistry
 
-1. Using CEPTR directly::
+1. Using CEPTR directly:
+
+   Executed from the ``${PELE_PHYSICS_HOME}/Support/ceptr`` directory, the most general usage of CEPTR is::
+
+     $ poetry run convert -f ${PELEPHYSICS_HOME}/Mechanisms/${chemistry}/mechanism.yaml \
+       --chemistry {chemistry-type} \
+       --gas_name {gas-name} \
+       --interface_name {interface-name}
+
+   The ``--chemistry``, or equivalently ``-c``,  argument allows users to convey if the ``${chemistry}`` of interest is either one of two valid options, namely, ``homogeneous`` or ``heterogeneous``.
+   Similarly, the ``--gas_name`` and ``--interface_name`` arguments allow users to specify the names of the homogeneous phase and gas-solid interface prescribed in the corresponding ``mechanism.yaml`` file.
+
+   The default ``chemistry-type``, ``gas-name`` are ``homogeneous`` and ``gas`` respectively while that for ``interface-name`` is ``None``.
+   Note that if a ``heterogeneous`` ``chemistry-type`` is specified, the user must necessarily specify a corresponding ``interface-name``.
+
+   An example of directly using CEPTR for homogeneous mechanisms is::
 
      $ cd ${PELE_PHYSICS_HOME}/Support/ceptr
      $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/LiDryer/mechanism.yaml
 
+   .. note:: CEPTR interpretations of heterogeneous mechanisms is currently a work in progress.
+
 2. Using a helper script in the directory containing the ``mechanism.yaml`` file::
 
      $ ./convert.sh

diff --git a/Mechanisms/Aromatic_KrNara/mechanism.H b/Mechanisms/Aromatic_KrNara/mechanism.H
@@ -172,10 +172,21 @@
 #define OC6H4O_ID 156
 #define N2_ID 157
 
-#define NUM_ELEMENTS 5
-#define NUM_SPECIES 158
+#define NUM_GAS_ELEMENTS 5     // Elements in the homogeneous phase
+#define NUM_GAS_SPECIES 158    // Species in the homogeneous phase
+#define NUM_GAS_REACTIONS 1049 // Reactions in the homogeneous phase
+
+#define SITE_DENSITY 0.000000E+00 // mol/cm^2
+
+#define NUM_SURFACE_ELEMENTS 0  // Additional elements in heterogeneous phase
+#define NUM_SURFACE_SPECIES 0   // Species in the heterogeneous phase
+#define NUM_SURFACE_REACTIONS 0 // Reactions in the heterogeneous phase
+
+#define NUM_ELEMENTS (NUM_GAS_ELEMENTS + NUM_SURFACE_ELEMENTS)
+#define NUM_SPECIES (NUM_GAS_SPECIES + NUM_SURFACE_SPECIES)
+#define NUM_REACTIONS (NUM_GAS_REACTIONS + NUM_SURFACE_REACTIONS)
+
 #define NUM_IONS 7
-#define NUM_REACTIONS 1049
 
 #define NUM_FIT 4
 
@@ -186439,7 +186450,7 @@ egtransetCOFD(amrex::Real* COFD)
   COFD[33806] = -4.21537415E-01;
   COFD[33807] = 1.63630500E-02;
   COFD[33808] = -2.25933772E+01;
-  COFD[33809] = 5.42562555E+00;
+  COFD[33809] = 5.42562556E+00;
   COFD[33810] = -4.48132861E-01;
   COFD[33811] = 1.77847329E-02;
   COFD[33812] = -2.24804061E+01;
@@ -202139,7 +202150,7 @@ egtransetCOFD(amrex::Real* COFD)
   COFD[49506] = -4.91225485E-01;
   COFD[49507] = 2.04057002E-02;
   COFD[49508] = -2.25933772E+01;
-  COFD[49509] = 5.42562555E+00;
+  COFD[49509] = 5.42562556E+00;
   COFD[49510] = -4.48132861E-01;
   COFD[49511] = 1.77847329E-02;
   COFD[49512] = -2.27399898E+01;
@@ -221355,19 +221366,19 @@ egtransetCOFD(amrex::Real* COFD)
   COFD[68722] = 3.67306611E-01;
   COFD[68723] = -2.15544181E-02;
   COFD[68724] = -1.25531803E+01;
-  COFD[68725] = -2.57908185E-02;
+  COFD[68725] = -2.57908186E-02;
   COFD[68726] = 3.65103624E-01;
   COFD[68727] = -2.14528891E-02;
   COFD[68728] = -1.25520156E+01;
-  COFD[68729] = -2.57908185E-02;
+  COFD[68729] = -2.57908186E-02;
   COFD[68730] = 3.65103624E-01;
   COFD[68731] = -2.14528891E-02;
   COFD[68732] = -1.25785265E+01;
-  COFD[68733] = -2.57908185E-02;
+  COFD[68733] = -2.57908186E-02;
   COFD[68734] = 3.65103624E-01;
   COFD[68735] = -2.14528891E-02;
   COFD[68736] = -1.25531803E+01;
-  COFD[68737] = -2.57908185E-02;
+  COFD[68737] = -2.57908186E-02;
   COFD[68738] = 3.65103624E-01;
   COFD[68739] = -2.14528891E-02;
   COFD[68740] = -1.91904086E+01;
@@ -221987,19 +221998,19 @@ egtransetCOFD(amrex::Real* COFD)
   COFD[69354] = 3.67306611E-01;
   COFD[69355] = -2.15544181E-02;
   COFD[69356] = -1.25516454E+01;
-  COFD[69357] = -2.57908185E-02;
+  COFD[69357] = -2.57908186E-02;
   COFD[69358] = 3.65103624E-01;
   COFD[69359] = -2.14528891E-02;
   COFD[69360] = -1.25504843E+01;
-  COFD[69361] = -2.57908185E-02;
+  COFD[69361] = -2.57908186E-02;
   COFD[69362] = 3.65103624E-01;
   COFD[69363] = -2.14528891E-02;
   COFD[69364] = -1.25769119E+01;
-  COFD[69365] = -2.57908185E-02;
+  COFD[69365] = -2.57908186E-02;
   COFD[69366] = 3.65103624E-01;
   COFD[69367] = -2.14528891E-02;
   COFD[69368] = -1.25516454E+01;
-  COFD[69369] = -2.57908185E-02;
+  COFD[69369] = -2.57908186E-02;
   COFD[69370] = 3.65103624E-01;
   COFD[69371] = -2.14528891E-02;
   COFD[69372] = -1.91896245E+01;
@@ -227007,11 +227018,11 @@ egtransetCOFD(amrex::Real* COFD)
   COFD[74374] = 3.64334842E-01;
   COFD[74375] = -2.14173756E-02;
   COFD[74376] = -1.25531803E+01;
-  COFD[74377] = -2.57908185E-02;
+  COFD[74377] = -2.57908186E-02;
   COFD[74378] = 3.65103624E-01;
   COFD[74379] = -2.14528891E-02;
   COFD[74380] = -1.25516454E+01;
-  COFD[74381] = -2.57908185E-02;
+  COFD[74381] = -2.57908186E-02;
   COFD[74382] = 3.65103624E-01;
   COFD[74383] = -2.14528891E-02;
   COFD[74384] = -1.38292265E+01;
@@ -227639,11 +227650,11 @@ egtransetCOFD(amrex::Real* COFD)
   COFD[75006] = 3.64334842E-01;
   COFD[75007] = -2.14173756E-02;
   COFD[75008] = -1.25520156E+01;
-  COFD[75009] = -2.57908185E-02;
+  COFD[75009] = -2.57908186E-02;
   COFD[75010] = 3.65103624E-01;
   COFD[75011] = -2.14528891E-02;
   COFD[75012] = -1.25504843E+01;
-  COFD[75013] = -2.57908185E-02;
+  COFD[75013] = -2.57908186E-02;
   COFD[75014] = 3.65103624E-01;
   COFD[75015] = -2.14528891E-02;
   COFD[75016] = -1.38281442E+01;
@@ -228271,11 +228282,11 @@ egtransetCOFD(amrex::Real* COFD)
   COFD[75638] = 3.64334842E-01;
   COFD[75639] = -2.14173756E-02;
   COFD[75640] = -1.25785265E+01;
-  COFD[75641] = -2.57908185E-02;
+  COFD[75641] = -2.57908186E-02;
   COFD[75642] = 3.65103624E-01;
   COFD[75643] = -2.14528891E-02;
   COFD[75644] = -1.25769119E+01;
-  COFD[75645] = -2.57908185E-02;
+  COFD[75645] = -2.57908186E-02;
   COFD[75646] = 3.65103624E-01;
   COFD[75647] = -2.14528891E-02;
   COFD[75648] = -1.38527338E+01;
@@ -228903,11 +228914,11 @@ egtransetCOFD(amrex::Real* COFD)
   COFD[76270] = 3.64334842E-01;
   COFD[76271] = -2.14173756E-02;
   COFD[76272] = -1.25531803E+01;
-  COFD[76273] = -2.57908185E-02;
+  COFD[76273] = -2.57908186E-02;
   COFD[76274] = 3.65103624E-01;
   COFD[76275] = -2.14528891E-02;
   COFD[76276] = -1.25516454E+01;
-  COFD[76277] = -2.57908185E-02;
+  COFD[76277] = -2.57908186E-02;
   COFD[76278] = 3.65103624E-01;
   COFD[76279] = -2.14528891E-02;
   COFD[76280] = -1.38292265E+01;

diff --git a/Mechanisms/Aromatic_KrNara/mechanism.cpp b/Mechanisms/Aromatic_KrNara/mechanism.cpp
@@ -1,5 +1,5 @@
 #include "mechanism.H"
-const int rmap[1049] = {
+const int rmap[NUM_REACTIONS] = {
   11,   13,   26,   44,   47,   49,   50,   51,   61,   74,   80,   81,   88,
   91,   97,   112,  120,  141,  152,  166,  191,  192,  200,  201,  209,  210,
   217,  220,  280,  391,  430,  823,  989,  4,    5,    6,    7,    8,    9,
@@ -86,7 +86,7 @@ const int rmap[1049] = {
 void
 GET_RMAP(int* _rmap)
 {
-  for (int j = 0; j < 1049; ++j) {
+  for (int j = 0; j < NUM_REACTIONS; ++j) {
     _rmap[j] = rmap[j];
   }
 }

diff --git a/Mechanisms/BurkeDryer/mechanism.H b/Mechanisms/BurkeDryer/mechanism.H
@@ -28,10 +28,21 @@
 #define CO_ID 11
 #define CO2_ID 12
 
-#define NUM_ELEMENTS 6
-#define NUM_SPECIES 13
+#define NUM_GAS_ELEMENTS 6   // Elements in the homogeneous phase
+#define NUM_GAS_SPECIES 13   // Species in the homogeneous phase
+#define NUM_GAS_REACTIONS 27 // Reactions in the homogeneous phase
+
+#define SITE_DENSITY 0.000000E+00 // mol/cm^2
+
+#define NUM_SURFACE_ELEMENTS 0  // Additional elements in heterogeneous phase
+#define NUM_SURFACE_SPECIES 0   // Species in the heterogeneous phase
+#define NUM_SURFACE_REACTIONS 0 // Reactions in the heterogeneous phase
+
+#define NUM_ELEMENTS (NUM_GAS_ELEMENTS + NUM_SURFACE_ELEMENTS)
+#define NUM_SPECIES (NUM_GAS_SPECIES + NUM_SURFACE_SPECIES)
+#define NUM_REACTIONS (NUM_GAS_REACTIONS + NUM_SURFACE_REACTIONS)
+
 #define NUM_IONS 0
-#define NUM_REACTIONS 27
 
 #define NUM_FIT 4
 

diff --git a/Mechanisms/BurkeDryer/mechanism.cpp b/Mechanisms/BurkeDryer/mechanism.cpp
@@ -1,12 +1,13 @@
 #include "mechanism.H"
-const int rmap[27] = {14, 21, 5,  6,  7,  8,  9,  10, 11, 12, 13, 0,  1, 2,
-                      3,  4,  15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26};
+const int rmap[NUM_REACTIONS] = {14, 21, 5,  6,  7,  8,  9,  10, 11,
+                                 12, 13, 0,  1,  2,  3,  4,  15, 16,
+                                 17, 18, 19, 20, 22, 23, 24, 25, 26};
 
 // Returns 0-based map of reaction order
 void
 GET_RMAP(int* _rmap)
 {
-  for (int j = 0; j < 27; ++j) {
+  for (int j = 0; j < NUM_REACTIONS; ++j) {
     _rmap[j] = rmap[j];
   }
 }

diff --git a/Mechanisms/C1-C2-NO/mechanism.H b/Mechanisms/C1-C2-NO/mechanism.H
@@ -58,10 +58,21 @@
 #define NCO_ID 42
 #define CH3O2_ID 43
 
-#define NUM_ELEMENTS 5
-#define NUM_SPECIES 44
+#define NUM_GAS_ELEMENTS 5    // Elements in the homogeneous phase
+#define NUM_GAS_SPECIES 44    // Species in the homogeneous phase
+#define NUM_GAS_REACTIONS 269 // Reactions in the homogeneous phase
+
+#define SITE_DENSITY 0.000000E+00 // mol/cm^2
+
+#define NUM_SURFACE_ELEMENTS 0  // Additional elements in heterogeneous phase
+#define NUM_SURFACE_SPECIES 0   // Species in the heterogeneous phase
+#define NUM_SURFACE_REACTIONS 0 // Reactions in the heterogeneous phase
+
+#define NUM_ELEMENTS (NUM_GAS_ELEMENTS + NUM_SURFACE_ELEMENTS)
+#define NUM_SPECIES (NUM_GAS_SPECIES + NUM_SURFACE_SPECIES)
+#define NUM_REACTIONS (NUM_GAS_REACTIONS + NUM_SURFACE_REACTIONS)
+
 #define NUM_IONS 0
-#define NUM_REACTIONS 269
 
 #define NUM_FIT 4
 

diff --git a/Mechanisms/C1-C2-NO/mechanism.cpp b/Mechanisms/C1-C2-NO/mechanism.cpp
@@ -1,5 +1,5 @@
 #include "mechanism.H"
-const int rmap[269] = {
+const int rmap[NUM_REACTIONS] = {
   11,  13,  41,  50,  52,  53,  61,  73,  78,  85,  87,  101, 104, 128, 139,
   145, 158, 172, 173, 188, 196, 203, 213, 220, 222, 29,  127, 4,   5,   6,
   7,   8,   9,   10,  38,  39,  245, 252, 0,   1,   2,   3,   12,  14,  15,
@@ -23,7 +23,7 @@ const int rmap[269] = {
 void
 GET_RMAP(int* _rmap)
 {
-  for (int j = 0; j < 269; ++j) {
+  for (int j = 0; j < NUM_REACTIONS; ++j) {
     _rmap[j] = rmap[j];
   }
 }

diff --git a/Mechanisms/C1-C2-NO_qss/mechanism.H b/Mechanisms/C1-C2-NO_qss/mechanism.H
@@ -53,10 +53,21 @@
 #define NCO_ID 37
 #define CH3O2_ID 38
 
-#define NUM_ELEMENTS 5
-#define NUM_SPECIES 39
+#define NUM_GAS_ELEMENTS 5      // Elements in the homogeneous phase
+#define NUM_QSSA_GAS_SPECIES 39 // Species in the homogeneous phase
+#define NUM_GAS_REACTIONS 269   // Reactions in the homogeneous phase
+
+#define SITE_DENSITY 0.000000E+00 // mol/cm^2
+
+#define NUM_SURFACE_ELEMENTS 0  // Additional elements in heterogeneous phase
+#define NUM_SURFACE_SPECIES 0   // Species in the heterogeneous phase
+#define NUM_SURFACE_REACTIONS 0 // Reactions in the heterogeneous phase
+
+#define NUM_ELEMENTS (NUM_GAS_ELEMENTS + NUM_SURFACE_ELEMENTS)
+#define NUM_SPECIES (NUM_QSSA_GAS_SPECIES + NUM_SURFACE_SPECIES)
+#define NUM_REACTIONS (NUM_GAS_REACTIONS + NUM_SURFACE_REACTIONS)
+
 #define NUM_IONS 0
-#define NUM_REACTIONS 269
 
 #define NUM_FIT 4
 

diff --git a/Mechanisms/C1-C2-NO_qss/mechanism.cpp b/Mechanisms/C1-C2-NO_qss/mechanism.cpp
@@ -1,5 +1,5 @@
 #include "mechanism.H"
-const int rmap[269] = {
+const int rmap[NUM_REACTIONS] = {
   0,   1,   2,   3,   4,   5,   6,   7,   8,   9,   10,  11,  12,  13,  14,
   15,  16,  17,  18,  19,  20,  21,  22,  23,  24,  25,  26,  27,  28,  29,
   30,  31,  32,  33,  34,  35,  36,  37,  38,  39,  40,  41,  42,  43,  44,
@@ -23,7 +23,7 @@ const int rmap[269] = {
 void
 GET_RMAP(int* _rmap)
 {
-  for (int j = 0; j < 269; ++j) {
+  for (int j = 0; j < NUM_REACTIONS; ++j) {
     _rmap[j] = rmap[j];
   }
 }

diff --git a/Mechanisms/CH4_lean/mechanism.H b/Mechanisms/CH4_lean/mechanism.H
@@ -21,7 +21,7 @@
 #define H2O_ID 5
 #define HO2_ID 6
 #define CH2_ID 7
-#define CH2S_ID 8
+#define CH2_S_ID 8
 #define CH3_ID 9
 #define CH4_ID 10
 #define CO_ID 11
@@ -31,10 +31,21 @@
 #define CH2OH_ID 15
 #define N2_ID 16
 
-#define NUM_ELEMENTS 5
-#define NUM_SPECIES 17
+#define NUM_GAS_ELEMENTS 5   // Elements in the homogeneous phase
+#define NUM_GAS_SPECIES 17   // Species in the homogeneous phase
+#define NUM_GAS_REACTIONS 73 // Reactions in the homogeneous phase
+
+#define SITE_DENSITY 0.000000E+00 // mol/cm^2
+
+#define NUM_SURFACE_ELEMENTS 0  // Additional elements in heterogeneous phase
+#define NUM_SURFACE_SPECIES 0   // Species in the heterogeneous phase
+#define NUM_SURFACE_REACTIONS 0 // Reactions in the heterogeneous phase
+
+#define NUM_ELEMENTS (NUM_GAS_ELEMENTS + NUM_SURFACE_ELEMENTS)
+#define NUM_SPECIES (NUM_GAS_SPECIES + NUM_SURFACE_SPECIES)
+#define NUM_REACTIONS (NUM_GAS_REACTIONS + NUM_SURFACE_REACTIONS)
+
 #define NUM_IONS 0
-#define NUM_REACTIONS 73
 
 #define NUM_FIT 4
 
@@ -14184,7 +14195,7 @@ egtransetCOFD(amrex::Real* COFD)
   COFD[805] = 5.11785645E+00;
   COFD[806] = -4.37867828E-01;
   COFD[807] = 1.85047543E-02;
-  COFD[808] = -1.99343635E+01;
+  COFD[808] = -1.99343636E+01;
   COFD[809] = 4.99746595E+00;
   COFD[810] = -4.23838963E-01;
   COFD[811] = 1.79592094E-02;
@@ -14440,7 +14451,7 @@ egtransetCOFD(amrex::Real* COFD)
   COFD[1061] = 5.35659323E+00;
   COFD[1062] = -4.62684013E-01;
   COFD[1063] = 1.93375283E-02;
-  COFD[1064] = -1.99343635E+01;
+  COFD[1064] = -1.99343636E+01;
   COFD[1065] = 4.99746595E+00;
   COFD[1066] = -4.23838963E-01;
   COFD[1067] = 1.79592094E-02;

diff --git a/Mechanisms/CH4_lean/mechanism.cpp b/Mechanisms/CH4_lean/mechanism.cpp
@@ -1,5 +1,5 @@
 #include "mechanism.H"
-const int rmap[73] = {
+const int rmap[NUM_REACTIONS] = {
   28, 29, 31, 33, 38, 0,  1,  8,  15, 16, 17, 18, 20, 21, 22, 23, 24, 69, 70,
   2,  3,  4,  5,  6,  7,  9,  10, 11, 12, 13, 14, 19, 25, 26, 27, 30, 32, 34,
   35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
@@ -9,7 +9,7 @@ const int rmap[73] = {
 void
 GET_RMAP(int* _rmap)
 {
-  for (int j = 0; j < 73; ++j) {
+  for (int j = 0; j < NUM_REACTIONS; ++j) {
     _rmap[j] = rmap[j];
   }
 }