with PelePhys, use NUM_SPECIES from PelePhys as MAX_SPECIES during

COMPILE time

Author: isriva

src_common/common_namespace.H

@@ -1,3 +1,6 @@
+#if defined(PELEPHYSICS)
+#include "mechanism.H"
+#endif
 namespace common {
 
 //////////////
@@ -7,6 +10,11 @@ namespace common {
 #define MAX_BONDS 12
 //////////////
 
+/// MAX_SPECIES and NUM_SPECIES consistency between PELEPHYSICS and FHD /////
+#if defined(PELEPHYSICS)
+#define MAX_SPECIES (NUM_SPECIES)
+#endif
+
     // misc global variables
     extern amrex::IntVect nodal_flag;
     extern amrex::Vector<amrex::IntVect> nodal_flag_dir;
@@ -326,4 +334,4 @@ namespace common {
     extern AMREX_GPU_MANAGED amrex::Real turb_alpha;
     extern AMREX_GPU_MANAGED int         turbForcing;
 
-}
+}

src_compressible/compressible_namespace.H

@@ -10,6 +10,7 @@ namespace compressible {
     extern AMREX_GPU_MANAGED int turbRestartRun;
     extern AMREX_GPU_MANAGED bool do_reservoir;
     extern AMREX_GPU_MANAGED amrex::Real zeta_ratio;
+    extern AMREX_GPU_MANAGED amrex::Real p_init;
 
 }
 

src_compressible_stag/main_driver.cpp

@@ -84,12 +84,26 @@ void main_driver(const char* argv)
     }
 #endif
 
-    int step_start, statsCount;
-    amrex::Real time;
+#if defined(PELEPHYSICS)
+    // Set nspecies = MAX_SPECIES
+    nspecies = int(MAX_SPECIES);
+    nvars = AMREX_SPACEDIM + 2 + nspecies;
+    nprimvars = AMREX_SPACEDIM + 3 + 2*nspecies;
+
+    // Set molmass
+    for (int i=0; i<MAX_SPECIES; ++i) {
+        molmass[i] = h_global_mw[i];
+    }
 
+    amrex::Print() << "starting simulation with " << nspecies <<  "\n";
+#else
     // if gas heat capacities in the namelist are negative, calculate them using using dofs.
     // This will only update the Fortran values.
     GetHcGas();
+#endif
+    
+    int step_start, statsCount;
+    amrex::Real time;
 
     // check bc_vel_lo/hi to determine the periodicity
     Vector<int> is_periodic(AMREX_SPACEDIM,0);  // set to 0 (not periodic) by default
@@ -771,6 +785,13 @@ void main_driver(const char* argv)
         //}
         conservedToPrimitiveStag(prim, vel, cu, cumom);
 
+        // get transport coefficients
+#if defined(PELEPHYSICS)
+            calculateTransportCoeffs(prim, eta, zeta, kappa, chi, D, trans_parms);
+#else
+            calculateTransportCoeffs(prim, eta, zeta, kappa, chi, D);
+#endif
+
         if (n_ads_spec>0) {
             init_surfcov(surfcov, geom);
         }