AMReX-Combustion · esclapez · Aug 17, 2021 · Aug 17, 2021 · Aug 17, 2021 · Aug 17, 2021
diff --git a/Exec/RegTests/FlameSheet/GNUmakefile b/Exec/RegTests/FlameSheet/GNUmakefile
@@ -22,10 +22,8 @@ USE_HIP         = FALSE
 
 # PelePhysics
 Chemistry_Model = drm19
-Reactions_dir	 = Fuego
-Eos_dir			 = Fuego
-Transport_dir   = Simple
-
-USE_SUNDIALS_PP = TRUE
+Reactor_dir	 	= cvode
+Eos_Model		= Fuego
+Transport_Model = Simple
 
 include $(PELELMEX_HOME)/Utils/Make.PeleLMeX
diff --git a/Exec/RegTests/HotBubble/GNUmakefile b/Exec/RegTests/HotBubble/GNUmakefile
@@ -22,9 +22,9 @@ USE_HIP         = FALSE
 
 # PelePhysics
 Chemistry_Model = air
-Reactions_dir	 = Null
-Eos_dir			 = Fuego
-Transport_dir   = Constant
+Reactor_dir     = null
+Eos_Model       = Fuego
+Transport_Model = Constant
 
 USE_SUNDIALS_PP = TRUE
 

diff --git a/Exec/RegTests/HotBubble/pelelm_prob.cpp b/Exec/RegTests/HotBubble/pelelm_prob.cpp
@@ -11,4 +11,12 @@ void PeleLM::readProbParm()
    pp.query("T_bubble", prob_parm->T_bubble);
    pp.query("bubble_radius", prob_parm->bubble_rad);
    pp.query("bubble_y0", prob_parm->bubble_y0);
+
+   auto& trans_parm = PeleLM::trans_parms.host_trans_parm();
+   amrex::ParmParse pptr("transport");
+   pp.query("const_viscosity", trans_parm.const_viscosity);
+   pp.query("const_bulk_viscosity", trans_parm.const_bulk_viscosity);
+   pp.query("const_conductivity", trans_parm.const_conductivity);
+   pp.query("const_diffusivity", trans_parm.const_diffusivity);
+   PeleLM::trans_parms.sync_to_device();
 }
diff --git a/Exec/RegTests/PeriodicCases/GNUmakefile b/Exec/RegTests/PeriodicCases/GNUmakefile
@@ -8,7 +8,7 @@ PELE_PHYSICS_HOME  ?= ${TOP}/PelePhysics
 DIM             = 2
 DEBUG           = FALSE
 PRECISION       = DOUBLE
-VERBOSE         = FALSE
+VERBOSE         = TRUE
 TINY_PROFILE    = FALSE
 
 # Compilation
@@ -22,8 +22,8 @@ USE_HIP         = FALSE
 
 # PelePhysics
 Chemistry_Model = air
-Reactions_dir	 = Null
-Eos_dir			 = Fuego
-Transport_dir   = Constant
+Reactor_dir     = null
+Eos_Model       = Fuego
+Transport_Model = Constant
 
 include $(PELELMEX_HOME)/Utils/Make.PeleLMeX
diff --git a/Exec/RegTests/PeriodicCases/pelelm_prob.cpp b/Exec/RegTests/PeriodicCases/pelelm_prob.cpp
@@ -56,4 +56,12 @@ void PeleLM::readProbParm()
        amrex::Print() << " Unknown prob.type ! Should be ConvectedVortex, ConvectedGaussian or DiffusedGaussian \n";
        amrex::Abort();
    }
+
+   auto& trans_parm = PeleLM::trans_parms.host_trans_parm();
+   amrex::ParmParse pptr("transport");
+   pp.query("const_viscosity", trans_parm.const_viscosity);
+   pp.query("const_bulk_viscosity", trans_parm.const_bulk_viscosity);
+   pp.query("const_conductivity", trans_parm.const_conductivity);
+   pp.query("const_diffusivity", trans_parm.const_diffusivity);
+   PeleLM::trans_parms.sync_to_device();
 }
diff --git a/Source/PeleLM.H b/Source/PeleLM.H
@@ -10,6 +10,7 @@
 #include <AMReX_VisMF.H>
 
 #include <mechanism.H>
+#include "PelePhysics.H"
 #include <PeleLM_Index.H>
 #include <PeleLMDerive.H>
 #include <pelelm_prob_parm.H>
@@ -781,6 +782,10 @@ class PeleLM : public amrex::AmrCore {
    // Problem parameters
    std::unique_ptr<ProbParm> prob_parm;
 
+   // Transport pointer
+   pele::physics::transport::TransportParams<
+         pele::physics::PhysicsType::transport_type> trans_parms;
+
    // Linear solvers
    std::unique_ptr<DiffusionOp> m_diffusion_op;
    std::unique_ptr<DiffusionTensorOp> m_diffusionTensor_op;

diff --git a/Source/PeleLMEvolve.cpp b/Source/PeleLMEvolve.cpp
@@ -58,6 +58,9 @@ void PeleLM::Evolve() {
    if ( m_check_int > 0 && !chk_justDidIt ) {
       WriteCheckPointFile();
    }
+
+   // TODO: set a clean up function.
+   trans_parms.deallocate();
 
 }
 

diff --git a/Source/PeleLMPlot.cpp b/Source/PeleLMPlot.cpp
@@ -76,7 +76,7 @@ void PeleLM::WritePlotFile() {
    //----------------------------------------------------------------
    // Components names
    Vector<std::string> names;
-   pele::physics::eos::speciesNames(names);
+   pele::physics::eos::speciesNames<pele::physics::PhysicsType::eos_type>(names);
 
    Vector<std::string> plt_VarsName;
    plt_VarsName.push_back("x_velocity");

diff --git a/Source/PeleLMReactions.cpp b/Source/PeleLMReactions.cpp
@@ -1,6 +1,6 @@
 #include <PeleLM.H>
 #include <PeleLM_K.H>
-#include <reactor.h>
+#include <reactor.H>
 #ifdef PLM_USE_EFIELD
 #include <PeleLMEF_Constants.H>
 #endif
@@ -107,8 +107,8 @@ void PeleLM::advanceChemistry(int lev,
 
       Real dt_incr     = a_dt;
       Real time_chem   = 0;
-#ifdef AMREX_USE_GPU
       int reactor_type = 2;
+#ifdef AMREX_USE_GPU
       int tmp_fctCn = 0;
       tmp_fctCn = react(bx, rhoY_n, extF_rhoY, temp_n, rhon, extF_rhoH, fcl, mask_arr, 
                         dt_incr, time_chem, reactor_type, amrex::Gpu::gpuStream());
@@ -118,7 +118,7 @@ void PeleLM::advanceChemistry(int lev,
       /* Solve */
       int tmp_fctCn = 0;
       tmp_fctCn = react(bx, rhoY_n, extF_rhoY, temp_n, rhoH_n, extF_rhoH, fcl, mask_arr,
-                        dt_incr, time_chem);
+                        dt_incr, time_chem, reactor_type);
       dt_incr   = a_dt;
       time_chem = 0;
 #endif
@@ -288,8 +288,8 @@ void PeleLM::advanceChemistry(int lev,
 
          Real dt_incr     = a_dt;
          Real time_chem   = 0;
-#ifdef AMREX_USE_GPU
          int reactor_type = 2;
+#ifdef AMREX_USE_GPU
          int tmp_fctCn = 0;
          tmp_fctCn = react(bx, rhoY_o, extF_rhoY, temp_o, rhoH_o, extF_rhoH, fcl, mask_arr, 
                            dt_incr, time_chem, reactor_type, amrex::Gpu::gpuStream());
@@ -299,7 +299,7 @@ void PeleLM::advanceChemistry(int lev,
          /* Solve */
          int tmp_fctCn = 0;
          tmp_fctCn = react(bx, rhoY_o, extF_rhoY, temp_o, rhoH_o, extF_rhoH, fcl, mask_arr,
-                           dt_incr, time_chem);
+                           dt_incr, time_chem, reactor_type);
          dt_incr   = a_dt;
          time_chem = 0;
 #endif

diff --git a/Source/PeleLMSetup.cpp b/Source/PeleLMSetup.cpp
@@ -2,7 +2,7 @@
 #include <AMReX_ParmParse.H>
 #include <PeleLMDeriveFunc.H>
 #include "PelePhysics.H"
-#include <reactor.h>
+#include <reactor.H>
 #ifdef PLM_USE_EFIELD
 #include "EOS_Extension.H"
 #endif
@@ -34,8 +34,7 @@ void PeleLM::Setup() {
    // Initialize EOS and others
    if (!m_incompressible) {
       amrex::Print() << " Initialization of Transport ... \n";
-      pele::physics::transport::InitTransport<
-         pele::physics::PhysicsType::eos_type>()();
+      trans_parms.allocate();
       if (m_do_react) {
          int reactor_type = 2;
          int ncells_chem = 1;
@@ -332,7 +331,7 @@ void PeleLM::variablesSetup() {
       stateComponents.emplace_back(DENSITY,"density");
       Print() << " First species: " << FIRSTSPEC << "\n";
       Vector<std::string> names;
-      pele::physics::eos::speciesNames(names);
+      pele::physics::eos::speciesNames<pele::physics::PhysicsType::eos_type>(names);
       for (int n = 0; n < NUM_SPECIES; n++ ) {
          stateComponents.emplace_back(FIRSTSPEC+n,"rho.Y("+names[n]+")");
       }
@@ -406,7 +405,7 @@ void PeleLM::derivedSetup()
 
       // Get species names
       Vector<std::string> spec_names;
-      pele::physics::eos::speciesNames(spec_names);
+      pele::physics::eos::speciesNames<pele::physics::PhysicsType::eos_type>(spec_names);
 
       // Set species mass fractions
       Vector<std::string> var_names_massfrac(NUM_SPECIES);

diff --git a/Source/PeleLMTransportProp.cpp b/Source/PeleLMTransportProp.cpp
@@ -18,8 +18,7 @@ void PeleLM::calcViscosity(const TimeStamp &a_time) {
       } else {
 
          // Transport data pointer
-         pele::physics::transport::TransParm const* ltransparm =
-            pele::physics::transport::trans_parm_g;
+         auto const* ltransparm = trans_parms.device_trans_parm();
 
 #ifdef _OPENMP
 #pragma omp parallel if (Gpu::notInLaunchRegion())
@@ -49,8 +48,7 @@ void PeleLM::calcDiffusivity(const TimeStamp &a_time) {
       auto ldata_p = getLevelDataPtr(lev,a_time);
 
       // Transport data pointer
-      pele::physics::transport::TransParm const* ltransparm =
-         pele::physics::transport::trans_parm_g;
+      auto const* ltransparm = trans_parms.device_trans_parm();
 
 #ifdef _OPENMP
 #pragma omp parallel if (Gpu::notInLaunchRegion())

diff --git a/Source/PeleLM_K.H b/Source/PeleLM_K.H
@@ -13,7 +13,8 @@ getTransportCoeff(int i, int j, int k,
                   amrex::Array4<      amrex::Real> const& rhoDi,
                   amrex::Array4<      amrex::Real> const& lambda,
                   amrex::Array4<      amrex::Real> const& mu,
-                  pele::physics::transport::TransParm const* trans_parm) noexcept
+                  pele::physics::transport::TransParm<pele::physics::PhysicsType::eos_type,
+                                                      pele::physics::PhysicsType::transport_type> const* trans_parm) noexcept
 {
    using namespace amrex::literals;
 
@@ -65,7 +66,8 @@ getVelViscosity(int i, int j, int k,
                 amrex::Array4<const amrex::Real> const& rhoY,
                 amrex::Array4<      amrex::Real> const& T,
                 amrex::Array4<      amrex::Real> const& mu,
-                pele::physics::transport::TransParm const* trans_parm) noexcept
+                pele::physics::transport::TransParm<pele::physics::PhysicsType::eos_type,
+                                                    pele::physics::PhysicsType::transport_type> const* trans_parm) noexcept
 {
    using namespace amrex::literals;
 

diff --git a/Utils/Make.PeleLMeX b/Utils/Make.PeleLMeX
@@ -28,12 +28,52 @@ Blocs += $(foreach dir, $(LMdirs), $(PELELMEX_HOME)/$(dir))
 #---------------
 # PelePhysics sources
 #---------------
+# EOS models switches
+ifeq ($(Eos_Model),$(filter $(Eos_Model),GammaLaw))
+   DEFINES += -DUSE_GAMMALAW_EOS
+endif
+ifeq ($(Eos_Model),$(filter $(Eos_Model),Fuego))
+   DEFINES += -DUSE_FUEGO_EOS
+endif
+ifeq ($(Eos_Model),$(filter $(Eos_Model),Soave-Redlich-Kwong))
+   DEFINES += -DUSE_SRK_EOS
+endif
+
+# Transport model switches
+ifeq ($(Transport_Model), Simple)
+  DEFINES += -DUSE_SIMPLE_TRANSPORT
+endif
+ifeq ($(Transport_Model), EGLib)
+  DEFINES += -DEGLIB_TRANSPORT
+  USE_FUEGO = TRUE
+endif
+ifeq ($(Transport_Model), Constant)
+  DEFINES += -DUSE_CONSTANT_TRANSPORT
+endif
+ifeq ($(Transport_Model), Sutherland)
+  DEFINES += -DUSE_SUTHERLAND_TRANSPORT
+endif
+
+# Reactor model switches
+ifeq ($(Reactor_dir), arkode)
+    USE_SUNDIALS_PP = TRUE
+    USE_ARKODE_PP = TRUE
+    ReacDirs  = Reactions Reactions/$(strip $(Reactor_dir))
+endif
+ifeq ($(Reactor_dir), cvode)
+    USE_SUNDIALS_PP = TRUE
+    USE_CVODE_PP = TRUE
+    USE_KLU_PP ?= FALSE
+    DEFINES += -DCOMPILE_JACOBIAN
+    ReacDirs  = Reactions Reactions/$(strip $(Reactor_dir))
+endif
+ifeq ($(Reactor_dir), null)
+    ReacDirs  = Reactions/$(strip $(Reactor_dir))
+endif
+
 ChemDir  = Support/Fuego/Mechanism/Models/$(Chemistry_Model)
-ReacDir  = Reactions/$(strip $(Reactions_dir))
-EosDir   = Eos/$(strip $(Eos_dir))
-TranDir  = Transport/$(strip $(Transport_dir))
 
-PPdirs  := Utility Source $(ChemDir) $(ReacDir) $(EosDir) $(TranDir)
+PPdirs  := Utility Source $(ChemDir) $(ReacDirs) Eos Transport
 PPHdirs := Support/Fuego/Evaluation
 Bpack += $(foreach dir, $(PPdirs), $(PELE_PHYSICS_HOME)/$(dir)/Make.package)
 Blocs += $(foreach dir, $(PPdirs), $(PELE_PHYSICS_HOME)/$(dir))
@@ -90,13 +130,13 @@ print-%::
 #---------------
 ifeq ($(USE_SUNDIALS_PP),TRUE)
   TPL:
-	cd $(PELE_PHYSICS_HOME)/ThirdParty; make AMREX_HOME=$(AMREX_HOME) USE_CUDA=$(USE_CUDA) USE_KLU=$(USE_KLU_PP) DEBUG=$(DEBUG) COMP=$(COMP) NVCC=$(COMP)
+	cd $(PELE_PHYSICS_HOME)/ThirdParty; make AMREX_HOME=$(AMREX_HOME) USE_CUDA=$(USE_CUDA) USE_KLU_PP=$(USE_KLU_PP) DEBUG=$(DEBUG) COMP=$(COMP) NVCC=$(COMP)
 
   TPLclean:
-	cd $(PELE_PHYSICS_HOME)/ThirdParty; make AMREX_HOME=$(AMREX_HOME) USE_CUDA=$(USE_CUDA) USE_KLU=$(USE_KLU_PP) DEBUG=$(DEBUG) COMP=$(HOSTCC) NVCC=$(COMP) clean
+	cd $(PELE_PHYSICS_HOME)/ThirdParty; make AMREX_HOME=$(AMREX_HOME) USE_CUDA=$(USE_CUDA) USE_KLU_PP=$(USE_KLU_PP) DEBUG=$(DEBUG) COMP=$(HOSTCC) NVCC=$(COMP) clean
 
   TPLrealclean:
-	cd $(PELE_PHYSICS_HOME)/ThirdParty; make AMREX_HOME=$(AMREX_HOME) USE_CUDA=$(USE_CUDA) USE_KLU=$(USE_KLU_PP) DEBUG=$(DEBUG) COMP=$(HOSTCC) NVCC=$(COMP) realclean
+	cd $(PELE_PHYSICS_HOME)/ThirdParty; make AMREX_HOME=$(AMREX_HOME) USE_CUDA=$(USE_CUDA) USE_KLU_PP=$(USE_KLU_PP) DEBUG=$(DEBUG) COMP=$(HOSTCC) NVCC=$(COMP) realclean
 else
   TPL:
   TPLclean: