updates needed for peleparams for PMF and transport

Exec/RegTests/EB_EnclosedVortex/pelelmex_prob.cpp

@@ -14,7 +14,7 @@ PeleLM::readProbParm() // NOLINT(readability-make-member-function-const)
   pp.query("forcevort", PeleLM::prob_parm->forcevort);
 
   if (m_incompressible == 0) {
-    auto& trans_parm = PeleLM::trans_parms.host_trans_parm();
+    auto& trans_parm = PeleLM::trans_parms.host_parm();
     amrex::ParmParse pptr("transport");
     pp.query("const_viscosity", trans_parm.const_viscosity);
     pp.query("const_bulk_viscosity", trans_parm.const_bulk_viscosity);

Exec/RegTests/EB_FlowPastCylinder/pelelmex_prob.cpp

@@ -12,7 +12,7 @@ PeleLM::readProbParm() // NOLINT(readability-make-member-function-const)
   pp.query("meanFlowMag", prob_parm->meanFlowMag);
 
   // if (!m_incompressible) {
-  //    auto& trans_parm = PeleLM::trans_parms.host_trans_parm();
+  //    auto& trans_parm = PeleLM::trans_parms.host_parm();
   //    amrex::ParmParse pptr("transport");
   //    pp.query("const_viscosity", trans_parm.const_viscosity);
   //    pp.query("const_bulk_viscosity", trans_parm.const_bulk_viscosity);

Exec/RegTests/EB_PipeFlow/pelelmex_prob.cpp

@@ -15,7 +15,7 @@ PeleLM::readProbParm() // NOLINT(readability-make-member-function-const)
 
   /*
   if (!m_incompressible) {
-     auto& trans_parm = PeleLM::trans_parms.host_trans_parm();
+     auto& trans_parm = PeleLM::trans_parms.host_parm();
      amrex::ParmParse pptr("transport");
      pp.query("const_viscosity", trans_parm.const_viscosity);
      pp.query("const_bulk_viscosity", trans_parm.const_bulk_viscosity);

Exec/RegTests/HotBubble/pelelmex_prob.cpp

@@ -14,7 +14,7 @@ PeleLM::readProbParm() // NOLINT(readability-make-member-function-const)
   pp.query("use_symmetry", prob_parm->is_sym);
   pp.query("use_mix_bubble", prob_parm->bubble_is_mix);
 
-  auto& trans_parm = PeleLM::trans_parms.host_trans_parm();
+  auto& trans_parm = PeleLM::trans_parms.host_parm();
   amrex::ParmParse pptr("transport");
   pp.query("const_viscosity", trans_parm.const_viscosity);
   pp.query("const_bulk_viscosity", trans_parm.const_bulk_viscosity);

Exec/RegTests/PeriodicCases/pelelmex_prob.cpp

@@ -81,7 +81,7 @@ PeleLM::readProbParm() // NOLINT(readability-make-member-function-const)
   }
 
   if (m_incompressible == 0) {
-    auto& trans_parm = PeleLM::trans_parms.host_trans_parm();
+    auto& trans_parm = PeleLM::trans_parms.host_parm();
     amrex::ParmParse pptr("transport");
     pp.query("const_viscosity", trans_parm.const_viscosity);
     pp.query("const_bulk_viscosity", trans_parm.const_bulk_viscosity);

Exec/RegTests/TaylorGreen/pelelmex_prob.cpp

@@ -37,7 +37,7 @@ PeleLM::readProbParm() // NOLINT(readability-make-member-function-const)
   // Transport
   amrex::Real cpmix_cgs;
   eos.TY2Cp(prob_parm->T_mean, massfrac, cpmix_cgs);
-  auto& trans_parm = PeleLM::trans_parms.host_trans_parm();
+  auto& trans_parm = PeleLM::trans_parms.host_parm();
   trans_parm.const_bulk_viscosity = 0.0;
   trans_parm.const_diffusivity = 0.0;
   trans_parm.const_viscosity =

Exec/RegTests/TurbInflow/pelelmex_prob.cpp

@@ -14,7 +14,7 @@ PeleLM::readProbParm() // NOLINT(readability-make-member-function-const)
 
   /*
   if (!m_incompressible) {
-     auto& trans_parm = PeleLM::trans_parms.host_trans_parm();
+     auto& trans_parm = PeleLM::trans_parms.host_parm();
      amrex::ParmParse pptr("transport");
      pp.query("const_viscosity", trans_parm.const_viscosity);
      pp.query("const_bulk_viscosity", trans_parm.const_bulk_viscosity);

Source/Efield/PeleLMeX_EFUtils.cpp

@@ -290,8 +290,7 @@ void
 PeleLM::fillPatchNLnE(Real a_time, Vector<MultiFab*> const& a_nE, int a_nGrow)
 {
   ProbParm const* lprobparm = prob_parm_d;
-  pele::physics::PMF::PmfData::DataContainer const* lpmfdata =
-    pmf_data.getDeviceData();
+  auto const* lpmfdata = pmf_data.device_parm();
 
   int lev = 0;
   {
@@ -324,8 +323,7 @@ PeleLM::fillPatchNLphiV(
   Real a_time, Vector<MultiFab*> const& a_phiV, int a_nGrow)
 {
   ProbParm const* lprobparm = prob_parm_d;
-  pele::physics::PMF::PmfData::DataContainer const* lpmfdata =
-    pmf_data.getDeviceData();
+  auto const* lpmfdata = pmf_data.device_parm();
 
   int lev = 0;
   {

Source/PeleLMeX.H

@@ -1742,11 +1742,13 @@ public:
   amrex::Vector<amrex::Real> m_ctrl_cntl_pts;
 
   // PMF parameters
-  pele::physics::PMF::PmfData pmf_data;
+  pele::physics::PeleParams<pele::physics::PMF::PmfData::DataContainer>
+    pmf_data;
 
   // Transport pointer
-  static pele::physics::transport::TransportParams<
-    pele::physics::PhysicsType::transport_type>
+  static pele::physics::PeleParams<pele::physics::transport::TransParm<
+    pele::physics::PhysicsType::eos_type,
+    pele::physics::PhysicsType::transport_type>>
     trans_parms;
 
   // Reactor pointer

Source/PeleLMeX.cpp

@@ -7,8 +7,9 @@
 
 using namespace amrex;
 
-pele::physics::transport::TransportParams<
-  pele::physics::PhysicsType::transport_type>
+pele::physics::PeleParams<pele::physics::transport::TransParm<
+  pele::physics::PhysicsType::eos_type,
+  pele::physics::PhysicsType::transport_type>>
   PeleLM::trans_parms;
 
 PeleLM::PeleLM() = default;

Source/PeleLMeX_BC.cpp

@@ -349,8 +349,7 @@ PeleLM::fillpatch_state(
   int lev, const amrex::Real a_time, amrex::MultiFab& a_state, int nGhost)
 {
   ProbParm const* lprobparm = prob_parm_d;
-  pele::physics::PMF::PmfData::DataContainer const* lpmfdata =
-    pmf_data.getDeviceData();
+  auto const* lpmfdata = pmf_data.device_parm();
 
   int nCompState = (m_incompressible) != 0 ? AMREX_SPACEDIM : NVAR;
 
@@ -404,8 +403,7 @@ PeleLM::fillpatch_density(
   int nGhost)
 {
   ProbParm const* lprobparm = prob_parm_d;
-  pele::physics::PMF::PmfData::DataContainer const* lpmfdata =
-    pmf_data.getDeviceData();
+  auto const* lpmfdata = pmf_data.device_parm();
   if (lev == 0) {
 
     // Density
@@ -451,8 +449,7 @@ PeleLM::fillpatch_species(
   int nGhost)
 {
   ProbParm const* lprobparm = prob_parm_d;
-  pele::physics::PMF::PmfData::DataContainer const* lpmfdata =
-    pmf_data.getDeviceData();
+  auto const* lpmfdata = pmf_data.device_parm();
   if (lev == 0) {
 
     // Species
@@ -497,8 +494,7 @@ PeleLM::fillpatch_temp(
   int nGhost)
 {
   ProbParm const* lprobparm = prob_parm_d;
-  pele::physics::PMF::PmfData::DataContainer const* lpmfdata =
-    pmf_data.getDeviceData();
+  auto const* lpmfdata = pmf_data.device_parm();
   if (lev == 0) {
     PhysBCFunct<GpuBndryFuncFab<PeleLMCCFillExtDirTemp>> bndry_func(
       geom[lev], fetchBCRecArray(TEMP, 1),
@@ -541,8 +537,7 @@ PeleLM::fillpatch_phiV(
   int nGhost)
 {
   ProbParm const* lprobparm = prob_parm_d;
-  pele::physics::PMF::PmfData::DataContainer const* lpmfdata =
-    pmf_data.getDeviceData();
+  auto const* lpmfdata = pmf_data.device_parm();
   if (lev == 0) {
     PhysBCFunct<GpuBndryFuncFab<PeleLMCCFillExtDirPhiV>> bndry_func(
       geom[lev], fetchBCRecArray(PHIV, 1),
@@ -745,8 +740,7 @@ PeleLM::fillcoarsepatch_state(
 {
   AMREX_ASSERT(lev > 0);
   ProbParm const* lprobparm = prob_parm_d;
-  pele::physics::PMF::PmfData::DataContainer const* lpmfdata =
-    pmf_data.getDeviceData();
+  auto const* lpmfdata = pmf_data.device_parm();
 
   int nCompState = (m_incompressible) != 0 ? AMREX_SPACEDIM : NVAR;
 
@@ -882,8 +876,7 @@ PeleLM::setInflowBoundaryVel(MultiFab& a_vel, int lev, TimeStamp a_time)
   fillTurbInflow(a_vel, 0, lev, time);
 
   ProbParm const* lprobparm = prob_parm_d;
-  pele::physics::PMF::PmfData::DataContainer const* lpmfdata =
-    pmf_data.getDeviceData();
+  auto const* lpmfdata = pmf_data.device_parm();
   PhysBCFunct<GpuBndryFuncFab<PeleLMCCFillExtDirState>> bndry_func(
     geom[lev], dummyVelBCRec,
     PeleLMCCFillExtDirState{

Source/PeleLMeX_DeriveFunc.cpp

@@ -1324,7 +1324,7 @@ pelelmex_dervisc(
     auto const& rhoY = statefab.const_array(FIRSTSPEC);
     auto const& T = statefab.array(TEMP);
     auto der = derfab.array(dcomp);
-    auto const* ltransparm = a_pelelm->trans_parms.device_trans_parm();
+    auto const* ltransparm = a_pelelm->trans_parms.device_parm();
     amrex::ParallelFor(
       bx, [rhoY, T, der,
            ltransparm] AMREX_GPU_DEVICE(int i, int j, int k) noexcept {
@@ -1370,7 +1370,7 @@ pelelmex_derdiffc(
   auto rhoD = derfab.array(dcomp);
   auto lambda = dummies.array(0);
   auto mu = dummies.array(1);
-  auto const* ltransparm = a_pelelm->trans_parms.device_trans_parm();
+  auto const* ltransparm = a_pelelm->trans_parms.device_parm();
   auto rhotheta = do_soret ? derfab.array(dcomp + NUM_SPECIES)
                            : dummies.array(2); // dummy for no soret
   amrex::Real LeInv = a_pelelm->m_Lewis_inv;
@@ -1417,7 +1417,7 @@ pelelmex_derlambda(
   auto lambda = derfab.array(dcomp);
   auto mu = dummies.array(0);
   auto rhotheta = dummies.array(NUM_SPECIES + 1);
-  auto const* ltransparm = a_pelelm->trans_parms.device_trans_parm();
+  auto const* ltransparm = a_pelelm->trans_parms.device_parm();
   amrex::Real LeInv = a_pelelm->m_Lewis_inv;
   amrex::Real PrInv = a_pelelm->m_Prandtl_inv;
   amrex::ParallelFor(

Source/PeleLMeX_FlowController.cpp

@@ -67,8 +67,7 @@ PeleLM::initActiveControl()
 
     // Extract data from BC: assumes flow comes in from lo side of ctrl_flameDir
     ProbParm const* lprobparm = prob_parm_d;
-    pele::physics::PMF::PmfData::DataContainer const* lpmfdata =
-      pmf_data.getDeviceData();
+    auto const* lpmfdata = pmf_data.device_parm();
 
     Gpu::DeviceVector<Real> s_ext_v(NVAR);
     Real* s_ext_d = s_ext_v.data();

Source/PeleLMeX_Init.cpp

@@ -338,8 +338,7 @@ PeleLM::initLevelData(int lev)
 
   // Prob/PMF data
   ProbParm const* lprobparm = prob_parm_d;
-  pele::physics::PMF::PmfData::DataContainer const* lpmfdata =
-    pmf_data.getDeviceData();
+  auto const* lpmfdata = pmf_data.device_parm();
 
 #ifdef AMREX_USE_OMP
 #pragma omp parallel if (Gpu::notInLaunchRegion())

Source/PeleLMeX_Setup.cpp

@@ -107,7 +107,7 @@ PeleLM::Setup()
   // Initialize EOS and others
   if (m_incompressible == 0) {
     amrex::Print() << " Initialization of Transport ... \n";
-    trans_parms.allocate();
+    trans_parms.initialize();
     if ((m_les_verbose != 0) and m_do_les) { // Say what transport model we're
                                              // going to use
       amrex::Print() << "    Using LES in transport with Sc = "

Source/PeleLMeX_SprayParticles.cpp

@@ -300,7 +300,7 @@ PeleLM::SprayMKDLevel(const int level, const Real time, const Real dt)
 
   // Advance the particle velocities to the half-time and the positions to
   // the new time
-  auto const* ltransparm = PeleLM::trans_parms.device_trans_parm();
+  auto const* ltransparm = PeleLM::trans_parms.device_parm();
 
   MultiFab& state = *(m_spraystate[level]);
   MultiFab& source = *(m_spraysource[level]);

Source/PeleLMeX_TransportProp.cpp

@@ -262,7 +262,7 @@ PeleLM::calcViscosity(const TimeStamp& a_time)
     } else {
 
       // Transport data pointer
-      auto const* ltransparm = trans_parms.device_trans_parm();
+      auto const* ltransparm = trans_parms.device_parm();
 
       // MultiArrays
       auto const& sma = ldata_p->state.const_arrays();
@@ -291,7 +291,7 @@ PeleLM::calcDiffusivity(const TimeStamp& a_time)
     auto* ldata_p = getLevelDataPtr(lev, a_time);
 
     // Transport data pointer
-    auto const* ltransparm = trans_parms.device_trans_parm();
+    auto const* ltransparm = trans_parms.device_parm();
 
     // MultiArrays
     auto const& sma = ldata_p->state.const_arrays();