merge devel in

.github/workflows/linux.yml

@@ -129,7 +129,7 @@ jobs:
     - name: Run
       working-directory: ./Exec/RegTests/EB_BackwardStepFlame/
       run: |
-        mpirun -n 2 ./PeleLMeX2d.gnu.MPI.ex eb_bfs.inp amr.max_step=2 amr.plot_int=-1 amr.check_int=-1 amrex.abort_on_unused_inputs=1
+        mpirun -n 2 ./PeleLMeX2d.gnu.MPI.ex eb_bfs.inp amr.max_step=2 amr.plot_int=-1 amr.check_int=-1 amrex.abort_on_unused_inputs=1 mac_proj.verbose=2 mac_proj.atol=5e-11 mac_proj.rtol=5e-11
 
   # Build and Run the Plasma flamesheet with GNU9.3 and MPI support
   PLASMA:

Docs/sphinx/manual/LMeXControls.rst

@@ -130,6 +130,7 @@ IO parameters
     amr.restart          = chk00100        # [OPT, DEF=""] Checkpoint from which to restart the simulation
     amr.initDataPlt      = plt01000        # [OPT, DEF=""] Provide a plotfile from which to extract initial data
     peleLM.initDataPlt_reset_time = 1               # [OPT, DEF=1] Resets time and nsteps to 0 after restarting from a plot file. (Warning: plot file will be rewritten if not renamed and argument value = 0)
+    peleLM.initDataPlt_specname_map = spec1 spec2 # [OPT, DEF=""] If specified, lookup these entries instead of species names when populating species from the init plot file (length must match NUM_SPECIES)
     peleLM.initDataPlt_patch_flow_variables = false # [OPT, DEF=false] Enable user-defined flow variable patching after reading a plot solution file
     amr.regrid_on_restart = 1              # [OPT, DEF="0"] Trigger a regrid after the data from checkpoint are loaded
     amr.n_files          = 64              # [OPT, DEF="min(256,NProcs)"] Number of files to write per level

Exec/Plasma/FlameSheetIons/pelelmex_prob.H

@@ -95,7 +95,7 @@ struct MyProblemSpecificFunctions : public DefaultProblemSpecificFunctions
     massfrac[E_ID] = 0.0;
     amrex::Real sum = 0.0;
     for (int n = 0; n < NUM_SPECIES; n++) {
-      massfrac[n] = std::max(0.0, massfrac[n]);
+      massfrac[n] = amrex::max(0.0, massfrac[n]);
       if (n != N2_ID)
         sum += massfrac[n];
     }
@@ -126,7 +126,7 @@ struct MyProblemSpecificFunctions : public DefaultProblemSpecificFunctions
     for (int n = 0; n < NUM_SPECIES; n++) {
       chargeDist += massfrac[n] * zk[n];
     }
-    state(i, j, k, NE) = std::max(1.0e-24, chargeDist / elemCharge);
+    state(i, j, k, NE) = amrex::max(1.0e-24, chargeDist / elemCharge);
 
     AMREX_D_TERM(state(i, j, k, VELX) = 0.0;
                  , state(i, j, k, VELY) = pmf_vals[1] * 0.01;

Exec/Production/CounterFlowSpray/SprayParticlesInitInsert.cpp

@@ -1,49 +1,46 @@
-
 #include "SprayParticles.H"
 #include "SprayInjection.H"
 #include "pelelmex_prob.H"
 
-using namespace amrex;
-
 class CounterFlowJet : public SprayJet
 {
 public:
   // Use default constructor
-  CounterFlowJet(const std::string jet_name, const Geometry& geom)
+  CounterFlowJet(const std::string jet_name, const amrex::Geometry& geom)
     : SprayJet(jet_name, geom)
   {
   }
 
   bool get_new_particle(
-    const Real time,
-    const Real& phi_radial,
-    const Real& cur_radius,
-    Real& umag,
-    Real& theta_spread,
-    Real& phi_swirl,
-    Real& dia_part,
-    Real& T_part,
-    Real* Y_part) override;
+    const amrex::Real time,
+    const amrex::Real& phi_radial,
+    const amrex::Real& cur_radius,
+    amrex::Real& umag,
+    amrex::Real& theta_spread,
+    amrex::Real& phi_swirl,
+    amrex::Real& dia_part,
+    amrex::Real& T_part,
+    amrex::Real* Y_part) override;
 };
 
 bool
 CounterFlowJet::get_new_particle(
-  const Real time,
-  const Real& phi_radial,
-  const Real& cur_radius,
-  Real& umag,
-  Real& theta_spread,
-  Real& phi_swirl,
-  Real& dia_part,
-  Real& T_part,
-  Real* Y_part)
+  const amrex::Real time,
+  const amrex::Real& phi_radial,
+  const amrex::Real& cur_radius,
+  amrex::Real& umag,
+  amrex::Real& theta_spread,
+  amrex::Real& phi_swirl,
+  amrex::Real& dia_part,
+  amrex::Real& T_part,
+  amrex::Real* Y_part)
 {
   umag = m_jetVel;
   T_part = m_jetT;
   dia_part = m_dropDist->get_dia();
   phi_swirl = 0.;
   // Random spread angle
-  Real tan_vel_comp = (2. * amrex::Random() - 1.) * 0.05;
+  amrex::Real tan_vel_comp = (2. * amrex::Random() - 1.) * 0.05;
   theta_spread = std::asin(tan_vel_comp);
   for (int sp = 0; sp < SPRAY_FUEL_NUM; ++sp) {
     Y_part[sp] = 0.;
@@ -54,7 +51,7 @@ CounterFlowJet::get_new_particle(
 
 bool
 SprayParticleContainer::injectParticles(
-  Real time, Real dt, int nstep, int lev, int finest_level)
+  amrex::Real time, amrex::Real dt, int nstep, int lev, int finest_level)
 {
   if (lev != 0) {
     return false;

Exec/RegTests/SprayTest/compareOutput.py

@@ -95,7 +95,7 @@ def pproc(args):
                             cer = float(line.split()[2])
                             if (cer > max_error):
                                 errfail += 1
-                                perr = "Error in {} on level {}: {} > {}".format(var,curlev,cer,maxerror)
+                                perr = "Error in {} on level {}: {} > {}".format(var,curlev,cer,max_error)
                                 print(perr)
         if (varcount != len(vars)):
             error = "Not all variables were found in plot file"

Exec/RegTests/Unit/pelelmex_prob_parm.H

@@ -3,14 +3,12 @@
 
 #include <AMReX_REAL.H>
 
-using namespace amrex::literals;
-
 struct ProbParm
 {
   // Shared params
   int probType = 0;
-  amrex::Real T_mean = 298.0_rt;
-  amrex::Real P_mean = 101325.0_rt;
+  amrex::Real T_mean = 298.0;
+  amrex::Real P_mean = 101325.0;
   amrex::Real meanFlowMag = 0.0;
   int meanFlowDir = 1;
 

Source/PeleLMeX.H

@@ -1505,6 +1505,7 @@ public:
     std::unique_ptr<AdvanceAdvData>& advData,
     std::unique_ptr<AdvanceDiffData>& diffData);
 
+  bool checkForNaNs();
   void copyTransportOldToNew();
   void copyStateNewToOld(int nGhost = 0);
   void copyPressNewToOld();
@@ -1900,6 +1901,7 @@ public:
   amrex::Vector<std::string> m_evaluatePlotVars;
   bool m_write_hdf5_pltfile = false;
   bool m_do_patch_flow_variables = false;
+  amrex::Vector<std::string> m_initDataPlt_specname_map = {};
 
   //-----------------------------------------------------------------------------
   // ALGORITHM