Extract restart read/write IO from M2ulPhyS

src/M2ulPhyS.cpp

@@ -329,9 +329,9 @@ void M2ulPhyS::initVariables() {
       if (config.isRestartSerialized("read")) {
         assert(serial_mesh->Conforming());
         partitioning_ = Array<int>(serial_mesh->GeneratePartitioning(nprocs_, defaultPartMethod), nelemGlobal_);
-        partitioning_file_hdf5("write");
+        partitioning_file_hdf5("write", config, groupsMPI, nelemGlobal_, partitioning_);
       } else {
-        partitioning_file_hdf5("read");
+        partitioning_file_hdf5("read", config, groupsMPI, nelemGlobal_, partitioning_);
       }
     }
 
@@ -359,7 +359,7 @@ void M2ulPhyS::initVariables() {
     if (nprocs_ > 1) {
       assert(serial_mesh->Conforming());
       partitioning_ = Array<int>(serial_mesh->GeneratePartitioning(nprocs_, defaultPartMethod), nelemGlobal_);
-      if (rank0_) partitioning_file_hdf5("write");
+      if (rank0_) partitioning_file_hdf5("write", config, groupsMPI, nelemGlobal_, partitioning_);
       MPI_Barrier(groupsMPI->getTPSCommWorld());
     }
 
@@ -655,7 +655,7 @@ void M2ulPhyS::initVariables() {
     ioData.registerIOVar("/rmsData", "vw", 5);
   }
 
-  ioData.initializeSerial(rank0_, (config.RestartSerial() != "no"), serial_mesh);
+  ioData.initializeSerial(rank0_, (config.RestartSerial() != "no"), serial_mesh, locToGlobElem, &partitioning_);
   projectInitialSolution();
 
   // Boundary attributes in present partition
@@ -1795,7 +1795,7 @@ void M2ulPhyS::initSolutionAndVisualizationVectors() {
   }
 
   // define solution parameters for i/o
-  ioData.registerIOFamily("Solution state variables", "/solution", U);
+  ioData.registerIOFamily("Solution state variables", "/solution", U, true, true, fec);
   ioData.registerIOVar("/solution", "density", 0);
   ioData.registerIOVar("/solution", "rho-u", 1);
   ioData.registerIOVar("/solution", "rho-v", 2);
@@ -1988,12 +1988,6 @@ void M2ulPhyS::solveStep() {
 
   const int vis_steps = config.GetNumItersOutput();
   if (iter % vis_steps == 0) {
-    // dump history
-    // NOTE(kevin): this routine is currently obsolete.
-    // It computes `dof`-averaged state and time-derivative, which are useless at this point.
-    // This will not be supported.
-    writeHistoryFile();
-
 #ifdef HAVE_MASA
     if (config.use_mms_) {
       if (config.mmsSaveDetails_) {

src/M2ulPhyS.hpp

@@ -343,18 +343,10 @@ class M2ulPhyS : public TPS::Solver {
   void initGradUp();
   void initilizeSpeciesFromLTE();
 
-  // NOTE(kevin): this routine is currently obsolete.
-  // It computes `dof`-averaged state and time-derivative, which are useless at this point.
-  // This will not be supported.
-  void writeHistoryFile();
-
   // i/o routines
-  void read_partitioned_soln_data(hid_t file, string varName, size_t index, double *data);
-  void read_serialized_soln_data(hid_t file, string varName, int numDof, int varOffset, double *data, IOFamily &fam);
   void restart_files_hdf5(string mode, string inputFileName = std::string());
-  void partitioning_file_hdf5(string mode);
-  void serialize_soln_for_write(IOFamily &fam);
-  void write_soln_data(hid_t group, string varName, hid_t dataspace, double *data);
+  void write_restart_files_hdf5(hid_t file, bool serialized_write);
+  void read_restart_files_hdf5(hid_t file, bool serialized_read);
 
   void Check_NAN();
   bool Check_JobResubmit();

src/cycle_avg_joule_coupling.cpp

@@ -313,7 +313,6 @@ void CycleAvgJouleCoupling::interpElectricFieldFromEMToFlow() {
   efieldR_->SetFromTrueDofs(interp_vals);
   efieldR_->HostRead();
 
-
   const ParGridFunction *efield_imag_gf = qmsa_solver_->getElectricFieldimag();
   interp_em_to_flow_->Interpolate(vxyz, *efield_imag_gf, interp_vals);
   efieldI_->SetFromTrueDofs(interp_vals);