make more reliable with explicit loops using exported nfield value

src/EXTRA-DUMP/dump_yaml.cpp

@@ -62,18 +62,21 @@ void DumpYAML::write_header(bigint ndump)
     Thermo *th = output->thermo;
     // output thermo data only on timesteps where it was computed
     if (update->ntimestep == th->get_timestep()) {
+      int nfield = th->get_nfield();
+      const auto &keywords = th->get_keywords();
+      const auto &fields = th->get_fields();
 
       thermo_data += "thermo:\n  - keywords: [ ";
-      for (const auto &key : th->get_keywords()) thermo_data += fmt::format("{}, ", key);
+      for (int i = 0; i < nfield; ++i) thermo_data += fmt::format("{}, ", keywords[i]);
       thermo_data += "]\n  - data: [ ";
 
-      for (const auto &val : th->get_fields()) {
+      for (int i = 0; i < nfield; ++i) {
-        if (val.type == multitype::DOUBLE)
+        if (fields[i].type == multitype::DOUBLE)
-          thermo_data += fmt::format("{}, ", val.data.d);
+          thermo_data += fmt::format("{}, ", fields[i].data.d);
-        else if (val.type == multitype::INT)
+        else if (fields[i].type == multitype::INT)
-          thermo_data += fmt::format("{}, ", val.data.i);
+          thermo_data += fmt::format("{}, ", fields[i].data.i);
-        else if (val.type == multitype::BIGINT)
+        else if (fields[i].type == multitype::BIGINT)
-          thermo_data += fmt::format("{}, ", val.data.b);
+          thermo_data += fmt::format("{}, ", fields[i].data.b);
         else
           thermo_data += ", ";
       }

src/NETCDF/dump_netcdf.cpp

@@ -195,6 +195,7 @@ DumpNetCDF::DumpNetCDF(LAMMPS *lmp, int narg, char **arg) :
   type_nc_real = NC_FLOAT;
 
   thermo = false;
+  thermo_warn = true;
   thermovar = nullptr;
 
   framei = 0;
@@ -223,7 +224,7 @@ void DumpNetCDF::openfile()
 
   if (thermo && !singlefile_opened) {
     delete[] thermovar;
-    thermovar = new int[output->thermo->get_keywords().size()];
+    thermovar = new int[output->thermo->get_nfield()];
   }
 
   // now the computes and fixes have been initialized, so we can query
@@ -320,8 +321,10 @@ void DumpNetCDF::openfile()
 
       // perframe variables
       if (thermo) {
-        const auto &keywords = output->thermo->get_keywords();
+        Thermo *th = output->thermo;
-        int nfield = keywords.size();
+        const auto &keywords = th->get_keywords();
+        const int nfield = th->get_nfield();
+
         for (int i = 0; i < nfield; i++) {
           NCERRX( nc_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
         }
@@ -433,9 +436,11 @@ void DumpNetCDF::openfile()
 
       // perframe variables
       if (thermo) {
-        const auto &fields = output->thermo->get_fields();
+        Thermo *th = output->thermo;
-        const auto &keywords = output->thermo->get_keywords();
+        const auto &fields = th->get_fields();
-        int nfield = fields.size();
+        const auto &keywords = th->get_keywords();
+        const int nfield = th->get_nfield();
+
         for (int i = 0; i < nfield; i++) {
           if (fields[i].type == multitype::DOUBLE) {
             NCERRX( nc_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
@@ -600,9 +605,23 @@ void DumpNetCDF::write()
   start[1] = 0;
 
   if (thermo) {
-    const auto &keywords = output->thermo->get_keywords();
+    Thermo *th = output->thermo;
-    const auto &fields = output->thermo->get_fields();
+
-    int nfield = fields.size();
+    // will output current thermo data only on timesteps where it was computed.
+    // warn (once) about using cached copy from old timestep.
+
+    if (thermo_warn && (update->ntimestep != th->get_timestep())) {
+      thermo_warn = false;
+      if (comm->me == 0) {
+        error->warning(FLERR, "Dump {} output on incompatible timestep with thermo output: {} vs {} \n"
+                       "         Dump netcdf always stores thermo data from last thermo output",
+                       id, th->get_timestep(), update->ntimestep);
+      }
+    }
+
+    const auto &keywords = th->get_keywords();
+    const auto &fields = th->get_fields();
+    int nfield = th->get_nfield();
     for (int i = 0; i < nfield; i++) {
       if (filewriter) {
         if (fields[i].type == multitype::DOUBLE) {

src/NETCDF/dump_netcdf.h

@@ -65,6 +65,7 @@ class DumpNetCDF : public DumpCustom {
 
   int type_nc_real;    // netcdf type to use for real variables: float or double
   bool thermo;         // write thermo output to netcdf file
+  bool thermo_warn;    // warn (once) that thermo output is on incompatible step
 
   bigint n_buffer;          // size of buffer
   bigint *int_buffer;       // buffer for passing data to netcdf

src/NETCDF/dump_netcdf_mpiio.cpp

@@ -192,6 +192,7 @@ DumpNetCDFMPIIO::DumpNetCDFMPIIO(LAMMPS *lmp, int narg, char **arg) :
   type_nc_real = NC_FLOAT;
 
   thermo = false;
+  thermo_warn = true;
   thermovar = nullptr;
 
   framei = 0;
@@ -220,7 +221,7 @@ void DumpNetCDFMPIIO::openfile()
 
   if (thermo && !singlefile_opened) {
     delete[] thermovar;
-    thermovar = new int[output->thermo->get_keywords().size()];
+    thermovar = new int[output->thermo->get_nfield()];
   }
 
   // now the computes and fixes have been initialized, so we can query
@@ -318,8 +319,10 @@ void DumpNetCDFMPIIO::openfile()
 
     // perframe variables
     if (thermo) {
-      const auto &keywords = output->thermo->get_keywords();
+      Thermo *th = output->thermo;
-      int nfield = keywords.size();
+      const auto &keywords = th->get_keywords();
+      const int nfield = th->get_nfield();
+
       for (int i = 0; i < nfield; i++) {
         NCERRX( ncmpi_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
       }
@@ -423,9 +426,11 @@ void DumpNetCDFMPIIO::openfile()
 
     // perframe variables
     if (thermo) {
-      const auto &fields = output->thermo->get_fields();
+      Thermo *th = output->thermo;
-      const auto &keywords = output->thermo->get_keywords();
+      const auto &fields = th->get_fields();
-      int nfield = fields.size();
+      const auto &keywords = th->get_keywords();
+      const int nfield = th->get_nfield();
+
       for (int i = 0; i < nfield; i++) {
         if (fields[i].type == multitype::DOUBLE) {
           NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
@@ -593,9 +598,23 @@ void DumpNetCDFMPIIO::write()
   NCERR( ncmpi_begin_indep_data(ncid) );
 
   if (thermo) {
-    const auto &keywords = output->thermo->get_keywords();
+    Thermo *th = output->thermo;
-    const auto &fields = output->thermo->get_fields();
+
-    int nfield = fields.size();
+    // will output current thermo data only on timesteps where it was computed.
+    // warn (once) about using cached copy from old timestep.
+
+    if (thermo_warn && (update->ntimestep != th->get_timestep())) {
+      thermo_warn = false;
+      if (comm->me == 0) {
+        error->warning(FLERR, "Dump {} output on incompatible timestep with thermo output: {} vs {} \n"
+                       "         Dump netcdf/mpiio always stores thermo data from last thermo output",
+                       id, th->get_timestep(), update->ntimestep);
+      }
+    }
+
+    const auto &keywords = th->get_keywords();
+    const auto &fields = th->get_fields();
+    int nfield = th->get_nfield();
     for (int i = 0; i < nfield; i++) {
       if (filewriter) {
         if (fields[i].type == multitype::DOUBLE) {

src/NETCDF/dump_netcdf_mpiio.h

@@ -62,6 +62,7 @@ class DumpNetCDFMPIIO : public DumpCustom {
 
   int type_nc_real;    // netcdf type to use for real variables: float or double
   bool thermo;         // write thermo output to netcdf file
+  bool thermo_warn;    // warn (once) that thermo output is on incompatible step
 
   bigint n_buffer;          // size of buffer
   bigint *int_buffer;       // buffer for passing data to netcdf