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make more reliable with explicit loops using exported nfield value

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This commit is contained in:
Axel Kohlmeyer
2023-06-07 15:19:58 -04:00
parent 620cca34d4
commit 30e6b8b9b6
5 changed files with 70 additions and 27 deletions
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39
src/NETCDF/dump_netcdf_mpiio.cpp
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@ -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();
int nfield = keywords.size();
Thermo *th = output->thermo;
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();
const auto &keywords = output->thermo->get_keywords();
int nfield = fields.size();
Thermo *th = output->thermo;
const auto &fields = th->get_fields();
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();
const auto &fields = output->thermo->get_fields();
int nfield = fields.size();
Thermo *th = output->thermo;
// 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) {
@ -609,7 +628,7 @@ void DumpNetCDFMPIIO::write()
}
}
// write timestep header
// write timestep header
write_time_and_cell();