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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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19
src/EXTRA-DUMP/dump_yaml.cpp
View File

@ -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()) {
if (val.type == multitype::DOUBLE)
thermo_data += fmt::format("{}, ", val.data.d);
else if (val.type == multitype::INT)
thermo_data += fmt::format("{}, ", val.data.i);
else if (val.type == multitype::BIGINT)
thermo_data += fmt::format("{}, ", val.data.b);
for (int i = 0; i < nfield; ++i) {
if (fields[i].type == multitype::DOUBLE)
thermo_data += fmt::format("{}, ", fields[i].data.d);
else if (fields[i].type == multitype::INT)
thermo_data += fmt::format("{}, ", fields[i].data.i);
else if (fields[i].type == multitype::BIGINT)
thermo_data += fmt::format("{}, ", fields[i].data.b);
else
thermo_data += ", ";
}

37
src/NETCDF/dump_netcdf.cpp
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@ -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();
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( 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();
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( 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();
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 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) {

1
src/NETCDF/dump_netcdf.h
View File

@ -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

37
src/NETCDF/dump_netcdf_mpiio.cpp
View File

@ -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) {

1
src/NETCDF/dump_netcdf_mpiio.h
View File

@ -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