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add API to library interface to access last thermo data

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This commit is contained in:
Axel Kohlmeyer
2023-06-07 16:21:01 -04:00
parent de561737a3
commit 491e152289
7 changed files with 116 additions and 17 deletions
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4
src/EXTRA-DUMP/dump_yaml.cpp
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@ -61,8 +61,8 @@ void DumpYAML::write_header(bigint ndump)
if (thermo) {
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();
if (update->ntimestep == *th->get_timestep()) {
int nfield = *th->get_nfield();
const auto &keywords = th->get_keywords();
const auto &fields = th->get_fields();

12
src/NETCDF/dump_netcdf.cpp
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@ -224,7 +224,7 @@ void DumpNetCDF::openfile()
if (thermo && !singlefile_opened) {
delete[] thermovar;
thermovar = new int[output->thermo->get_nfield()];
thermovar = new int[*output->thermo->get_nfield()];
}
// now the computes and fixes have been initialized, so we can query
@ -323,7 +323,7 @@ void DumpNetCDF::openfile()
if (thermo) {
Thermo *th = output->thermo;
const auto &keywords = th->get_keywords();
const int nfield = th->get_nfield();
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() );
@ -439,7 +439,7 @@ void DumpNetCDF::openfile()
Thermo *th = output->thermo;
const auto &fields = th->get_fields();
const auto &keywords = th->get_keywords();
const int nfield = th->get_nfield();
const int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (fields[i].type == multitype::DOUBLE) {
@ -610,18 +610,18 @@ void DumpNetCDF::write()
// 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())) {
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);
id, *th->get_timestep(), update->ntimestep);
}
}
const auto &keywords = th->get_keywords();
const auto &fields = th->get_fields();
int nfield = th->get_nfield();
int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (filewriter) {
if (fields[i].type == multitype::DOUBLE) {

12
src/NETCDF/dump_netcdf_mpiio.cpp
View File

@ -221,7 +221,7 @@ void DumpNetCDFMPIIO::openfile()
if (thermo && !singlefile_opened) {
delete[] thermovar;
thermovar = new int[output->thermo->get_nfield()];
thermovar = new int[*output->thermo->get_nfield()];
}
// now the computes and fixes have been initialized, so we can query
@ -321,7 +321,7 @@ void DumpNetCDFMPIIO::openfile()
if (thermo) {
Thermo *th = output->thermo;
const auto &keywords = th->get_keywords();
const int nfield = th->get_nfield();
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() );
@ -429,7 +429,7 @@ void DumpNetCDFMPIIO::openfile()
Thermo *th = output->thermo;
const auto &fields = th->get_fields();
const auto &keywords = th->get_keywords();
const int nfield = th->get_nfield();
const int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (fields[i].type == multitype::DOUBLE) {
@ -603,18 +603,18 @@ void DumpNetCDFMPIIO::write()
// 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())) {
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);
id, *th->get_timestep(), update->ntimestep);
}
}
const auto &keywords = th->get_keywords();
const auto &fields = th->get_fields();
int nfield = th->get_nfield();
int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (filewriter) {
if (fields[i].type == multitype::DOUBLE) {

99
src/library.cpp
View File

@ -719,7 +719,7 @@ double lammps_get_natoms(void *handle)
/* ---------------------------------------------------------------------- */
/** Get current value of a thermo keyword.
/** Evaluate a thermo keyword.
*
\verbatim embed:rst
@ -750,6 +750,103 @@ double lammps_get_thermo(void *handle, const char *keyword)
/* ---------------------------------------------------------------------- */
/** Access cached data from last thermo output
*
\verbatim embed:rst
This function provides access to cached data from the last thermo
output. This differs from :cpp:func:`lammps_get_thermo` in that it does
not trigger an evaluation. It provides direct access to a a read-only
location of the last thermo output data and the corresponding keyword
strings. The output depends on the value of the *what* argument string.
.. list-table::
:header-rows: 1
:widths: auto
* - Value of *what
- Description of return value
- Data type
- Uses index
* - step
- timestep when the last thermo output was generated or -1 when no data available
- pointer to bigint cast to void pointer
- no
* - num
- number of fields in thermo output
- pointer to int cast to void pointer
- no
* - keyword
- column keyword for thermo output
- const char pointer cast to void pointer
- yes
* - type
- data type of thermo output column. LAMMPS_INT, LAMMPS_DOUBLE, or LAMMPS_INT64
- const int cast to void pointer
- yes
* - data
- actual field data for column
- pointer to either int, int64_t or double cast to void pointer
- yes
\endverbatim
*
* \param handle pointer to a previously created LAMMPS instance
* \param what string with the kind of data requested
* \param idx integer with index into data arrays, ignored for scalar data
* \return pointer to location of requested data cast to void or NULL */
void *lammps_last_thermo(void *handle, const char *what, int idx)
{
auto lmp = (LAMMPS *) handle;
void *val = nullptr;
Thermo *th = lmp->output->thermo;
if (!th) return nullptr;
const int nfield = *th->get_nfield();
BEGIN_CAPTURE
{
if (strcmp(what, "step") == 0) {
val = (void *) th->get_timestep();
} else if (strcmp(what, "num") == 0) {
val = (void *) th->get_nfield();
} else if (strcmp(what, "keyword") == 0) {
if ((idx < 0) || (idx >= nfield)) return nullptr;
const auto &keywords = th->get_keywords();
val = (void *) keywords[idx].c_str();
} else if (strcmp(what, "type") == 0) {
if ((idx < 0) || (idx >= nfield)) return nullptr;
const auto &field = th->get_fields()[idx];
if (field.type == multitype::INT) {
val = (void *) LAMMPS_INT;
} else if (field.type == multitype::BIGINT) {
val = (void *) LAMMPS_INT64;
} else if (field.type == multitype::DOUBLE) {
val = (void *) LAMMPS_DOUBLE;
}
} else if (strcmp(what, "data") == 0) {
if ((idx < 0) || (idx >= nfield)) return nullptr;
const auto &field = th->get_fields()[idx];
if (field.type == multitype::INT) {
val = (void *) &field.data.i;
} else if (field.type == multitype::BIGINT) {
val = (void *) &field.data.b;
} else if (field.type == multitype::DOUBLE) {
val = (void *) &field.data.d;
}
} else val = nullptr;
}
END_CAPTURE
return val;
}
/* ---------------------------------------------------------------------- */
/** Extract simulation box parameters.
*
\verbatim embed:rst

1
src/library.h
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@ -148,6 +148,7 @@ void lammps_commands_string(void *handle, const char *str);
double lammps_get_natoms(void *handle);
double lammps_get_thermo(void *handle, const char *keyword);
void *lammps_last_thermo(void *handle, const char *what, int idx);
void lammps_extract_box(void *handle, double *boxlo, double *boxhi, double *xy, double *yz,
double *xz, int *pflags, int *boxflag);

1
src/thermo.cpp
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@ -111,6 +111,7 @@ Thermo::Thermo(LAMMPS *_lmp, int narg, char **arg) :
lostflag = lostbond = Thermo::ERROR;
lostbefore = warnbefore = 0;
flushflag = 0;
ntimestep = -1;
// set style and corresponding lineflag
// custom style builds its own line of keywords, including wildcard expansion

4
src/thermo.h
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@ -43,8 +43,8 @@ class Thermo : protected Pointers {
int evaluate_keyword(const std::string &, double *);
// for accessing cached thermo data
int get_nfield() const { return nfield; }
bigint get_timestep() const { return ntimestep; }
const int *get_nfield() const { return &nfield; }
const bigint *get_timestep() const { return &ntimestep; }
const std::vector<multitype> &get_fields() const { return field_data; }
const std::vector<std::string> &get_keywords() const { return keyword; }