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initial support for write_data

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This commit is contained in:
Steve Plimpton
2023-09-13 10:03:05 -06:00
parent dec245c67b
commit c7e794146f
8 changed files with 124 additions and 32 deletions
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33
src/write_data.cpp
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@ -97,7 +97,7 @@ void WriteData::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"nofix") == 0) {
fixflag = 0;
iarg++;
} else if (strcmp(arg[iarg],"triclinic") == 0) {
} else if (strcmp(arg[iarg],"triclinic/general") == 0) {
triclinic_general = 1;
iarg++;
} else if (strcmp(arg[iarg],"nolabelmap") == 0) {
@ -213,32 +213,14 @@ void WriteData::write(const std::string &file)
if (coeffflag) force_fields();
}
// per atom info in Atoms and Velocities sections
// if general triclinic:
// save restricted triclinic atom coords
// transform atom coords from restricted to general
// restore saved atom coords after output
// reset internal per-atom data that needs rotation
atom->avec->write_data_restricted_to_general();
double **xstore = nullptr;
if (triclinic_general) {
double **x = atom->x;
int nlocal = atom->nlocal;
memory->create(xstore,nlocal,3,"write_data:xstore");
if (nlocal) memcpy(&xstore[0][0],&x[0][0],3*nlocal*sizeof(double));
for (int i = 0; i < nlocal; i++)
domain->restricted_to_general_coords(x[i]);
}
// per atom info in Atoms and Velocities sections
if (natoms) atoms();
if (triclinic_general) {
double **x = atom->x;
int nlocal = atom->nlocal;
if (nlocal) memcpy(&x[0][0],&xstore[0][0],3*nlocal*sizeof(double));
memory->destroy(xstore);
}
if (natoms) velocities();
// molecular topology info if defined
@ -265,6 +247,11 @@ void WriteData::write(const std::string &file)
if (ifix->wd_section)
for (int m = 0; m < ifix->wd_section; m++) fix(ifix,m);
// if general triclinic:
// restore internal per-atom data that was rotated
atom->avec->write_data_restore_restricted();
// close data file
if (me == 0) fclose(fp);