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add general tri options to read and write data commands and Domain class

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This commit is contained in:
Steve Plimpton
2023-08-31 14:34:37 -06:00
parent dc3c8da52b
commit db72d4b73a
9 changed files with 426 additions and 73 deletions
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59
src/write_data.cpp
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@ -72,8 +72,11 @@ void WriteData::command(int narg, char **arg)
pairflag = II;
coeffflag = 1;
fixflag = 1;
triclinic_general = 0;
lmapflag = 1;
// store current (default) setting since we may change it.
// store current (default) setting since we may change it
int types_style = atom->types_style;
int noinit = 0;
@ -94,6 +97,9 @@ void WriteData::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"nofix") == 0) {
fixflag = 0;
iarg++;
} else if (strcmp(arg[iarg],"triclinic") == 0) {
triclinic_general = 1;
iarg++;
} else if (strcmp(arg[iarg],"nolabelmap") == 0) {
lmapflag = 0;
iarg++;
@ -135,7 +141,9 @@ void WriteData::command(int narg, char **arg)
}
write(file);
// restore saved setting
atom->types_style = types_style;
}
@ -206,8 +214,32 @@ void WriteData::write(const std::string &file)
}
// per atom info in Atoms and Velocities sections
// if general triclinic:
// save restricted triclinic atom coords
// transform atom coords from restricted to general
// restore save atom coords after output
// NOTE: do same for velocities as well ?
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(x[i]);
}
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
@ -289,15 +321,22 @@ void WriteData::header()
for (int m = 0; m < ifix->wd_header; m++)
ifix->write_data_header(fp,m);
// box info
// box info: orthogonal, restricted triclinic, or general triclinic (if requested)
auto box = fmt::format("\n{} {} xlo xhi\n{} {} ylo yhi\n{} {} zlo zhi\n",
domain->boxlo[0],domain->boxhi[0],
domain->boxlo[1],domain->boxhi[1],
domain->boxlo[2],domain->boxhi[2]);
if (domain->triclinic)
box += fmt::format("{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz);
fputs(box.c_str(),fp);
if (!triclinic_general) {
fmt::print(fp,"\n{} {} xlo xhi\n{} {} ylo yhi\n{} {} zlo zhi\n",
domain->boxlo[0],domain->boxhi[0],
domain->boxlo[1],domain->boxhi[1],
domain->boxlo[2],domain->boxhi[2]);
if (domain->triclinic)
fmt::print(fp,"{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz);
} else if (triclinic_general) {
fmt::print(fp,"\n{} {} {} {} avec\n{} {} {} {} bvec\n{} {} {} {} cvec\n",
domain->avec[0],domain->avec[1],domain->avec[2],domain->tri_origin[0],
domain->bvec[0],domain->bvec[1],domain->bvec[2],domain->tri_origin[1],
domain->cvec[0],domain->cvec[1],domain->cvec[2],domain->tri_origin[2]);
}
}
/* ----------------------------------------------------------------------