ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

undo "boxgeom" changes

Browse Source
This commit is contained in:
Axel Kohlmeyer
2023-11-03 16:40:18 -04:00
parent a0f7612f13
commit 0fbe388cbd
2 changed files with 14 additions and 30 deletions
Download Patch File Download Diff File Expand all files Collapse all files

41
src/read_dump.cpp
View File

@ -48,19 +48,6 @@ ReadDump::ReadDump(LAMMPS *lmp) :
nfield = 0;
readerstyle = utils::strdup("native");
scaled = wrapped = 0;
boxgeom = UNKNOWN;
if (domain->triclinic)
boxgeom |= TRICLINIC;
else
boxgeom |= ORTHOGONAL;
if (domain->dimension == 2)
boxgeom |= TWO_D;
else
boxgeom |= THREE_D;
nreader = 0;
clustercomm = MPI_COMM_NULL;
filereader = 0;
@ -518,8 +505,8 @@ void ReadDump::header(int fieldinfo)
if (boxflag) {
if (!boxinfo)
error->all(FLERR,"No box information in dump, must use 'box no'");
else if ((triclinic_snap && (boxgeom & ORTHOGONAL)) ||
(!triclinic_snap && (boxgeom & TRICLINIC)))
else if ((triclinic_snap && !domain->triclinic) ||
(!triclinic_snap && domain->triclinic))
error->one(FLERR,"Read_dump triclinic status does not match simulation");
}
@ -563,11 +550,11 @@ void ReadDump::header(int fieldinfo)
// set yindex,zindex = column index of Y and Z fields in fields array
// needed for unscaling to absolute coords in xfield(), yfield(), zfield()
if (scaled && (boxgeom & TRICLINIC)) {
if (scaled && domain->triclinic == 1) {
int flag = 0;
if (xflag == Reader::UNSET) flag = 1;
if (yflag == Reader::UNSET) flag = 1;
if ((boxgeom & THREE_D) && zflag == Reader::UNSET) flag = 1;
if (domain->dimension == 3 && zflag == Reader::UNSET) flag = 1;
if (flag)
error->one(FLERR,"All read_dump x,y,z fields must be specified for "
"scaled, triclinic coords");
@ -653,13 +640,13 @@ void ReadDump::atoms()
domain->boxhi[0] = xhi;
domain->boxlo[1] = ylo;
domain->boxhi[1] = yhi;
if (boxgeom & THREE_D) {
if (domain->dimension == 3) {
domain->boxlo[2] = zlo;
domain->boxhi[2] = zhi;
}
if (boxgeom & TRICLINIC) {
if (domain->triclinic) {
domain->xy = xy;
if (boxgeom & THREE_D) {
if (domain->dimension == 3) {
domain->xz = xz;
domain->yz = yz;
}
@ -1132,12 +1119,12 @@ void ReadDump::migrate_atoms_by_coords()
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
if (boxgeom & TRICLINIC) domain->x2lamda(atom->nlocal);
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->reset_box();
auto irregular = new Irregular(lmp);
irregular->migrate_atoms(1);
delete irregular;
if (boxgeom & TRICLINIC) domain->lamda2x(atom->nlocal);
if (domain->triclinic) domain->lamda2x(atom->nlocal);
}
/* ----------------------------------------------------------------------
@ -1185,7 +1172,7 @@ int ReadDump::fields_and_keywords(int narg, char **arg)
if (fieldtype[nfield-1] == Reader::ID || fieldtype[nfield-1] == Reader::TYPE)
error->all(FLERR,"Read_dump must use at least either 'id' or 'type' field");
if (boxgeom & TWO_D) {
if (domain->dimension == 2) {
for (int i = 0; i < nfield; i++)
if (fieldtype[i] == Reader::Z || fieldtype[i] == Reader::VZ ||
fieldtype[i] == Reader::IZ || fieldtype[i] == Reader::FZ)
@ -1319,8 +1306,8 @@ int ReadDump::whichtype(char *str)
double ReadDump::xfield(int i, int j)
{
if (!scaled) return fields[i][j];
else if (boxgeom & ORTHOGONAL) return fields[i][j]*xprd + xlo;
else if (boxgeom & TWO_D)
else if (!domain->triclinic) return fields[i][j]*xprd + xlo;
else if (domain->dimension == 2)
return xprd*fields[i][j] + xy*fields[i][yindex] + xlo;
return xprd*fields[i][j] + xy*fields[i][yindex] + xz*fields[i][zindex] + xlo;
}
@ -1328,8 +1315,8 @@ double ReadDump::xfield(int i, int j)
double ReadDump::yfield(int i, int j)
{
if (!scaled) return fields[i][j];
else if (boxgeom & ORTHOGONAL) return fields[i][j]*yprd + ylo;
else if (boxgeom & TWO_D) return yprd*fields[i][j] + ylo;
else if (!domain->triclinic) return fields[i][j]*yprd + ylo;
else if (domain->dimension == 2) return yprd*fields[i][j] + ylo;
return yprd*fields[i][j] + yz*fields[i][zindex] + ylo;
}