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

alter how lattice interacts with create_box and create_atoms for general triclinic

Browse Source
This commit is contained in:
Steve Plimpton
2023-11-17 17:10:45 -07:00
parent 4ccd59af80
commit 56b2c7ed46
11 changed files with 383 additions and 206 deletions
Download Patch File Download Diff File Expand all files Collapse all files

54
src/create_atoms.cpp
View File

@ -154,9 +154,10 @@ void CreateAtoms::command(int narg, char **arg)
overlapflag = 0;
maxtry = DEFAULT_MAXTRY;
radscale = 1.0;
radthresh = domain->lattice->xlattice;
mesh_style = BISECTION;
mesh_density = 1.0;
radthresh = domain->lattice->xlattice; // NOTE to Axel - I think this should be 1.0 by default
mesh_density = 1.0; // similar to how this setting is 1.0
// see rescaling of both below if units = lattice
nbasis = domain->lattice->nbasis;
basistype = new int[nbasis];
for (int i = 0; i < nbasis; i++) basistype[i] = ntype;
@ -354,19 +355,27 @@ void CreateAtoms::command(int narg, char **arg)
}
}
// demand non-none lattice be defined for BOX and REGION
// else setup scaling for SINGLE and RANDOM
// could use domain->lattice->lattice2box() to do conversion of
// lattice to box, but not consistent with other uses of units=lattice
// triclinic remapping occurs in add_single()
// require non-none lattice be defined for BOX or REGION styles
if ((style == BOX) || (style == REGION)) {
if (nbasis == 0) error->all(FLERR, "Cannot create atoms with undefined lattice");
} else if (scaleflag == 1) {
// apply scaling factor for styles that use distance-dependent factors
if (scaleflag) {
if (style == SINGLE) {
xone[0] *= domain->lattice->xlattice;
xone[1] *= domain->lattice->ylattice;
xone[2] *= domain->lattice->zlattice;
overlap *= domain->lattice->xlattice;
} else if (style == RANDOM) {
if (overlapflag) overlap *= domain->lattice->xlattice;
} else if (style == MESH) { // NOTE to Axel - here is the rescaling of both params
if (mesh_style == BISECT) { // by lattice spacings if units = lattice, similar to xone,overlap
radthresh *= domain->lattice->xlattice;
} else if (mesh_style = QUASIRANDOM) {
mesh_density /= (domain->lattice->xlattice * domain->lattice->xlattice);
}
}
}
// set bounds for my proc in sublo[3] & subhi[3]
@ -710,7 +719,7 @@ void CreateAtoms::add_single()
void CreateAtoms::add_random()
{
double xlo, ylo, zlo, xhi, yhi, zhi, zmid;
double xlo, ylo, zlo, xhi, yhi, zhi;
double delx, dely, delz, distsq, odistsq;
double lamda[3], *coord;
double *boxlo, *boxhi;
@ -729,7 +738,6 @@ void CreateAtoms::add_random()
for (int ii = 0; ii < 30; ii++) random->uniform();
// bounding box for atom creation
// in real units, even if triclinic
// only limit bbox by region if its bboxflag is set (interior region)
if (triclinic == 0) {
@ -739,7 +747,6 @@ void CreateAtoms::add_random()
yhi = domain->boxhi[1];
zlo = domain->boxlo[2];
zhi = domain->boxhi[2];
zmid = zlo + 0.5 * (zhi - zlo);
} else {
xlo = domain->boxlo_bound[0];
xhi = domain->boxhi_bound[0];
@ -747,7 +754,6 @@ void CreateAtoms::add_random()
yhi = domain->boxhi_bound[1];
zlo = domain->boxlo_bound[2];
zhi = domain->boxhi_bound[2];
zmid = zlo + 0.5 * (zhi - zlo);
boxlo = domain->boxlo_lamda;
boxhi = domain->boxhi_lamda;
}
@ -783,7 +789,7 @@ void CreateAtoms::add_random()
xone[0] = xlo + random->uniform() * (xhi - xlo);
xone[1] = ylo + random->uniform() * (yhi - ylo);
xone[2] = zlo + random->uniform() * (zhi - zlo);
if (domain->dimension == 2) xone[2] = zmid;
if (domain->dimension == 2) xone[2] = 0.0;
if (region && (region->match(xone[0], xone[1], xone[2]) == 0)) continue;
if (varflag && vartest(xone) == 0) continue;
@ -1168,16 +1174,12 @@ void CreateAtoms::add_mesh(const char *filename)
void CreateAtoms::add_lattice()
{
// add atoms on general triclinic lattice if Domain has setting for it
// verify lattice is valid for general triclinic
int triclinic_general = domain->triclinic_general;
// verify lattice was defined with triclinic/general option
if (triclinic_general) {
if (!domain->lattice->is_custom())
error->all(FLERR,"Create_atoms for general triclinic requires custom lattice");
if (domain->lattice->is_oriented())
error->all(FLERR,"Create_atoms for general triclinic requires lattice with default orientation");
}
if (!domain->triclinic_general && domain->lattice->is_general_triclinic())
error->all(FLERR,"Create_atoms for non general triclinic box cannot use triclinic/general lattice");
if (domain->triclinic_general && !domain->lattice->is_general_triclinic())
error->all(FLERR,"Create_atoms for general triclinic box requires triclnic/general lattice");
// convert 8 corners of my subdomain from box coords to lattice coords
// for orthogonal, use corner pts of my subbox
@ -1224,7 +1226,7 @@ void CreateAtoms::add_lattice()
// compute new bounding box (xyz min/max) in lattice coords
// for orthogonal or restricted triclinic, use 8 corner points of bbox lo/hi
if (!triclinic_general) {
if (!domain->triclinic_general) {
domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
@ -1238,7 +1240,7 @@ void CreateAtoms::add_lattice()
// new set of 8 points is no longer an orthogonal bounding box
// instead invoke lattice->bbox() on each of 8 points
} else if (triclinic_general) {
} else if (domain->triclinic_general) {
double point[3];
point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2];