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work on create_atoms command

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This commit is contained in:
Steve Plimpton
2023-09-01 14:38:22 -06:00
parent 7462439b5d
commit 817a16b48c
5 changed files with 90 additions and 23 deletions
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90
src/create_atoms.cpp
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@ -450,8 +450,8 @@ void CreateAtoms::command(int narg, char **arg)
atom->nghost = 0;
atom->avec->clear_bonus();
// add atoms/molecules in one of 3 ways
// add atoms/molecules with appropriate add() method
bigint natoms_previous = atom->natoms;
int nlocal_previous = atom->nlocal;
@ -1155,12 +1155,34 @@ void CreateAtoms::add_mesh(const char *filename)
}
}
/* ----------------------------------------------------------------------
add many atoms to general triclinic box by looping over lattice
------------------------------------------------------------------------- */
void CreateAtoms::add_lattice_triclinic_general()
{
}
/* ----------------------------------------------------------------------
add many atoms by looping over lattice
------------------------------------------------------------------------- */
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;
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");
}
// convert 8 corners of my subdomain from box coords to lattice coords
// for orthogonal, use corner pts of my subbox
// for triclinic, use bounding box of my subbox
@ -1202,17 +1224,56 @@ void CreateAtoms::add_lattice()
xmin = ymin = zmin = BIG;
xmax = ymax = zmax = -BIG;
// convert to lattice coordinates and set bounding box
// convert 8 corner points of bounding box to lattice coordinates
// 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) {
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);
domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
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);
domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
// for general triclinic, convert 8 corner points of bbox to general triclinic coords
// 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) {
double point[3];
point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2];
domain->restricted_to_general(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxhi[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2];
domain->restricted_to_general(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxlo[0]; point[1] = bboxhi[1]; point[2] = bboxlo[2];
domain->restricted_to_general(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxhi[0]; point[1] = bboxhi[1]; point[2] = bboxlo[2];
domain->restricted_to_general(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxhi[2];
domain->restricted_to_general(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxhi[0]; point[1] = bboxlo[1]; point[2] = bboxhi[2];
domain->restricted_to_general(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxlo[0]; point[1] = bboxhi[1]; point[2] = bboxhi[2];
domain->restricted_to_general(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxhi[0]; point[1] = bboxhi[1]; point[2] = bboxhi[2];
domain->restricted_to_general(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
}
// ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my subbox
// overlap = any part of a unit cell (face,edge,pt) in common with my subbox
// in lattice space, subbox is a tilted box
@ -1233,6 +1294,8 @@ void CreateAtoms::add_lattice()
if (ymin < 0.0) jlo--;
if (zmin < 0.0) klo--;
printf("LOOP LATTICE bounds: %d %d: %d %d: %d %d\n",ilo,ihi,jlo,jhi,klo,khi);
// count lattice sites on each proc
nlatt_overflow = 0;
@ -1298,6 +1361,7 @@ void CreateAtoms::loop_lattice(int action)
{
int i, j, k, m;
int triclinic_general = domain->triclinic_general;
const double *const *const basis = domain->lattice->basis;
nlatt = 0;
@ -1317,6 +1381,10 @@ void CreateAtoms::loop_lattice(int action)
domain->lattice->lattice2box(x[0], x[1], x[2]);
// convert from general to restricted triclinic coords
if (triclinic_general) domain->general_to_restricted(x);
// if a region was specified, test if atom is in it
if (style == REGION)

1
src/create_atoms.h
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@ -69,6 +69,7 @@ class CreateAtoms : public Command {
void add_mesh(const char *);
int add_bisection(const double[3][3], tagint);
int add_quasirandom(const double[3][3], tagint);
void add_lattice_triclinic_general();
void add_lattice();
void loop_lattice(int);
void add_molecule(double *);

13
src/create_box.cpp
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@ -115,8 +115,10 @@ void CreateBox::command(int narg, char **arg)
double chi = utils::numeric(FLERR, arg[iarg + 5], false, lmp);
iarg += 6;
// use lattice2box() to generate avec, bvec, cvec and origin
// use lattice2box() to generate origin and ABC vectors
// origin = abc lo
// ABC vector = hi in one dim - orign
double avec[3],bvec[3],cvec[3],origin[3];
double px,py,pz;
@ -144,12 +146,7 @@ void CreateBox::command(int narg, char **arg)
cvec[1] = py - origin[1];
cvec[2] = pz - origin[2];
printf("ORIGIN %g %g %g\n",origin[0],origin[1],origin[2]);
printf("AVEC %g %g %g\n",avec[0],avec[1],avec[2]);
printf("BVEC %g %g %g\n",bvec[0],bvec[1],bvec[2]);
printf("CVEC %g %g %g\n",cvec[0],cvec[1],cvec[2]);
// setup general triclinic box in Domain
// setup general triclinic box within Domain
domain->set_general_triclinic(avec,bvec,cvec,origin);
}

4
src/domain.cpp
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@ -667,7 +667,7 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller,
}
/* ----------------------------------------------------------------------
transform one atom's coords from general triclinic to restricted triclinic
transform atom coords from general triclinic to restricted triclinic
------------------------------------------------------------------------- */
void Domain::general_to_restricted(double *x)
@ -681,7 +681,7 @@ void Domain::general_to_restricted(double *x)
}
/* ----------------------------------------------------------------------
transform one atom's coords from restricted triclinic to general triclinic
transform atom coords from restricted triclinic to general triclinic
------------------------------------------------------------------------- */
void Domain::restricted_to_general(double *x)

5
src/lattice.cpp
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@ -582,8 +582,9 @@ void Lattice::cross(double *x, double *y, double *z)
}
/* ----------------------------------------------------------------------
convert x,y,z from lattice coords to box coords (flag = 0) or vice versa
use new point to expand bounding box (min to max)
convert x,y,z from lattice coords to box coords (flag = 0)
or from box coords to lattice coords (flag = 1)
either way, use new point to expand bounding box (min to max)
------------------------------------------------------------------------- */
void Lattice::bbox(int flag, double x, double y, double z,