git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/create_atoms.cpp
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339
src/create_atoms.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdlib.h"
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#include "string.h"
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#include "create_atoms.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "domain.h"
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#include "update.h"
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#include "region.h"
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#include "error.h"
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#define SC 1
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#define BCC 2
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#define FCC 3
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#define SQ 4
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#define SQ2 5
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#define HEX 6
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#define DIAMOND 7
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#define MINATOMS 1000
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#define MAXATOMS 0x7FFFFFFF
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#define EPSILON 1.0e-6
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/* ---------------------------------------------------------------------- */
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void CreateAtoms::command(int narg, char **arg)
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{
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if (domain->box_exist == 0)
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error->all("Create_atoms command before simulation box is defined");
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if (narg != 1 && narg != 2) error->all("Illegal create_atoms command");
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create_type = atoi(arg[0]);
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if (create_type > atom->ntypes)
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error->all("Too large an atom type in create_atoms command");
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if (strcmp(domain->lattice_style,"none") == 0)
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error->all("Cannot create atoms with undefined lattice");
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if (!domain->orthogonality()) error->all("Non-orthogonal lattice vectors");
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if (!domain->right_handed())
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error->all("Orientation vectors are not right-handed");
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// iregion = specified region (-1 if not specified)
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iregion = -1;
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if (narg == 2) {
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for (iregion = 0; iregion < domain->nregion; iregion++)
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if (strcmp(arg[1],domain->regions[iregion]->id) == 0) break;
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if (iregion == domain->nregion)
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error->all("Create_atoms region ID does not exist");
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}
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// local copies of domain properties
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subxlo = domain->subxlo;
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subxhi = domain->subxhi;
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subylo = domain->subylo;
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subyhi = domain->subyhi;
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subzlo = domain->subzlo;
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subzhi = domain->subzhi;
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boxxhi = domain->boxxhi;
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boxyhi = domain->boxyhi;
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boxzhi = domain->boxzhi;
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// ilo:ihi,jlo:jhi,klo:khi = loop bounds of simple cubic lattice
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// that entirely overlaps my proc's sub-box
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int ilo,ihi,jlo,jhi,klo,khi;
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loop_bounds(0,&ilo,&ihi);
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loop_bounds(1,&jlo,&jhi);
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loop_bounds(2,&klo,&khi);
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// initialize 3d periodic lattice using overlapping loop bounds
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// lattice style determines how many atoms in cubic unit cell
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// sc = 1, bcc = 2, fcc = 4, sq = 1, sq2 = 2, hex = 2, diamond = 8
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double natoms_previous = atom->natoms;
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int nlocal_previous = atom->nlocal;
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int style;
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if (strcmp(domain->lattice_style,"sc") == 0) style = SC;
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else if (strcmp(domain->lattice_style,"bcc") == 0) style = BCC;
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else if (strcmp(domain->lattice_style,"fcc") == 0) style = FCC;
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else if (strcmp(domain->lattice_style,"sq") == 0) style = SQ;
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else if (strcmp(domain->lattice_style,"sq2") == 0) style = SQ2;
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else if (strcmp(domain->lattice_style,"hex") == 0) style = HEX;
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else if (strcmp(domain->lattice_style,"diamond") == 0) style = DIAMOND;
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double ifull,ihalf,jfull,jhalf,kfull,khalf;
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double iquart,i3quart,jquart,j3quart,kquart,k3quart;
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int i,j,k;
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for (k = klo; k <= khi; k++) {
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kfull = (double) k;
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khalf = k + 0.5;
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kquart = k + 0.25;
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k3quart = k + 0.75;
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for (j = jlo; j <= jhi; j++) {
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jfull = (double) j;
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jhalf = j + 0.5;
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jquart = j + 0.25;
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j3quart = j + 0.75;
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for (i = ilo; i <= ihi; i++) {
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ifull = (double) i;
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ihalf = i + 0.5;
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iquart = i + 0.25;
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i3quart = i + 0.75;
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if (style == SC)
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add_atom(ifull,jfull,kfull);
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else if (style == BCC) {
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add_atom(ifull,jfull,kfull);
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add_atom(ihalf,jhalf,khalf);
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} else if (style == FCC) {
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add_atom(ifull,jfull,kfull);
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add_atom(ihalf,jhalf,kfull);
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add_atom(ihalf,jfull,khalf);
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add_atom(ifull,jhalf,khalf);
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} else if (style == SQ) {
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add_atom(ifull,jfull,kfull);
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} else if (style == SQ2) {
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add_atom(ifull,jfull,kfull);
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add_atom(ihalf,jhalf,kfull);
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} else if (style == HEX) {
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add_atom(ifull,jfull,kfull);
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add_atom(ihalf,jhalf,kfull);
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} else if (style == DIAMOND) {
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add_atom(ifull,jfull,kfull);
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add_atom(ifull,jhalf,khalf);
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add_atom(ihalf,jfull,khalf);
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add_atom(ihalf,jhalf,kfull);
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add_atom(iquart,jquart,kquart);
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add_atom(iquart,j3quart,k3quart);
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add_atom(i3quart,jquart,k3quart);
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add_atom(i3quart,j3quart,kquart);
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}
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}
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}
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}
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// new total # of atoms
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double rlocal = atom->nlocal;
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MPI_Allreduce(&rlocal,&atom->natoms,1,MPI_DOUBLE,MPI_SUM,world);
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// print status
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if (comm->me == 0) {
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if (screen)
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fprintf(screen,"Created %.15g atoms\n",atom->natoms-natoms_previous);
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if (logfile)
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fprintf(logfile,"Created %.15g atoms\n",atom->natoms-natoms_previous);
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}
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// reset simulation now that more atoms are defined
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// add tags for newly created atoms if possible
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// if global map exists, reset it
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// if a molecular system, set nspecial to 0 for new atoms
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if (atom->natoms > MAXATOMS) atom->tag_enable = 0;
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if (atom->natoms <= MAXATOMS) atom->tag_extend();
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if (atom->map_style) {
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atom->map_init();
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atom->map_set();
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}
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if (atom->molecular) {
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int **nspecial = atom->nspecial;
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for (i = nlocal_previous; i < atom->nlocal; i++) {
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nspecial[i][0] = 0;
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nspecial[i][1] = 0;
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nspecial[i][2] = 0;
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}
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}
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}
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/* ----------------------------------------------------------------------
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add an atom at x,y,z in lattice coords if it meets all criteria
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------------------------------------------------------------------------- */
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void CreateAtoms::add_atom(double x, double y, double z)
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{
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// convert from lattice coords to box coords
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domain->lattice2box(&x,&y,&z);
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// if a region was specified, test if atom is in it
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if (iregion >= 0)
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if (!domain->regions[iregion]->match(x,y,z)) return;
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// test if atom is in my subbox
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if (x < subxlo || x >= subxhi ||
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y < subylo || y >= subyhi ||
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z < subzlo || z >= subzhi) return;
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// don't put atoms within EPSILON of upper periodic boundary
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// else may overlap image atom at lower boundary
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if (domain->xperiodic && fabs(x-boxxhi) < EPSILON) return;
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if (domain->yperiodic && fabs(y-boxyhi) < EPSILON) return;
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if (domain->zperiodic && fabs(z-boxzhi) < EPSILON) return;
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// add the atom to my list of atoms
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atom->create_one(create_type,x,y,z);
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}
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/* ----------------------------------------------------------------------
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search for 2 bounding lattice planes that completely enclose my sub-box
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do this by testing if all corner points of my sub-box lie on correct side
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of a lattice plane via same_side function
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dim = 0,1,2 for x,y,z directions
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lo,hi = returned indices of 2 bounding lattice planes
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a lattice plane is defined by:
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point = point in lattice space through which the plane passes
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normal = vector normal to lattice plane
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------------------------------------------------------------------------- */
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void CreateAtoms::loop_bounds(int dim, int *lo, int *hi)
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{
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int normal[3],point[3];
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// start search at origin
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point[0] = point[1] = point[2] = 0;
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// set lattice plane direction along positive lattice axis
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normal[0] = normal[1] = normal[2] = 0;
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normal[dim] = 1;
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// step down (if needed) until entire box is above the plane
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// step up until 1st time entire box is not above the plane
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while (!same_side(point,normal)) point[dim]--;
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while (same_side(point,normal)) point[dim]++;
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// lower loop bound = current loc minus 1 (subtract 1 more for safety)
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*lo = point[dim] - 2;
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// flip plane direction
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// step up until entire box is below the plane
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normal[dim] = -1;
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while (!same_side(point,normal)) point[dim]++;
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// lower loop bound = current loc (add 1 more for safety)
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*hi = point[dim] + 1;
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}
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/* ----------------------------------------------------------------------
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test if all 8 corner points of my sub-box are on "correct" side of a plane
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plane is defined by point[3] it goes thru and a normal[3]
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normal also defines the correct side
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------------------------------------------------------------------------- */
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int CreateAtoms::same_side(int *point, int *normal)
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{
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// p1 = plane center point in box coords
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// p2 = point on correct side of plane, in box coords
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double p1x = point[0];
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double p1y = point[1];
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double p1z = point[2];
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domain->lattice2box(&p1x,&p1y,&p1z);
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double p2x = point[0] + normal[0];
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double p2y = point[1] + normal[1];
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double p2z = point[2] + normal[2];
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domain->lattice2box(&p2x,&p2y,&p2z);
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// for each of 8 sub-box corner points, dot these 2 vectors:
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// v1 = from plane center point to point on correct side of plane
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// v2 = from plane center point to box corner point
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// negative result = portion of box is on wrong side of plane, return 0
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double v1[3],v2[3];
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points2vec(p1x,p1y,p1z,p2x,p2y,p2z,v1);
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points2vec(p1x,p1y,p1z,subxlo,subylo,subzlo,v2);
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if (dot(v1,v2) < 0.0) return 0;
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points2vec(p1x,p1y,p1z,subxhi,subylo,subzlo,v2);
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if (dot(v1,v2) < 0.0) return 0;
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points2vec(p1x,p1y,p1z,subxlo,subyhi,subzlo,v2);
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if (dot(v1,v2) < 0.0) return 0;
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points2vec(p1x,p1y,p1z,subxhi,subyhi,subzlo,v2);
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if (dot(v1,v2) < 0.0) return 0;
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points2vec(p1x,p1y,p1z,subxlo,subylo,subzhi,v2);
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if (dot(v1,v2) < 0.0) return 0;
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points2vec(p1x,p1y,p1z,subxhi,subylo,subzhi,v2);
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if (dot(v1,v2) < 0.0) return 0;
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points2vec(p1x,p1y,p1z,subxlo,subyhi,subzhi,v2);
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if (dot(v1,v2) < 0.0) return 0;
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points2vec(p1x,p1y,p1z,subxhi,subyhi,subzhi,v2);
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if (dot(v1,v2) < 0.0) return 0;
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// all 8 points were on correct side
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return 1;
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}
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/* ---------------------------------------------------------------------- */
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double CreateAtoms::dot(double *vec1, double *vec2)
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{
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double sum = vec1[0]*vec2[0] + vec1[1]*vec2[1] + vec1[2]*vec2[2];
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return sum;
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}
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/* ---------------------------------------------------------------------- */
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void CreateAtoms::points2vec(double p1x, double p1y, double p1z,
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double p2x, double p2y, double p2z, double *v)
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{
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v[0] = p2x - p1x;
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v[1] = p2y - p1y;
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v[2] = p2z - p1z;
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}
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