361 lines
9.8 KiB
C++
361 lines
9.8 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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 "compute_coord_atom.h"
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#include <cmath>
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#include <cstring>
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#include "compute_orientorder_atom.h"
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "force.h"
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#include "pair.h"
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#include "comm.h"
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#include "group.h"
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#include "memory.h"
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#include "error.h"
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#include "utils.h"
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using namespace LAMMPS_NS;
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#define INVOKED_PERATOM 8
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/* ---------------------------------------------------------------------- */
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ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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typelo(NULL), typehi(NULL), cvec(NULL), carray(NULL),
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group2(NULL), id_orientorder(NULL), normv(NULL)
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{
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if (narg < 5) error->all(FLERR,"Illegal compute coord/atom command");
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jgroup = group->find("all");
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jgroupbit = group->bitmask[jgroup];
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cstyle = NONE;
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if (strcmp(arg[3],"cutoff") == 0) {
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cstyle = CUTOFF;
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double cutoff = force->numeric(FLERR,arg[4]);
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cutsq = cutoff*cutoff;
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int iarg = 5;
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if ((narg > 6) && (strcmp(arg[5],"group") == 0)) {
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int len = strlen(arg[6])+1;
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group2 = new char[len];
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strcpy(group2,arg[6]);
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iarg += 2;
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jgroup = group->find(group2);
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if (jgroup == -1)
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error->all(FLERR,"Compute coord/atom group2 ID does not exist");
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jgroupbit = group->bitmask[jgroup];
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}
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ncol = narg-iarg + 1;
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int ntypes = atom->ntypes;
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typelo = new int[ncol];
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typehi = new int[ncol];
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if (narg == iarg) {
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ncol = 1;
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typelo[0] = 1;
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typehi[0] = ntypes;
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} else {
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ncol = 0;
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while (iarg < narg) {
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force->bounds(FLERR,arg[iarg],ntypes,typelo[ncol],typehi[ncol]);
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if (typelo[ncol] > typehi[ncol])
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error->all(FLERR,"Illegal compute coord/atom command");
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ncol++;
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iarg++;
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}
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}
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} else if (strcmp(arg[3],"orientorder") == 0) {
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cstyle = ORIENT;
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if (narg != 6) error->all(FLERR,"Illegal compute coord/atom command");
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int n = strlen(arg[4]) + 1;
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id_orientorder = new char[n];
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strcpy(id_orientorder,arg[4]);
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int iorientorder = modify->find_compute(id_orientorder);
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if (iorientorder < 0)
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error->all(FLERR,"Could not find compute coord/atom compute ID");
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if (!utils::strmatch(modify->compute[iorientorder]->style,"^orientorder/atom"))
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error->all(FLERR,"Compute coord/atom compute ID is not orientorder/atom");
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threshold = force->numeric(FLERR,arg[5]);
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if (threshold <= -1.0 || threshold >= 1.0)
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error->all(FLERR,"Compute coord/atom threshold not between -1 and 1");
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ncol = 1;
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typelo = new int[ncol];
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typehi = new int[ncol];
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typelo[0] = 1;
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typehi[0] = atom->ntypes;
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} else error->all(FLERR,"Invalid cstyle in compute coord/atom");
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peratom_flag = 1;
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if (ncol == 1) size_peratom_cols = 0;
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else size_peratom_cols = ncol;
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nmax = 0;
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}
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/* ---------------------------------------------------------------------- */
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ComputeCoordAtom::~ComputeCoordAtom()
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{
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if (copymode) return;
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delete [] group2;
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delete [] typelo;
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delete [] typehi;
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memory->destroy(cvec);
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memory->destroy(carray);
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delete [] id_orientorder;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCoordAtom::init()
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{
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if (cstyle == ORIENT) {
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int iorientorder = modify->find_compute(id_orientorder);
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c_orientorder = (ComputeOrientOrderAtom*)(modify->compute[iorientorder]);
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cutsq = c_orientorder->cutsq;
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l = c_orientorder->qlcomp;
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// communicate real and imaginary 2*l+1 components of the normalized vector
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comm_forward = 2*(2*l+1);
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if (!(c_orientorder->qlcompflag))
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error->all(FLERR,"Compute coord/atom requires components "
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"option in compute orientorder/atom");
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}
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if (force->pair == NULL)
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error->all(FLERR,"Compute coord/atom requires a pair style be defined");
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if (sqrt(cutsq) > force->pair->cutforce)
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error->all(FLERR,
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"Compute coord/atom cutoff is longer than pairwise cutoff");
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// need an occasional full neighbor list
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int irequest = neighbor->request(this,instance_me);
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neighbor->requests[irequest]->pair = 0;
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neighbor->requests[irequest]->compute = 1;
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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neighbor->requests[irequest]->occasional = 1;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCoordAtom::init_list(int /*id*/, NeighList *ptr)
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{
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list = ptr;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCoordAtom::compute_peratom()
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{
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int i,j,m,ii,jj,inum,jnum,jtype,n;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *ilist,*jlist,*numneigh,**firstneigh;
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double *count;
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invoked_peratom = update->ntimestep;
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// grow coordination array if necessary
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if (atom->nmax > nmax) {
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if (ncol == 1) {
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memory->destroy(cvec);
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nmax = atom->nmax;
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memory->create(cvec,nmax,"coord/atom:cvec");
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vector_atom = cvec;
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} else {
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memory->destroy(carray);
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nmax = atom->nmax;
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memory->create(carray,nmax,ncol,"coord/atom:carray");
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array_atom = carray;
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}
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}
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if (cstyle == ORIENT) {
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if (!(c_orientorder->invoked_flag & INVOKED_PERATOM)) {
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c_orientorder->compute_peratom();
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c_orientorder->invoked_flag |= INVOKED_PERATOM;
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}
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nqlist = c_orientorder->nqlist;
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normv = c_orientorder->array_atom;
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comm->forward_comm_compute(this);
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}
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// invoke full neighbor list (will copy or build if necessary)
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neighbor->build_one(list);
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// compute coordination number(s) for each atom in group
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// use full neighbor list to count atoms less than cutoff
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double **x = atom->x;
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int *type = atom->type;
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int *mask = atom->mask;
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if (cstyle == CUTOFF) {
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if (ncol == 1) {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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n = 0;
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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if (mask[j] & jgroupbit) {
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jtype = type[j];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0])
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n++;
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}
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}
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cvec[i] = n;
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} else cvec[i] = 0.0;
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}
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} else {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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count = carray[i];
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for (m = 0; m < ncol; m++) count[m] = 0.0;
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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jtype = type[j];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq) {
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for (m = 0; m < ncol; m++)
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if (jtype >= typelo[m] && jtype <= typehi[m])
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count[m] += 1.0;
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}
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}
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}
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}
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}
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} else if (cstyle == ORIENT) {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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n = 0;
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq) {
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double dot_product = 0.0;
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for (int m=0; m < 2*(2*l+1); m++) {
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dot_product += normv[i][nqlist+m]*normv[j][nqlist+m];
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}
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if (dot_product > threshold) n++;
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}
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}
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cvec[i] = n;
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} else cvec[i] = 0.0;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf,
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int /*pbc_flag*/, int * /*pbc*/)
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{
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int i,m=0,j;
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for (i = 0; i < n; ++i) {
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for (j = nqlist; j < nqlist + 2*(2*l+1); ++j) {
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buf[m++] = normv[list[i]][j];
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCoordAtom::unpack_forward_comm(int n, int first, double *buf)
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{
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int i,last,m=0,j;
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last = first + n;
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for (i = first; i < last; ++i) {
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for (j = nqlist; j < nqlist + 2*(2*l+1); ++j) {
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normv[i][j] = buf[m++];
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}
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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double ComputeCoordAtom::memory_usage()
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{
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double bytes = ncol*nmax * sizeof(double);
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return bytes;
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}
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