268 lines
7.1 KiB
C++
268 lines
7.1 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 "math.h"
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#include "string.h"
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#include "stdlib.h"
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#include "compute_pair_local.h"
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#include "atom.h"
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#include "update.h"
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#include "force.h"
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#include "pair.h"
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#include "neighbor.h"
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#include "neigh_request.h"
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#include "neigh_list.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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using namespace LAMMPS_NS;
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#define DELTA 10000
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enum{DIST,ENG,FORCE,FX,FY,FZ,PN};
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/* ---------------------------------------------------------------------- */
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ComputePairLocal::ComputePairLocal(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg < 4) error->all(FLERR,"Illegal compute pair/local command");
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local_flag = 1;
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nvalues = narg - 3;
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if (nvalues == 1) size_local_cols = 0;
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else size_local_cols = nvalues;
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pstyle = new int[nvalues];
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pindex = new int[nvalues];
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nvalues = 0;
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for (int iarg = 3; iarg < narg; iarg++) {
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if (strcmp(arg[iarg],"dist") == 0) pstyle[nvalues++] = DIST;
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else if (strcmp(arg[iarg],"eng") == 0) pstyle[nvalues++] = ENG;
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else if (strcmp(arg[iarg],"force") == 0) pstyle[nvalues++] = FORCE;
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else if (strcmp(arg[iarg],"fx") == 0) pstyle[nvalues++] = FX;
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else if (strcmp(arg[iarg],"fy") == 0) pstyle[nvalues++] = FY;
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else if (strcmp(arg[iarg],"fz") == 0) pstyle[nvalues++] = FZ;
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else if (arg[iarg][0] == 'p') {
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int n = atoi(&arg[iarg][1]);
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if (n <= 0) error->all(FLERR,
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"Invalid keyword in compute pair/local command");
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pstyle[nvalues] = PN;
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pindex[nvalues++] = n-1;
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} else error->all(FLERR,"Invalid keyword in compute pair/local command");
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}
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// set singleflag if need to call pair->single()
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singleflag = 0;
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for (int i = 0; i < nvalues; i++)
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if (pstyle[i] != DIST) singleflag = 1;
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nmax = 0;
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vector = NULL;
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array = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputePairLocal::~ComputePairLocal()
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{
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memory->destroy(vector);
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memory->destroy(array);
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delete [] pstyle;
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delete [] pindex;
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}
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/* ---------------------------------------------------------------------- */
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void ComputePairLocal::init()
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{
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if (singleflag && force->pair == NULL)
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error->all(FLERR,"No pair style is defined for compute pair/local");
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if (singleflag && force->pair->single_enable == 0)
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error->all(FLERR,"Pair style does not support compute pair/local");
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for (int i = 0; i < nvalues; i++)
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if (pstyle[i] == PN && pindex[i] >= force->pair->single_extra)
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error->all(FLERR,"Pair style does not have extra field"
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" requested by compute pair/local");
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// need an occasional half neighbor list
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int irequest = neighbor->request((void *) this);
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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]->occasional = 1;
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}
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/* ---------------------------------------------------------------------- */
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void ComputePairLocal::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 ComputePairLocal::compute_local()
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{
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invoked_local = update->ntimestep;
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// count local entries and compute pair info
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ncount = compute_pairs(0);
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if (ncount > nmax) reallocate(ncount);
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size_local_rows = ncount;
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compute_pairs(1);
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}
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/* ----------------------------------------------------------------------
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count pairs and compute pair info on this proc
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only count pair once if newton_pair is off
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both atom I,J must be in group
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if flag is set, compute requested info about pair
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------------------------------------------------------------------------- */
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int ComputePairLocal::compute_pairs(int flag)
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{
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int i,j,m,n,ii,jj,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz;
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double rsq,eng,fpair,factor_coul,factor_lj;
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int *ilist,*jlist,*numneigh,**firstneigh;
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double *ptr;
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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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int nlocal = atom->nlocal;
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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// invoke half neighbor list (will copy or build if necessary)
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if (flag == 0) neighbor->build_one(list->index);
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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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// loop over neighbors of my atoms
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// skip if I or J are not in group
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// for flag = 0, just count pair interactions within force cutoff
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// for flag = 1, calculate requested output fields
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Pair *pair = force->pair;
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double **cutsq = force->pair->cutsq;
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m = 0;
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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)) continue;
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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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itype = type[i];
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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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factor_lj = special_lj[sbmask(j)];
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factor_coul = special_coul[sbmask(j)];
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j &= NEIGHMASK;
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if (!(mask[j] & groupbit)) continue;
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if (newton_pair == 0 && j >= nlocal) continue;
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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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jtype = type[j];
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if (rsq >= cutsq[itype][jtype]) continue;
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if (flag) {
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if (singleflag)
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eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
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if (nvalues == 1) ptr = &vector[m];
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else ptr = array[m];
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for (n = 0; n < nvalues; n++) {
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switch (pstyle[n]) {
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case DIST:
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ptr[n] = sqrt(rsq);
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break;
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case ENG:
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ptr[n] = eng;
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break;
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case FORCE:
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ptr[n] = sqrt(rsq)*fpair;
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break;
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case FX:
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ptr[n] = delx*fpair;
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break;
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case FY:
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ptr[n] = dely*fpair;
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break;
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case FZ:
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ptr[n] = delz*fpair;
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break;
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case PN:
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ptr[n] = pair->svector[pindex[n]];
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break;
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}
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}
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}
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m++;
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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 ComputePairLocal::reallocate(int n)
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{
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// grow vector or array and indices array
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while (nmax < n) nmax += DELTA;
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if (nvalues == 1) {
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memory->destroy(vector);
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memory->create(vector,nmax,"pair/local:vector");
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vector_local = vector;
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} else {
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memory->destroy(array);
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memory->create(array,nmax,nvalues,"pair/local:array");
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array_local = array;
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local data
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------------------------------------------------------------------------- */
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double ComputePairLocal::memory_usage()
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{
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double bytes = nmax*nvalues * sizeof(double);
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return bytes;
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}
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