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lammps/src/compute_pair_local.cpp
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compute_pair_local.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include "compute_pair_local.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
enum{DIST,ENG,FORCE,FX,FY,FZ,PN};
enum{TYPE,RADIUS};
/* ---------------------------------------------------------------------- */
ComputePairLocal::ComputePairLocal(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
pstyle(NULL), pindex(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal compute pair/local command");
local_flag = 1;
nvalues = narg - 3;
if (nvalues == 1) size_local_cols = 0;
else size_local_cols = nvalues;
pstyle = new int[nvalues];
pindex = new int[nvalues];
nvalues = 0;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"dist") == 0) pstyle[nvalues++] = DIST;
else if (strcmp(arg[iarg],"eng") == 0) pstyle[nvalues++] = ENG;
else if (strcmp(arg[iarg],"force") == 0) pstyle[nvalues++] = FORCE;
else if (strcmp(arg[iarg],"fx") == 0) pstyle[nvalues++] = FX;
else if (strcmp(arg[iarg],"fy") == 0) pstyle[nvalues++] = FY;
else if (strcmp(arg[iarg],"fz") == 0) pstyle[nvalues++] = FZ;
else if (arg[iarg][0] == 'p') {
int n = atoi(&arg[iarg][1]);
if (n <= 0) error->all(FLERR,
"Invalid keyword in compute pair/local command");
pstyle[nvalues] = PN;
pindex[nvalues++] = n-1;
} else break;
iarg++;
}
// optional args
cutstyle = TYPE;
while (iarg < narg) {
if (strcmp(arg[iarg],"cutoff") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute pair/local command");
if (strcmp(arg[iarg+1],"type") == 0) cutstyle = TYPE;
else if (strcmp(arg[iarg+1],"radius") == 0) cutstyle = RADIUS;
else error->all(FLERR,"Illegal compute pair/local command");
iarg += 2;
} else error->all(FLERR,"Illegal compute pair/local command");
}
// error check
if (cutstyle == RADIUS && !atom->radius_flag)
error->all(FLERR,"Compute pair/local requires atom attribute radius");
// set singleflag if need to call pair->single()
singleflag = 0;
for (int i = 0; i < nvalues; i++)
if (pstyle[i] != DIST) singleflag = 1;
nmax = 0;
}
/* ---------------------------------------------------------------------- */
ComputePairLocal::~ComputePairLocal()
{
memory->destroy(vector);
memory->destroy(array);
delete [] pstyle;
delete [] pindex;
}
/* ---------------------------------------------------------------------- */
void ComputePairLocal::init()
{
if (singleflag && force->pair == NULL)
error->all(FLERR,"No pair style is defined for compute pair/local");
if (singleflag && force->pair->single_enable == 0)
error->all(FLERR,"Pair style does not support compute pair/local");
for (int i = 0; i < nvalues; i++)
if (pstyle[i] == PN && pindex[i] >= force->pair->single_extra)
error->all(FLERR,"Pair style does not have extra field"
" requested by compute pair/local");
// need an occasional half neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
}
/* ---------------------------------------------------------------------- */
void ComputePairLocal::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputePairLocal::compute_local()
{
invoked_local = update->ntimestep;
// count local entries and compute pair info
ncount = compute_pairs(0);
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
compute_pairs(1);
}
/* ----------------------------------------------------------------------
count pairs and compute pair info on this proc
only count pair once if newton_pair is off
both atom I,J must be in group
if flag is set, compute requested info about pair
------------------------------------------------------------------------- */
int ComputePairLocal::compute_pairs(int flag)
{
int i,j,m,n,ii,jj,inum,jnum,itype,jtype;
tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,radsum,eng,fpair,factor_coul,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
double *ptr;
double **x = atom->x;
double *radius = atom->radius;
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
// invoke half neighbor list (will copy or build if necessary)
if (flag == 0) neighbor->build_one(list);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
// skip if I or J are not in group
// for newton = 0 and J = ghost atom,
// need to insure I,J pair is only output by one proc
// use same itag,jtag logic as in Neighbor::neigh_half_nsq()
// for flag = 0, just count pair interactions within force cutoff
// for flag = 1, calculate requested output fields
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
m = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (!(mask[i] & groupbit)) continue;
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itag = tag[i];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
if (!(mask[j] & groupbit)) continue;
// itag = jtag is possible for long cutoffs that include images of self
if (newton_pair == 0 && j >= nlocal) {
jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
}
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (cutstyle == TYPE) {
if (rsq >= cutsq[itype][jtype]) continue;
} else {
radsum = radius[i] + radius[j];
if (rsq >= radsum*radsum) continue;
}
if (flag) {
if (singleflag)
eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
else eng = fpair = 0.0;
if (nvalues == 1) ptr = &vector[m];
else ptr = array[m];
for (n = 0; n < nvalues; n++) {
switch (pstyle[n]) {
case DIST:
ptr[n] = sqrt(rsq);
break;
case ENG:
ptr[n] = eng;
break;
case FORCE:
ptr[n] = sqrt(rsq)*fpair;
break;
case FX:
ptr[n] = delx*fpair;
break;
case FY:
ptr[n] = dely*fpair;
break;
case FZ:
ptr[n] = delz*fpair;
break;
case PN:
ptr[n] = pair->svector[pindex[n]];
break;
}
}
}
m++;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputePairLocal::reallocate(int n)
{
// grow vector or array and indices array
while (nmax < n) nmax += DELTA;
if (nvalues == 1) {
memory->destroy(vector);
memory->create(vector,nmax,"pair/local:vector");
vector_local = vector;
} else {
memory->destroy(array);
memory->create(array,nmax,nvalues,"pair/local:array");
array_local = array;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputePairLocal::memory_usage()
{
double bytes = nmax*nvalues * sizeof(double);
return bytes;
}
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