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compute_cna_atom.cpp
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Fri, Nov 1, 22:26

compute_cna_atom.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Wan Liang (Chinese Academy of Sciences)
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "compute_cna_atom.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "math.h"
using namespace LAMMPS_NS;
#define MAXNEAR 16
#define MAXCOMMON 8
enum{UNKNOWN,FCC,HCP,BCC,ICOS,OTHER};
enum{NCOMMON,NBOND,MAXBOND,MINBOND};
/* ---------------------------------------------------------------------- */
ComputeCNAAtom::ComputeCNAAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute cna/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
double cutoff = atof(arg[3]);
if (cutoff < 0.0) error->all(FLERR,"Illegal compute cna/atom command");
cutsq = cutoff*cutoff;
nmax = 0;
nearest = NULL;
nnearest = NULL;
pattern = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeCNAAtom::~ComputeCNAAtom()
{
memory->destroy(nearest);
memory->destroy(nnearest);
memory->destroy(pattern);
}
/* ---------------------------------------------------------------------- */
void ComputeCNAAtom::init()
{
if (force->pair == NULL)
error->all(FLERR,"Compute cna/atom requires a pair style be defined");
if (sqrt(cutsq) > force->pair->cutforce)
error->all(FLERR,"Compute cna/atom cutoff is longer than pairwise cutoff");
// cannot use neighbor->cutneighmax b/c neighbor has not yet been init
if (2.0*sqrt(cutsq) > force->pair->cutforce + neighbor->skin &&
comm->me == 0)
error->warning(FLERR,"Compute cna/atom cutoff may be too large to find "
"ghost atom neighbors");
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"cna/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute cna/atom defined");
// need an occasional full neighbor list
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
}
/* ---------------------------------------------------------------------- */
void ComputeCNAAtom::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeCNAAtom::compute_peratom()
{
int i,j,k,ii,jj,kk,m,n,inum,jnum,inear,jnear;
int firstflag,ncommon,nbonds,maxbonds,minbonds;
int nfcc,nhcp,nbcc4,nbcc6,nico,cj,ck,cl,cm;
int *ilist,*jlist,*numneigh,**firstneigh;
int cna[MAXNEAR][4],onenearest[MAXNEAR];
int common[MAXCOMMON],bonds[MAXCOMMON];
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
invoked_peratom = update->ntimestep;
// grow arrays if necessary
if (atom->nlocal > nmax) {
memory->destroy(nearest);
memory->destroy(nnearest);
memory->destroy(pattern);
nmax = atom->nmax;
memory->create(nearest,nmax,MAXNEAR,"cna:nearest");
memory->create(nnearest,nmax,"cna:nnearest");
memory->create(pattern,nmax,"cna:cna_pattern");
vector_atom = pattern;
}
// invoke full neighbor list (will copy or build if necessary)
neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// find the neigbours of each atom within cutoff using full neighbor list
// nearest[] = atom indices of nearest neighbors, up to MAXNEAR
// do this for all atoms, not just compute group
// since CNA calculation requires neighbors of neighbors
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nerror = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
n = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
if (n < MAXNEAR) nearest[i][n++] = j;
else {
nerror++;
break;
}
}
}
nnearest[i] = n;
}
// warning message
int nerrorall;
MPI_Allreduce(&nerror,&nerrorall,1,MPI_INT,MPI_SUM,world);
if (nerrorall && comm->me == 0) {
char str[128];
sprintf(str,"Too many neighbors in CNA for %d atoms",nerrorall);
error->warning(FLERR,str,0);
}
// compute CNA for each atom in group
// only performed if # of nearest neighbors = 12 or 14 (fcc,hcp)
nerror = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (!(mask[i] & groupbit)) {
pattern[i] = UNKNOWN;
continue;
}
if (nnearest[i] != 12 && nnearest[i] != 14) {
pattern[i] = OTHER;
continue;
}
// loop over near neighbors of I to build cna data structure
// cna[k][NCOMMON] = # of common neighbors of I with each of its neighs
// cna[k][NBONDS] = # of bonds between those common neighbors
// cna[k][MAXBOND] = max # of bonds of any common neighbor
// cna[k][MINBOND] = min # of bonds of any common neighbor
for (m = 0; m < nnearest[i]; m++) {
j = nearest[i][m];
// common = list of neighbors common to atom I and atom J
// if J is an owned atom, use its near neighbor list to find them
// if J is a ghost atom, use full neighbor list of I to find them
// in latter case, must exclude J from I's neighbor list
if (j < nlocal) {
firstflag = 1;
ncommon = 0;
for (inear = 0; inear < nnearest[i]; inear++)
for (jnear = 0; jnear < nnearest[j]; jnear++)
if (nearest[i][inear] == nearest[j][jnear]) {
if (ncommon < MAXCOMMON) common[ncommon++] = nearest[i][inear];
else if (firstflag) {
nerror++;
firstflag = 0;
}
}
} else {
xtmp = x[j][0];
ytmp = x[j][1];
ztmp = x[j][2];
jlist = firstneigh[i];
jnum = numneigh[i];
n = 0;
for (kk = 0; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
if (k == j) continue;
delx = xtmp - x[k][0];
dely = ytmp - x[k][1];
delz = ztmp - x[k][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
if (n < MAXNEAR) onenearest[n++] = k;
else break;
}
}
firstflag = 1;
ncommon = 0;
for (inear = 0; inear < nnearest[i]; inear++)
for (jnear = 0; jnear < n; jnear++)
if (nearest[i][inear] == onenearest[jnear]) {
if (ncommon < MAXCOMMON) common[ncommon++] = nearest[i][inear];
else if (firstflag) {
nerror++;
firstflag = 0;
}
}
}
cna[m][NCOMMON] = ncommon;
// calculate total # of bonds between common neighbor atoms
// also max and min # of common atoms any common atom is bonded to
// bond = pair of atoms within cutoff
for (n = 0; n < ncommon; n++) bonds[n] = 0;
nbonds = 0;
for (jj = 0; jj < ncommon; jj++) {
j = common[jj];
xtmp = x[j][0];
ytmp = x[j][1];
ztmp = x[j][2];
for (kk = jj+1; kk < ncommon; kk++) {
k = common[kk];
delx = xtmp - x[k][0];
dely = ytmp - x[k][1];
delz = ztmp - x[k][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
nbonds++;
bonds[jj]++;
bonds[kk]++;
}
}
}
cna[m][NBOND] = nbonds;
maxbonds = 0;
minbonds = MAXCOMMON;
for (n = 0; n < ncommon; n++) {
maxbonds = MAX(bonds[n],maxbonds);
minbonds = MIN(bonds[n],minbonds);
}
cna[m][MAXBOND] = maxbonds;
cna[m][MINBOND] = minbonds;
}
// detect CNA pattern of the atom
nfcc = nhcp = nbcc4 = nbcc6 = nico = 0;
pattern[i] = OTHER;
if (nnearest[i] == 12) {
for (inear = 0; inear < 12; inear++) {
cj = cna[inear][NCOMMON];
ck = cna[inear][NBOND];
cl = cna[inear][MAXBOND];
cm = cna[inear][MINBOND];
if (cj == 4 && ck == 2 && cl == 1 && cm == 1) nfcc++;
else if (cj == 4 && ck == 2 && cl == 2 && cm == 0) nhcp++;
else if (cj == 5 && ck == 5 && cl == 2 && cm == 2) nico++;
}
if (nfcc == 12) pattern[i] = FCC;
else if (nfcc == 6 && nhcp == 6) pattern[i] = HCP;
else if (nico == 12) pattern[i] = ICOS;
} else if (nnearest[i] == 14) {
for (inear = 0; inear < 14; inear++) {
cj = cna[inear][NCOMMON];
ck = cna[inear][NBOND];
cl = cna[inear][MAXBOND];
cm = cna[inear][MINBOND];
if (cj == 4 && ck == 4 && cl == 2 && cm == 2) nbcc4++;
else if (cj == 6 && ck == 6 && cl == 2 && cm == 2) nbcc6++;
}
if (nbcc4 == 6 && nbcc6 == 8) pattern[i] = BCC;
}
}
// warning message
MPI_Allreduce(&nerror,&nerrorall,1,MPI_INT,MPI_SUM,world);
if (nerrorall && comm->me == 0) {
char str[128];
sprintf(str,"Too many common neighbors in CNA %d times",nerrorall);
error->warning(FLERR,str);
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeCNAAtom::memory_usage()
{
double bytes = nmax * sizeof(int);
bytes += nmax * MAXNEAR * sizeof(int);
bytes += nmax * sizeof(double);
return bytes;
}

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