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compute_coord_atom.cpp
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Fri, Jul 5, 15:55

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

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