Homec4science
Diffusion lammps (lammm-master) Browse

lammps/src/compute_contact_atom.cpp
1111c8ba93c9lammm-master

Last Change
Raw File

compute_contact_atom.cpp
View Options

/* ----------------------------------------------------------------------
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_contact_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;
/* ---------------------------------------------------------------------- */
ComputeContactAtom::ComputeContactAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute contact/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
comm_reverse = 1;
nmax = 0;
contact = NULL;
// error checks
if (!atom->sphere_flag)
error->all(FLERR,"Compute contact/atom requires atom style sphere");
}
/* ---------------------------------------------------------------------- */
ComputeContactAtom::~ComputeContactAtom()
{
memory->destroy(contact);
}
/* ---------------------------------------------------------------------- */
void ComputeContactAtom::init()
{
if (force->pair == NULL)
error->all(FLERR,"Compute contact/atom requires a pair style be defined");
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"contact/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute contact/atom");
// need an occasional neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->gran = 1;
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
}
/* ---------------------------------------------------------------------- */
void ComputeContactAtom::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeContactAtom::compute_peratom()
{
int i,j,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,radsumsq;
int *ilist,*jlist,*numneigh,**firstneigh;
invoked_peratom = update->ntimestep;
// grow contact array if necessary
if (atom->nmax > nmax) {
memory->destroy(contact);
nmax = atom->nmax;
memory->create(contact,nmax,"contact/atom:contact");
vector_atom = contact;
}
// invoke 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 number of contacts for each atom in group
// contact if distance <= sum of radii
// tally for both I and J
double **x = atom->x;
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
for (i = 0; i < nall; i++) contact[i] = 0.0;
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];
radi = radius[i];
jlist = firstneigh[i];
jnum = numneigh[i];
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;
radsum = radi + radius[j];
radsumsq = radsum*radsum;
if (rsq <= radsumsq) {
contact[i] += 1.0;
contact[j] += 1.0;
}
}
}
}
// communicate ghost atom counts between neighbor procs if necessary
if (force->newton_pair) comm->reverse_comm_compute(this);
}
/* ---------------------------------------------------------------------- */
int ComputeContactAtom::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++)
buf[m++] = contact[i];
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeContactAtom::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
contact[j] += buf[m++];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeContactAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}
c4science · Help