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compute_body_local.cpp
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Tue, Nov 19, 01:32

compute_body_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 "compute_body_local.h"
#include "atom.h"
#include "atom_vec_body.h"
#include "body.h"
#include "update.h"
#include "domain.h"
#include "force.h"
#include "bond.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
enum{ID,TYPE,INDEX};
/* ---------------------------------------------------------------------- */
ComputeBodyLocal::ComputeBodyLocal(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute body/local command");
local_flag = 1;
nvalues = narg - 3;
if (nvalues == 1) size_local_cols = 0;
else size_local_cols = nvalues;
which = new int[nvalues];
index = new int[nvalues];
nvalues = 0;
for (int iarg = 3; iarg < narg; iarg++) {
if (strcmp(arg[iarg],"id") == 0) which[nvalues++] = ID;
else if (strcmp(arg[iarg],"type") == 0) which[nvalues++] = TYPE;
else {
which[nvalues] = INDEX;
index[nvalues] = force->inumeric(FLERR,arg[iarg]) - 1;
nvalues++;
}
}
avec = (AtomVecBody *) atom->style_match("body");
if (!avec) error->all(FLERR,"Compute body/local requires atom style body");
bptr = avec->bptr;
int indexmax = bptr->noutcol();
for (int i = 0; i < nvalues; i++) {
if (which[i] == INDEX && (index[i] < 0 || index[i] >= indexmax))
error->all(FLERR,"Invalid index in compute body/local command");
}
nmax = 0;
vector = NULL;
array = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeBodyLocal::~ComputeBodyLocal()
{
delete [] which;
delete [] index;
memory->destroy(vector);
memory->destroy(array);
}
/* ---------------------------------------------------------------------- */
void ComputeBodyLocal::init()
{
// if non-body particles in group insure only indices 1,2,3 are used
int nonbody = 0;
int *mask = atom->mask;
int *body = atom->body;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (body[i] < 0) nonbody = 1;
int flag;
MPI_Allreduce(&nonbody,&flag,1,MPI_INT,MPI_SUM,world);
if (flag) {
for (int i = 0; i < nvalues; i++)
if (which[i] == INDEX && index[i] > 2)
error->all(FLERR,"Invalid index for non-body particles "
"in compute body/local command");
}
// do initial memory allocation so that memory_usage() is correct
int ncount = compute_body(0);
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
}
/* ---------------------------------------------------------------------- */
void ComputeBodyLocal::compute_local()
{
invoked_local = update->ntimestep;
// count local entries and compute body info
int ncount = compute_body(0);
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
ncount = compute_body(1);
}
/* ----------------------------------------------------------------------
count body info and compute body info on this proc
flag = 0, only count
flag = 1, also compute
------------------------------------------------------------------------- */
int ComputeBodyLocal::compute_body(int flag)
{
// perform count
int *mask = atom->mask;
int *body = atom->body;
int nlocal = atom->nlocal;
int ncount = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (body[i] < 0) ncount++;
else ncount += bptr->noutrow(body[i]);
}
if (flag == 0) return ncount;
// perform computation and fill output vector/array
int m,n,ibonus;
double *values = new double[bptr->noutcol()];
double **x = atom->x;
tagint *tag = atom->tag;
int *type = atom->type;
ncount = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (body[i] < 0) {
if (nvalues == 1) {
if (which[0] == ID) vector[ncount] = tag[i];
else if (which[0] == TYPE) vector[ncount] = type[i];
else vector[ncount] = x[i][index[0]];
} else {
for (m = 0; m < nvalues; m++) {
if (which[m] == ID) array[ncount][m] = tag[i];
else if (which[m] == TYPE) array[ncount][m] = type[i];
else array[ncount][m] = x[i][index[m]];
}
}
ncount++;
} else {
ibonus = body[i];
n = bptr->noutrow(ibonus);
for (int j = 0; j < n; j++) {
bptr->output(ibonus,j,values);
if (nvalues == 1) {
if (which[0] == ID) vector[ncount] = tag[i];
else if (which[0] == TYPE) vector[ncount] = type[i];
else vector[ncount] = values[index[0]];
} else {
for (m = 0; m < nvalues; m++) {
if (which[m] == ID) array[ncount][m] = tag[i];
else if (which[m] == TYPE) array[ncount][m] = type[i];
else array[ncount][m] = values[index[m]];
}
}
ncount++;
}
}
}
}
delete [] values;
return ncount;
}
/* ---------------------------------------------------------------------- */
void ComputeBodyLocal::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,"body/local:vector");
vector_local = vector;
} else {
memory->destroy(array);
memory->create(array,nmax,nvalues,"body/local:array");
array_local = array;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeBodyLocal::memory_usage()
{
double bytes = nmax*nvalues * sizeof(double);
return bytes;
}

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