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lammps/src/compute_sum_atom.cpp
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compute_sum_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 "string.h"
#include "compute_sum_atom.h"
#include "atom.h"
#include "modify.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSumAtom::ComputeSumAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 5) error->all("Illegal compute sum/atom command");
// store pre-compute IDs
npre = narg - 3;
id_pre = new char*[npre];
for (int i = 0; i < npre; i++) {
int iarg = i + 3;
int n = strlen(arg[iarg]) + 1;
id_pre[i] = new char[n];
strcpy(id_pre[i],arg[iarg]);
}
compute = new Compute*[npre];
// all sub-computes must be peratom
// check consistency of sub-computes for scalar & vector output
int icompute;
for (int i = 0; i < npre; i++) {
icompute = modify->find_compute(id_pre[i]);
if (icompute < 0)
error->all("Could not find compute sum/atom pre-compute ID");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Compute sum/atom compute is not a per-atom compute");
}
peratom_flag = 1;
icompute = modify->find_compute(id_pre[0]);
size_peratom = modify->compute[icompute]->size_peratom;
for (int i = 1; i < npre; i++) {
icompute = modify->find_compute(id_pre[i]);
if (modify->compute[icompute]->size_peratom != size_peratom)
error->all("Inconsistent sizes of compute sum/atom compute quantities");
}
// values generated by this compute
nmax = 0;
s_value = NULL;
v_value = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSumAtom::~ComputeSumAtom()
{
delete [] compute;
memory->sfree(s_value);
memory->destroy_2d_double_array(v_value);
}
/* ---------------------------------------------------------------------- */
void ComputeSumAtom::init()
{
// set ptrs to Computes used as pre-computes by this compute
for (int i = 0; i < npre; i++) {
int icompute = modify->find_compute(id_pre[i]);
if (icompute < 0)
error->all("Could not find compute sum/atom pre-compute ID");
compute[i] = modify->compute[icompute];
}
}
/* ---------------------------------------------------------------------- */
void ComputeSumAtom::compute_peratom()
{
int i,j,m;
// grow sum array if necessary
if (atom->nlocal > nmax) {
nmax = atom->nmax;
if (size_peratom == 0) {
memory->sfree(s_value);
s_value = (double *)
memory->smalloc(nmax*sizeof(double),"compute/sum/atom:s_value");
scalar_atom = s_value;
} else {
memory->destroy_2d_double_array(v_value);
v_value = memory->create_2d_double_array(nmax,size_peratom,
"compute/sum/atom:v_value");
vector_atom = v_value;
}
}
// sum over pre-computes
// pre-computes of the pre-computes are not invoked
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (size_peratom == 0) {
double *scalar = compute[0]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_value[i] = scalar[i];
else s_value[i] = 0.0;
for (m = 1; m < npre; m++) {
scalar = compute[m]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) s_value[i] += scalar[i];
}
} else {
double **vector = compute[0]->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
for (j = 0; j < size_peratom; j++)
v_value[i][j] = vector[i][j];
else
for (j = 0; j < size_peratom; j++)
v_value[i][j] = 0.0;
for (m = 1; m < npre; m++) {
vector = compute[m]->vector_atom;
for (j = 0; j < size_peratom; j++)
if (mask[i] & groupbit) v_value[i][j] += vector[i][j];
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeSumAtom::memory_usage()
{
double bytes = 0.0;
if (size_peratom == 0) bytes = nmax * sizeof(double);
else bytes = nmax*size_peratom * sizeof(double);
return bytes;
}
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