Homec4science
Diffusion lammps (master) Browse

lammps/src/USER-TALLY/compute_force_tally.cpp
2fe1d1b90451master

Last Change
Raw File

compute_force_tally.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 <string.h>
#include "compute_force_tally.h"
#include "atom.h"
#include "group.h"
#include "pair.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeForceTally::ComputeForceTally(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute force/tally command");
igroup2 = group->find(arg[3]);
if (igroup2 == -1)
error->all(FLERR,"Could not find compute force/tally second group ID");
groupbit2 = group->bitmask[igroup2];
scalar_flag = 1;
vector_flag = 0;
peratom_flag = 1;
timeflag = 1;
comm_reverse = size_peratom_cols = 3;
extscalar = 1;
peflag = 1; // we need Pair::ev_tally() to be run
did_setup = invoked_peratom = invoked_scalar = -1;
nmax = -1;
fatom = NULL;
vector = new double[size_peratom_cols];
}
/* ---------------------------------------------------------------------- */
ComputeForceTally::~ComputeForceTally()
{
if (force && force->pair) force->pair->del_tally_callback(this);
memory->destroy(fatom);
delete[] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeForceTally::init()
{
if (force->pair == NULL)
error->all(FLERR,"Trying to use compute force/tally without pair style");
else
force->pair->add_tally_callback(this);
if (comm->me == 0) {
if (force->pair->single_enable == 0 || force->pair->manybody_flag)
error->warning(FLERR,"Compute force/tally used with incompatible pair style");
if (force->bond || force->angle || force->dihedral
|| force->improper || force->kspace)
error->warning(FLERR,"Compute force/tally only called from pair style");
}
did_setup = -1;
}
/* ---------------------------------------------------------------------- */
void ComputeForceTally::pair_setup_callback(int, int)
{
const int ntotal = atom->nlocal + atom->nghost;
// grow per-atom storage, if needed
if (atom->nmax > nmax) {
memory->destroy(fatom);
nmax = atom->nmax;
memory->create(fatom,nmax,size_peratom_cols,"force/tally:fatom");
array_atom = fatom;
}
// clear storage
for (int i=0; i < ntotal; ++i)
for (int j=0; j < size_peratom_cols; ++j)
fatom[i][j] = 0.0;
for (int i=0; i < size_peratom_cols; ++i)
vector[i] = ftotal[i] = 0.0;
did_setup = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
void ComputeForceTally::pair_tally_callback(int i, int j, int nlocal, int newton,
double, double, double fpair,
double dx, double dy, double dz)
{
const int * const mask = atom->mask;
if ( ((mask[i] & groupbit) && (mask[j] & groupbit2))
|| ((mask[i] & groupbit2) && (mask[j] & groupbit)) ) {
if (newton || i < nlocal) {
if (mask[i] & groupbit) {
ftotal[0] += fpair*dx;
ftotal[1] += fpair*dy;
ftotal[2] += fpair*dz;
}
fatom[i][0] += fpair*dx;
fatom[i][1] += fpair*dy;
fatom[i][2] += fpair*dz;
}
if (newton || j < nlocal) {
if (mask[j] & groupbit) {
ftotal[0] -= fpair*dx;
ftotal[1] -= fpair*dy;
ftotal[2] -= fpair*dz;
}
fatom[j][0] -= fpair*dx;
fatom[j][1] -= fpair*dy;
fatom[j][2] -= fpair*dz;
}
}
}
/* ---------------------------------------------------------------------- */
int ComputeForceTally::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++] = fatom[i][0];
buf[m++] = fatom[i][1];
buf[m++] = fatom[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeForceTally::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
fatom[j][0] += buf[m++];
fatom[j][1] += buf[m++];
fatom[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
double ComputeForceTally::compute_scalar()
{
invoked_scalar = update->ntimestep;
if ((did_setup != invoked_scalar)
|| (update->eflag_global != invoked_scalar))
error->all(FLERR,"Energy was not tallied on needed timestep");
// sum accumulated forces across procs
MPI_Allreduce(ftotal,vector,size_peratom_cols,MPI_DOUBLE,MPI_SUM,world);
scalar = sqrt(vector[0]*vector[0]+vector[1]*vector[1]+vector[2]*vector[2]);
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeForceTally::compute_peratom()
{
invoked_peratom = update->ntimestep;
if ((did_setup != invoked_peratom)
|| (update->eflag_global != invoked_peratom))
error->all(FLERR,"Energy was not tallied on needed timestep");
// collect contributions from ghost atoms
if (force->newton_pair) {
comm->reverse_comm_compute(this);
// clear out ghost atom data after it has been collected to local atoms
const int nall = atom->nlocal + atom->nghost;
for (int i = atom->nlocal; i < nall; ++i)
for (int j = 0; j < size_peratom_cols; ++j)
fatom[i][j] = 0.0;
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeForceTally::memory_usage()
{
double bytes = (nmax < 0) ? 0 : nmax*size_peratom_cols * sizeof(double);
return bytes;
}
c4science · Help