Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/compute_displace_atom.cpp
49804d97059fefficient_neuronet

Last Change
Raw File

compute_displace_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 "compute_displace_atom.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "fix_store.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
displace(NULL), id_fix(NULL)
{
if (narg != 3) error->all(FLERR,"Illegal compute displace/atom command");
peratom_flag = 1;
size_peratom_cols = 4;
create_attribute = 1;
// create a new fix STORE style
// id = compute-ID + COMPUTE_STORE, fix group = compute group
int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
id_fix = new char[n];
strcpy(id_fix,id);
strcat(id_fix,"_COMPUTE_STORE");
char **newarg = new char*[6];
newarg[0] = id_fix;
newarg[1] = group->names[igroup];
newarg[2] = (char *) "STORE";
newarg[3] = (char *) "peratom";
newarg[4] = (char *) "1";
newarg[5] = (char *) "3";
modify->add_fix(6,newarg);
fix = (FixStore *) modify->fix[modify->nfix-1];
delete [] newarg;
// calculate xu,yu,zu for fix store array
// skip if reset from restart file
if (fix->restart_reset) fix->restart_reset = 0;
else {
double **xoriginal = fix->astore;
double **x = atom->x;
int *mask = atom->mask;
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
}
// per-atom displacement array
nmax = 0;
}
/* ---------------------------------------------------------------------- */
ComputeDisplaceAtom::~ComputeDisplaceAtom()
{
// check nfix in case all fixes have already been deleted
if (modify->nfix) modify->delete_fix(id_fix);
delete [] id_fix;
memory->destroy(displace);
}
/* ---------------------------------------------------------------------- */
void ComputeDisplaceAtom::init()
{
// set fix which stores original atom coords
int ifix = modify->find_fix(id_fix);
if (ifix < 0) error->all(FLERR,"Could not find compute displace/atom fix ID");
fix = (FixStore *) modify->fix[ifix];
}
/* ---------------------------------------------------------------------- */
void ComputeDisplaceAtom::compute_peratom()
{
invoked_peratom = update->ntimestep;
// grow local displacement array if necessary
if (atom->nmax > nmax) {
memory->destroy(displace);
nmax = atom->nmax;
memory->create(displace,nmax,4,"displace/atom:displace");
array_atom = displace;
}
// dx,dy,dz = displacement of atom from original position
// original unwrapped position is stored by fix
// for triclinic, need to unwrap current atom coord via h matrix
double **xoriginal = fix->astore;
double **x = atom->x;
int *mask = atom->mask;
imageint *image = atom->image;
int nlocal = atom->nlocal;
double *h = domain->h;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
int xbox,ybox,zbox;
double dx,dy,dz;
if (domain->triclinic == 0) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = x[i][0] + xbox*xprd - xoriginal[i][0];
dy = x[i][1] + ybox*yprd - xoriginal[i][1];
dz = x[i][2] + zbox*zprd - xoriginal[i][2];
displace[i][0] = dx;
displace[i][1] = dy;
displace[i][2] = dz;
displace[i][3] = sqrt(dx*dx + dy*dy + dz*dz);
} else displace[i][0] = displace[i][1] =
displace[i][2] = displace[i][3] = 0.0;
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];
dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];
dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
displace[i][0] = dx;
displace[i][1] = dy;
displace[i][2] = dz;
displace[i][3] = sqrt(dx*dx + dy*dy + dz*dz);
} else displace[i][0] = displace[i][1] =
displace[i][2] = displace[i][3] = 0.0;
}
}
/* ----------------------------------------------------------------------
initialize one atom's storage values, called when atom is created
------------------------------------------------------------------------- */
void ComputeDisplaceAtom::set_arrays(int i)
{
double **xoriginal = fix->astore;
double **x = atom->x;
xoriginal[i][0] = x[i][0];
xoriginal[i][1] = x[i][1];
xoriginal[i][2] = x[i][2];
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeDisplaceAtom::memory_usage()
{
double bytes = nmax*4 * sizeof(double);
return bytes;
}
c4science · Help