Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/REPLICA/fix_event.cpp
b247eeb103f5lammm-master-deprecated

Last Change
Raw File

fix_event.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL), Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "fix_event.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "neighbor.h"
#include "comm.h"
#include "universe.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixEvent::FixEvent(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal fix event command");
restart_global = 1;
// perform initial allocation of atom-based array
// register with Atom class
xevent = NULL;
xold = NULL;
vold = NULL;
imageold = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
}
/* ---------------------------------------------------------------------- */
FixEvent::~FixEvent()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
// delete locally stored array
memory->destroy(xevent);
memory->destroy(xold);
memory->destroy(vold);
memory->destroy(imageold);
}
/* ---------------------------------------------------------------------- */
int FixEvent::setmask()
{
return 0;
}
/* ----------------------------------------------------------------------
save current atom coords as an event
called when an event occurs
------------------------------------------------------------------------- */
void FixEvent::store_event()
{
double **x = atom->x;
int *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
domain->unmap(x[i],image[i],xevent[i]);
}
/* ----------------------------------------------------------------------
restore atom coords to quenched initial state
called prior to NEB calculation
------------------------------------------------------------------------- */
void FixEvent::restore_event()
{
double **x = atom->x;
int *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
x[i][0] = xevent[i][0];
x[i][1] = xevent[i][1];
x[i][2] = xevent[i][2];
// Since xevent is unwrapped coordinate, need to
// adjust image flags when remapping
image[i] = (512 << 20) | (512 << 10) | 512;
domain->remap(x[i],image[i]);
// domain->remap(x[i]);
}
}
/* ----------------------------------------------------------------------
store state of all atoms
called before quench and subsequent check for event
so can later restore pre-quench state if no event occurs
------------------------------------------------------------------------- */
void FixEvent::store_state()
{
double **x = atom->x;
double **v = atom->v;
int *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
xold[i][0] = x[i][0];
xold[i][1] = x[i][1];
xold[i][2] = x[i][2];
vold[i][0] = v[i][0];
vold[i][1] = v[i][1];
vold[i][2] = v[i][2];
imageold[i] = image[i];
}
}
/* ----------------------------------------------------------------------
restore state of all atoms to pre-quench state
called after no event detected so can continue
------------------------------------------------------------------------- */
void FixEvent::restore_state()
{
double **x = atom->x;
double **v = atom->v;
int *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
x[i][0] = xold[i][0];
x[i][1] = xold[i][1];
x[i][2] = xold[i][2];
v[i][0] = vold[i][0];
v[i][1] = vold[i][1];
v[i][2] = vold[i][2];
image[i] = imageold[i];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double FixEvent::memory_usage()
{
double bytes = 6*atom->nmax * sizeof(double);
bytes += atom->nmax*sizeof(int);
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based array
------------------------------------------------------------------------- */
void FixEvent::grow_arrays(int nmax)
{
memory->grow(xevent,nmax,3,"event:xevent");
memory->grow(xold,nmax,3,"event:xold");
memory->grow(vold,nmax,3,"event:vold");
memory->grow(imageold,nmax,"event:imageold");
// allow compute event to access stored event coords
array_atom = xevent;
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixEvent::copy_arrays(int i, int j)
{
xevent[j][0] = xevent[i][0];
xevent[j][1] = xevent[i][1];
xevent[j][2] = xevent[i][2];
xold[j][0] = xold[i][0];
xold[j][1] = xold[i][1];
xold[j][2] = xold[i][2];
vold[j][0] = vold[i][0];
vold[j][1] = vold[i][1];
vold[j][2] = vold[i][2];
imageold[j] = imageold[i];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixEvent::pack_exchange(int i, double *buf)
{
buf[0] = xevent[i][0];
buf[1] = xevent[i][1];
buf[2] = xevent[i][2];
buf[3] = xold[i][0];
buf[4] = xold[i][1];
buf[5] = xold[i][2];
buf[6] = vold[i][0];
buf[7] = vold[i][1];
buf[8] = vold[i][2];
buf[9] = imageold[i];
return 10;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixEvent::unpack_exchange(int nlocal, double *buf)
{
xevent[nlocal][0] = buf[0];
xevent[nlocal][1] = buf[1];
xevent[nlocal][2] = buf[2];
xold[nlocal][0] = buf[3];
xold[nlocal][1] = buf[4];
xold[nlocal][2] = buf[5];
vold[nlocal][0] = buf[6];
vold[nlocal][1] = buf[7];
vold[nlocal][2] = buf[8];
imageold[nlocal] = static_cast<int>(buf[9]);
return 10;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixEvent::write_restart(FILE *fp)
{
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixEvent::restart(char *buf)
{
}
c4science · Help