265 lines
7.2 KiB
C++
265 lines
7.2 KiB
C++
/* ----------------------------------------------------------------------
|
|
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)
|
|
{
|
|
}
|