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Added tad example

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5475 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
2011-01-05 00:23:34 +00:00
parent 4e99c5022e
commit c69f3aea57
16 changed files with 1597 additions and 128 deletions
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108
src/REPLICA/fix_event.cpp
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@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
Contributing author: Mike Brown (SNL), Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include "stdlib.h"
@ -43,13 +43,10 @@ FixEvent::FixEvent(LAMMPS *lmp, int narg, char **arg) :
xevent = NULL;
xold = NULL;
vold = NULL;
imageold = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
event_number = 0;
event_timestep = update->ntimestep;
clock = 0;
}
/* ---------------------------------------------------------------------- */
@ -64,6 +61,7 @@ FixEvent::~FixEvent()
memory->destroy_2d_double_array(xevent);
memory->destroy_2d_double_array(xold);
memory->destroy_2d_double_array(vold);
memory->sfree(imageold);
}
@ -76,12 +74,10 @@ int FixEvent::setmask()
/* ----------------------------------------------------------------------
save current atom coords as an event
called when an event occurs in some replica
set event_timestep = when event occurred in a particular replica
update clock = elapsed time since last event, across all replicas
called when an event occurs
------------------------------------------------------------------------- */
void FixEvent::store_event(int timestep, int delta_clock)
void FixEvent::store_event()
{
double **x = atom->x;
int *image = atom->image;
@ -90,9 +86,41 @@ void FixEvent::store_event(int timestep, int delta_clock)
for (int i = 0; i < nlocal; i++)
domain->unmap(x[i],image[i],xevent[i]);
event_timestep = timestep;
clock += delta_clock;
event_number++;
// printf("store_event %g %d %g %d \n",
// x[8][1],image[8],xevent[8][1],0);
}
/* ----------------------------------------------------------------------
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;
// printf("restore_event1 %g %d %g %d \n",
// x[8][1],image[8],xevent[8][1],0);
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]);
}
// printf("restore_event2 %g %d %g %d \n",
// x[8][1],image[8],xevent[8][1],0);
}
/* ----------------------------------------------------------------------
@ -104,14 +132,20 @@ void FixEvent::store_event(int timestep, int delta_clock)
void FixEvent::store_state()
{
double **x = atom->x;
double **f = atom->f;
double **v = atom->v;
int *image = atom->image;
int nlocal = atom->nlocal;
// printf("store_state %g %d %g %d \n",
// xold[8][1],imageold[8],x[8][1],image[8]);
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];
}
}
@ -124,13 +158,20 @@ void FixEvent::store_state()
void FixEvent::restore_state()
{
double **x = atom->x;
double **v = atom->v;
int *image = atom->image;
int nlocal = atom->nlocal;
// printf("restore_state %g %d %g %d \n",
// xold[8][1],imageold[8],x[8][1],image[8]);
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];
}
}
@ -154,6 +195,7 @@ void FixEvent::grow_arrays(int nmax)
{
xevent = memory->grow_2d_double_array(xevent,nmax,3,"event:xevent");
xold = memory->grow_2d_double_array(xold,nmax,3,"event:xold");
vold = memory->grow_2d_double_array(vold,nmax,3,"event:vold");
imageold = (int *)
memory->srealloc(imageold,nmax*sizeof(int),"event:imageold");
@ -174,6 +216,9 @@ void FixEvent::copy_arrays(int i, int j)
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];
}
@ -189,9 +234,12 @@ int FixEvent::pack_exchange(int i, double *buf)
buf[3] = xold[i][0];
buf[4] = xold[i][1];
buf[5] = xold[i][2];
buf[6] = imageold[i];
buf[6] = vold[i][0];
buf[7] = vold[i][1];
buf[8] = vold[i][2];
buf[9] = imageold[i];
return 7;
return 10;
}
/* ----------------------------------------------------------------------
@ -206,9 +254,12 @@ int FixEvent::unpack_exchange(int nlocal, double *buf)
xold[nlocal][0] = buf[3];
xold[nlocal][1] = buf[4];
xold[nlocal][2] = buf[5];
imageold[nlocal] = static_cast<int>(buf[6]);
vold[nlocal][0] = buf[6];
vold[nlocal][1] = buf[7];
vold[nlocal][2] = buf[8];
imageold[nlocal] = static_cast<int>(buf[9]);
return 7;
return 10;
}
/* ----------------------------------------------------------------------
@ -217,20 +268,6 @@ int FixEvent::unpack_exchange(int nlocal, double *buf)
void FixEvent::write_restart(FILE *fp)
{
int n = 0;
double list[5];
list[n++] = event_number;
list[n++] = event_timestep;
list[n++] = clock;
list[n++] = replica_number;
list[n++] = correlated_event;
list[n++] = ncoincident;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
@ -239,13 +276,4 @@ void FixEvent::write_restart(FILE *fp)
void FixEvent::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
event_number = static_cast<int> (list[n++]);
event_timestep = static_cast<int> (list[n++]);
clock = static_cast<int> (list[n++]);
replica_number = static_cast<int> (list[n++]);
correlated_event = static_cast<int> (list[n++]);
ncoincident = static_cast<int> (list[n++]);
}