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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1219 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-12-06 16:23:12 +00:00
parent 0bb3fd9b06
commit b2af7fb88f
3 changed files with 61 additions and 22 deletions
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25
src/domain.cpp
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@ -678,7 +678,7 @@ void Domain::remap(double *x, int &image)
/* ----------------------------------------------------------------------
unmap the point via image flags
don't reset image flag
x overwritten with result, don't reset image flag
for triclinic, use h[] to add in tilt factors in other dims as needed
------------------------------------------------------------------------- */
@ -699,6 +699,29 @@ void Domain::unmap(double *x, int image)
}
}
/* ----------------------------------------------------------------------
unmap the point via image flags
result returned in y, don't reset image flag
for triclinic, use h[] to add in tilt factors in other dims as needed
------------------------------------------------------------------------- */
void Domain::unmap(double *x, int image, double *y)
{
int xbox = (image & 1023) - 512;
int ybox = (image >> 10 & 1023) - 512;
int zbox = (image >> 20) - 512;
if (triclinic == 0) {
y[0] = x[0] + xbox*xprd;
y[1] = x[1] + ybox*yprd;
y[2] = x[2] + zbox*zprd;
} else {
y[0] = x[0] + h[0]*xbox + h[5]*ybox + h[4]*zbox;
y[1] = x[1] + h[1]*ybox + h[3]*zbox;
y[2] = x[2] + h[2]*zbox;
}
}
/* ----------------------------------------------------------------------
create a lattice
delete it if style = none

1
src/domain.h
View File

@ -91,6 +91,7 @@ class Domain : protected Pointers {
void pbc();
void remap(double *, int &);
void unmap(double *, int);
void unmap(double *, int, double *);
void minimum_image(double &, double &, double &);
void minimum_image(double *);
void set_lattice(int, char **);

57
src/fix_msd.cpp
View File

@ -72,14 +72,8 @@ FixMSD::FixMSD(LAMMPS *lmp, int narg, char **arg) :
int xbox,ybox,zbox;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
xoriginal[i][0] = x[i][0] + xbox*xprd;
xoriginal[i][1] = x[i][1] + ybox*yprd;
xoriginal[i][2] = x[i][2] + zbox*zprd;
} else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
}
// nmsd = # of atoms in group
@ -149,6 +143,7 @@ void FixMSD::end_of_step()
int *image = atom->image;
int nlocal = atom->nlocal;
double *h = domain->h;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
@ -157,19 +152,39 @@ void FixMSD::end_of_step()
double msd[4];
msd[0] = msd[1] = msd[2] = msd[3] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
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];
msd[0] += dx*dx;
msd[1] += dy*dy;
msd[2] += dz*dz;
msd[3] += dx*dx + dy*dy + dz*dz;
}
// dx,dy,dz = displacement of atom from original position
// for triclinic, need to unwrap current atom coord via h matrix
if (domain->triclinic == 0) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
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];
msd[0] += dx*dx;
msd[1] += dy*dy;
msd[2] += dz*dz;
msd[3] += dx*dx + dy*dy + dz*dz;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
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];
msd[0] += dx*dx;
msd[1] += dy*dy;
msd[2] += dz*dz;
msd[3] += dx*dx + dy*dy + dz*dz;
}
}
double msd_all[4];
MPI_Allreduce(msd,msd_all,4,MPI_DOUBLE,MPI_SUM,world);