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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8008 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-04-10 15:02:16 +00:00
parent e75bdb13f0
commit fb1c3d6019
8 changed files with 102 additions and 42 deletions
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42
src/fix_nh.cpp
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@ -85,7 +85,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (domain->xz != 0.0) scalexz = 1;
}
// Set fixed-point to default = center of cell
// set fixed-point to default = center of cell
fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]);
fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]);
@ -116,7 +116,8 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
t_stop = atof(arg[iarg+2]);
t_period = atof(arg[iarg+3]);
if (t_start < 0.0 || t_stop <= 0.0)
error->all(FLERR,"Target temperature for fix nvt/npt/nph cannot be 0.0");
error->all(FLERR,
"Target temperature for fix nvt/npt/nph cannot be 0.0");
iarg += 4;
} else if (strcmp(arg[iarg],"iso") == 0) {
@ -2137,12 +2138,16 @@ void FixNH::nh_omega_dot()
}
/* ----------------------------------------------------------------------
if any tilt ratios exceed 0.5, set flip = 1 & compute new tilt_flip values
do not flip in x or y if non-periodic
when yz flips and xy is non-zero, xz must also change
this is to keep the edge vectors of the flipped shape matrix
an integer combination of the edge vectors of the unflipped shape matrix
perform irregular on atoms in lamda coords to get atoms to new procs
if any tilt ratios exceed 0.5, set flip = 1 and compute new tilt values
do not flip in x or y if non-periodic (can tilt but not flip)
this is b/c the box length would be changed (dramatically) by flip
if yz tilt exceeded, adjust C vector by one B vector
if xz tilt exceeded, adjust C vector by one A vector
if xy tilt exceeded, adjust B vector by one A vector
if any flip occurs, create new box in domain
remap() puts atoms outside the new box back into the new box
image_tilt() adjusts image flags due to box shape change induced by flip
perform irregular on atoms in lamda coords to migrate atoms to new procs
------------------------------------------------------------------------- */
void FixNH::pre_exchange()
@ -2156,37 +2161,41 @@ void FixNH::pre_exchange()
double xtiltmax = (0.5+DELTAFLIP)*xprd;
double ytiltmax = (0.5+DELTAFLIP)*yprd;
int flip = 0;
int flipxy,flipxz,flipyz;
flipxy = flipxz = flipyz = 0;
if (domain->yperiodic) {
if (domain->yz < -ytiltmax) {
flip = 1;
domain->yz += yprd;
domain->xz += domain->xy;
flipyz = 1;
} else if (domain->yz >= ytiltmax) {
flip = 1;
domain->yz -= yprd;
domain->xz -= domain->xy;
flipyz = -1;
}
}
if (domain->xperiodic) {
if (domain->xz < -xtiltmax) {
flip = 1;
domain->xz += xprd;
flipxz = 1;
} else if (domain->xz >= xtiltmax) {
flip = 1;
domain->xz -= xprd;
flipxz = -1;
}
if (domain->xy < -xtiltmax) {
flip = 1;
domain->xy += xprd;
flipxy = 1;
} else if (domain->xy >= xtiltmax) {
flip = 1;
domain->xy -= xprd;
flipxy = -1;
}
}
int flip = 0;
if (flipxy || flipxz || flipyz) flip = 1;
if (flip) {
domain->set_global_box();
domain->set_local_box();
@ -2195,7 +2204,8 @@ void FixNH::pre_exchange()
int *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
domain->image_flip(flipxy,flipxz,flipyz);
domain->x2lamda(atom->nlocal);
irregular->migrate_atoms();
domain->lamda2x(atom->nlocal);