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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8037 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-05-03 14:58:24 +00:00
parent 301022e272
commit 2e1b7a0f0e
3 changed files with 12 additions and 5 deletions
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3
src/domain.cpp
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@ -758,7 +758,7 @@ void Domain::closest_image(const double * const xi, const double * const xj,
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
remap the point into the periodic box no matter how far away remap the point into the periodic box no matter how far away
adjust image accordingly adjust 3 image flags encoded in image accordingly
resulting coord must satisfy lo <= coord < hi resulting coord must satisfy lo <= coord < hi
MAX is important since coord - prd < lo can happen when coord = hi MAX is important since coord - prd < lo can happen when coord = hi
for triclinic, point is converted to lamda coords (0-1) before doing remap for triclinic, point is converted to lamda coords (0-1) before doing remap
@ -849,6 +849,7 @@ void Domain::remap(double *x, int &image)
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
remap the point into the periodic box no matter how far away remap the point into the periodic box no matter how far away
no image flag calculation
resulting coord must satisfy lo <= coord < hi resulting coord must satisfy lo <= coord < hi
MAX is important since coord - prd < lo can happen when coord = hi MAX is important since coord - prd < lo can happen when coord = hi
for triclinic, point is converted to lamda coords (0-1) before remap for triclinic, point is converted to lamda coords (0-1) before remap

7
src/fix_deform.cpp
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@ -636,9 +636,11 @@ void FixDeform::init()
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
box flipped on previous step box flipped on previous step
reset box tilts for flipped config and create new box in domain reset box tilts for flipped config and create new box in domain
image_flip() adjusts image flags due to box shape change induced by flip
remap() puts atoms outside the new box back into the new box 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 perform irregular on atoms in lamda coords to migrate atoms to new procs
important that image_flip comes before remap, since remap may change
image flags to new values, making eqs in doc of Domain:image_flip incorrect
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void FixDeform::pre_exchange() void FixDeform::pre_exchange()
@ -651,11 +653,12 @@ void FixDeform::pre_exchange()
domain->set_global_box(); domain->set_global_box();
domain->set_local_box(); domain->set_local_box();
domain->image_flip(flipxy,flipxz,flipyz);
double **x = atom->x; double **x = atom->x;
int *image = atom->image; int *image = atom->image;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]); for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
domain->image_flip(flipxy,flipxz,flipyz);
domain->x2lamda(atom->nlocal); domain->x2lamda(atom->nlocal);
irregular->migrate_atoms(); irregular->migrate_atoms();

7
src/fix_nh.cpp
View File

@ -2146,9 +2146,11 @@ void FixNH::nh_omega_dot()
if xy tilt exceeded, adjust B vector by one A vector if xy tilt exceeded, adjust B vector by one A vector
check yz first since it may change xz, then xz check comes after check yz first since it may change xz, then xz check comes after
if any flip occurs, create new box in domain if any flip occurs, create new box in domain
remap() puts atoms outside the new box back into the new box
image_flip() adjusts image flags due to box shape change induced by flip image_flip() adjusts image flags due to box shape change induced by flip
remap() puts atoms outside the new box back into the new box
perform irregular on atoms in lamda coords to migrate atoms to new procs perform irregular on atoms in lamda coords to migrate atoms to new procs
important that image_flip comes before remap, since remap may change
image flags to new values, making eqs in doc of Domain:image_flip incorrect
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void FixNH::pre_exchange() void FixNH::pre_exchange()
@ -2201,11 +2203,12 @@ void FixNH::pre_exchange()
domain->set_global_box(); domain->set_global_box();
domain->set_local_box(); domain->set_local_box();
domain->image_flip(flipxy,flipxz,flipyz);
double **x = atom->x; double **x = atom->x;
int *image = atom->image; int *image = atom->image;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]); for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
domain->image_flip(flipxy,flipxz,flipyz);
domain->x2lamda(atom->nlocal); domain->x2lamda(atom->nlocal);
irregular->migrate_atoms(); irregular->migrate_atoms();