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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@622 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-06-20 13:17:59 +00:00
parent bde732bced
commit aaed6ebc33
131 changed files with 4277 additions and 2222 deletions
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66
src/domain.cpp
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@ -26,6 +26,7 @@
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "fix_deform.h"
#include "region.h"
#include "lattice.h"
#include "comm.h"
@ -44,6 +45,8 @@ using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
/* ----------------------------------------------------------------------
default is periodic
------------------------------------------------------------------------- */
@ -67,6 +70,12 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp)
boxhi[0] = boxhi[1] = boxhi[2] = 0.5;
xy = xz = yz = 0.0;
h[3] = h[4] = h[5] = 0.0;
h_inv[3] = h_inv[4] = h_inv[5] = 0.0;
h_rate[0] = h_rate[1] = h_rate[2] =
h_rate[3] = h_rate[4] = h_rate[5] = 0.0;
h_ratelo[0] = h_ratelo[1] = h_ratelo[2] = 0.0;
prd_lamda[0] = prd_lamda[1] = prd_lamda[2] = 1.0;
boxlo_lamda[0] = boxlo_lamda[1] = boxlo_lamda[2] = 0.0;
boxhi_lamda[0] = boxhi_lamda[1] = boxhi_lamda[2] = 1.0;
@ -96,6 +105,18 @@ void Domain::init()
if (nonperiodic == 2) box_change = 1;
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->box_change) box_change = 1;
// check for fix deform
deform_flag = deform_remap = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
deform_flag = 1;
if (((FixDeform *) modify->fix[i])->remapflag == V_REMAP) {
deform_remap = 1;
deform_groupbit = modify->fix[i]->groupbit;
} else deform_remap = 0;
}
}
/* ----------------------------------------------------------------------
@ -120,11 +141,11 @@ void Domain::set_initial_box()
if (yz != 0.0 && (!yperiodic || !zperiodic))
error->all("Triclinic box must be periodic in skewed dimensions");
if (fabs(xy/(boxhi[1]-boxlo[1])) > 0.5)
if (fabs(xy/(boxhi[0]-boxlo[0])) > 0.5)
error->all("Triclinic box skew is too large");
if (fabs(xz/(boxhi[2]-boxlo[2])) > 0.5)
if (fabs(xz/(boxhi[0]-boxlo[0])) > 0.5)
error->all("Triclinic box skew is too large");
if (fabs(yz/(boxhi[2]-boxlo[2])) > 0.5)
if (fabs(yz/(boxhi[1]-boxlo[1])) > 0.5)
error->all("Triclinic box skew is too large");
}
@ -157,21 +178,21 @@ void Domain::set_global_box()
prd[1] = yprd = boxhi[1] - boxlo[1];
prd[2] = zprd = boxhi[2] - boxlo[2];
h[0] = xprd;
h[1] = yprd;
h[2] = zprd;
h_inv[0] = 1.0/h[0];
h_inv[1] = 1.0/h[1];
h_inv[2] = 1.0/h[2];
xprd_half = 0.5*xprd;
yprd_half = 0.5*yprd;
zprd_half = 0.5*zprd;
if (triclinic) {
h[0] = xprd;
h[1] = yprd;
h[2] = zprd;
h[3] = yz;
h[4] = xz;
h[5] = xy;
h_inv[0] = 1.0/h[0];
h_inv[1] = 1.0/h[1];
h_inv[2] = 1.0/h[2];
h_inv[3] = -h[3] / (h[1]*h[2]);
h_inv[4] = (h[3]*h[5] - h[1]*h[4]) / (h[0]*h[1]*h[2]);
h_inv[5] = -h[5] / (h[0]*h[1]);
@ -318,6 +339,7 @@ void Domain::reset_box()
called every reneighboring and by other commands that change atoms
resulting coord must satisfy lo <= coord < hi
MAX is important since coord - prd < lo can happen when coord = hi
if fix deform, remap velocity of fix group atoms by box edge velocities
for triclinic, atoms must be in lamda coords (0-1) before pbc is called
image = 10 bits for each dimension
increment/decrement in wrap-around fashion
@ -329,6 +351,8 @@ void Domain::pbc()
double *lo,*hi,*period;
int nlocal = atom->nlocal;
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int *image = atom->image;
if (triclinic == 0) {
@ -345,6 +369,7 @@ void Domain::pbc()
if (xperiodic) {
if (x[i][0] < lo[0]) {
x[i][0] += period[0];
if (deform_remap && mask[i] & deform_groupbit) v[i][0] += h_rate[0];
idim = image[i] & 1023;
otherdims = image[i] ^ idim;
idim--;
@ -354,6 +379,7 @@ void Domain::pbc()
if (x[i][0] >= hi[0]) {
x[i][0] -= period[0];
x[i][0] = MAX(x[i][0],lo[0]);
if (deform_remap && mask[i] & deform_groupbit) v[i][0] -= h_rate[0];
idim = image[i] & 1023;
otherdims = image[i] ^ idim;
idim++;
@ -365,6 +391,10 @@ void Domain::pbc()
if (yperiodic) {
if (x[i][1] < lo[1]) {
x[i][1] += period[1];
if (deform_remap && mask[i] & deform_groupbit) {
v[i][0] += h_rate[5];
v[i][1] += h_rate[1];
}
idim = (image[i] >> 10) & 1023;
otherdims = image[i] ^ (idim << 10);
idim--;
@ -374,6 +404,10 @@ void Domain::pbc()
if (x[i][1] >= hi[1]) {
x[i][1] -= period[1];
x[i][1] = MAX(x[i][1],lo[1]);
if (deform_remap && mask[i] & deform_groupbit) {
v[i][0] -= h_rate[5];
v[i][1] -= h_rate[1];
}
idim = (image[i] >> 10) & 1023;
otherdims = image[i] ^ (idim << 10);
idim++;
@ -385,6 +419,11 @@ void Domain::pbc()
if (zperiodic) {
if (x[i][2] < lo[2]) {
x[i][2] += period[2];
if (deform_remap && mask[i] & deform_groupbit) {
v[i][0] += h_rate[4];
v[i][1] += h_rate[3];
v[i][2] += h_rate[2];
}
idim = image[i] >> 20;
otherdims = image[i] ^ (idim << 20);
idim--;
@ -394,6 +433,11 @@ void Domain::pbc()
if (x[i][2] >= hi[2]) {
x[i][2] -= period[2];
x[i][2] = MAX(x[i][2],lo[2]);
if (deform_remap && mask[i] & deform_groupbit) {
v[i][0] -= h_rate[4];
v[i][1] -= h_rate[3];
v[i][2] -= h_rate[2];
}
idim = image[i] >> 20;
otherdims = image[i] ^ (idim << 20);
idim++;
@ -533,7 +577,7 @@ void Domain::minimum_image(double *delta)
adjust image accordingly
resulting coord must satisfy lo <= coord < hi
MAX is important since coord - prd < lo can happen when coord = hi
for triclinic, convert atom to lamda coords (0-1) before doing remap
for triclinic, atom is converted to lamda coords (0-1) before doing remap
image = 10 bits for each dimension
increment/decrement in wrap-around fashion
------------------------------------------------------------------------- */