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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8395 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-25 22:03:31 +00:00
parent 8f6a8d13d5
commit 66c5617afb
83 changed files with 10821 additions and 639 deletions
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92
src/group.cpp
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@ -733,7 +733,7 @@ void Group::xcm(int igroup, double masstotal, double *cm)
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
tagint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
@ -750,9 +750,9 @@ void Group::xcm(int igroup, double masstotal, double *cm)
if (rmass) {
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;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
massone = rmass[i];
cmone[0] += (x[i][0] + xbox*xprd) * massone;
cmone[1] += (x[i][1] + ybox*yprd) * massone;
@ -761,9 +761,9 @@ void Group::xcm(int igroup, double masstotal, double *cm)
} 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;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
massone = mass[type[i]];
cmone[0] += (x[i][0] + xbox*xprd) * massone;
cmone[1] += (x[i][1] + ybox*yprd) * massone;
@ -794,7 +794,7 @@ void Group::xcm(int igroup, double masstotal, double *cm, int iregion)
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
tagint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
@ -811,9 +811,9 @@ void Group::xcm(int igroup, double masstotal, double *cm, int iregion)
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
massone = rmass[i];
cmone[0] += (x[i][0] + xbox*xprd) * massone;
cmone[1] += (x[i][1] + ybox*yprd) * massone;
@ -822,9 +822,9 @@ void Group::xcm(int igroup, double masstotal, double *cm, int iregion)
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
massone = mass[type[i]];
cmone[0] += (x[i][0] + xbox*xprd) * massone;
cmone[1] += (x[i][1] + ybox*yprd) * massone;
@ -1071,7 +1071,7 @@ double Group::gyration(int igroup, double masstotal, double *cm)
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
tagint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
@ -1085,9 +1085,9 @@ double Group::gyration(int igroup, double masstotal, double *cm)
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;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
@ -1116,7 +1116,7 @@ double Group::gyration(int igroup, double masstotal, double *cm, int iregion)
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
tagint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
@ -1130,9 +1130,9 @@ double Group::gyration(int igroup, double masstotal, double *cm, int iregion)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
@ -1161,7 +1161,7 @@ void Group::angmom(int igroup, double *cm, double *lmom)
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
tagint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
@ -1176,9 +1176,9 @@ void Group::angmom(int igroup, double *cm, double *lmom)
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;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
@ -1207,7 +1207,7 @@ void Group::angmom(int igroup, double *cm, double *lmom, int iregion)
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
tagint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
@ -1222,9 +1222,9 @@ void Group::angmom(int igroup, double *cm, double *lmom, int iregion)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
@ -1251,7 +1251,7 @@ void Group::torque(int igroup, double *cm, double *tq)
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int *image = atom->image;
tagint *image = atom->image;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
@ -1264,9 +1264,9 @@ void Group::torque(int igroup, double *cm, double *tq)
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;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
@ -1292,7 +1292,7 @@ void Group::torque(int igroup, double *cm, double *tq, int iregion)
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int *image = atom->image;
tagint *image = atom->image;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
@ -1305,9 +1305,9 @@ void Group::torque(int igroup, double *cm, double *tq, int iregion)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
@ -1333,7 +1333,7 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3])
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
tagint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
@ -1350,9 +1350,9 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3])
for (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;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
@ -1387,7 +1387,7 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3], int iregion)
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
tagint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
@ -1404,9 +1404,9 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3], int iregion)
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];