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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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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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132
src/dump_custom.cpp
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@ -532,61 +532,61 @@ int DumpCustom::count()
} else if (thresh_array[ithresh] == XU) {
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double xprd = domain->xprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = x[i][0] + ((image[i] & 1023) - 512) * xprd;
dchoose[i] = x[i][0] + ((image[i] & IMGMASK) - IMGMAX) * xprd;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YU) {
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double yprd = domain->yprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd;
dchoose[i] = x[i][1] + ((image[i] >> IMGBITS & IMGMASK) - IMGMAX) * yprd;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZU) {
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double zprd = domain->zprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = x[i][2] + ((image[i] >> 20) - 512) * zprd;
dchoose[i] = x[i][2] + ((image[i] >> IMG2BITS) - IMGMAX) * zprd;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == XUTRI) {
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double *h = domain->h;
int xbox,ybox,zbox;
for (i = 0; i < nlocal; i++) {
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;
dchoose[i] = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox;
}
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YUTRI) {
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double *h = domain->h;
int ybox,zbox;
for (i = 0; i < nlocal; i++) {
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dchoose[i] = x[i][1] + h[1]*ybox + h[3]*zbox;
}
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZUTRI) {
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double *h = domain->h;
int zbox;
for (i = 0; i < nlocal; i++) {
zbox = (image[i] >> 20) - 512;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dchoose[i] = x[i][2] + h[2]*zbox;
}
ptr = dchoose;
@ -594,85 +594,85 @@ int DumpCustom::count()
} else if (thresh_array[ithresh] == XSU) {
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double boxxlo = domain->boxlo[0];
double invxprd = 1.0/domain->xprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = (x[i][0] - boxxlo) * invxprd + (image[i] & 1023) - 512;
dchoose[i] = (x[i][0] - boxxlo) * invxprd + (image[i] & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YSU) {
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double boxylo = domain->boxlo[1];
double invyprd = 1.0/domain->yprd;
for (i = 0; i < nlocal; i++)
dchoose[i] =
(x[i][1] - boxylo) * invyprd + (image[i] >> 10 & 1023) - 512;
(x[i][1] - boxylo) * invyprd + (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZSU) {
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double boxzlo = domain->boxlo[2];
double invzprd = 1.0/domain->zprd;
for (i = 0; i < nlocal; i++)
dchoose[i] = (x[i][2] - boxzlo) * invzprd + (image[i] >> 20) - 512;
dchoose[i] = (x[i][2] - boxzlo) * invzprd + (image[i] >> IMG2BITS) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == XSUTRI) {
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (i = 0; i < nlocal; i++)
dchoose[i] = h_inv[0]*(x[i][0]-boxlo[0]) +
h_inv[5]*(x[i][1]-boxlo[1]) +
h_inv[4]*(x[i][2]-boxlo[2]) +
(image[i] & 1023) - 512;
(image[i] & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == YSUTRI) {
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (i = 0; i < nlocal; i++)
dchoose[i] = h_inv[1]*(x[i][1]-boxlo[1]) +
h_inv[3]*(x[i][2]-boxlo[2]) +
(image[i] >> 10 & 1023) - 512;
(image[i] >> IMGBITS & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == ZSUTRI) {
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (i = 0; i < nlocal; i++)
dchoose[i] = h_inv[2]*(x[i][2]-boxlo[2]) +
(image[i] >> 20) - 512;
(image[i] >> IMG2BITS) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == IX) {
int *image = atom->image;
tagint *image = atom->image;
for (i = 0; i < nlocal; i++)
dchoose[i] = (image[i] & 1023) - 512;
dchoose[i] = (image[i] & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == IY) {
int *image = atom->image;
tagint *image = atom->image;
for (i = 0; i < nlocal; i++)
dchoose[i] = (image[i] >> 10 & 1023) - 512;
dchoose[i] = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
} else if (thresh_array[ithresh] == IZ) {
int *image = atom->image;
tagint *image = atom->image;
for (i = 0; i < nlocal; i++)
dchoose[i] = (image[i] >> 20) - 512;
dchoose[i] = (image[i] >> IMG2BITS) - IMGMAX;
ptr = dchoose;
nstride = 1;
@ -1847,13 +1847,13 @@ void DumpCustom::pack_xu(int n)
{
int j;
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double xprd = domain->xprd;
for (int i = 0; i < nchoose; i++) {
j = clist[i];
buf[n] = x[j][0] + ((image[j] & 1023) - 512) * xprd;
buf[n] = x[j][0] + ((image[j] & IMGMASK) - IMGMAX) * xprd;
n += size_one;
}
}
@ -1864,13 +1864,13 @@ void DumpCustom::pack_yu(int n)
{
int j;
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double yprd = domain->yprd;
for (int i = 0; i < nchoose; i++) {
j = clist[i];
buf[n] = x[j][1] + ((image[j] >> 10 & 1023) - 512) * yprd;
buf[n] = x[j][1] + ((image[j] >> IMGBITS & IMGMASK) - IMGMAX) * yprd;
n += size_one;
}
}
@ -1881,13 +1881,13 @@ void DumpCustom::pack_zu(int n)
{
int j;
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double zprd = domain->zprd;
for (int i = 0; i < nchoose; i++) {
j = clist[i];
buf[n] = x[j][2] + ((image[j] >> 20) - 512) * zprd;
buf[n] = x[j][2] + ((image[j] >> IMG2BITS) - IMGMAX) * zprd;
n += size_one;
}
}
@ -1898,16 +1898,16 @@ void DumpCustom::pack_xu_triclinic(int n)
{
int j;
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double *h = domain->h;
int xbox,ybox,zbox;
for (int i = 0; i < nchoose; i++) {
j = clist[i];
xbox = (image[j] & 1023) - 512;
ybox = (image[j] >> 10 & 1023) - 512;
zbox = (image[j] >> 20) - 512;
xbox = (image[j] & IMGMASK) - IMGMAX;
ybox = (image[j] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[j] >> IMG2BITS) - IMGMAX;
buf[n] = x[j][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox;
n += size_one;
}
@ -1919,15 +1919,15 @@ void DumpCustom::pack_yu_triclinic(int n)
{
int j;
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double *h = domain->h;
int ybox,zbox;
for (int i = 0; i < nchoose; i++) {
j = clist[i];
ybox = (image[j] >> 10 & 1023) - 512;
zbox = (image[j] >> 20) - 512;
ybox = (image[j] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[j] >> IMG2BITS) - IMGMAX;
buf[n] = x[j][1] + h[1]*ybox + h[3]*zbox;
n += size_one;
}
@ -1939,14 +1939,14 @@ void DumpCustom::pack_zu_triclinic(int n)
{
int j;
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double *h = domain->h;
int zbox;
for (int i = 0; i < nchoose; i++) {
j = clist[i];
zbox = (image[j] >> 20) - 512;
zbox = (image[j] >> IMG2BITS) - IMGMAX;
buf[n] = x[j][2] + h[2]*zbox;
n += size_one;
}
@ -1958,14 +1958,14 @@ void DumpCustom::pack_xsu(int n)
{
int j;
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double boxxlo = domain->boxlo[0];
double invxprd = 1.0/domain->xprd;
for (int i = 0; i < nchoose; i++) {
j = clist[i];
buf[n] = (x[j][0] - boxxlo) * invxprd + (image[j] & 1023) - 512;
buf[n] = (x[j][0] - boxxlo) * invxprd + (image[j] & IMGMASK) - IMGMAX;
n += size_one;
}
}
@ -1976,14 +1976,14 @@ void DumpCustom::pack_ysu(int n)
{
int j;
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double boxylo = domain->boxlo[1];
double invyprd = 1.0/domain->yprd;
for (int i = 0; i < nchoose; i++) {
j = clist[i];
buf[n] = (x[j][1] - boxylo) * invyprd + (image[j] >> 10 & 1023) - 512;
buf[n] = (x[j][1] - boxylo) * invyprd + (image[j] >> IMGBITS & IMGMASK) - IMGMAX;
n += size_one;
}
}
@ -1994,14 +1994,14 @@ void DumpCustom::pack_zsu(int n)
{
int j;
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double boxzlo = domain->boxlo[2];
double invzprd = 1.0/domain->zprd;
for (int i = 0; i < nchoose; i++) {
j = clist[i];
buf[n] = (x[j][2] - boxzlo) * invzprd + (image[j] >> 20) - 512;
buf[n] = (x[j][2] - boxzlo) * invzprd + (image[j] >> IMG2BITS) - IMGMAX;
n += size_one;
}
}
@ -2012,7 +2012,7 @@ void DumpCustom::pack_xsu_triclinic(int n)
{
int j;
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
@ -2020,7 +2020,7 @@ void DumpCustom::pack_xsu_triclinic(int n)
for (int i = 0; i < nchoose; i++) {
j = clist[i];
buf[n] = h_inv[0]*(x[j][0]-boxlo[0]) + h_inv[5]*(x[j][1]-boxlo[1]) +
h_inv[4]*(x[j][2]-boxlo[2]) + (image[j] & 1023) - 512;
h_inv[4]*(x[j][2]-boxlo[2]) + (image[j] & IMGMASK) - IMGMAX;
n += size_one;
}
}
@ -2031,7 +2031,7 @@ void DumpCustom::pack_ysu_triclinic(int n)
{
int j;
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
@ -2039,7 +2039,7 @@ void DumpCustom::pack_ysu_triclinic(int n)
for (int i = 0; i < nchoose; i++) {
j = clist[i];
buf[n] = h_inv[1]*(x[j][1]-boxlo[1]) + h_inv[3]*(x[j][2]-boxlo[2]) +
(image[j] >> 10 & 1023) - 512;
(image[j] >> IMGBITS & IMGMASK) - IMGMAX;
n += size_one;
}
}
@ -2050,14 +2050,14 @@ void DumpCustom::pack_zsu_triclinic(int n)
{
int j;
double **x = atom->x;
int *image = atom->image;
tagint *image = atom->image;
double *boxlo = domain->boxlo;
double *h_inv = domain->h_inv;
for (int i = 0; i < nchoose; i++) {
j = clist[i];
buf[n] = h_inv[2]*(x[j][2]-boxlo[2]) + (image[j] >> 20) - 512;
buf[n] = h_inv[2]*(x[j][2]-boxlo[2]) + (image[j] >> IMG2BITS) - IMGMAX;
n += size_one;
}
}
@ -2066,10 +2066,10 @@ void DumpCustom::pack_zsu_triclinic(int n)
void DumpCustom::pack_ix(int n)
{
int *image = atom->image;
tagint *image = atom->image;
for (int i = 0; i < nchoose; i++) {
buf[n] = (image[clist[i]] & 1023) - 512;
buf[n] = (image[clist[i]] & IMGMASK) - IMGMAX;
n += size_one;
}
}
@ -2078,10 +2078,10 @@ void DumpCustom::pack_ix(int n)
void DumpCustom::pack_iy(int n)
{
int *image = atom->image;
tagint *image = atom->image;
for (int i = 0; i < nchoose; i++) {
buf[n] = (image[clist[i]] >> 10 & 1023) - 512;
buf[n] = (image[clist[i]] >> IMGBITS & IMGMASK) - IMGMAX;
n += size_one;
}
}
@ -2090,10 +2090,10 @@ void DumpCustom::pack_iy(int n)
void DumpCustom::pack_iz(int n)
{
int *image = atom->image;
tagint *image = atom->image;
for (int i = 0; i < nchoose; i++) {
buf[n] = (image[clist[i]] >> 20) - 512;
buf[n] = (image[clist[i]] >> IMG2BITS) - IMGMAX;
n += size_one;
}
}