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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4405 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2010-07-20 18:17:24 +00:00
parent 71fa7dbfd9
commit c4f3b2fe6d
3 changed files with 69 additions and 30 deletions
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52
src/XTC/dump_xtc.cpp
View File

@ -53,8 +53,6 @@ DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
{
if (narg != 5) error->all("Illegal dump xtc command");
if (igroup != group->find("all")) error->all("Dump xtc must use group all");
if (domain->triclinic)
error->all("Dump xtc does not yet support triclinic simulation boxes");
if (binary || compressed || multifile || multiproc)
error->all("Invalid dump xtc filename");
@ -175,15 +173,28 @@ void DumpXTC::write_header(int n)
xdr_float(&xd,&time_value);
// cell basis vectors
if (domain->triclinic) {
float zero = 0.0;
float xdim = sfactor * (domain->boxhi[0] - domain->boxlo[0]);
float ydim = sfactor * (domain->boxhi[1] - domain->boxlo[1]);
float zdim = sfactor * (domain->boxhi[2] - domain->boxlo[2]);
float xy = sfactor * domain->xy;
float xz = sfactor * domain->xz;
float yz = sfactor * domain->yz;
float zero = 0.0;
float xdim = sfactor * (domain->boxhi[0] - domain->boxlo[0]);
float ydim = sfactor * (domain->boxhi[1] - domain->boxlo[1]);
float zdim = sfactor * (domain->boxhi[2] - domain->boxlo[2]);
xdr_float(&xd,&xdim); xdr_float(&xd,&zero); xdr_float(&xd,&zero);
xdr_float(&xd,&xy ); xdr_float(&xd,&ydim); xdr_float(&xd,&zero);
xdr_float(&xd,&xz ); xdr_float(&xd,&yz ); xdr_float(&xd,&zdim);
} else {
float zero = 0.0;
float xdim = sfactor * (domain->boxhi[0] - domain->boxlo[0]);
float ydim = sfactor * (domain->boxhi[1] - domain->boxlo[1]);
float zdim = sfactor * (domain->boxhi[2] - domain->boxlo[2]);
xdr_float(&xd,&xdim); xdr_float(&xd,&zero); xdr_float(&xd,&zero);
xdr_float(&xd,&zero); xdr_float(&xd,&ydim); xdr_float(&xd,&zero);
xdr_float(&xd,&zero); xdr_float(&xd,&zero); xdr_float(&xd,&zdim);
xdr_float(&xd,&xdim); xdr_float(&xd,&zero); xdr_float(&xd,&zero);
xdr_float(&xd,&zero); xdr_float(&xd,&ydim); xdr_float(&xd,&zero);
xdr_float(&xd,&zero); xdr_float(&xd,&zero); xdr_float(&xd,&zdim);
}
}
/* ---------------------------------------------------------------------- */
@ -209,14 +220,27 @@ int DumpXTC::pack()
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double xy = domain->xy;
double xz = domain->xz;
double yz = domain->yz;
for (int i = 0; i < nlocal; i++) {
buf[m++] = tag[i];
buf[m++] = sfactor*(x[i][0] + ((image[i] & 1023) - 512) * xprd);
buf[m++] = sfactor*(x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd);
buf[m++] = sfactor*(x[i][2] + ((image[i] >> 20) - 512) * zprd);
}
int ix = (image[i] & 1023) - 512;
int iy = (image[i] >> 10 & 1023) - 512;
int iz = (image[i] >> 20) - 512;
if (domain->triclinic) {
buf[m++] = tag[i];
buf[m++] = sfactor * (x[i][0] + ix * xprd + iy * xy + iz * xz);
buf[m++] = sfactor * (x[i][1] + iy * yprd + iz * yz);
buf[m++] = sfactor * (x[i][2] + iz * zprd);
} else {
buf[m++] = tag[i];
buf[m++] = sfactor * (x[i][0] + ix * xprd);
buf[m++] = sfactor * (x[i][1] + iy * yprd);
buf[m++] = sfactor * (x[i][2] + iz * zprd);
}
}
} else {
for (int i = 0; i < nlocal; i++) {
buf[m++] = tag[i];

45
src/dump_dcd.cpp
View File

@ -55,8 +55,6 @@ DumpDCD::DumpDCD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
{
if (narg != 5) error->all("Illegal dump dcd command");
if (igroup != group->find("all")) error->all("Dump dcd must use group all");
if (domain->triclinic)
error->all("Dump dcd does not yet support triclinic simulation boxes");
if (binary || compressed || multifile || multiproc)
error->all("Invalid dump dcd filename");
@ -92,9 +90,6 @@ DumpDCD::~DumpDCD()
void DumpDCD::init()
{
if (unwrap_flag == 1 && domain->triclinic)
error->all("Dump dcd cannot dump unwrapped coords with triclinic box");
// check that dump frequency has not changed
if (nevery_save == 0) {
@ -161,24 +156,31 @@ void DumpDCD::write_header(int n)
}
// dim[] = size and angle cosines of orthogonal or triclinic box
// dim[0] = a = length of unit cell vector along x-axis
// dim[1] = alpha = cosine of angle between b and c
// dim[2] = b = length of unit cell vector in xy-plane
// dim[3] = beta = cosine of angle between a and c
// dim[4] = gamma = cosine of angle between a and b
// dim[5] = c = length of final unit cell vector
// 48 = 6 doubles
double dim[6];
dim[0] = domain->xprd;
dim[2] = domain->yprd;
dim[5] = domain->zprd;
if (domain->triclinic == 0) dim[1] = dim[3] = dim[4] = 0.0;
else {
if (domain->triclinic) {
double *h = domain->h;
double alen = h[0];
double blen = sqrt(h[5]*h[5] + h[1]*h[1]);
double clen = sqrt(h[4]*h[4] + h[3]*h[3] + h[2]*h[2]);
dim[0] = alen;
dim[2] = blen;
dim[5] = clen;
dim[1] = (h[5]*h[4] + h[1]*h[3]) / blen/clen;
dim[3] = (h[0]*h[4]) / alen/clen;
dim[4] = (h[0]*h[5]) / alen/blen;
} else {
dim[0] = domain->xprd;
dim[2] = domain->yprd;
dim[5] = domain->zprd;
dim[1] = dim[3] = dim[4] = 0.0;
}
if (me == 0) {
@ -213,14 +215,27 @@ int DumpDCD::pack()
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double xy = domain->xy;
double xz = domain->xz;
double yz = domain->yz;
for (int i = 0; i < nlocal; i++) {
buf[m++] = tag[i];
buf[m++] = x[i][0] + ((image[i] & 1023) - 512) * xprd;
buf[m++] = x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd;
buf[m++] = x[i][2] + ((image[i] >> 20) - 512) * zprd;
}
int ix = (image[i] & 1023) - 512;
int iy = (image[i] >> 10 & 1023) - 512;
int iz = (image[i] >> 20) - 512;
if (domain->triclinic) {
buf[m++] = tag[i];
buf[m++] = x[i][0] + ix * xprd + iy * xy + iz * xz;
buf[m++] = x[i][1] + iy * yprd + iz * yz;
buf[m++] = x[i][2] + iz * zprd;
} else {
buf[m++] = tag[i];
buf[m++] = x[i][0] + ix * xprd;
buf[m++] = x[i][1] + iy * yprd;
buf[m++] = x[i][2] + iz * zprd;
}
}
} else {
for (int i = 0; i < nlocal; i++) {
buf[m++] = tag[i];

2
src/region_sphere.cpp
View File

@ -63,7 +63,7 @@ RegSphere::~RegSphere()
inside = 0 if x,y,z is outside and not on surface
------------------------------------------------------------------------- */
int RegSphere:: inside(double x, double y, double z)
int RegSphere::inside(double x, double y, double z)
{
double delx = x - xc;
double dely = y - yc;