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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@371 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-03-08 00:54:02 +00:00
parent a70ee2eadc
commit 9e1f8bcd6a
64 changed files with 1785 additions and 772 deletions
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72
src/atom.cpp
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@ -35,18 +35,17 @@
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define DELTA 1
#define DELTA_MEMSTR 1024
#define EPSILON 1.0e-6
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
{
// no atoms
natoms = nlocal = nghost = nmax = 0;
ntypes = 0;
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
@ -620,8 +619,9 @@ int Atom::count_words(char *line)
void Atom::data_atoms(int n, char *buf, int ihybrid)
{
int m,imagetmp,xptr,iptr;
double xtmp,ytmp,ztmp;
int m,imagedata,xptr,iptr;
double xdata[3],lamda[3],sublo[3],subhi[3];
double *coord;
char *next;
next = strchr(buf,'\n');
@ -635,12 +635,33 @@ void Atom::data_atoms(int n, char *buf, int ihybrid)
char **values = new char*[nwords];
double subxlo = domain->subxlo;
double subxhi = domain->subxhi;
double subylo = domain->subylo;
double subyhi = domain->subyhi;
double subzlo = domain->subzlo;
double subzhi = domain->subzhi;
// set bounds for my proc
// if periodic and I am lo/hi proc, adjust bounds by EPSILON
// insures all data atoms will be owned even with round-off
int triclinic = domain->triclinic;
if (triclinic == 0) {
sublo[0] = domain->sublo[0]; subhi[0] = domain->subhi[0];
sublo[1] = domain->sublo[1]; subhi[1] = domain->subhi[1];
sublo[2] = domain->sublo[2]; subhi[2] = domain->subhi[2];
} else {
sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
}
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= EPSILON;
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += EPSILON;
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= EPSILON;
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += EPSILON;
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= EPSILON;
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += EPSILON;
}
// xptr = which word in line starts xyz coords
// iptr = which word in line starts ix,iy,iz image flags
@ -662,20 +683,25 @@ void Atom::data_atoms(int n, char *buf, int ihybrid)
for (m = 1; m < nwords; m++)
values[m] = strtok(NULL," \t\n\r\f");
xtmp = atof(values[xptr]);
ytmp = atof(values[xptr+1]);
ztmp = atof(values[xptr+2]);
if (imageflag)
imagetmp = ((atoi(values[iptr+2]) + 512 & 1023) << 20) |
imagedata = ((atoi(values[iptr+2]) + 512 & 1023) << 20) |
((atoi(values[iptr+1]) + 512 & 1023) << 10) |
(atoi(values[iptr]) + 512 & 1023);
else imagetmp = (512 << 20) | (512 << 10) | 512;
else imagedata = (512 << 20) | (512 << 10) | 512;
domain->remap(xtmp,ytmp,ztmp,imagetmp);
if (xtmp >= subxlo && xtmp < subxhi &&
ytmp >= subylo && ytmp < subyhi &&
ztmp >= subzlo && ztmp < subzhi)
avec->data_atom(xtmp,ytmp,ztmp,imagetmp,values,ihybrid);
xdata[0] = atof(values[xptr]);
xdata[1] = atof(values[xptr+1]);
xdata[2] = atof(values[xptr+2]);
domain->remap(xdata,imagedata);
if (triclinic) {
domain->x2lamda(xdata,lamda);
coord = lamda;
} else coord = xdata;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2])
avec->data_atom(xdata,imagedata,values,ihybrid);
buf = next + 1;
}