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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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50
src/atom_vec_atomic.cpp
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@ -14,7 +14,6 @@
#include "stdlib.h"
#include "atom_vec_atomic.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
@ -102,12 +101,13 @@ void AtomVecAtomic::copy(int i, int j)
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_comm(int n, int *list, double *buf, int *pbc_flags)
int AtomVecAtomic::pack_comm(int n, int *list, double *buf,
int pbc_flag, double *pbc_dist)
{
int i,j,m;
m = 0;
if (pbc_flags[0] == 0) {
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
@ -115,14 +115,11 @@ int AtomVecAtomic::pack_comm(int n, int *list, double *buf, int *pbc_flags)
buf[m++] = x[j][2];
}
} else {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + pbc_flags[1]*xprd;
buf[m++] = x[j][1] + pbc_flags[2]*yprd;
buf[m++] = x[j][2] + pbc_flags[3]*zprd;
buf[m++] = x[j][0] + pbc_dist[0];
buf[m++] = x[j][1] + pbc_dist[1];
buf[m++] = x[j][2] + pbc_dist[2];
}
}
return m;
@ -176,12 +173,13 @@ void AtomVecAtomic::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_border(int n, int *list, double *buf, int *pbc_flags)
int AtomVecAtomic::pack_border(int n, int *list, double *buf,
int pbc_flag, double *pbc_dist)
{
int i,j,m;
m = 0;
if (pbc_flags[0] == 0) {
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
@ -192,14 +190,11 @@ int AtomVecAtomic::pack_border(int n, int *list, double *buf, int *pbc_flags)
buf[m++] = mask[j];
}
} else {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + pbc_flags[1]*xprd;
buf[m++] = x[j][1] + pbc_flags[2]*yprd;
buf[m++] = x[j][2] + pbc_flags[3]*zprd;
buf[m++] = x[j][0] + pbc_dist[0];
buf[m++] = x[j][1] + pbc_dist[1];
buf[m++] = x[j][2] + pbc_dist[2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
@ -378,21 +373,20 @@ int AtomVecAtomic::unpack_restart(double *buf)
}
/* ----------------------------------------------------------------------
create one atom of type itype at x0,y0,z0
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecAtomic::create_atom(int itype, double x0, double y0, double z0,
int ihybrid)
void AtomVecAtomic::create_atom(int itype, double *coord, int ihybrid)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = x0;
x[nlocal][1] = y0;
x[nlocal][2] = z0;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
@ -407,8 +401,8 @@ void AtomVecAtomic::create_atom(int itype, double x0, double y0, double z0,
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecAtomic::data_atom(double xtmp, double ytmp, double ztmp,
int imagetmp, char **values, int ihybrid)
void AtomVecAtomic::data_atom(double *coord, int imagetmp, char **values,
int ihybrid)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
@ -421,9 +415,9 @@ void AtomVecAtomic::data_atom(double xtmp, double ytmp, double ztmp,
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
x[nlocal][0] = xtmp;
x[nlocal][1] = ytmp;
x[nlocal][2] = ztmp;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;