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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3355 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2009-11-09 18:20:20 +00:00
parent e8f3d7542d
commit 0c76e65560
40 changed files with 1935 additions and 468 deletions
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136
src/atom_vec_atomic.cpp
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@ -29,10 +29,14 @@ using namespace LAMMPS_NS;
AtomVecAtomic::AtomVecAtomic(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 0;
mass_type = 1;
size_comm = 3;
comm_x_only = comm_f_only = 1;
size_forward = 3;
size_reverse = 3;
size_border = 6;
size_velocity = 3;
size_data_atom = 5;
size_data_vel = 4;
xcol_data = 3;
@ -125,6 +129,48 @@ int AtomVecAtomic::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomic::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
@ -140,6 +186,24 @@ void AtomVecAtomic::unpack_comm(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
void AtomVecAtomic::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
@ -213,6 +277,54 @@ int AtomVecAtomic::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomic::unpack_border(int n, int first, double *buf)
{
int i,m,last;
@ -230,6 +342,28 @@ void AtomVecAtomic::unpack_border(int n, int first, double *buf)
}
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomic::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them