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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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224
src/atom_vec_hybrid.cpp
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@ -57,7 +57,7 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
// hybrid settings are MAX or MIN of sub-style settings
// hybrid sizes are minimial values plus extra values for each sub-style
size_comm = 3;
size_forward = 3;
size_reverse = 3;
size_border = 6;
size_data_atom = 5;
@ -73,16 +73,19 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
mass_type = MAX(mass_type,styles[k]->mass_type);
shape_type = MAX(shape_type,styles[k]->shape_type);
dipole_type = MAX(dipole_type,styles[k]->dipole_type);
comm_x_only = MIN(comm_x_only,styles[k]->comm_x_only);
comm_f_only = MIN(comm_f_only,styles[k]->comm_f_only);
ghost_velocity = MAX(ghost_velocity,styles[k]->ghost_velocity);
size_comm += styles[k]->size_comm - 3;
size_forward += styles[k]->size_forward - 3;
size_reverse += styles[k]->size_reverse - 3;
size_border += styles[k]->size_border - 6;
size_data_atom += styles[k]->size_data_atom - 5;
size_data_vel += styles[k]->size_data_vel - 4;
}
size_velocity = 3;
if (atom->omega_flag) size_velocity += 3;
if (atom->angmom_flag) size_velocity += 3;
}
/* ---------------------------------------------------------------------- */
@ -122,6 +125,9 @@ void AtomVecHybrid::grow(int n)
v = atom->v;
f = atom->f;
omega = atom->omega;
angmom = atom->angmom;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
@ -192,6 +198,74 @@ int AtomVecHybrid::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
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];
if (omega_flag) {
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
if (angmom_flag) {
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_comm_one(j,&buf[m]);
}
} 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];
if (omega_flag) {
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
if (angmom_flag) {
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_comm_one(j,&buf[m]);
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::unpack_comm(int n, int first, double *buf)
{
int i,k,last;
@ -209,6 +283,38 @@ void AtomVecHybrid::unpack_comm(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::unpack_comm_vel(int n, int first, double *buf)
{
int i,k,last;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
int 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++];
if (omega_flag) {
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
}
if (angmom_flag) {
angmom[i][0] = buf[m++];
angmom[i][1] = buf[m++];
angmom[i][2] = buf[m++];
}
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_comm_one(i,&buf[m]);
}
}
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_reverse(int n, int first, double *buf)
{
int i,k,last;
@ -290,6 +396,80 @@ int AtomVecHybrid::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
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];
if (omega_flag) {
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
if (angmom_flag) {
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_border_one(j,&buf[m]);
}
} 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];
if (omega_flag) {
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
if (angmom_flag) {
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_border_one(j,&buf[m]);
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::unpack_border(int n, int first, double *buf)
{
int i,k,m,last;
@ -309,6 +489,42 @@ void AtomVecHybrid::unpack_border(int n, int first, double *buf)
}
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::unpack_border_vel(int n, int first, double *buf)
{
int i,k,m,last;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
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++];
if (omega_flag) {
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
}
if (angmom_flag) {
angmom[i][0] = buf[m++];
angmom[i][1] = buf[m++];
angmom[i][2] = buf[m++];
}
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_border_one(i,&buf[m]);
}
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
pack each sub-style one after the other