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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5753 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-03-07 22:46:48 +00:00
parent cdcce9fed8
commit 649ea52fbd
3 changed files with 189 additions and 63 deletions
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12
src/atom_vec.cpp
View File

@ -14,6 +14,7 @@
#include "stdlib.h" #include "stdlib.h"
#include "atom_vec.h" #include "atom_vec.h"
#include "atom.h" #include "atom.h"
#include "domain.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -26,6 +27,17 @@ AtomVec::AtomVec(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
mass_type = shape_type = dipole_type = 0; mass_type = shape_type = dipole_type = 0;
} }
/* ----------------------------------------------------------------------
copy of velocity remap settings from Domain
------------------------------------------------------------------------- */
void AtomVec::init()
{
deform_vremap = domain->deform_vremap;
deform_groupbit = domain->deform_groupbit;
h_rate = domain->h_rate;
}
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
unpack one line from Velocities section of data file unpack one line from Velocities section of data file
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

87
src/atom_vec_atomic.cpp
View File

@ -147,7 +147,7 @@ int AtomVecAtomic::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc) int pbc_flag, int *pbc)
{ {
int i,j,m; int i,j,m;
double dx,dy,dz; double dx,dy,dz,dvx,dvy,dvz;
m = 0; m = 0;
if (pbc_flag == 0) { if (pbc_flag == 0) {
@ -170,14 +170,35 @@ int AtomVecAtomic::pack_comm_vel(int n, int *list, double *buf,
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd; dz = pbc[2]*domain->zprd;
} }
for (i = 0; i < n; i++) { if (!deform_vremap) {
j = list[i]; for (i = 0; i < n; i++) {
buf[m++] = x[j][0] + dx; j = list[i];
buf[m++] = x[j][1] + dy; buf[m++] = x[j][0] + dx;
buf[m++] = x[j][2] + dz; buf[m++] = x[j][1] + dy;
buf[m++] = v[j][0]; buf[m++] = x[j][2] + dz;
buf[m++] = v[j][1]; buf[m++] = v[j][0];
buf[m++] = v[j][2]; buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[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;
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
} }
} }
return m; return m;
@ -295,7 +316,7 @@ int AtomVecAtomic::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc) int pbc_flag, int *pbc)
{ {
int i,j,m; int i,j,m;
double dx,dy,dz; double dx,dy,dz,dvx,dvy,dvz;
m = 0; m = 0;
if (pbc_flag == 0) { if (pbc_flag == 0) {
@ -321,17 +342,41 @@ int AtomVecAtomic::pack_border_vel(int n, int *list, double *buf,
dy = pbc[1]; dy = pbc[1];
dz = pbc[2]; dz = pbc[2];
} }
for (i = 0; i < n; i++) { if (!deform_vremap) {
j = list[i]; for (i = 0; i < n; i++) {
buf[m++] = x[j][0] + dx; j = list[i];
buf[m++] = x[j][1] + dy; buf[m++] = x[j][0] + dx;
buf[m++] = x[j][2] + dz; buf[m++] = x[j][1] + dy;
buf[m++] = tag[j]; buf[m++] = x[j][2] + dz;
buf[m++] = type[j]; buf[m++] = tag[j];
buf[m++] = mask[j]; buf[m++] = type[j];
buf[m++] = v[j][0]; buf[m++] = mask[j];
buf[m++] = v[j][1]; buf[m++] = v[j][0];
buf[m++] = v[j][2]; buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[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];
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
} }
} }
return m; return m;

153
src/atom_vec_hybrid.cpp
View File

@ -211,7 +211,7 @@ int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc) int pbc_flag, int *pbc)
{ {
int i,j,k,m; int i,j,k,m;
double dx,dy,dz; double dx,dy,dz,dvx,dvy,dvz;
int omega_flag = atom->omega_flag; int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag; int angmom_flag = atom->angmom_flag;
@ -248,26 +248,59 @@ int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd; dz = pbc[2]*domain->zprd;
} }
for (i = 0; i < n; i++) { if (!deform_vremap) {
j = list[i]; for (i = 0; i < n; i++) {
buf[m++] = x[j][0] + dx; j = list[i];
buf[m++] = x[j][1] + dy; buf[m++] = x[j][0] + dx;
buf[m++] = x[j][2] + dz; buf[m++] = x[j][1] + dy;
buf[m++] = v[j][0]; buf[m++] = x[j][2] + dz;
buf[m++] = v[j][1]; buf[m++] = v[j][0];
buf[m++] = v[j][2]; buf[m++] = v[j][1];
if (omega_flag) { buf[m++] = v[j][2];
buf[m++] = omega[j][0]; if (omega_flag) {
buf[m++] = omega[j][1]; buf[m++] = omega[j][0];
buf[m++] = omega[j][2]; 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]);
} }
if (angmom_flag) { } else {
buf[m++] = angmom[j][0]; dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
buf[m++] = angmom[j][1]; dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
buf[m++] = angmom[j][2]; dvz = pbc[2]*h_rate[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;
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
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]);
} }
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_comm_one(j,&buf[m]);
} }
} }
return m; return m;
@ -409,7 +442,7 @@ int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc) int pbc_flag, int *pbc)
{ {
int i,j,k,m; int i,j,k,m;
double dx,dy,dz; double dx,dy,dz,dvx,dvy,dvz;
int omega_flag = atom->omega_flag; int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag; int angmom_flag = atom->angmom_flag;
@ -449,29 +482,65 @@ int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf,
dy = pbc[1]; dy = pbc[1];
dz = pbc[2]; dz = pbc[2];
} }
for (i = 0; i < n; i++) { if (!deform_vremap) {
j = list[i]; for (i = 0; i < n; i++) {
buf[m++] = x[j][0] + dx; j = list[i];
buf[m++] = x[j][1] + dy; buf[m++] = x[j][0] + dx;
buf[m++] = x[j][2] + dz; buf[m++] = x[j][1] + dy;
buf[m++] = tag[j]; buf[m++] = x[j][2] + dz;
buf[m++] = type[j]; buf[m++] = tag[j];
buf[m++] = mask[j]; buf[m++] = type[j];
buf[m++] = v[j][0]; buf[m++] = mask[j];
buf[m++] = v[j][1]; buf[m++] = v[j][0];
buf[m++] = v[j][2]; buf[m++] = v[j][1];
if (omega_flag) { buf[m++] = v[j][2];
buf[m++] = omega[j][0]; if (omega_flag) {
buf[m++] = omega[j][1]; buf[m++] = omega[j][0];
buf[m++] = omega[j][2]; buf[m++] = omega[j][1];
} buf[m++] = omega[j][2];
if (angmom_flag) { }
buf[m++] = angmom[j][0]; if (angmom_flag) {
buf[m++] = angmom[j][1]; buf[m++] = angmom[j][0];
buf[m++] = angmom[j][2]; buf[m++] = angmom[j][1];
} buf[m++] = angmom[j][2];
for (k = 0; k < nstyles; k++) }
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_border_one(j,&buf[m]); m += styles[k]->pack_border_one(j,&buf[m]);
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[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];
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
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; return m;