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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5751 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-03-07 22:46:24 +00:00
parent de606547aa
commit 4170b9f339
3 changed files with 322 additions and 185 deletions
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273
src/USER-EFF/atom_vec_electron.cpp
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@ -40,10 +40,10 @@ AtomVecElectron::AtomVecElectron(LAMMPS *lmp, int narg, char **arg) :
mass_type = 1;
molecular = 0;
size_forward = 5;
size_forward = 4;
size_reverse = 4;
size_border = 10;
size_velocity = 4;
size_border = 9;
size_velocity = 3;
size_data_atom = 8;
size_data_vel = 5;
xcol_data = 6;
@ -102,7 +102,8 @@ void AtomVecElectron::grow_reset()
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
q = atom->q; eradius = atom->eradius; ervel = atom->ervel; erforce = atom->erforce;
q = atom->q;
eradius = atom->eradius; ervel = atom->ervel; erforce = atom->erforce;
}
/* ---------------------------------------------------------------------- */
@ -146,7 +147,6 @@ int AtomVecElectron::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
} else {
if (domain->triclinic == 0) {
@ -164,7 +164,6 @@ int AtomVecElectron::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
}
return m;
@ -176,7 +175,7 @@ int AtomVecElectron::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
double dx,dy,dz,dvx,dvy,dvz;
m = 0;
if (pbc_flag == 0) {
@ -185,11 +184,10 @@ int AtomVecElectron::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = eradius[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
} else {
if (domain->triclinic == 0) {
@ -201,16 +199,37 @@ int AtomVecElectron::pack_comm_vel(int n, int *list, double *buf,
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];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
if (!deform_vremap) {
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++] = eradius[j];
buf[m++] = v[j][0];
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++] = eradius[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;
@ -229,7 +248,6 @@ void AtomVecElectron::unpack_comm(int n, int first, double *buf)
x[i][1] = buf[m++];
x[i][2] = buf[m++];
eradius[i] = buf[m++];
ervel[i] = buf[m++];
}
}
@ -245,11 +263,10 @@ void AtomVecElectron::unpack_comm_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
eradius[i] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
eradius[i] = buf[m++];
ervel[i] = buf[m++];
}
}
@ -258,9 +275,7 @@ void AtomVecElectron::unpack_comm_vel(int n, int first, double *buf)
int AtomVecElectron::pack_comm_one(int i, double *buf)
{
buf[0] = eradius[i];
buf[1] = ervel[i];
return 2;
return 1;
}
/* ---------------------------------------------------------------------- */
@ -268,9 +283,7 @@ int AtomVecElectron::pack_comm_one(int i, double *buf)
int AtomVecElectron::unpack_comm_one(int i, double *buf)
{
eradius[i] = buf[0];
ervel[i] = buf[1];
return 2;
return 1;
}
/* ---------------------------------------------------------------------- */
@ -295,7 +308,6 @@ int AtomVecElectron::pack_reverse(int n, int first, double *buf)
int AtomVecElectron::pack_reverse_one(int i, double *buf)
{
buf[0] = erforce[i];
return 1;
}
@ -320,94 +332,11 @@ void AtomVecElectron::unpack_reverse(int n, int *list, double *buf)
int AtomVecElectron::unpack_reverse_one(int i, double *buf)
{
erforce[i] += buf[0];
return 1;
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::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];
buf[m++] = q[j];
buf[m++] = spin[j];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
} 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];
buf[m++] = q[j];
buf[m++] = spin[j];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecElectron::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++];
q[i] = buf[m++];
spin[i] = static_cast<int> (buf[m++]);
eradius[i] = buf[m++];
ervel[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
@ -427,7 +356,6 @@ int AtomVecElectron::pack_border(int n, int *list, double *buf,
buf[m++] = q[j];
buf[m++] = spin[j];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
} else {
if (domain->triclinic == 0) {
@ -450,7 +378,87 @@ int AtomVecElectron::pack_border(int n, int *list, double *buf,
buf[m++] = q[j];
buf[m++] = spin[j];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
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++] = q[j];
buf[m++] = spin[j];
buf[m++] = eradius[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];
}
if (domain->triclinic == 0) {
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++] = q[j];
buf[m++] = spin[j];
buf[m++] = eradius[j];
buf[m++] = v[j][0];
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];
buf[m++] = q[j];
buf[m++] = spin[j];
buf[m++] = eradius[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;
@ -463,9 +471,7 @@ int AtomVecElectron::pack_border_one(int i, double *buf)
buf[0] = q[i];
buf[1] = spin[i];
buf[2] = eradius[i];
buf[3] = ervel[i];
return 4;
return 3;
}
/* ---------------------------------------------------------------------- */
@ -487,7 +493,31 @@ void AtomVecElectron::unpack_border(int n, int first, double *buf)
q[i] = buf[m++];
spin[i] = static_cast<int> (buf[m++]);
eradius[i] = buf[m++];
ervel[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecElectron::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++]);
q[i] = buf[m++];
spin[i] = static_cast<int> (buf[m++]);
eradius[i] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
@ -498,9 +528,7 @@ int AtomVecElectron::unpack_border_one(int i, double *buf)
q[i] = buf[0];
spin[i] = static_cast<int> (buf[1]);
eradius[i] = buf[2];
ervel[i] = buf[3];
return 4;
return 3;
}
/* ----------------------------------------------------------------------
@ -746,7 +774,7 @@ int AtomVecElectron::data_atom_hybrid(int nlocal, char **values)
v[nlocal][2] = 0.0;
ervel[nlocal] = 0.0;
return 2;
return 3;
}
/* ----------------------------------------------------------------------
@ -768,7 +796,6 @@ void AtomVecElectron::data_vel(int m, char **values)
int AtomVecElectron::data_vel_hybrid(int m, char **values)
{
ervel[m] = atof(values[0]);
return 1;
}