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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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236
src/atom_vec_hybrid.cpp
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@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -42,9 +42,9 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
for (i = 0; i < narg; i++) {
for (k = 0; k < i; k++)
if (strcmp(arg[i],keywords[k]) == 0)
error->all(FLERR,"Atom style hybrid cannot use same atom style twice");
if (strcmp(arg[i],"hybrid") == 0)
if (strcmp(arg[i],keywords[k]) == 0)
error->all(FLERR,"Atom style hybrid cannot use same atom style twice");
if (strcmp(arg[i],"hybrid") == 0)
error->all(FLERR,"Atom style hybrid cannot have hybrid as an argument");
styles[i] = atom->new_avec(arg[i],0,NULL,NULL,dummy);
keywords[i] = new char[strlen(arg[i])+1];
@ -108,7 +108,7 @@ void AtomVecHybrid::init()
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecHybrid::grow(int n)
@ -134,7 +134,7 @@ void AtomVecHybrid::grow(int n)
grow_reset();
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
@ -164,7 +164,7 @@ void AtomVecHybrid::copy(int i, int j, int delflag)
atom->nextra_grow = tmp;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
@ -178,7 +178,7 @@ void AtomVecHybrid::clear_bonus()
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz;
@ -220,7 +220,7 @@ 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 pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz,dvx,dvy,dvz;
@ -238,14 +238,14 @@ int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
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];
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];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
}
} else {
@ -260,52 +260,52 @@ int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
}
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++] = 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];
}
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];
}
}
} 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];
}
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];
}
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];
}
}
}
}
@ -418,7 +418,7 @@ void AtomVecHybrid::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz;
@ -466,7 +466,7 @@ 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 pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz,dvx,dvy,dvz;
@ -487,14 +487,14 @@ int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf,
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];
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];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
}
} else {
@ -509,58 +509,58 @@ int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf,
}
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++] = 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];
}
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];
}
}
} 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];
}
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];
}
}
}
}
@ -649,13 +649,13 @@ int AtomVecHybrid::pack_exchange(int i, double *buf)
atom->nextra_grow = 0;
m = 0;
for (k = 0; k < nstyles; k++)
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_exchange(i,&buf[m]);
atom->nextra_grow = tmp;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@ -687,9 +687,9 @@ int AtomVecHybrid::unpack_exchange(double *buf)
atom->nextra_grow = tmp;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@ -713,9 +713,9 @@ int AtomVecHybrid::size_restart()
int nlocal = atom->nlocal;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (int i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@ -738,7 +738,7 @@ int AtomVecHybrid::pack_restart(int i, double *buf)
atom->nextra_restart = tmp;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@ -840,7 +840,7 @@ void AtomVecHybrid::data_atom(double *coord, int imagetmp, char **values)
// each sub-style parses sub-style specific values
int m = 5;
for (int k = 0; k < nstyles; k++)
for (int k = 0; k < nstyles; k++)
m += styles[k]->data_atom_hybrid(nlocal,&values[m]);
atom->nlocal++;
@ -859,7 +859,7 @@ void AtomVecHybrid::data_vel(int m, char **values)
// each sub-style parses sub-style specific values
int n = 3;
for (int k = 0; k < nstyles; k++)
for (int k = 0; k < nstyles; k++)
n += styles[k]->data_vel_hybrid(m,&values[n]);
}