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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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316
src/atom_vec_ellipsoid.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.
@ -120,7 +120,7 @@ void AtomVecEllipsoid::grow_bonus()
error->one(FLERR,"Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
"atom:bonus");
"atom:bonus");
}
/* ----------------------------------------------------------------------
@ -189,8 +189,8 @@ void AtomVecEllipsoid::clear_bonus()
this may create or delete entry in bonus data
------------------------------------------------------------------------- */
void AtomVecEllipsoid::set_shape(int i,
double shapex, double shapey, double shapez)
void AtomVecEllipsoid::set_shape(int i,
double shapex, double shapey, double shapez)
{
if (ellipsoid[i] < 0) {
if (shapex == 0.0 && shapey == 0.0 && shapez == 0.0) return;
@ -221,7 +221,7 @@ void AtomVecEllipsoid::set_shape(int i,
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@ -235,11 +235,11 @@ int AtomVecEllipsoid::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][1];
buf[m++] = x[j][2];
if (ellipsoid[j] >= 0) {
quat = bonus[ellipsoid[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
quat = bonus[ellipsoid[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
}
} else {
@ -258,11 +258,11 @@ int AtomVecEllipsoid::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
if (ellipsoid[j] >= 0) {
quat = bonus[ellipsoid[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
quat = bonus[ellipsoid[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
}
}
@ -272,7 +272,7 @@ int AtomVecEllipsoid::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@ -286,11 +286,11 @@ int AtomVecEllipsoid::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = x[j][1];
buf[m++] = x[j][2];
if (ellipsoid[j] >= 0) {
quat = bonus[ellipsoid[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
quat = bonus[ellipsoid[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
@ -311,52 +311,52 @@ int AtomVecEllipsoid::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;
if (ellipsoid[j] >= 0) {
quat = bonus[ellipsoid[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
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 (ellipsoid[j] >= 0) {
quat = bonus[ellipsoid[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
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 (ellipsoid[j] >= 0) {
quat = bonus[ellipsoid[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
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];
}
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 (ellipsoid[j] >= 0) {
quat = bonus[ellipsoid[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
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];
}
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
}
}
@ -529,7 +529,7 @@ int AtomVecEllipsoid::unpack_reverse_hybrid(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@ -547,16 +547,16 @@ int AtomVecEllipsoid::pack_border(int n, int *list, double *buf,
buf[m++] = mask[j];
if (ellipsoid[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
shape = bonus[ellipsoid[j]].shape;
quat = bonus[ellipsoid[j]].quat;
buf[m++] = shape[0];
buf[m++] = shape[1];
buf[m++] = shape[2];
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = 1;
shape = bonus[ellipsoid[j]].shape;
quat = bonus[ellipsoid[j]].quat;
buf[m++] = shape[0];
buf[m++] = shape[1];
buf[m++] = shape[2];
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
}
} else {
@ -579,16 +579,16 @@ int AtomVecEllipsoid::pack_border(int n, int *list, double *buf,
buf[m++] = mask[j];
if (ellipsoid[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
shape = bonus[ellipsoid[j]].shape;
quat = bonus[ellipsoid[j]].quat;
buf[m++] = shape[0];
buf[m++] = shape[1];
buf[m++] = shape[2];
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = 1;
shape = bonus[ellipsoid[j]].shape;
quat = bonus[ellipsoid[j]].quat;
buf[m++] = shape[0];
buf[m++] = shape[1];
buf[m++] = shape[2];
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
}
}
@ -598,7 +598,7 @@ int AtomVecEllipsoid::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@ -616,16 +616,16 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf,
buf[m++] = mask[j];
if (ellipsoid[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
shape = bonus[ellipsoid[j]].shape;
quat = bonus[ellipsoid[j]].quat;
buf[m++] = shape[0];
buf[m++] = shape[1];
buf[m++] = shape[2];
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = 1;
shape = bonus[ellipsoid[j]].shape;
quat = bonus[ellipsoid[j]].quat;
buf[m++] = shape[0];
buf[m++] = shape[1];
buf[m++] = shape[2];
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
@ -646,69 +646,69 @@ int AtomVecEllipsoid::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];
if (ellipsoid[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
quat = bonus[ellipsoid[j]].quat;
buf[m++] = shape[0];
buf[m++] = shape[1];
buf[m++] = shape[2];
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
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 (ellipsoid[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
quat = bonus[ellipsoid[j]].quat;
buf[m++] = shape[0];
buf[m++] = shape[1];
buf[m++] = shape[2];
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
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 (ellipsoid[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
shape = bonus[ellipsoid[j]].shape;
quat = bonus[ellipsoid[j]].quat;
buf[m++] = shape[0];
buf[m++] = shape[1];
buf[m++] = shape[2];
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
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];
}
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 (ellipsoid[j] < 0) buf[m++] = 0;
else {
buf[m++] = 1;
shape = bonus[ellipsoid[j]].shape;
quat = bonus[ellipsoid[j]].quat;
buf[m++] = shape[0];
buf[m++] = shape[1];
buf[m++] = shape[2];
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
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];
}
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
}
}
@ -893,7 +893,7 @@ int AtomVecEllipsoid::pack_exchange(int i, double *buf)
buf[m++] = quat[2];
buf[m++] = quat[3];
}
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
@ -946,7 +946,7 @@ int AtomVecEllipsoid::unpack_exchange(double *buf)
if (atom->nextra_grow)
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;
@ -970,7 +970,7 @@ int AtomVecEllipsoid::size_restart()
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (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;
}
@ -1030,7 +1030,7 @@ int AtomVecEllipsoid::unpack_restart(double *buf)
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
if (atom->nextra_store)
memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
}
@ -1067,7 +1067,7 @@ int AtomVecEllipsoid::unpack_restart(double *buf)
bonus[nlocal_bonus].ilocal = nlocal;
ellipsoid[nlocal] = nlocal_bonus++;
}
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
@ -1098,7 +1098,7 @@ void AtomVecEllipsoid::create_atom(int itype, double *coord)
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
rmass[nlocal] = 1.0;
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
@ -1232,7 +1232,7 @@ int AtomVecEllipsoid::data_vel_hybrid(int m, char **values)
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecEllipsoid::memory_usage()
@ -1251,7 +1251,7 @@ bigint AtomVecEllipsoid::memory_usage()
if (atom->memcheck("angmom")) bytes += memory->usage(angmom,nmax,3);
if (atom->memcheck("torque")) bytes += memory->usage(torque,nmax*comm->nthreads,3);
if (atom->memcheck("ellipsoid")) bytes += memory->usage(ellipsoid,nmax);
bytes += nmax_bonus*sizeof(Bonus);
return bytes;