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atom_vec_ellipsoid.cpp
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Mon, Jul 21, 06:17

atom_vec_ellipsoid.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "atom_vec_ellipsoid.h"
#include "math_extra.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
mass_type = 1;
shape_type = 1;
comm_x_only = comm_f_only = 0;
size_comm = 7;
size_reverse = 6;
size_border = 10;
size_data_atom = 9;
size_data_vel = 7;
xcol_data = 3;
atom->angmom_flag = atom->torque_flag = atom->quat_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecEllipsoid::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
quat = atom->quat =
memory->grow_2d_double_array(atom->quat,nmax,4,"atom:quat");
angmom = atom->angmom =
memory->grow_2d_double_array(atom->angmom,nmax,3,"atom:angmom");
torque = atom->torque =
memory->grow_2d_double_array(atom->torque,nmax,3,"atom:torque");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ---------------------------------------------------------------------- */
void AtomVecEllipsoid::copy(int i, int j)
{
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
quat[j][0] = quat[i][0];
quat[j][1] = quat[i][1];
quat[j][2] = quat[i][2];
quat[j][3] = quat[i][3];
angmom[j][0] = angmom[i][0];
angmom[j][1] = angmom[i][1];
angmom[j][2] = angmom[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_comm(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++] = quat[j][0];
buf[m++] = quat[j][1];
buf[m++] = quat[j][2];
buf[m++] = quat[j][3];
}
} 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++] = quat[j][0];
buf[m++] = quat[j][1];
buf[m++] = quat[j][2];
buf[m++] = quat[j][3];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_comm_one(int i, double *buf)
{
buf[0] = quat[i][0];
buf[1] = quat[i][1];
buf[2] = quat[i][2];
buf[3] = quat[i][3];
return 4;
}
/* ---------------------------------------------------------------------- */
void AtomVecEllipsoid::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
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++];
quat[i][0] = buf[m++];
quat[i][1] = buf[m++];
quat[i][2] = buf[m++];
quat[i][3] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::unpack_comm_one(int i, double *buf)
{
quat[i][0] = buf[0];
quat[i][1] = buf[1];
quat[i][2] = buf[2];
quat[i][3] = buf[3];
return 4;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
buf[m++] = torque[i][0];
buf[m++] = torque[i][1];
buf[m++] = torque[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_reverse_one(int i, double *buf)
{
buf[0] = torque[i][0];
buf[1] = torque[i][1];
buf[2] = torque[i][2];
return 3;
}
/* ---------------------------------------------------------------------- */
void AtomVecEllipsoid::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
torque[j][0] += buf[m++];
torque[j][1] += buf[m++];
torque[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::unpack_reverse_one(int i, double *buf)
{
torque[i][0] += buf[0];
torque[i][1] += buf[1];
torque[i][2] += buf[2];
return 3;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_border(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++] = quat[j][0];
buf[m++] = quat[j][1];
buf[m++] = quat[j][2];
buf[m++] = quat[j][3];
}
} 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++] = quat[j][0];
buf[m++] = quat[j][1];
buf[m++] = quat[j][2];
buf[m++] = quat[j][3];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_border_one(int i, double *buf)
{
buf[0] = quat[i][0];
buf[1] = quat[i][1];
buf[2] = quat[i][2];
buf[3] = quat[i][3];
return 4;
}
/* ---------------------------------------------------------------------- */
void AtomVecEllipsoid::unpack_border(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++]);
quat[i][0] = buf[m++];
quat[i][1] = buf[m++];
quat[i][2] = buf[m++];
quat[i][3] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::unpack_border_one(int i, double *buf)
{
quat[i][0] = buf[0];
quat[i][1] = buf[1];
quat[i][2] = buf[2];
quat[i][3] = buf[3];
return 4;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_exchange(int i, double *buf)
{
int m = 1;
buf[m++] = 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++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = quat[i][0];
buf[m++] = quat[i][1];
buf[m++] = quat[i][2];
buf[m++] = quat[i][3];
buf[m++] = angmom[i][0];
buf[m++] = angmom[i][1];
buf[m++] = angmom[i][2];
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]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
quat[nlocal][0] = buf[m++];
quat[nlocal][1] = buf[m++];
quat[nlocal][2] = buf[m++];
quat[nlocal][3] = buf[m++];
angmom[nlocal][0] = buf[m++];
angmom[nlocal][1] = buf[m++];
angmom[nlocal][2] = buf[m++];
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]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecEllipsoid::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 18 * nlocal;
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);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_restart(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = quat[i][0];
buf[m++] = quat[i][1];
buf[m++] = quat[i][2];
buf[m++] = quat[i][3];
buf[m++] = angmom[i][0];
buf[m++] = angmom[i][1];
buf[m++] = angmom[i][2];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecEllipsoid::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
quat[nlocal][0] = buf[m++];
quat[nlocal][1] = buf[m++];
quat[nlocal][2] = buf[m++];
quat[nlocal][3] = buf[m++];
angmom[nlocal][0] = buf[m++];
angmom[nlocal][1] = buf[m++];
angmom[nlocal][2] = buf[m++];
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecEllipsoid::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
quat[nlocal][0] = 1.0;
quat[nlocal][1] = 0.0;
quat[nlocal][2] = 0.0;
quat[nlocal][3] = 0.0;
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
angmom[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecEllipsoid::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
quat[nlocal][0] = atof(values[5]);
quat[nlocal][1] = atof(values[6]);
quat[nlocal][2] = atof(values[7]);
quat[nlocal][3] = atof(values[8]);
MathExtra::normalize4(quat[nlocal]);
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
angmom[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecEllipsoid::data_atom_hybrid(int nlocal, char **values)
{
quat[nlocal][0] = atof(values[0]);
quat[nlocal][1] = atof(values[1]);
quat[nlocal][2] = atof(values[2]);
quat[nlocal][3] = atof(values[3]);
MathExtra::normalize4(quat[nlocal]);
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
angmom[nlocal][2] = 0.0;
return 0;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecEllipsoid::data_vel(int m, char **values)
{
v[m][0] = atof(values[0]);
v[m][1] = atof(values[1]);
v[m][2] = atof(values[2]);
angmom[m][0] = atof(values[3]);
angmom[m][1] = atof(values[4]);
angmom[m][2] = atof(values[5]);
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int AtomVecEllipsoid::data_vel_hybrid(int m, char **values)
{
angmom[m][0] = atof(values[0]);
angmom[m][1] = atof(values[1]);
angmom[m][2] = atof(values[2]);
return 3;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecEllipsoid::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("quat")) bytes += nmax*4 * sizeof(double);
if (atom->memcheck("angmom")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("torque")) bytes += nmax*3 * sizeof(double);
return bytes;
}

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