Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F120856874
atom_vec_ellipsoid.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Mon, Jul 7, 13:02
Size
17 KB
Mime Type
text/x-c
Expires
Wed, Jul 9, 13:02 (2 d)
Engine
blob
Format
Raw Data
Handle
27187302
Attached To
rLAMMPS lammps
atom_vec_ellipsoid.cpp
View Options
/* ----------------------------------------------------------------------
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;
}
Event Timeline
Log In to Comment