Homec4science
Diffusion lammps (runner) Browse

lammps/src/PERI/atom_vec_peri.cpp
7518fae9bcffrunner

Last Change
Raw File

atom_vec_peri.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 Parks (SNL)
------------------------------------------------------------------------- */
#include "float.h"
#include "stdlib.h"
#include "string.h"
#include "atom_vec_peri.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
static const char cite_peri_package[] =
"PERI package for Peridynamics:\n\n"
"@Article{Parks08,\n"
" author = {M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling},\n"
" title = {Implementing peridynamics within a molecular dynamics code},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" year = 2008,\n"
" volume = 179,\n"
" pages = {777--783}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
AtomVecPeri::AtomVecPeri(LAMMPS *lmp) : AtomVec(lmp)
{
if (lmp->citeme) lmp->citeme->add(cite_peri_package);
molecular = 0;
comm_x_only = 0;
comm_f_only = 1;
size_forward = 4;
size_reverse = 3;
size_border = 11;
size_velocity = 3;
size_data_atom = 7;
size_data_vel = 4;
xcol_data = 5;
atom->peri_flag = 1;
atom->vfrac_flag = atom->rmass_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecPeri::grow(int n)
{
if (n == 0) grow_nmax();
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one(FLERR,"Per-processor system is too big");
tag = memory->grow(atom->tag,nmax,"atom:tag");
type = memory->grow(atom->type,nmax,"atom:type");
mask = memory->grow(atom->mask,nmax,"atom:mask");
image = memory->grow(atom->image,nmax,"atom:image");
x = memory->grow(atom->x,nmax,3,"atom:x");
v = memory->grow(atom->v,nmax,3,"atom:v");
f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f");
vfrac = memory->grow(atom->vfrac,nmax,"atom:vfrac");
rmass = memory->grow(atom->rmass,nmax,"atom:rmass");
s0 = memory->grow(atom->s0,nmax,"atom:s0");
x0 = memory->grow(atom->x0,nmax,3,"atom:x0");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecPeri::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
vfrac = atom->vfrac; rmass = atom->rmass;
s0 = atom->s0; x0 = atom->x0;
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void AtomVecPeri::copy(int i, int j, int delflag)
{
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];
vfrac[j] = vfrac[i];
rmass[j] = rmass[i];
s0[j] = s0[i];
x0[j][0] = x0[i][0];
x0[j][1] = x0[i][1];
x0[j][2] = x0[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,delflag);
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::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++] = s0[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]*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++] = s0[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::pack_comm_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++] = s0[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]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
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++] = s0[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++] = s0[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;
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::pack_comm_hybrid(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = s0[j];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecPeri::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++];
s0[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecPeri::unpack_comm_vel(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++];
s0[i] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::unpack_comm_hybrid(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++)
s0[i] = buf[m++];
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::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];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecPeri::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++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = vfrac[j];
buf[m++] = s0[j];
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[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];
}
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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = vfrac[j];
buf[m++] = s0[j];
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[j][2];
}
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = vfrac[j];
buf[m++] = s0[j];
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[j][2];
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 (!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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = vfrac[j];
buf[m++] = s0[j];
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[j][2];
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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = vfrac[j];
buf[m++] = s0[j];
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[j][2];
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 (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::pack_border_hybrid(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = vfrac[j];
buf[m++] = s0[j];
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[j][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecPeri::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] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
vfrac[i] = buf[m++];
s0[i] = buf[m++];
x0[i][0] = buf[m++];
x0[i][1] = buf[m++];
x0[i][2] = buf[m++];
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->
unpack_border(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
void AtomVecPeri::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] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
vfrac[i] = buf[m++];
s0[i] = buf[m++];
x0[i][0] = buf[m++];
x0[i][1] = buf[m++];
x0[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->
unpack_border(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::unpack_border_hybrid(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
vfrac[i] = buf[m++];
s0[i] = buf[m++];
x0[i][0] = buf[m++];
x0[i][1] = buf[m++];
x0[i][2] = buf[m++];
}
return m;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecPeri::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++] = ubuf(tag[i]).d;
buf[m++] = ubuf(type[i]).d;
buf[m++] = ubuf(mask[i]).d;
buf[m++] = ubuf(image[i]).d;
buf[m++] = vfrac[i];
buf[m++] = rmass[i];
buf[m++] = s0[i];
buf[m++] = x0[i][0];
buf[m++] = x0[i][1];
buf[m++] = x0[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 AtomVecPeri::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] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
vfrac[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
s0[nlocal] = buf[m++];
x0[nlocal][0] = buf[m++];
x0[nlocal][1] = buf[m++];
x0[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 AtomVecPeri::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 17 * 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 AtomVecPeri::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++] = ubuf(tag[i]).d;
buf[m++] = ubuf(type[i]).d;
buf[m++] = ubuf(mask[i]).d;
buf[m++] = ubuf(image[i]).d;
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = vfrac[i];
buf[m++] = rmass[i];
buf[m++] = s0[i];
buf[m++] = x0[i][0];
buf[m++] = x0[i][1];
buf[m++] = x0[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 AtomVecPeri::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
memory->grow(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] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
vfrac[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
s0[nlocal] = buf[m++];
x0[nlocal][0] = buf[m++];
x0[nlocal][1] = buf[m++];
x0[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 AtomVecPeri::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] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
vfrac[nlocal] = 1.0;
rmass[nlocal] = 1.0;
s0[nlocal] = DBL_MAX;
x0[nlocal][0] = coord[0];
x0[nlocal][1] = coord[1];
x0[nlocal][2] = coord[2];
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecPeri::data_atom(double *coord, imageint imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
vfrac[nlocal] = atof(values[2]);
rmass[nlocal] = atof(values[3]);
if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid mass value");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
s0[nlocal] = DBL_MAX;
x0[nlocal][0] = coord[0];
x0[nlocal][1] = coord[1];
x0[nlocal][2] = coord[2];
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecPeri::data_atom_hybrid(int nlocal, char **values)
{
vfrac[nlocal] = atof(values[0]);
rmass[nlocal] = atof(values[1]);
if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid mass value");
s0[nlocal] = DBL_MAX;
x0[nlocal][0] = x[nlocal][0];
x0[nlocal][1] = x[nlocal][1];
x0[nlocal][2] = x[nlocal][2];
return 2;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecPeri::pack_data(double **buf)
{
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = ubuf(tag[i]).d;
buf[i][1] = ubuf(type[i]).d;
buf[i][2] = vfrac[i];
buf[i][3] = rmass[i];
buf[i][4] = x[i][0];
buf[i][5] = x[i][1];
buf[i][6] = x[i][2];
buf[i][7] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
buf[i][8] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
buf[i][9] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
}
}
/* ----------------------------------------------------------------------
pack hybrid atom info for data file
------------------------------------------------------------------------- */
int AtomVecPeri::pack_data_hybrid(int i, double *buf)
{
buf[0] = vfrac[i];
buf[1] = rmass[i];
return 2;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecPeri::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT
" %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],buf[i][4],buf[i][5],buf[i][6],
(int) ubuf(buf[i][7]).i,(int) ubuf(buf[i][8]).i,
(int) ubuf(buf[i][9]).i);
}
/* ----------------------------------------------------------------------
write hybrid atom info to data file
------------------------------------------------------------------------- */
int AtomVecPeri::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %-1.16e %-1.16e",buf[0],buf[1]);
return 2;
}
/* ----------------------------------------------------------------------
assign an index to named atom property and return index
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecPeri::property_atom(char *name)
{
if (strcmp(name,"vfrac") == 0) return 0;
if (strcmp(name,"s0") == 0) return 1;
return -1;
}
/* ----------------------------------------------------------------------
pack per-atom data into buf for ComputePropertyAtom
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecPeri::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
int n = 0;
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = vfrac[i];
else buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = s0[i];
else buf[n] = 0.0;
n += nvalues;
}
}
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecPeri::memory_usage()
{
bigint bytes = 0;
if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3);
if (atom->memcheck("vfrac")) bytes += memory->usage(vfrac,nmax);
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
if (atom->memcheck("s0")) bytes += memory->usage(s0,nmax);
if (atom->memcheck("x0")) bytes += memory->usage(x0,nmax,3);
return bytes;
}
c4science · Help