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lammps/src/atom_vec_body.cpp
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atom_vec_body.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.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "atom_vec_body.h"
#include "style_body.h"
#include "body.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "force.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
AtomVecBody::AtomVecBody(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 0;
// size_forward and size_border set in settings(), via Body class
comm_x_only = comm_f_only = 0;
size_forward = 0;
size_reverse = 6;
size_border = 0;
size_velocity = 6;
size_data_atom = 7;
size_data_vel = 7;
xcol_data = 5;
atom->body_flag = 1;
atom->rmass_flag = 1;
atom->angmom_flag = atom->torque_flag = 1;
atom->radius_flag = 1;
nlocal_bonus = nghost_bonus = nmax_bonus = 0;
bonus = NULL;
bptr = NULL;
if (sizeof(double) == sizeof(int)) intdoubleratio = 1;
else if (sizeof(double) == 2*sizeof(int)) intdoubleratio = 2;
else error->all(FLERR,"Internal error in atom_style body");
}
/* ---------------------------------------------------------------------- */
AtomVecBody::~AtomVecBody()
{
int nall = nlocal_bonus + nghost_bonus;
for (int i = 0; i < nall; i++) {
icp->put(bonus[i].iindex);
dcp->put(bonus[i].dindex);
}
memory->sfree(bonus);
delete bptr;
}
/* ----------------------------------------------------------------------
process additional args
instantiate Body class
set size_forward and size_border to max sizes
------------------------------------------------------------------------- */
void AtomVecBody::process_args(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Invalid atom_style body command");
if (0) bptr = NULL;
#define BODY_CLASS
#define BodyStyle(key,Class) \
else if (strcmp(arg[0],#key) == 0) bptr = new Class(lmp,narg,arg);
#include "style_body.h"
#undef BodyStyle
#undef BODY_CLASS
else error->all(FLERR,"Unknown body style");
bptr->avec = this;
icp = bptr->icp;
dcp = bptr->dcp;
// max size of forward/border comm
// 7,16 are packed in pack_comm/pack_border
// bptr values = max number of additional ivalues/dvalues from Body class
size_forward = 7 + bptr->size_forward;
size_border = 18 + bptr->size_border;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecBody::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");
radius = memory->grow(atom->radius,nmax,"atom:radius");
rmass = memory->grow(atom->rmass,nmax,"atom:rmass");
angmom = memory->grow(atom->angmom,nmax,3,"atom:angmom");
torque = memory->grow(atom->torque,nmax*comm->nthreads,3,"atom:torque");
body = memory->grow(atom->body,nmax,"atom:body");
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 AtomVecBody::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
radius = atom->radius; rmass = atom->rmass;
angmom = atom->angmom; torque = atom->torque;
body = atom->body;
}
/* ----------------------------------------------------------------------
grow bonus data structure
------------------------------------------------------------------------- */
void AtomVecBody::grow_bonus()
{
nmax_bonus = grow_nmax_bonus(nmax_bonus);
if (nmax_bonus < 0)
error->one(FLERR,"Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
"atom:bonus");
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
if delflag and atom J has bonus data, then delete it
------------------------------------------------------------------------- */
void AtomVecBody::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];
radius[j] = radius[i];
rmass[j] = rmass[i];
angmom[j][0] = angmom[i][0];
angmom[j][1] = angmom[i][1];
angmom[j][2] = angmom[i][2];
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && body[j] >= 0) {
int k = body[j];
icp->put(bonus[k].iindex);
dcp->put(bonus[k].dindex);
copy_bonus(nlocal_bonus-1,k);
nlocal_bonus--;
}
// if atom I has bonus data, reset I's bonus.ilocal to loc J
// do NOT do this if self-copy (I=J) since I's bonus data is already deleted
if (body[i] >= 0 && i != j) bonus[body[i]].ilocal = j;
body[j] = body[i];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
}
/* ----------------------------------------------------------------------
copy bonus data from I to J, effectively deleting the J entry
also reset body that points to I to now point to J
------------------------------------------------------------------------- */
void AtomVecBody::copy_bonus(int i, int j)
{
body[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
}
/* ----------------------------------------------------------------------
clear ghost info in bonus data
called before ghosts are recommunicated in comm and irregular
------------------------------------------------------------------------- */
void AtomVecBody::clear_bonus()
{
int nall = nlocal_bonus + nghost_bonus;
for (int i = nlocal_bonus; i < nall; i++) {
icp->put(bonus[i].iindex);
dcp->put(bonus[i].dindex);
}
nghost_bonus = 0;
}
/* ---------------------------------------------------------------------- */
int AtomVecBody::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
double *quat;
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];
if (body[j] >= 0) {
quat = bonus[body[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
}
}
} 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;
if (body[j] >= 0) {
quat = bonus[body[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecBody::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;
double *quat;
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];
if (body[j] >= 0) {
quat = bonus[body[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
}
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 {
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;
if (body[j] >= 0) {
quat = bonus[body[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
}
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 (body[j] >= 0) {
quat = bonus[body[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
}
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];
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecBody::pack_comm_hybrid(int n, int *list, double *buf)
{
int i,j,m;
double *quat;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (body[j] >= 0) {
quat = bonus[body[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecBody::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
double *quat;
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++];
if (body[i] >= 0) {
quat = bonus[body[i]].quat;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
m += bptr->unpack_comm_body(&bonus[body[i]],&buf[m]);
}
}
}
/* ---------------------------------------------------------------------- */
void AtomVecBody::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
double *quat;
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++];
if (body[i] >= 0) {
quat = bonus[body[i]].quat;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
m += bptr->unpack_comm_body(&bonus[body[i]],&buf[m]);
}
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
angmom[i][0] = buf[m++];
angmom[i][1] = buf[m++];
angmom[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecBody::unpack_comm_hybrid(int n, int first, double *buf)
{
int i,m,last;
double *quat;
m = 0;
last = first + n;
for (i = first; i < last; i++)
if (body[i] >= 0) {
quat = bonus[body[i]].quat;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
m += bptr->unpack_comm_body(&bonus[body[i]],&buf[m]);
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecBody::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 AtomVecBody::pack_reverse_hybrid(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = torque[i][0];
buf[m++] = torque[i][1];
buf[m++] = torque[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecBody::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 AtomVecBody::unpack_reverse_hybrid(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
torque[j][0] += buf[m++];
torque[j][1] += buf[m++];
torque[j][2] += buf[m++];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecBody::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
double *quat,*inertia;
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++] = radius[j];
buf[m++] = rmass[j];
if (body[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[body[j]].quat;
inertia = bonus[body[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
}
}
} 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++] = radius[j];
buf[m++] = rmass[j];
if (body[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[body[j]].quat;
inertia = bonus[body[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
}
}
}
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 AtomVecBody::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;
double *quat,*inertia;
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++] = radius[j];
buf[m++] = rmass[j];
if (body[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[body[j]].quat;
inertia = bonus[body[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
}
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 {
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++] = radius[j];
buf[m++] = rmass[j];
if (body[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[body[j]].quat;
inertia = bonus[body[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
}
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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
if (body[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[body[j]].quat;
inertia = bonus[body[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
}
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];
}
}
}
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 AtomVecBody::pack_border_hybrid(int n, int *list, double *buf)
{
int i,j,m;
double *quat,*inertia;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (body[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[body[j]].quat;
inertia = bonus[body[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecBody::unpack_border(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*inertia;
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;
radius[i] = buf[m++];
rmass[i] = buf[m++];
body[i] = (int) ubuf(buf[m++]).i;
if (body[i] == 0) body[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
quat = bonus[j].quat;
inertia = bonus[j].inertia;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
inertia[0] = buf[m++];
inertia[1] = buf[m++];
inertia[2] = buf[m++];
bonus[j].ninteger = (int) ubuf(buf[m++]).i;
bonus[j].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in clear_bonus()
bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
m += bptr->unpack_border_body(&bonus[j],&buf[m]);
bonus[j].ilocal = i;
body[i] = j;
nghost_bonus++;
}
}
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 AtomVecBody::unpack_border_vel(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*inertia;
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;
radius[i] = buf[m++];
rmass[i] = buf[m++];
body[i] = (int) ubuf(buf[m++]).i;
if (body[i] == 0) body[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
quat = bonus[j].quat;
inertia = bonus[j].inertia;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
inertia[0] = buf[m++];
inertia[1] = buf[m++];
inertia[2] = buf[m++];
bonus[j].ninteger = (int) ubuf(buf[m++]).i;
bonus[j].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in clear_bonus()
bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
m += bptr->unpack_border_body(&bonus[j],&buf[m]);
bonus[j].ilocal = i;
body[i] = j;
nghost_bonus++;
}
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
angmom[i][0] = buf[m++];
angmom[i][1] = buf[m++];
angmom[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 AtomVecBody::unpack_border_hybrid(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*inertia;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
radius[i] = buf[m++];
rmass[i] = buf[m++];
body[i] = (int) ubuf(buf[m++]).i;
if (body[i] == 0) body[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
quat = bonus[j].quat;
inertia = bonus[j].inertia;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
inertia[0] = buf[m++];
inertia[1] = buf[m++];
inertia[2] = buf[m++];
bonus[j].ninteger = (int) ubuf(buf[m++]).i;
bonus[j].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in clear_bonus()
bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
m += bptr->unpack_border_body(&bonus[j],&buf[m]);
bonus[j].ilocal = i;
body[i] = j;
nghost_bonus++;
}
}
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 AtomVecBody::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++] = radius[i];
buf[m++] = rmass[i];
buf[m++] = angmom[i][0];
buf[m++] = angmom[i][1];
buf[m++] = angmom[i][2];
if (body[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = body[i];
double *quat = bonus[j].quat;
double *inertia = bonus[j].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[j].ninteger).d;
buf[m++] = ubuf(bonus[j].ndouble).d;
memcpy(&buf[m],bonus[j].ivalue,bonus[j].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[j].ninteger;
else m += (bonus[j].ninteger+1)/2;
memcpy(&buf[m],bonus[j].dvalue,bonus[j].ndouble*sizeof(double));
m += bonus[j].ndouble;
}
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 AtomVecBody::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;
radius[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
angmom[nlocal][0] = buf[m++];
angmom[nlocal][1] = buf[m++];
angmom[nlocal][2] = buf[m++];
body[nlocal] = (int) ubuf(buf[m++]).i;
if (body[nlocal] == 0) body[nlocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
double *inertia = bonus[nlocal_bonus].inertia;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
inertia[0] = buf[m++];
inertia[1] = buf[m++];
inertia[2] = buf[m++];
bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in copy()
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
bonus[nlocal_bonus].dindex);
memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
bonus[nlocal_bonus].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[nlocal_bonus].ninteger;
else m += (bonus[nlocal_bonus].ninteger+1)/2;
memcpy(bonus[nlocal_bonus].dvalue,&buf[m],
bonus[nlocal_bonus].ndouble*sizeof(double));
m += bonus[nlocal_bonus].ndouble;
bonus[nlocal_bonus].ilocal = nlocal;
body[nlocal] = nlocal_bonus++;
}
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 AtomVecBody::size_restart()
{
int i;
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (body[i] >= 0) {
n += 26;
if (intdoubleratio == 1) n += bonus[body[i]].ninteger;
else n += (bonus[body[i]].ninteger+1)/2;
n += bonus[body[i]].ndouble;
} else n += 17;
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 AtomVecBody::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++] = radius[i];
buf[m++] = rmass[i];
buf[m++] = angmom[i][0];
buf[m++] = angmom[i][1];
buf[m++] = angmom[i][2];
if (body[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = body[i];
double *quat = bonus[j].quat;
double *inertia = bonus[j].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[j].ninteger).d;
buf[m++] = ubuf(bonus[j].ndouble).d;
memcpy(&buf[m],bonus[j].ivalue,bonus[j].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[j].ninteger;
else m += (bonus[j].ninteger+1)/2;
memcpy(&buf[m],bonus[j].dvalue,bonus[j].ndouble*sizeof(double));
m += bonus[j].ndouble;
}
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 AtomVecBody::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++];
radius[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
angmom[nlocal][0] = buf[m++];
angmom[nlocal][1] = buf[m++];
angmom[nlocal][2] = buf[m++];
body[nlocal] = (int) ubuf(buf[m++]).i;
if (body[nlocal] == 0) body[nlocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
double *inertia = bonus[nlocal_bonus].inertia;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
inertia[0] = buf[m++];
inertia[1] = buf[m++];
inertia[2] = buf[m++];
bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
bonus[nlocal_bonus].dindex);
memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
bonus[nlocal_bonus].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[nlocal_bonus].ninteger;
else m += (bonus[nlocal_bonus].ninteger+1)/2;
memcpy(bonus[nlocal_bonus].dvalue,&buf[m],
bonus[nlocal_bonus].ndouble*sizeof(double));
m += bonus[nlocal_bonus].ndouble;
bonus[nlocal_bonus].ilocal = nlocal;
body[nlocal] = nlocal_bonus++;
}
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 AtomVecBody::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;
radius[nlocal] = 0.5;
rmass[nlocal] = 1.0;
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
angmom[nlocal][2] = 0.0;
body[nlocal] = -1;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecBody::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");
body[nlocal] = atoi(values[2]);
if (body[nlocal] == 0) body[nlocal] = -1;
else if (body[nlocal] == 1) body[nlocal] = 0;
else error->one(FLERR,"Invalid atom type in Atoms section of data file");
rmass[nlocal] = atof(values[3]);
if (rmass[nlocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
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;
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
angmom[nlocal][2] = 0.0;
radius[nlocal] = 0.5;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecBody::data_atom_hybrid(int nlocal, char **values)
{
body[nlocal] = atoi(values[0]);
if (body[nlocal] == 0) body[nlocal] = -1;
else if (body[nlocal] == 1) body[nlocal] = 0;
else error->one(FLERR,"Invalid atom type in Atoms section of data file");
rmass[nlocal] = atof(values[1]);
if (rmass[nlocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
return 2;
}
/* ----------------------------------------------------------------------
unpack one body from Bodies section of data file
------------------------------------------------------------------------- */
void AtomVecBody::data_body(int m, int ninteger, int ndouble,
int *ivalues, double *dvalues)
{
if (body[m]) error->one(FLERR,"Assigning body parameters to non-body atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
bonus[nlocal_bonus].ilocal = m;
bptr->data_body(nlocal_bonus,ninteger,ndouble,ivalues,dvalues);
body[m] = nlocal_bonus++;
}
/* ----------------------------------------------------------------------
unpack one tri from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecBody::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 body in Velocities section of data file
------------------------------------------------------------------------- */
int AtomVecBody::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;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecBody::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;
if (body[i] < 0) buf[i][2] = ubuf(0).d;
else buf[i][2] = ubuf(1).d;
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 AtomVecBody::pack_data_hybrid(int i, double *buf)
{
if (body[i] < 0) buf[0] = ubuf(0).d;
else buf[0] = ubuf(1).d;
buf[1] = rmass[i];
return 2;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecBody::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT " %d %d %g %g %g %g %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,
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 AtomVecBody::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %d %g",(int) ubuf(buf[0]).i,buf[1]);
return 2;
}
/* ----------------------------------------------------------------------
pack velocity info for data file
------------------------------------------------------------------------- */
void AtomVecBody::pack_vel(double **buf)
{
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = ubuf(tag[i]).d;
buf[i][1] = v[i][0];
buf[i][2] = v[i][1];
buf[i][3] = v[i][2];
buf[i][4] = angmom[i][0];
buf[i][5] = angmom[i][1];
buf[i][6] = angmom[i][2];
}
}
/* ----------------------------------------------------------------------
pack hybrid velocity info for data file
------------------------------------------------------------------------- */
int AtomVecBody::pack_vel_hybrid(int i, double *buf)
{
buf[0] = angmom[i][0];
buf[1] = angmom[i][1];
buf[2] = angmom[i][2];
return 3;
}
/* ----------------------------------------------------------------------
write velocity info to data file
------------------------------------------------------------------------- */
void AtomVecBody::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT " %g %g %g %g %g %g\n",
(tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6]);
}
/* ----------------------------------------------------------------------
write hybrid velocity info to data file
------------------------------------------------------------------------- */
int AtomVecBody::write_vel_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %g %g %g",buf[0],buf[1],buf[2]);
return 3;
}
/* ----------------------------------------------------------------------
body computes its size based on ivalues/dvalues and returns it
------------------------------------------------------------------------- */
double AtomVecBody::radius_body(int ninteger, int ndouble,
int *ivalues, double *dvalues)
{
return bptr->radius_body(ninteger,ndouble,ivalues,dvalues);
}
/* ----------------------------------------------------------------------
reset quat orientation for atom M to quat_external
called by Atom:add_molecule_atom()
------------------------------------------------------------------------- */
void AtomVecBody::set_quat(int m, double *quat_external)
{
if (body[m] < 0) error->one(FLERR,"Assigning quat to non-body atom");
double *quat = bonus[body[m]].quat;
quat[0] = quat_external[0]; quat[1] = quat_external[1];
quat[2] = quat_external[2]; quat[3] = quat_external[3];
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecBody::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("radius")) bytes += memory->usage(radius,nmax);
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
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("body")) bytes += memory->usage(body,nmax);
bytes += nmax_bonus*sizeof(Bonus);
bytes += icp->size + dcp->size;
int nall = nlocal_bonus + nghost_bonus;
for (int i = 0; i < nall; i++) {
bytes += bonus[i].ninteger * sizeof(int);
bytes += bonus[i].ndouble * sizeof(double);
}
return bytes;
}
/* ----------------------------------------------------------------------
debug method for sanity checking of own/bonus data pointers
------------------------------------------------------------------------- */
/*
void AtomVecBody::check(int flag)
{
for (int i = 0; i < atom->nlocal; i++) {
if (atom->body[i] >= 0 && atom->body[i] >= nlocal_bonus) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD AAA");
}
}
for (int i = atom->nlocal; i < atom->nlocal+atom->nghost; i++) {
if (atom->body[i] >= 0 &&
(atom->body[i] < nlocal_bonus ||
atom->body[i] >= nlocal_bonus+nghost_bonus)) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD BBB");
}
}
for (int i = 0; i < nlocal_bonus; i++) {
if (bonus[i].ilocal < 0 || bonus[i].ilocal >= atom->nlocal) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD CCC");
}
}
for (int i = 0; i < nlocal_bonus; i++) {
if (atom->body[bonus[i].ilocal] != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD DDD");
}
}
for (int i = nlocal_bonus; i < nlocal_bonus+nghost_bonus; i++) {
if (bonus[i].ilocal < atom->nlocal ||
bonus[i].ilocal >= atom->nlocal+atom->nghost) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD EEE");
}
}
for (int i = nlocal_bonus; i < nlocal_bonus+nghost_bonus; i++) {
if (atom->body[bonus[i].ilocal] != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD FFF");
}
}
}
*/
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