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lammps/src/atom_vec_tri.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_tri.h"
#include "math_extra.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "force.h"
#include "fix.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define EPSILON 0.001
/* ---------------------------------------------------------------------- */
AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 0;
comm_x_only = comm_f_only = 0;
size_forward = 7;
size_reverse = 6;
size_border = 26;
size_velocity = 9;
size_data_atom = 8;
size_data_vel = 7;
size_data_bonus = 10;
xcol_data = 6;
atom->tri_flag = 1;
atom->molecule_flag = atom->rmass_flag = 1;
atom->radius_flag = atom->omega_flag = atom->angmom_flag = 1;
atom->torque_flag = 1;
atom->sphere_flag = 1;
nlocal_bonus = nghost_bonus = nmax_bonus = 0;
bonus = NULL;
if (domain->dimension != 3)
error->all(FLERR,"Atom_style tri can only be used in 3d simulations");
}
/* ---------------------------------------------------------------------- */
AtomVecTri::~AtomVecTri()
{
memory->sfree(bonus);
}
/* ---------------------------------------------------------------------- */
void AtomVecTri::init()
{
AtomVec::init();
if (domain->dimension != 3)
error->all(FLERR,"Atom_style tri can only be used in 3d simulations");
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecTri::grow(int n)
{
if (n == 0) grow_nmax();
else nmax = n;
atom->nmax = nmax;
if (nmax < 0)
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");
molecule = memory->grow(atom->molecule,nmax,"atom:molecule");
rmass = memory->grow(atom->rmass,nmax,"atom:rmass");
radius = memory->grow(atom->radius,nmax,"atom:radius");
omega = memory->grow(atom->omega,nmax,3,"atom:omega");
angmom = memory->grow(atom->angmom,nmax,3,"atom:angmom");
torque = memory->grow(atom->torque,nmax*comm->nthreads,3,"atom:torque");
tri = memory->grow(atom->tri,nmax,"atom:tri");
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 AtomVecTri::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
molecule = atom->molecule; rmass = atom->rmass;
radius = atom->radius; omega = atom->omega;
angmom = atom->angmom; torque = atom->torque;
tri = atom->tri;
}
/* ----------------------------------------------------------------------
grow bonus data structure
------------------------------------------------------------------------- */
void AtomVecTri::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 AtomVecTri::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];
molecule[j] = molecule[i];
rmass[j] = rmass[i];
radius[j] = radius[i];
omega[j][0] = omega[i][0];
omega[j][1] = omega[i][1];
omega[j][2] = omega[i][2];
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 && tri[j] >= 0) {
copy_bonus(nlocal_bonus-1,tri[j]);
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 (tri[i] >= 0 && i != j) bonus[tri[i]].ilocal = j;
tri[j] = tri[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 tri that points to I to now point to J
------------------------------------------------------------------------- */
void AtomVecTri::copy_bonus(int i, int j)
{
tri[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 AtomVecTri::clear_bonus()
{
nghost_bonus = 0;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->clear_bonus();
}
/* ----------------------------------------------------------------------
set equilateral tri of size in bonus data for particle I
oriented symmetrically in xy plane
this may create or delete entry in bonus data
------------------------------------------------------------------------- */
void AtomVecTri::set_equilateral(int i, double size)
{
// also set radius = distance from center to corner-pt = len(c1)
// unless size = 0.0, then set diameter = 1.0
if (tri[i] < 0) {
if (size == 0.0) return;
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
double *c1 = bonus[nlocal_bonus].c1;
double *c2 = bonus[nlocal_bonus].c2;
double *c3 = bonus[nlocal_bonus].c3;
double *inertia = bonus[nlocal_bonus].inertia;
quat[0] = 1.0;
quat[1] = 0.0;
quat[2] = 0.0;
quat[3] = 0.0;
c1[0] = -size/2.0;
c1[1] = -sqrt(3.0)/2.0 * size / 3.0;
c1[2] = 0.0;
c2[0] = size/2.0;
c2[1] = -sqrt(3.0)/2.0 * size / 3.0;
c2[2] = 0.0;
c3[0] = 0.0;
c3[1] = sqrt(3.0)/2.0 * size * 2.0/3.0;
c3[2] = 0.0;
inertia[0] = sqrt(3.0)/96.0 * size*size*size*size;
inertia[1] = sqrt(3.0)/96.0 * size*size*size*size;
inertia[2] = sqrt(3.0)/48.0 * size*size*size*size;
radius[i] = MathExtra::len3(c1);
bonus[nlocal_bonus].ilocal = i;
tri[i] = nlocal_bonus++;
} else if (size == 0.0) {
radius[i] = 0.5;
copy_bonus(nlocal_bonus-1,tri[i]);
nlocal_bonus--;
tri[i] = -1;
} else {
double *c1 = bonus[tri[i]].c1;
double *c2 = bonus[tri[i]].c2;
double *c3 = bonus[tri[i]].c3;
double *inertia = bonus[tri[i]].inertia;
c1[0] = -size/2.0;
c1[1] = -sqrt(3.0)/2.0 * size / 3.0;
c1[2] = 0.0;
c2[0] = size/2.0;
c2[1] = -sqrt(3.0)/2.0 * size / 3.0;
c2[2] = 0.0;
c3[0] = 0.0;
c3[1] = sqrt(3.0)/2.0 * size * 2.0/3.0;
c3[2] = 0.0;
inertia[0] = sqrt(3.0)/96.0 * size*size*size*size;
inertia[1] = sqrt(3.0)/96.0 * size*size*size*size;
inertia[2] = sqrt(3.0)/48.0 * size*size*size*size;
radius[i] = MathExtra::len3(c1);
}
}
/* ---------------------------------------------------------------------- */
int AtomVecTri::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 (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[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;
if (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecTri::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 (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[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 (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[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 (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecTri::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 (tri[j] >= 0) {
quat = bonus[tri[j]].quat;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecTri::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 (tri[i] >= 0) {
quat = bonus[tri[i]].quat;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
}
}
}
/* ---------------------------------------------------------------------- */
void AtomVecTri::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 (tri[i] >= 0) {
quat = bonus[tri[i]].quat;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
}
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
angmom[i][0] = buf[m++];
angmom[i][1] = buf[m++];
angmom[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecTri::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 (tri[i] >= 0) {
quat = bonus[tri[i]].quat;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecTri::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 AtomVecTri::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 AtomVecTri::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 AtomVecTri::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 AtomVecTri::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
double *quat,*c1,*c2,*c3,*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++] = ubuf(molecule[j]).d;
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (tri[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[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++] = ubuf(molecule[j]).d;
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (tri[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[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 AtomVecTri::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,*c1,*c2,*c3,*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++] = ubuf(molecule[j]).d;
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (tri[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[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++] = ubuf(molecule[j]).d;
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (tri[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
}
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[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;
buf[m++] = ubuf(molecule[j]).d;
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (tri[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[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];
}
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[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 AtomVecTri::pack_border_hybrid(int n, int *list, double *buf)
{
int i,j,m;
double *quat,*c1,*c2,*c3,*inertia;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(molecule[j]).d;
buf[m++] = radius[j];
buf[m++] = rmass[j];
if (tri[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[tri[j]].quat;
c1 = bonus[tri[j]].c1;
c2 = bonus[tri[j]].c2;
c3 = bonus[tri[j]].c3;
inertia = bonus[tri[j]].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecTri::unpack_border(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*c1,*c2,*c3,*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;
molecule[i] = (tagint) ubuf(buf[m++]).i;
radius[i] = buf[m++];
rmass[i] = buf[m++];
tri[i] = (int) ubuf(buf[m++]).i;
if (tri[i] == 0) tri[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
quat = bonus[j].quat;
c1 = bonus[j].c1;
c2 = bonus[j].c2;
c3 = bonus[j].c3;
inertia = bonus[j].inertia;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
c1[0] = buf[m++];
c1[1] = buf[m++];
c1[2] = buf[m++];
c2[0] = buf[m++];
c2[1] = buf[m++];
c2[2] = buf[m++];
c3[0] = buf[m++];
c3[1] = buf[m++];
c3[2] = buf[m++];
inertia[0] = buf[m++];
inertia[1] = buf[m++];
inertia[2] = buf[m++];
bonus[j].ilocal = i;
tri[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 AtomVecTri::unpack_border_vel(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*c1,*c2,*c3,*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;
molecule[i] = (tagint) ubuf(buf[m++]).i;
radius[i] = buf[m++];
rmass[i] = buf[m++];
tri[i] = (int) ubuf(buf[m++]).i;
if (tri[i] == 0) tri[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
quat = bonus[j].quat;
c1 = bonus[j].c1;
c2 = bonus[j].c2;
c3 = bonus[j].c3;
inertia = bonus[j].inertia;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
c1[0] = buf[m++];
c1[1] = buf[m++];
c1[2] = buf[m++];
c2[0] = buf[m++];
c2[1] = buf[m++];
c2[2] = buf[m++];
c3[0] = buf[m++];
c3[1] = buf[m++];
c3[2] = buf[m++];
inertia[0] = buf[m++];
inertia[1] = buf[m++];
inertia[2] = buf[m++];
bonus[j].ilocal = i;
tri[i] = j;
nghost_bonus++;
}
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[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 AtomVecTri::unpack_border_hybrid(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*c1,*c2,*c3,*inertia;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
molecule[i] = (tagint) ubuf(buf[m++]).i;
radius[i] = buf[m++];
rmass[i] = buf[m++];
tri[i] = (int) ubuf(buf[m++]).i;
if (tri[i] == 0) tri[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
quat = bonus[j].quat;
c1 = bonus[j].c1;
c2 = bonus[j].c2;
c3 = bonus[j].c3;
inertia = bonus[j].inertia;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
c1[0] = buf[m++];
c1[1] = buf[m++];
c1[2] = buf[m++];
c2[0] = buf[m++];
c2[1] = buf[m++];
c2[2] = buf[m++];
c3[0] = buf[m++];
c3[1] = buf[m++];
c3[2] = buf[m++];
inertia[0] = buf[m++];
inertia[1] = buf[m++];
inertia[2] = buf[m++];
bonus[j].ilocal = i;
tri[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 AtomVecTri::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++] = ubuf(molecule[i]).d;
buf[m++] = rmass[i];
buf[m++] = radius[i];
buf[m++] = omega[i][0];
buf[m++] = omega[i][1];
buf[m++] = omega[i][2];
buf[m++] = angmom[i][0];
buf[m++] = angmom[i][1];
buf[m++] = angmom[i][2];
if (tri[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = tri[i];
double *quat = bonus[j].quat;
double *c1 = bonus[j].c1;
double *c2 = bonus[j].c2;
double *c3 = bonus[j].c3;
double *inertia = bonus[j].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[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 AtomVecTri::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;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
rmass[nlocal] = buf[m++];
radius[nlocal] = buf[m++];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
omega[nlocal][2] = buf[m++];
angmom[nlocal][0] = buf[m++];
angmom[nlocal][1] = buf[m++];
angmom[nlocal][2] = buf[m++];
tri[nlocal] = (int) ubuf(buf[m++]).i;
if (tri[nlocal] == 0) tri[nlocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
double *c1 = bonus[nlocal_bonus].c1;
double *c2 = bonus[nlocal_bonus].c2;
double *c3 = bonus[nlocal_bonus].c3;
double *inertia = bonus[nlocal_bonus].inertia;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
c1[0] = buf[m++];
c1[1] = buf[m++];
c1[2] = buf[m++];
c2[0] = buf[m++];
c2[1] = buf[m++];
c2[2] = buf[m++];
c3[0] = buf[m++];
c3[1] = buf[m++];
c3[2] = buf[m++];
inertia[0] = buf[m++];
inertia[1] = buf[m++];
inertia[2] = buf[m++];
bonus[nlocal_bonus].ilocal = nlocal;
tri[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 AtomVecTri::size_restart()
{
int i;
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (tri[i] >= 0) n += 37;
else n += 21;
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 AtomVecTri::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++] = ubuf(molecule[i]).d;
buf[m++] = rmass[i];
buf[m++] = radius[i];
buf[m++] = omega[i][0];
buf[m++] = omega[i][1];
buf[m++] = omega[i][2];
buf[m++] = angmom[i][0];
buf[m++] = angmom[i][1];
buf[m++] = angmom[i][2];
if (tri[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = tri[i];
double *quat = bonus[j].quat;
double *c1 = bonus[j].c1;
double *c2 = bonus[j].c2;
double *c3 = bonus[j].c3;
double *inertia = bonus[j].inertia;
buf[m++] = quat[0];
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
buf[m++] = c1[0];
buf[m++] = c1[1];
buf[m++] = c1[2];
buf[m++] = c2[0];
buf[m++] = c2[1];
buf[m++] = c2[2];
buf[m++] = c3[0];
buf[m++] = c3[1];
buf[m++] = c3[2];
buf[m++] = inertia[0];
buf[m++] = inertia[1];
buf[m++] = inertia[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 AtomVecTri::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++];
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
rmass[nlocal] = buf[m++];
radius[nlocal] = buf[m++];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
omega[nlocal][2] = buf[m++];
angmom[nlocal][0] = buf[m++];
angmom[nlocal][1] = buf[m++];
angmom[nlocal][2] = buf[m++];
tri[nlocal] = (int) ubuf(buf[m++]).i;
if (tri[nlocal] == 0) tri[nlocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
double *c1 = bonus[nlocal_bonus].c1;
double *c2 = bonus[nlocal_bonus].c2;
double *c3 = bonus[nlocal_bonus].c3;
double *inertia = bonus[nlocal_bonus].inertia;
quat[0] = buf[m++];
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
c1[0] = buf[m++];
c1[1] = buf[m++];
c1[2] = buf[m++];
c2[0] = buf[m++];
c2[1] = buf[m++];
c2[2] = buf[m++];
c3[0] = buf[m++];
c3[1] = buf[m++];
c3[2] = buf[m++];
inertia[0] = buf[m++];
inertia[1] = buf[m++];
inertia[2] = buf[m++];
bonus[nlocal_bonus].ilocal = nlocal;
tri[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 AtomVecTri::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;
molecule[nlocal] = 0;
radius[nlocal] = 0.5;
rmass[nlocal] = 4.0*MY_PI/3.0 * radius[nlocal]*radius[nlocal]*radius[nlocal];
omega[nlocal][0] = 0.0;
omega[nlocal][1] = 0.0;
omega[nlocal][2] = 0.0;
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
angmom[nlocal][2] = 0.0;
tri[nlocal] = -1;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecTri::data_atom(double *coord, imageint imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = ATOTAGINT(values[1]);
type[nlocal] = atoi(values[2]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
tri[nlocal] = atoi(values[3]);
if (tri[nlocal] == 0) tri[nlocal] = -1;
else if (tri[nlocal] == 1) tri[nlocal] = 0;
else error->one(FLERR,"Invalid atom type in Atoms section of data file");
rmass[nlocal] = atof(values[4]);
if (rmass[nlocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (tri[nlocal] < 0) {
radius[nlocal] = 0.5;
rmass[nlocal] *= 4.0*MY_PI/3.0 *
radius[nlocal]*radius[nlocal]*radius[nlocal];
} else radius[nlocal] = 0.0;
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;
omega[nlocal][0] = 0.0;
omega[nlocal][1] = 0.0;
omega[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 tri in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecTri::data_atom_hybrid(int nlocal, char **values)
{
molecule[nlocal] = ATOTAGINT(values[0]);
tri[nlocal] = atoi(values[1]);
if (tri[nlocal] == 0) tri[nlocal] = -1;
else if (tri[nlocal] == 1) tri[nlocal] = 0;
else error->one(FLERR,"Invalid atom type in Atoms section of data file");
rmass[nlocal] = atof(values[2]);
if (rmass[nlocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (tri[nlocal] < 0) {
radius[nlocal] = 0.5;
rmass[nlocal] *= 4.0*MY_PI/3.0 *
radius[nlocal]*radius[nlocal]*radius[nlocal];
} else radius[nlocal] = 0.0;
return 3;
}
/* ----------------------------------------------------------------------
unpack one line from Tris section of data file
------------------------------------------------------------------------- */
void AtomVecTri::data_atom_bonus(int m, char **values)
{
if (tri[m]) error->one(FLERR,"Assigning tri parameters to non-tri atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
double c1[3],c2[3],c3[3];
c1[0] = atof(values[0]);
c1[1] = atof(values[1]);
c1[2] = atof(values[2]);
c2[0] = atof(values[3]);
c2[1] = atof(values[4]);
c2[2] = atof(values[5]);
c3[0] = atof(values[6]);
c3[1] = atof(values[7]);
c3[2] = atof(values[8]);
// check for duplicate points
if (c1[0] == c2[0] && c1[1] == c2[1] && c1[2] == c2[2])
error->one(FLERR,"Invalid shape in Triangles section of data file");
if (c1[0] == c3[0] && c1[1] == c3[1] && c1[2] == c3[2])
error->one(FLERR,"Invalid shape in Triangles section of data file");
if (c2[0] == c3[0] && c2[1] == c3[1] && c2[2] == c3[2])
error->one(FLERR,"Invalid shape in Triangles section of data file");
// size = length of one edge
double c2mc1[3],c3mc1[3];
MathExtra::sub3(c2,c1,c2mc1);
MathExtra::sub3(c3,c1,c3mc1);
double size = MAX(MathExtra::len3(c2mc1),MathExtra::len3(c3mc1));
// centroid = 1/3 of sum of vertices
double centroid[3];
centroid[0] = (c1[0]+c2[0]+c3[0]) / 3.0;
centroid[1] = (c1[1]+c2[1]+c3[1]) / 3.0;
centroid[2] = (c1[2]+c2[2]+c3[2]) / 3.0;
double dx = centroid[0] - x[m][0];
double dy = centroid[1] - x[m][1];
double dz = centroid[2] - x[m][2];
double delta = sqrt(dx*dx + dy*dy + dz*dz);
if (delta/size > EPSILON)
error->one(FLERR,"Inconsistent triangle in data file");
x[m][0] = centroid[0];
x[m][1] = centroid[1];
x[m][2] = centroid[2];
// reset tri radius and mass
// rmass currently holds density
// tri area = 0.5 len(U x V), where U,V are edge vectors from one vertex
double c4[3];
MathExtra::sub3(c1,centroid,c4);
radius[m] = MathExtra::lensq3(c4);
MathExtra::sub3(c2,centroid,c4);
radius[m] = MAX(radius[m],MathExtra::lensq3(c4));
MathExtra::sub3(c3,centroid,c4);
radius[m] = MAX(radius[m],MathExtra::lensq3(c4));
radius[m] = sqrt(radius[m]);
double norm[3];
MathExtra::cross3(c2mc1,c3mc1,norm);
double area = 0.5 * MathExtra::len3(norm);
rmass[m] *= area;
// inertia = inertia tensor of triangle as 6-vector in Voigt notation
double inertia[6];
MathExtra::inertia_triangle(c1,c2,c3,rmass[m],inertia);
// diagonalize inertia tensor via Jacobi rotations
// bonus[].inertia = 3 eigenvalues = principal moments of inertia
// evectors and exzy_space = 3 evectors = principal axes of triangle
double tensor[3][3],evectors[3][3];
tensor[0][0] = inertia[0];
tensor[1][1] = inertia[1];
tensor[2][2] = inertia[2];
tensor[1][2] = tensor[2][1] = inertia[3];
tensor[0][2] = tensor[2][0] = inertia[4];
tensor[0][1] = tensor[1][0] = inertia[5];
int ierror = MathExtra::jacobi(tensor,bonus[nlocal_bonus].inertia,evectors);
if (ierror) error->one(FLERR,"Insufficient Jacobi rotations for triangle");
double ex_space[3],ey_space[3],ez_space[3];
ex_space[0] = evectors[0][0];
ex_space[1] = evectors[1][0];
ex_space[2] = evectors[2][0];
ey_space[0] = evectors[0][1];
ey_space[1] = evectors[1][1];
ey_space[2] = evectors[2][1];
ez_space[0] = evectors[0][2];
ez_space[1] = evectors[1][2];
ez_space[2] = evectors[2][2];
// enforce 3 orthogonal vectors as a right-handed coordinate system
// flip 3rd vector if needed
MathExtra::cross3(ex_space,ey_space,norm);
if (MathExtra::dot3(norm,ez_space) < 0.0) MathExtra::negate3(ez_space);
// create initial quaternion
MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus[nlocal_bonus].quat);
// bonus c1,c2,c3 = displacement of c1,c2,c3 from centroid
// in basis of principal axes
double disp[3];
MathExtra::sub3(c1,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
disp,bonus[nlocal_bonus].c1);
MathExtra::sub3(c2,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
disp,bonus[nlocal_bonus].c2);
MathExtra::sub3(c3,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
disp,bonus[nlocal_bonus].c3);
bonus[nlocal_bonus].ilocal = m;
tri[m] = nlocal_bonus++;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecTri::data_vel(int m, char **values)
{
v[m][0] = atof(values[0]);
v[m][1] = atof(values[1]);
v[m][2] = atof(values[2]);
omega[m][0] = atof(values[3]);
omega[m][1] = atof(values[4]);
omega[m][2] = atof(values[5]);
angmom[m][0] = atof(values[6]);
angmom[m][1] = atof(values[7]);
angmom[m][2] = atof(values[8]);
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int AtomVecTri::data_vel_hybrid(int m, char **values)
{
omega[m][0] = atof(values[0]);
omega[m][1] = atof(values[1]);
omega[m][2] = atof(values[2]);
angmom[m][0] = atof(values[3]);
angmom[m][1] = atof(values[4]);
angmom[m][2] = atof(values[5]);
return 6;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecTri::pack_data(double **buf)
{
double c2mc1[3],c3mc1[3],norm[3];
double area;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = ubuf(tag[i]).d;
buf[i][1] = ubuf(molecule[i]).d;
buf[i][2] = ubuf(type[i]).d;
if (tri[i] < 0) buf[i][3] = ubuf(0).d;
else buf[i][3] = ubuf(1).d;
if (tri[i] < 0)
buf[i][4] = rmass[i] / (4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i]);
else {
MathExtra::sub3(bonus[tri[i]].c2,bonus[tri[i]].c1,c2mc1);
MathExtra::sub3(bonus[tri[i]].c3,bonus[tri[i]].c1,c3mc1);
MathExtra::cross3(c2mc1,c3mc1,norm);
area = 0.5 * MathExtra::len3(norm);
buf[i][4] = rmass[i]/area;
}
buf[i][5] = x[i][0];
buf[i][6] = x[i][1];
buf[i][7] = x[i][2];
buf[i][8] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
buf[i][9] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
buf[i][10] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
}
}
/* ----------------------------------------------------------------------
pack hybrid atom info for data file
------------------------------------------------------------------------- */
int AtomVecTri::pack_data_hybrid(int i, double *buf)
{
buf[0] = ubuf(molecule[i]).d;
if (tri[i] < 0) buf[1] = ubuf(0).d;
else buf[1] = ubuf(1).d;
if (tri[i] < 0)
buf[2] = rmass[i] / (4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i]);
else {
double c2mc1[3],c3mc1[3],norm[3];
MathExtra::sub3(bonus[tri[i]].c2,bonus[tri[i]].c1,c2mc1);
MathExtra::sub3(bonus[tri[i]].c3,bonus[tri[i]].c1,c3mc1);
MathExtra::cross3(c2mc1,c3mc1,norm);
double area = 0.5 * MathExtra::len3(norm);
buf[2] = rmass[i]/area;
}
return 3;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecTri::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
" %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(tagint) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,(int) ubuf(buf[i][3]).i,
buf[i][4],buf[i][5],buf[i][6],buf[i][7],
(int) ubuf(buf[i][8]).i,(int) ubuf(buf[i][9]).i,
(int) ubuf(buf[i][10]).i);
}
/* ----------------------------------------------------------------------
write hybrid atom info to data file
------------------------------------------------------------------------- */
int AtomVecTri::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," " TAGINT_FORMAT " %d %-1.16e",
(tagint) ubuf(buf[0]).i,(int) ubuf(buf[1]).i,buf[2]);
return 3;
}
/* ----------------------------------------------------------------------
pack velocity info for data file
------------------------------------------------------------------------- */
void AtomVecTri::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] = omega[i][0];
buf[i][5] = omega[i][1];
buf[i][6] = omega[i][2];
buf[i][7] = angmom[i][0];
buf[i][8] = angmom[i][1];
buf[i][9] = angmom[i][2];
}
}
/* ----------------------------------------------------------------------
pack hybrid velocity info for data file
------------------------------------------------------------------------- */
int AtomVecTri::pack_vel_hybrid(int i, double *buf)
{
buf[0] = omega[i][0];
buf[1] = omega[i][1];
buf[2] = omega[i][2];
buf[3] = angmom[i][0];
buf[4] = angmom[i][1];
buf[5] = angmom[i][2];
return 6;
}
/* ----------------------------------------------------------------------
write velocity info to data file
------------------------------------------------------------------------- */
void AtomVecTri::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT
" %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
"%-1.16e %-1.16e %-1.16e\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],buf[i][7],buf[i][8],buf[i][9]);
}
/* ----------------------------------------------------------------------
write hybrid velocity info to data file
------------------------------------------------------------------------- */
int AtomVecTri::write_vel_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",
buf[0],buf[1],buf[2],buf[3],buf[4],buf[5]);
return 6;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecTri::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("molecule")) bytes += memory->usage(molecule,nmax);
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
if (atom->memcheck("radius")) bytes += memory->usage(radius,nmax);
if (atom->memcheck("omega")) bytes += memory->usage(omega,nmax,3);
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("tri")) bytes += memory->usage(tri,nmax);
bytes += nmax_bonus*sizeof(Bonus);
return bytes;
}
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