atom_vec_line.cpp
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Created: Sun, May 26, 07:07

atom_vec_line.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_line.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

	/* ---------------------------------------------------------------------- */

	AtomVecLine::AtomVecLine(LAMMPS *lmp) : AtomVec(lmp)
	{
	molecular = 0;

	comm_x_only = comm_f_only = 0;
	size_forward = 4;
	size_reverse = 6;
	size_border = 12;
	size_velocity = 6;
	size_data_atom = 8;
	size_data_vel = 7;
	size_data_bonus = 5;
	xcol_data = 6;

	atom->line_flag = 1;
	atom->molecule_flag = atom->rmass_flag = 1;
	atom->radius_flag = atom->omega_flag = atom->torque_flag = 1;
	atom->sphere_flag = 1;

	nlocal_bonus = nghost_bonus = nmax_bonus = 0;
	bonus = NULL;
	}

	/* ---------------------------------------------------------------------- */

	AtomVecLine::~AtomVecLine()
	{
	memory->sfree(bonus);
	}

	/* ---------------------------------------------------------------------- */

	void AtomVecLine::init()
	{
	AtomVec::init();

	if (domain->dimension != 2)
	error->all(FLERR,"Atom_style line can only be used in 2d simulations");
	}

	/* ----------------------------------------------------------------------
	grow atom arrays
	n = 0 grows arrays by a chunk
	n > 0 allocates arrays to size n
	------------------------------------------------------------------------- */

	void AtomVecLine::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");

	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");
	torque = memory->grow(atom->torque,nmax*comm->nthreads,3,"atom:torque");
	line = memory->grow(atom->line,nmax,"atom:line");

	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 AtomVecLine::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; torque = atom->torque;
	line = atom->line;
	}

	/* ----------------------------------------------------------------------
	grow bonus data structure
	------------------------------------------------------------------------- */

	void AtomVecLine::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_bonussizeof(Bonus),
	"atom:bonus");
	}

	/* ----------------------------------------------------------------------
	copy atom I info to atom J
	------------------------------------------------------------------------- */

	void AtomVecLine::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];

	// if deleting atom J via delflag and J has bonus data, then delete it

	if (delflag && line[j] >= 0) {
	copy_bonus(nlocal_bonus-1,line[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 (line[i] >= 0 && i != j) bonus[line[i]].ilocal = j;
	line[j] = line[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 line that points to I to now point to J
	------------------------------------------------------------------------- */

	void AtomVecLine::copy_bonus(int i, int j)
	{
	line[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 AtomVecLine::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 length value in bonus data for particle I
	oriented along x axis
	this may create or delete entry in bonus data
	------------------------------------------------------------------------- */

	void AtomVecLine::set_length(int i, double value)
	{
	if (line[i] < 0) {
	if (value == 0.0) return;
	if (nlocal_bonus == nmax_bonus) grow_bonus();
	bonus[nlocal_bonus].length = value;
	bonus[nlocal_bonus].theta = 0.0;
	bonus[nlocal_bonus].ilocal = i;
	line[i] = nlocal_bonus++;
	} else if (value == 0.0) {
	copy_bonus(nlocal_bonus-1,line[i]);
	nlocal_bonus--;
	line[i] = -1;
	} else bonus[line[i]].length = value;

	// also set radius = half of length
	// unless value = 0.0, then set diameter = 1.0

	radius[i] = 0.5 * value;
	if (value == 0.0) radius[i] = 0.5;
	}

	/* ---------------------------------------------------------------------- */

	int AtomVecLine::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];
	if (line[j] >= 0) buf[m++] = bonus[line[j]].theta;
	}
	} 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 (line[j] >= 0) buf[m++] = bonus[line[j]].theta;
	}
	}

	return m;
	}

	/* ---------------------------------------------------------------------- */

	int AtomVecLine::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];
	if (line[j] >= 0) buf[m++] = bonus[line[j]].theta;
	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];
	}
	} 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 (line[j] >= 0) buf[m++] = bonus[line[j]].theta;
	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];
	}
	} 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 (line[j] >= 0) buf[m++] = bonus[line[j]].theta;
	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];
	}
	}
	}

	return m;
	}

	/* ---------------------------------------------------------------------- */

	int AtomVecLine::pack_comm_hybrid(int n, int list, double buf)
	{
	int i,j,m;

	m = 0;
	for (i = 0; i < n; i++) {
	j = list[i];
	if (line[j] >= 0) buf[m++] = bonus[line[j]].theta;
	}
	return m;
	}

	/* ---------------------------------------------------------------------- */

	void AtomVecLine::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++];
	if (line[i] >= 0) bonus[line[i]].theta = buf[m++];
	}
	}

	/* ---------------------------------------------------------------------- */

	void AtomVecLine::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++];
	if (line[i] >= 0) bonus[line[i]].theta = 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++];
	}
	}

	/* ---------------------------------------------------------------------- */

	int AtomVecLine::unpack_comm_hybrid(int n, int first, double *buf)
	{
	int i,m,last;

	m = 0;
	last = first + n;
	for (i = first; i < last; i++)
	if (line[i] >= 0) bonus[line[i]].theta = buf[m++];
	return m;
	}

	/* ---------------------------------------------------------------------- */

	int AtomVecLine::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 AtomVecLine::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 AtomVecLine::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 AtomVecLine::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 AtomVecLine::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++] = ubuf(molecule[j]).d;
	buf[m++] = radius[j];
	buf[m++] = rmass[j];
	if (line[j] < 0) buf[m++] = ubuf(0).d;
	else {
	buf[m++] = ubuf(1).d;
	buf[m++] = bonus[line[j]].length;
	buf[m++] = bonus[line[j]].theta;
	}
	}
	} 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 (line[j] < 0) buf[m++] = ubuf(0).d;
	else {
	buf[m++] = ubuf(1).d;
	buf[m++] = bonus[line[j]].length;
	buf[m++] = bonus[line[j]].theta;
	}
	}
	}

	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 AtomVecLine::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++] = ubuf(molecule[j]).d;
	buf[m++] = radius[j];
	buf[m++] = rmass[j];
	if (line[j] < 0) buf[m++] = ubuf(0).d;
	else {
	buf[m++] = ubuf(1).d;
	buf[m++] = bonus[line[j]].length;
	buf[m++] = bonus[line[j]].theta;
	}
	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];
	}
	} 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 (line[j] < 0) buf[m++] = ubuf(0).d;
	else {
	buf[m++] = ubuf(1).d;
	buf[m++] = bonus[line[j]].length;
	buf[m++] = bonus[line[j]].theta;
	}
	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];
	}
	} 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 (line[j] < 0) buf[m++] = ubuf(0).d;
	else {
	buf[m++] = ubuf(1).d;
	buf[m++] = bonus[line[j]].length;
	buf[m++] = bonus[line[j]].theta;
	}
	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];
	}
	}
	}

	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 AtomVecLine::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++] = ubuf(molecule[j]).d;
	buf[m++] = radius[j];
	buf[m++] = rmass[j];
	if (line[j] < 0) buf[m++] = ubuf(0).d;
	else {
	buf[m++] = ubuf(1).d;
	buf[m++] = bonus[line[j]].length;
	buf[m++] = bonus[line[j]].theta;
	}
	}
	return m;
	}

	/* ---------------------------------------------------------------------- */

	void AtomVecLine::unpack_border(int n, int first, double *buf)
	{
	int i,j,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;
	molecule[i] = (tagint) ubuf(buf[m++]).i;
	radius[i] = buf[m++];
	rmass[i] = buf[m++];
	line[i] = (int) ubuf(buf[m++]).i;
	if (line[i] == 0) line[i] = -1;
	else {
	j = nlocal_bonus + nghost_bonus;
	if (j == nmax_bonus) grow_bonus();
	bonus[j].length = buf[m++];
	bonus[j].theta = buf[m++];
	bonus[j].ilocal = i;
	line[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 AtomVecLine::unpack_border_vel(int n, int first, double *buf)
	{
	int i,j,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;
	molecule[i] = (tagint) ubuf(buf[m++]).i;
	radius[i] = buf[m++];
	rmass[i] = buf[m++];
	line[i] = (int) ubuf(buf[m++]).i;
	if (line[i] == 0) line[i] = -1;
	else {
	j = nlocal_bonus + nghost_bonus;
	if (j == nmax_bonus) grow_bonus();
	bonus[j].length = buf[m++];
	bonus[j].theta = buf[m++];
	bonus[j].ilocal = i;
	line[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++];
	}

	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 AtomVecLine::unpack_border_hybrid(int n, int first, double *buf)
	{
	int i,j,m,last;

	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++];
	line[i] = (int) ubuf(buf[m++]).i;
	if (line[i] == 0) line[i] = -1;
	else {
	j = nlocal_bonus + nghost_bonus;
	if (j == nmax_bonus) grow_bonus();
	bonus[j].length = buf[m++];
	bonus[j].theta = buf[m++];
	bonus[j].ilocal = i;
	line[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 AtomVecLine::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];

	if (line[i] < 0) buf[m++] = ubuf(0).d;
	else {
	buf[m++] = ubuf(1).d;
	int j = line[i];
	buf[m++] = bonus[j].length;
	buf[m++] = bonus[j].theta;
	}

	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 AtomVecLine::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++];

	line[nlocal] = (int) ubuf(buf[m++]).i;
	if (line[nlocal] == 0) line[nlocal] = -1;
	else {
	if (nlocal_bonus == nmax_bonus) grow_bonus();
	bonus[nlocal_bonus].length = buf[m++];
	bonus[nlocal_bonus].theta = buf[m++];
	bonus[nlocal_bonus].ilocal = nlocal;
	line[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 AtomVecLine::size_restart()
	{
	int i;

	int n = 0;
	int nlocal = atom->nlocal;
	for (i = 0; i < nlocal; i++)
	if (line[i] >= 0) n += 20;
	else n += 18;

	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 AtomVecLine::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];

	if (line[i] < 0) buf[m++] = ubuf(0).d;
	else {
	buf[m++] = ubuf(1).d;
	int j = line[i];
	buf[m++] = bonus[j].length;
	buf[m++] = bonus[j].theta;
	}

	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 AtomVecLine::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++];

	line[nlocal] = (int) ubuf(buf[m++]).i;
	if (line[nlocal] == 0) line[nlocal] = -1;
	else {
	if (nlocal_bonus == nmax_bonus) grow_bonus();
	bonus[nlocal_bonus].length = buf[m++];
	bonus[nlocal_bonus].theta = buf[m++];
	bonus[nlocal_bonus].ilocal = nlocal;
	line[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 AtomVecLine::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] = 4.0MY_PI/3.0 radius[nlocal]radius[nlocal]radius[nlocal];
	omega[nlocal][0] = 0.0;
	omega[nlocal][1] = 0.0;
	omega[nlocal][2] = 0.0;
	line[nlocal] = -1;

	atom->nlocal++;
	}

	/* ----------------------------------------------------------------------
	unpack one line from Atoms section of data file
	initialize other atom quantities
	------------------------------------------------------------------------- */

	void AtomVecLine::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");

	line[nlocal] = atoi(values[3]);
	if (line[nlocal] == 0) line[nlocal] = -1;
	else if (line[nlocal] == 1) line[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 (line[nlocal] < 0) {
	radius[nlocal] = 0.5;
	rmass[nlocal] = 4.0MY_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;

	atom->nlocal++;
	}

	/* ----------------------------------------------------------------------
	unpack hybrid quantities from one line in Atoms section of data file
	initialize other atom quantities for this sub-style
	------------------------------------------------------------------------- */

	int AtomVecLine::data_atom_hybrid(int nlocal, char **values)
	{
	molecule[nlocal] = ATOTAGINT(values[0]);

	line[nlocal] = atoi(values[1]);
	if (line[nlocal] == 0) line[nlocal] = -1;
	else if (line[nlocal] == 1) line[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 (line[nlocal] < 0) {
	radius[nlocal] = 0.5;
	rmass[nlocal] = 4.0MY_PI/3.0 *
	radius[nlocal]radius[nlocal]radius[nlocal];
	} else radius[nlocal] = 0.0;

	return 3;
	}

	/* ----------------------------------------------------------------------
	unpack one line from Lines section of data file
	------------------------------------------------------------------------- */

	void AtomVecLine::data_atom_bonus(int m, char **values)
	{
	if (line[m]) error->one(FLERR,"Assigning line parameters to non-line atom");

	if (nlocal_bonus == nmax_bonus) grow_bonus();

	double x1 = atof(values[0]);
	double y1 = atof(values[1]);
	double x2 = atof(values[2]);
	double y2 = atof(values[3]);
	double dx = x2 - x1;
	double dy = y2 - y1;
	double length = sqrt(dxdx + dydy);

	bonus[nlocal_bonus].length = length;
	if (dy >= 0.0) bonus[nlocal_bonus].theta = acos(dx/length);
	else bonus[nlocal_bonus].theta = -acos(dx/length);

	double xc = 0.5*(x1+x2);
	double yc = 0.5*(y1+y2);
	dx = xc - x[m][0];
	dy = yc - x[m][1];
	double delta = sqrt(dxdx + dydy);

	if (delta/length > EPSILON)
	error->one(FLERR,"Inconsistent line segment in data file");

	x[m][0] = xc;
	x[m][1] = yc;

	// reset line radius and mass
	// rmass currently holds density

	radius[m] = 0.5 * length;
	rmass[m] *= length;

	bonus[nlocal_bonus].ilocal = m;
	line[m] = nlocal_bonus++;
	}

	/* ----------------------------------------------------------------------
	unpack one line from Velocities section of data file
	------------------------------------------------------------------------- */

	void AtomVecLine::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]);
	}

	/* ----------------------------------------------------------------------
	unpack hybrid quantities from one line in Velocities section of data file
	------------------------------------------------------------------------- */

	int AtomVecLine::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]);
	return 3;
	}

	/* ----------------------------------------------------------------------
	pack atom info for data file including 3 image flags
	------------------------------------------------------------------------- */

	void AtomVecLine::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(molecule[i]).d;
	buf[i][2] = ubuf(type[i]).d;
	if (line[i] < 0) buf[i][3] = ubuf(0).d;
	else buf[i][3] = ubuf(1).d;
	if (line[i] < 0)
	buf[i][4] = rmass[i] / (4.0MY_PI/3.0 radius[i]radius[i]radius[i]);
	else buf[i][4] = rmass[i]/bonus[line[i]].length;
	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 AtomVecLine::pack_data_hybrid(int i, double *buf)
	{
	buf[0] = ubuf(molecule[i]).d;
	if (line[i] < 0) buf[1] = ubuf(0).d;
	else buf[1] = ubuf(1).d;
	if (line[i] < 0)
	buf[2] = rmass[i] / (4.0MY_PI/3.0 radius[i]radius[i]radius[i]);
	else buf[2] = rmass[i]/bonus[line[i]].length;
	return 3;
	}

	/* ----------------------------------------------------------------------
	write atom info to data file including 3 image flags
	------------------------------------------------------------------------- */

	void AtomVecLine::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 AtomVecLine::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 AtomVecLine::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];
	}
	}

	/* ----------------------------------------------------------------------
	pack hybrid velocity info for data file
	------------------------------------------------------------------------- */

	int AtomVecLine::pack_vel_hybrid(int i, double *buf)
	{
	buf[0] = omega[i][0];
	buf[1] = omega[i][1];
	buf[2] = omega[i][2];
	return 3;
	}

	/* ----------------------------------------------------------------------
	write velocity info to data file
	------------------------------------------------------------------------- */

	void AtomVecLine::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\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 AtomVecLine::write_vel_hybrid(FILE fp, double buf)
	{
	fprintf(fp," %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2]);
	return 3;
	}

	/* ----------------------------------------------------------------------
	return # of bytes of allocated memory
	------------------------------------------------------------------------- */

	bigint AtomVecLine::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("torque"))
	bytes += memory->usage(torque,nmax*comm->nthreads,3);
	if (atom->memcheck("line")) bytes += memory->usage(line,nmax);

	bytes += nmax_bonus*sizeof(Bonus);

	return bytes;
	}

	/* ----------------------------------------------------------------------
	check consistency of internal Bonus data structure
	n = # of atoms in regular structure to check against
	------------------------------------------------------------------------- */

	/*
	void AtomVecLine::consistency_check(int n, char *str)
	{
	int iflag = 0;
	int count = 0;
	for (int i = 0; i < n; i++) {

	if (line[i] >= 0) {
	count++;
	if (line[i] >= nlocal_bonus) iflag++;
	if (bonus[line[i]].ilocal != i) iflag++;
	//if (comm->me == 1 && update->ntimestep == 873)
	// printf("CCHK %s: %d %d: %d %d: %d %d\n",
	// str,i,n,line[i],nlocal_bonus,bonus[line[i]].ilocal,iflag);
	}
	}

	if (iflag) {
	printf("BAD vecline ptrs: %s: %d %d: %d\n",str,comm->me,
	update->ntimestep,iflag);
	MPI_Abort(world,1);
	}

	if (count != nlocal_bonus) {
	char msg[128];
	printf("BAD vecline count: %s: %d %d: %d %d\n",
	str,comm->me,update->ntimestep,count,nlocal_bonus);
	MPI_Abort(world,1);
	}
	}
	*/

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