atom_vec_template.cpp
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Created: Sun, Nov 10, 13:43

atom_vec_template.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 <string.h>
	#include <stdlib.h>
	#include "atom_vec_template.h"
	#include "atom.h"
	#include "molecule.h"
	#include "comm.h"
	#include "domain.h"
	#include "modify.h"
	#include "fix.h"
	#include "memory.h"
	#include "error.h"

	using namespace LAMMPS_NS;

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

	AtomVecTemplate::AtomVecTemplate(LAMMPS *lmp) : AtomVec(lmp)
	{
	molecular = 2;
	mass_type = 1;

	comm_x_only = comm_f_only = 1;
	size_forward = 3;
	size_reverse = 3;
	size_border = 9;
	size_velocity = 3;
	size_data_atom = 8;
	size_data_vel = 4;
	xcol_data = 6;

	atom->molecule_flag = 1;
	}

	/* ----------------------------------------------------------------------
	process additional arg = molecule template ID
	------------------------------------------------------------------------- */

	void AtomVecTemplate::process_args(int narg, char **arg)
	{
	if (narg != 1) error->all(FLERR,"Illegal atom_style template command");

	int imol = atom->find_molecule(arg[0]);
	if (imol == -1) error->all(FLERR,"Molecule template ID for "
	"atom_style template does not exist");

	onemols = &atom->molecules[imol];
	nset = atom->molecules[imol]->nset;

	// error check on molecule template fields

	for (int i = 0; i < nset; i++)
	if (onemols[i]->typeflag == 0)
	error->all(FLERR,"Atom style template molecule must have atom types");

	// set bonds_allow,angles_allow,etc based on the molecules in template set
	// similar to how atom_style bond,angle,full set it

	for (int i = 0; i < nset; i++) {
	if (onemols[i]->bondflag) bonds_allow = 1;
	if (onemols[i]->angleflag) angles_allow = 1;
	if (onemols[i]->dihedralflag) dihedrals_allow = 1;
	if (onemols[i]->improperflag) impropers_allow = 1;
	}

	// set nbondtypes,nangletypes,etc based on the molecules in template set
	// do this here b/c data file will typically not contain these settings

	for (int i = 0; i < nset; i++) {
	atom->nbondtypes = MAX(atom->nbondtypes,onemols[i]->nbondtypes);
	atom->nangletypes = MAX(atom->nangletypes,onemols[i]->nangletypes);
	atom->ndihedraltypes = MAX(atom->ndihedraltypes,onemols[i]->ndihedraltypes);
	atom->nimpropertypes = MAX(atom->nimpropertypes,onemols[i]->nimpropertypes);
	}
	}

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

	void AtomVecTemplate::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");
	molindex = memory->grow(atom->molindex,nmax,"atom:molindex");
	molatom = memory->grow(atom->molatom,nmax,"atom:molatom");

	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 AtomVecTemplate::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;
	molindex = atom->molindex; molatom = atom->molatom;
	}

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

	void AtomVecTemplate::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];
	molindex[j] = molindex[i];
	molatom[j] = molatom[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);
	}

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

	int AtomVecTemplate::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];
	}
	} 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;
	}
	}
	return m;
	}

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

	int AtomVecTemplate::pack_comm_vel(int n, int list, double buf,
	int pbc_flag, int *pbc)
	{
	int i,j,m;
	double dx,dy,dz,dvx,dvy,dvz;

	m = 0;
	if (pbc_flag == 0) {
	for (i = 0; i < n; i++) {
	j = list[i];
	buf[m++] = x[j][0];
	buf[m++] = x[j][1];
	buf[m++] = x[j][2];
	buf[m++] = v[j][0];
	buf[m++] = v[j][1];
	buf[m++] = v[j][2];
	}
	} else {
	if (domain->triclinic == 0) {
	dx = pbc[0]*domain->xprd;
	dy = pbc[1]*domain->yprd;
	dz = pbc[2]*domain->zprd;
	} else {
	dx = pbc[0]domain->xprd + pbc[5]domain->xy + pbc[4]*domain->xz;
	dy = pbc[1]domain->yprd + pbc[3]domain->yz;
	dz = pbc[2]*domain->zprd;
	}
	if (!deform_vremap) {
	for (i = 0; i < n; i++) {
	j = list[i];
	buf[m++] = x[j][0] + dx;
	buf[m++] = x[j][1] + dy;
	buf[m++] = x[j][2] + dz;
	buf[m++] = v[j][0];
	buf[m++] = v[j][1];
	buf[m++] = v[j][2];
	}
	} else {
	dvx = pbc[0]h_rate[0] + pbc[5]h_rate[5] + pbc[4]*h_rate[4];
	dvy = pbc[1]h_rate[1] + pbc[3]h_rate[3];
	dvz = pbc[2]*h_rate[2];
	for (i = 0; i < n; i++) {
	j = list[i];
	buf[m++] = x[j][0] + dx;
	buf[m++] = x[j][1] + dy;
	buf[m++] = x[j][2] + dz;
	if (mask[i] & deform_groupbit) {
	buf[m++] = v[j][0] + dvx;
	buf[m++] = v[j][1] + dvy;
	buf[m++] = v[j][2] + dvz;
	} else {
	buf[m++] = v[j][0];
	buf[m++] = v[j][1];
	buf[m++] = v[j][2];
	}
	}
	}
	}
	return m;
	}

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

	void AtomVecTemplate::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++];
	}
	}

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

	void AtomVecTemplate::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++];
	v[i][0] = buf[m++];
	v[i][1] = buf[m++];
	v[i][2] = buf[m++];
	}
	}

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

	int AtomVecTemplate::pack_reverse(int n, int first, double *buf)
	{
	int i,m,last;

	m = 0;
	last = first + n;
	for (i = first; i < last; i++) {
	buf[m++] = f[i][0];
	buf[m++] = f[i][1];
	buf[m++] = f[i][2];
	}
	return m;
	}

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

	void AtomVecTemplate::unpack_reverse(int n, int list, double buf)
	{
	int i,j,m;

	m = 0;
	for (i = 0; i < n; i++) {
	j = list[i];
	f[j][0] += buf[m++];
	f[j][1] += buf[m++];
	f[j][2] += buf[m++];
	}
	}

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

	int AtomVecTemplate::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++] = ubuf(molindex[j]).d;
	buf[m++] = ubuf(molatom[j]).d;
	}
	} 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++] = ubuf(molindex[j]).d;
	buf[m++] = ubuf(molatom[j]).d;
	}
	}

	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 AtomVecTemplate::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++] = ubuf(molindex[j]).d;
	buf[m++] = ubuf(molatom[j]).d;
	buf[m++] = v[j][0];
	buf[m++] = v[j][1];
	buf[m++] = v[j][2];
	}
	} else {
	if (domain->triclinic == 0) {
	dx = pbc[0]*domain->xprd;
	dy = pbc[1]*domain->yprd;
	dz = pbc[2]*domain->zprd;
	} else {
	dx = pbc[0];
	dy = pbc[1];
	dz = pbc[2];
	}
	if (!deform_vremap) {
	for (i = 0; i < n; i++) {
	j = list[i];
	buf[m++] = x[j][0] + dx;
	buf[m++] = x[j][1] + dy;
	buf[m++] = x[j][2] + dz;
	buf[m++] = ubuf(tag[j]).d;
	buf[m++] = ubuf(type[j]).d;
	buf[m++] = ubuf(mask[j]).d;
	buf[m++] = ubuf(molecule[j]).d;
	buf[m++] = ubuf(molindex[j]).d;
	buf[m++] = ubuf(molatom[j]).d;
	buf[m++] = v[j][0];
	buf[m++] = v[j][1];
	buf[m++] = v[j][2];
	}
	} else {
	dvx = pbc[0]h_rate[0] + pbc[5]h_rate[5] + pbc[4]*h_rate[4];
	dvy = pbc[1]h_rate[1] + pbc[3]h_rate[3];
	dvz = pbc[2]*h_rate[2];
	for (i = 0; i < n; i++) {
	j = list[i];
	buf[m++] = x[j][0] + dx;
	buf[m++] = x[j][1] + dy;
	buf[m++] = x[j][2] + dz;
	buf[m++] = ubuf(tag[j]).d;
	buf[m++] = ubuf(type[j]).d;
	buf[m++] = ubuf(mask[j]).d;
	buf[m++] = ubuf(molecule[j]).d;
	buf[m++] = ubuf(molindex[j]).d;
	buf[m++] = ubuf(molatom[j]).d;
	if (mask[i] & deform_groupbit) {
	buf[m++] = v[j][0] + dvx;
	buf[m++] = v[j][1] + dvy;
	buf[m++] = v[j][2] + dvz;
	} else {
	buf[m++] = v[j][0];
	buf[m++] = v[j][1];
	buf[m++] = v[j][2];
	}
	}
	}
	}

	if (atom->nextra_border)
	for (int iextra = 0; iextra < atom->nextra_border; iextra++)
	m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);

	return m;
	}

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

	int AtomVecTemplate::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++] = ubuf(molindex[j]).d;
	buf[m++] = ubuf(molatom[j]).d;
	}
	return m;
	}

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

	void AtomVecTemplate::unpack_border(int n, int first, double *buf)
	{
	int i,m,last;

	m = 0;
	last = first + n;
	for (i = first; i < last; i++) {
	if (i == nmax) grow(0);
	x[i][0] = buf[m++];
	x[i][1] = buf[m++];
	x[i][2] = buf[m++];
	tag[i] = (tagint) ubuf(buf[m++]).i;
	type[i] = (int) ubuf(buf[m++]).i;
	mask[i] = (int) ubuf(buf[m++]).i;
	molecule[i] = (tagint) ubuf(buf[m++]).i;
	molindex[i] = (int) ubuf(buf[m++]).i;
	molatom[i] = (int) ubuf(buf[m++]).i;
	}

	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 AtomVecTemplate::unpack_border_vel(int n, int first, double *buf)
	{
	int i,m,last;

	m = 0;
	last = first + n;
	for (i = first; i < last; i++) {
	if (i == nmax) grow(0);
	x[i][0] = buf[m++];
	x[i][1] = buf[m++];
	x[i][2] = buf[m++];
	tag[i] = (tagint) ubuf(buf[m++]).i;
	type[i] = (int) ubuf(buf[m++]).i;
	mask[i] = (int) ubuf(buf[m++]).i;
	molecule[i] = (tagint) ubuf(buf[m++]).i;
	molindex[i] = (int) ubuf(buf[m++]).i;
	molatom[i] = (int) ubuf(buf[m++]).i;
	v[i][0] = buf[m++];
	v[i][1] = buf[m++];
	v[i][2] = buf[m++];
	}

	if (atom->nextra_border)
	for (int iextra = 0; iextra < atom->nextra_border; iextra++)
	m += modify->fix[atom->extra_border[iextra]]->
	unpack_border(n,first,&buf[m]);
	}

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

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

	m = 0;
	last = first + n;
	for (i = first; i < last; i++) {
	molecule[i] = (tagint) ubuf(buf[m++]).i;
	molindex[i] = (int) ubuf(buf[m++]).i;
	molatom[i] = (int) ubuf(buf[m++]).i;
	}
	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 AtomVecTemplate::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++] = ubuf(molindex[i]).d;
	buf[m++] = ubuf(molatom[i]).d;

	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 AtomVecTemplate::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;
	molindex[nlocal] = (int) ubuf(buf[m++]).i;
	molatom[nlocal] = (int) ubuf(buf[m++]).i;

	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 AtomVecTemplate::size_restart()
	{
	int i;

	int nlocal = atom->nlocal;
	int n = 14 * nlocal;

	if (atom->nextra_restart)
	for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
	for (i = 0; i < nlocal; i++)
	n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);

	return n;
	}

	/* ----------------------------------------------------------------------
	pack atom I's data for restart file including extra quantities
	xyz must be 1st 3 values, so that read_restart can test on them
	molecular types may be negative, but write as positive
	------------------------------------------------------------------------- */

	int AtomVecTemplate::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++] = ubuf(molindex[i]).d;
	buf[m++] = ubuf(molatom[i]).d;

	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 AtomVecTemplate::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;
	molindex[nlocal] = (int) ubuf(buf[m++]).i;
	molatom[nlocal] = (int) ubuf(buf[m++]).i;

	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 AtomVecTemplate::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;
	molindex[nlocal] = -1;
	molatom[nlocal] = -1;

	atom->nlocal++;
	}

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

	void AtomVecTemplate::data_atom(double coord, imageint imagetmp, char *values)
	{
	int nlocal = atom->nlocal;
	if (nlocal == nmax) grow(0);

	tag[nlocal] = ATOTAGINT(values[0]);
	if (tag[nlocal] <= 0)
	error->one(FLERR,"Invalid atom ID in Atoms section of data file");

	molecule[nlocal] = ATOTAGINT(values[1]);
	molindex[nlocal] = atoi(values[2]) - 1;
	molatom[nlocal] = atoi(values[3]) - 1;

	if (molindex[nlocal] < 0 \|\| molindex[nlocal] >= nset)
	error->one(FLERR,"Invalid template index in Atoms section of data file");
	if (molatom[nlocal] < 0 \|\|
	molatom[nlocal] >= onemols[molindex[nlocal]]->natoms)
	error->one(FLERR,"Invalid template atom in Atoms section of data file");

	type[nlocal] = atoi(values[4]);
	if (type[nlocal] <= 0 \|\| type[nlocal] > atom->ntypes)
	error->one(FLERR,"Invalid atom type 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;

	atom->nlocal++;
	}

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

	int AtomVecTemplate::data_atom_hybrid(int nlocal, char **values)
	{
	molecule[nlocal] = ATOTAGINT(values[0]);
	molindex[nlocal] = atoi(values[1]) - 1;
	molatom[nlocal] = atoi(values[2]) - 1;
	return 3;
	}

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

	void AtomVecTemplate::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(molindex[i]+1).d;
	buf[i][3] = ubuf(molatom[i]+1).d;
	buf[i][4] = ubuf(type[i]).d;
	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 AtomVecTemplate::pack_data_hybrid(int i, double *buf)
	{
	buf[0] = ubuf(molecule[i]).d;
	buf[1] = ubuf(molindex[i]+1).d;
	buf[2] = ubuf(molatom[i]+1).d;
	return 3;
	}

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

	void AtomVecTemplate::write_data(FILE fp, int n, double *buf)
	{
	for (int i = 0; i < n; i++)
	fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
	" %d %d %d %-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,
	(int) ubuf(buf[i][4]).i,
	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 AtomVecTemplate::write_data_hybrid(FILE fp, double buf)
	{
	fprintf(fp," " TAGINT_FORMAT " %d %d",
	(tagint) ubuf(buf[0]).i,(int) ubuf(buf[1]).i,(int) ubuf(buf[2]).i);
	return 3;
	}

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

	bigint AtomVecTemplate::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("molindex")) bytes += memory->usage(molindex,nmax);
	if (atom->memcheck("molatom")) bytes += memory->usage(molatom,nmax);

	return bytes;
	}

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