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atom.cpp
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atom.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 "mpi.h"
			#include "stdio.h"
			#include "stdlib.h"
			#include "string.h"
			#include "limits.h"
			#include "atom.h"
			#include "style_atom.h"
			#include "atom_vec.h"
			#include "comm.h"
			#include "neighbor.h"
			#include "force.h"
			#include "modify.h"
			#include "fix.h"
			#include "output.h"
			#include "thermo.h"
			#include "update.h"
			#include "domain.h"
			#include "group.h"
			#include "memory.h"
			#include "error.h"

			using namespace LAMMPS_NS;

			#define DELTA 1
			#define DELTA_MEMSTR 1024
			#define EPSILON 1.0e-6

			#define MIN(A,B) ((A) < (B)) ? (A) : (B)
			#define MAX(A,B) ((A) > (B)) ? (A) : (B)

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

			Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
			{
			natoms = 0;
			nlocal = nghost = nmax = 0;
			ntypes = 0;
			nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
			nbonds = nangles = ndihedrals = nimpropers = 0;
			bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
			extra_bond_per_atom = 0;

			firstgroupname = NULL;
			sortfreq = 1000;
			userbinsize = 0.0;
			maxbin = maxnext = 0;
			binhead = NULL;
			next = permute = NULL;

			// initialize atom arrays
			// customize by adding new array

			tag = type = mask = image = NULL;
			x = v = f = NULL;

			molecule = NULL;
			q = NULL;
			mu = NULL;
			quat = omega = angmom = torque = NULL;
			radius = density = rmass = NULL;
			vfrac = s0 = NULL;
			x0 = NULL;

			spin = NULL;
			eradius = ervel = erforce = NULL;

			maxspecial = 1;
			nspecial = NULL;
			special = NULL;

			num_bond = NULL;
			bond_type = bond_atom = NULL;

			num_angle = NULL;
			angle_type = angle_atom1 = angle_atom2 = angle_atom3 = NULL;

			num_dihedral = NULL;
			dihedral_type = dihedral_atom1 = dihedral_atom2 = NULL;
			dihedral_atom3 = dihedral_atom4 = NULL;

			num_improper = NULL;
			improper_type = improper_atom1 = improper_atom2 = NULL;
			improper_atom3 = improper_atom4 = NULL;

			// initialize atom array existence flags
			// customize by adding new flag

			molecule_flag = 0;
			q_flag = mu_flag = 0;
			quat_flag = omega_flag = angmom_flag = torque_flag = 0;
			radius_flag = density_flag = rmass_flag = vfrac_flag = 0;
			spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;

			// ntype-length arrays

			mass = NULL;
			mass_setflag = NULL;
			shape = NULL;
			shape_setflag = NULL;
			dipole = NULL;
			dipole_setflag = NULL;

			// callback lists & extra restart info

			nextra_grow = nextra_restart = 0;
			extra_grow = extra_restart = NULL;
			nextra_grow_max = nextra_restart_max = 0;
			nextra_store = 0;
			extra = NULL;

			// default mapping values and hash table primes

			tag_enable = 1;
			map_style = 0;
			map_tag_max = 0;
			map_nhash = 0;

			nprimes = 38;
			primes = new int[nprimes];
			int plist[] = {5041,10007,20011,30011,40009,50021,60013,70001,80021,
			90001,100003,110017,120011,130003,140009,150001,160001,
			170003,180001,190027,200003,210011,220009,230003,240007,
			250007,260003,270001,280001,290011,300007,310019,320009,
			330017,340007,350003,362881,3628801};
			for (int i = 0; i < nprimes; i++) primes[i] = plist[i];

			// default atom style = atomic

			atom_style = NULL;
			avec = NULL;
			create_avec("atomic",0,NULL);
			}

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

			Atom::~Atom()
			{
			delete [] atom_style;
			delete avec;

			delete [] firstgroupname;
			memory->destroy(binhead);
			memory->destroy(next);
			memory->destroy(permute);

			// delete atom arrays
			// customize by adding new array

			memory->destroy(tag);
			memory->destroy(type);
			memory->destroy(mask);
			memory->destroy(image);
			memory->destroy(x);
			memory->destroy(v);
			memory->destroy(f);

			memory->destroy(q);
			memory->destroy(mu);
			memory->destroy(quat);
			memory->destroy(omega);
			memory->destroy(angmom);
			memory->destroy(torque);

			memory->destroy(radius);
			memory->destroy(density);
			memory->destroy(rmass);
			memory->destroy(vfrac);
			memory->destroy(s0);
			memory->destroy(x0);

			memory->destroy(spin);
			memory->destroy(eradius);
			memory->destroy(ervel);
			memory->destroy(erforce);

			memory->destroy(molecule);

			memory->destroy(nspecial);
			memory->destroy(special);

			memory->destroy(num_bond);
			memory->destroy(bond_type);
			memory->destroy(bond_atom);

			memory->destroy(num_angle);
			memory->destroy(angle_type);
			memory->destroy(angle_atom1);
			memory->destroy(angle_atom2);
			memory->destroy(angle_atom3);

			memory->destroy(num_dihedral);
			memory->destroy(dihedral_type);
			memory->destroy(dihedral_atom1);
			memory->destroy(dihedral_atom2);
			memory->destroy(dihedral_atom3);
			memory->destroy(dihedral_atom4);

			memory->destroy(num_improper);
			memory->destroy(improper_type);
			memory->destroy(improper_atom1);
			memory->destroy(improper_atom2);
			memory->destroy(improper_atom3);
			memory->destroy(improper_atom4);

			// delete per-type arrays

			delete [] mass;
			delete [] mass_setflag;
			memory->destroy(shape);
			delete [] shape_setflag;
			delete [] dipole;
			delete [] dipole_setflag;

			// delete extra arrays

			memory->destroy(extra_grow);
			memory->destroy(extra_restart);
			memory->destroy(extra);

			// delete mapping data structures

			map_delete();
			delete [] primes;
			}

			/* ----------------------------------------------------------------------
			copy modify settings from old Atom class to current Atom class
			------------------------------------------------------------------------- */

			void Atom::settings(Atom *old)
			{
			map_style = old->map_style;
			}

			/* ----------------------------------------------------------------------
			create an AtomVec style
			called from input script, restart file, replicate
			------------------------------------------------------------------------- */

			void Atom::create_avec(const char style, int narg, char *arg)
			{
			delete [] atom_style;
			if (avec) delete avec;

			// unset atom array existence flags that may have been set by old avec
			// customize by adding new flag

			molecule_flag = 0;
			q_flag = mu_flag = 0;
			quat_flag = omega_flag = angmom_flag = torque_flag = 0;
			radius_flag = density_flag = rmass_flag = vfrac_flag = 0;
			spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;

			avec = new_avec(style,narg,arg);
			int n = strlen(style) + 1;
			atom_style = new char[n];
			strcpy(atom_style,style);

			// if molecular system, default is to have array map

			molecular = avec->molecular;
			if (map_style == 0 && molecular) map_style = 1;
			}

			/* ----------------------------------------------------------------------
			generate an AtomVec class
			------------------------------------------------------------------------- */

			AtomVec Atom::new_avec(const char style, int narg, char **arg)
			{
			if (0) return NULL;

			#define ATOM_CLASS
			#define AtomStyle(key,Class) \
			else if (strcmp(style,#key) == 0) return new Class(lmp,narg,arg);
			#include "style_atom.h"
			#undef ATOM_CLASS

			else error->all("Invalid atom style");
			return NULL;
			}

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

			void Atom::init()
			{
			// delete extra array since it doesn't persist past first run

			if (nextra_store) {
			memory->destroy(extra);
			extra = NULL;
			nextra_store = 0;
			}

			// check arrays that are atom type in length

			check_mass();
			check_shape();
			check_dipole();

			// setup of firstgroup

			if (firstgroupname) {
			firstgroup = group->find(firstgroupname);
			if (firstgroup < 0)
			error->all("Could not find atom_modify first group ID");
			} else firstgroup = -1;

			// init AtomVec

			avec->init();
			}

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

			void Atom::setup()
			{
			// setup bins for sorting
			// cannot do this in init() because uses neighbor cutoff

			if (sortfreq > 0) setup_sort_bins();
			}

			/* ----------------------------------------------------------------------
			return 1 if style matches atom style or hybrid sub-style
			else return 0
			------------------------------------------------------------------------- */

			int Atom::style_match(const char *style)
			{
			if (strcmp(atom_style,style) == 0) return 1;
			else if (strcmp(atom_style,"hybrid") == 0) {
			AtomVecHybrid avec_hybrid = (AtomVecHybrid ) avec;
			for (int i = 0; i < avec_hybrid->nstyles; i++)
			if (strcmp(avec_hybrid->keywords[i],style) == 0) return 1;
			}
			return 0;
			}

			/* ----------------------------------------------------------------------
			modify parameters of the atom style
			some options can only be invoked before simulation box is defined
			first and sort options cannot be used together
			------------------------------------------------------------------------- */

			void Atom::modify_params(int narg, char **arg)
			{
			if (narg == 0) error->all("Illegal atom_modify command");

			int iarg = 0;
			while (iarg < narg) {
			if (strcmp(arg[iarg],"map") == 0) {
			if (iarg+2 > narg) error->all("Illegal atom_modify command");
			if (strcmp(arg[iarg+1],"array") == 0) map_style = 1;
			else if (strcmp(arg[iarg+1],"hash") == 0) map_style = 2;
			else error->all("Illegal atom_modify command");
			if (domain->box_exist)
			error->all("Atom_modify map command after simulation box is defined");
			iarg += 2;
			} else if (strcmp(arg[iarg],"first") == 0) {
			if (iarg+2 > narg) error->all("Illegal atom_modify command");
			if (strcmp(arg[iarg+1],"all") == 0) {
			delete [] firstgroupname;
			firstgroupname = NULL;
			} else {
			int n = strlen(arg[iarg+1]) + 1;
			firstgroupname = new char[n];
			strcpy(firstgroupname,arg[iarg+1]);
			sortfreq = 0;
			}
			iarg += 2;
			} else if (strcmp(arg[iarg],"sort") == 0) {
			if (iarg+3 > narg) error->all("Illegal atom_modify command");
			sortfreq = atoi(arg[iarg+1]);
			userbinsize = atof(arg[iarg+2]);
			if (sortfreq < 0 \|\| userbinsize < 0.0)
			error->all("Illegal atom_modify command");
			if (sortfreq >= 0 && firstgroupname)
			error->all("Atom_modify sort and first options "
			"cannot be used together");
			iarg += 3;
			} else error->all("Illegal atom_modify command");
			}
			}

			/* ----------------------------------------------------------------------
			allocate and initialize array or hash table for global -> local map
			set map_tag_max = largest atom ID (may be larger than natoms)
			for array option:
			array length = 1 to largest tag of any atom
			set entire array to -1 as initial values
			for hash option:
			map_nhash = length of hash table
			map_nbucket = # of hash buckets, prime larger than map_nhash
			so buckets will only be filled with 0 or 1 atoms on average
			------------------------------------------------------------------------- */

			void Atom::map_init()
			{
			map_delete();

			if (tag_enable == 0)
			error->all("Cannot create an atom map unless atoms have IDs");

			int max = 0;
			for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
			MPI_Allreduce(&max,&map_tag_max,1,MPI_INT,MPI_MAX,world);

			if (map_style == 1) {
			memory->create(map_array,map_tag_max+1,"atom:map_array");
			for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;

			} else {

			// map_nhash = max of atoms/proc or total atoms, times 2, at least 1000

			int nper = static_cast<int> (natoms/comm->nprocs);
			map_nhash = MAX(nper,nmax);
			if (map_nhash > natoms) map_nhash = static_cast<int> (natoms);
			if (comm->nprocs > 1) map_nhash *= 2;
			map_nhash = MAX(map_nhash,1000);

			// map_nbucket = prime just larger than map_nhash

			int n = map_nhash/10000;
			n = MIN(n,nprimes-1);
			map_nbucket = primes[n];
			if (map_nbucket < map_nhash && n < nprimes-1) map_nbucket = primes[n+1];

			// set all buckets to empty
			// set hash to map_nhash in length
			// put all hash entries in free list and point them to each other

			map_bucket = new int[map_nbucket];
			for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1;

			map_hash = new HashElem[map_nhash];
			map_nused = 0;
			map_free = 0;
			for (int i = 0; i < map_nhash; i++) map_hash[i].next = i+1;
			map_hash[map_nhash-1].next = -1;
			}
			}

			/* ----------------------------------------------------------------------
			clear global -> local map for all of my own and ghost atoms
			for hash table option:
			global ID may not be in table if image atom was already cleared
			------------------------------------------------------------------------- */

			void Atom::map_clear()
			{
			if (map_style == 1) {
			int nall = nlocal + nghost;
			for (int i = 0; i < nall; i++) map_array[tag[i]] = -1;

			} else {
			int previous,global,ibucket,index;
			int nall = nlocal + nghost;
			for (int i = 0; i < nall; i++) {

			// search for key
			// if don't find it, done

			previous = -1;
			global = tag[i];
			ibucket = global % map_nbucket;
			index = map_bucket[ibucket];
			while (index > -1) {
			if (map_hash[index].global == global) break;
			previous = index;
			index = map_hash[index].next;
			}
			if (index == -1) continue;

			// delete the hash entry and add it to free list
			// special logic if entry is 1st in the bucket

			if (previous == -1) map_bucket[ibucket] = map_hash[index].next;
			else map_hash[previous].next = map_hash[index].next;

			map_hash[index].next = map_free;
			map_free = index;
			map_nused--;
			}
			}
			}

			/* ----------------------------------------------------------------------
			set global -> local map for all of my own and ghost atoms
			loop in reverse order so that nearby images take precedence over far ones
			and owned atoms take precedence over images
			this enables valid lookups of bond topology atoms
			for hash table option:
			if hash table too small, re-init
			global ID may already be in table if image atom was set
			------------------------------------------------------------------------- */

			void Atom::map_set()
			{
			if (map_style == 1) {
			int nall = nlocal + nghost;
			for (int i = nall-1; i >= 0 ; i--) map_array[tag[i]] = i;

			} else {
			int previous,global,ibucket,index;
			int nall = nlocal + nghost;
			if (nall > map_nhash) map_init();

			for (int i = nall-1; i >= 0 ; i--) {

			// search for key
			// if found it, just overwrite local value with index

			previous = -1;
			global = tag[i];
			ibucket = global % map_nbucket;
			index = map_bucket[ibucket];
			while (index > -1) {
			if (map_hash[index].global == global) break;
			previous = index;
			index = map_hash[index].next;
			}
			if (index > -1) {
			map_hash[index].local = i;
			continue;
			}

			// take one entry from free list
			// add the new global/local pair as entry at end of bucket list
			// special logic if this entry is 1st in bucket

			index = map_free;
			map_free = map_hash[map_free].next;
			if (previous == -1) map_bucket[ibucket] = index;
			else map_hash[previous].next = index;
			map_hash[index].global = global;
			map_hash[index].local = i;
			map_hash[index].next = -1;
			map_nused++;
			}
			}
			}

			/* ----------------------------------------------------------------------
			set global to local map for one atom
			for hash table option:
			global ID may already be in table if atom was already set
			------------------------------------------------------------------------- */

			void Atom::map_one(int global, int local)
			{
			if (map_style == 1) map_array[global] = local;

			else {
			// search for key
			// if found it, just overwrite local value with index

			int previous = -1;
			int ibucket = global % map_nbucket;
			int index = map_bucket[ibucket];
			while (index > -1) {
			if (map_hash[index].global == global) break;
			previous = index;
			index = map_hash[index].next;
			}
			if (index > -1) {
			map_hash[index].local = local;
			return;
			}

			// take one entry from free list
			// add the new global/local pair as entry at end of bucket list
			// special logic if this entry is 1st in bucket

			index = map_free;
			map_free = map_hash[map_free].next;
			if (previous == -1) map_bucket[ibucket] = index;
			else map_hash[previous].next = index;
			map_hash[index].global = global;
			map_hash[index].local = local;
			map_hash[index].next = -1;
			map_nused++;
			}
			}

			/* ----------------------------------------------------------------------
			free the array or hash table for global to local mapping
			------------------------------------------------------------------------- */

			void Atom::map_delete()
			{
			if (map_style == 1) {
			if (map_tag_max) memory->destroy(map_array);
			} else {
			if (map_nhash) {
			delete [] map_bucket;
			delete [] map_hash;
			}
			map_nhash = 0;
			}
			map_tag_max = 0;
			}

			/* ----------------------------------------------------------------------
			lookup global ID in hash table, return local index
			------------------------------------------------------------------------- */

			int Atom::map_find_hash(int global)
			{
			int local = -1;
			int index = map_bucket[global % map_nbucket];
			while (index > -1) {
			if (map_hash[index].global == global) {
			local = map_hash[index].local;
			break;
			}
			index = map_hash[index].next;
			}
			return local;
			}

			/* ----------------------------------------------------------------------
			add unique tags to any atoms with tag = 0
			new tags are grouped by proc and start after max current tag
			called after creating new atoms
			------------------------------------------------------------------------- */

			void Atom::tag_extend()
			{
			// maxtag_all = max tag for all atoms

			int maxtag = 0;
			for (int i = 0; i < nlocal; i++) maxtag = MAX(maxtag,tag[i]);
			int maxtag_all;
			MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_INT,MPI_MAX,world);

			// notag = # of atoms I own with no tag (tag = 0)
			// notag_sum = # of total atoms on procs <= me with no tag

			int notag = 0;
			for (int i = 0; i < nlocal; i++) if (tag[i] == 0) notag++;
			int notag_sum;
			MPI_Scan(&notag,&notag_sum,1,MPI_INT,MPI_SUM,world);

			// itag = 1st new tag that my untagged atoms should use

			int itag = maxtag_all + notag_sum - notag + 1;
			for (int i = 0; i < nlocal; i++) if (tag[i] == 0) tag[i] = itag++;
			}

			/* ----------------------------------------------------------------------
			check that atom IDs span range from 1 to Natoms
			return 0 if mintag != 1 or maxtag != Natoms
			return 1 if OK
			doesn't actually check if all tag values are used
			------------------------------------------------------------------------- */

			int Atom::tag_consecutive()
			{
			int idmin = static_cast<int> (natoms);
			int idmax = 0;

			for (int i = 0; i < nlocal; i++) {
			idmin = MIN(idmin,tag[i]);
			idmax = MAX(idmax,tag[i]);
			}
			int idminall,idmaxall;
			MPI_Allreduce(&idmin,&idminall,1,MPI_INT,MPI_MIN,world);
			MPI_Allreduce(&idmax,&idmaxall,1,MPI_INT,MPI_MAX,world);

			if (idminall != 1 \|\| idmaxall != static_cast<int> (natoms)) return 0;
			return 1;
			}

			/* ----------------------------------------------------------------------
			count and return words in a single line
			make copy of line before using strtok so as not to change line
			trim anything from '#' onward
			------------------------------------------------------------------------- */

			int Atom::count_words(const char *line)
			{
			int n = strlen(line) + 1;
			char *copy;
			memory->create(copy,n,"atom:copy");
			strcpy(copy,line);

			char *ptr;
			if (ptr = strchr(copy,'#')) *ptr = '\0';

			if (strtok(copy," \t\n\r\f") == NULL) {
			memory->destroy(copy);
			return 0;
			}
			n = 1;
			while (strtok(NULL," \t\n\r\f")) n++;

			memory->destroy(copy);
			return n;
			}

			/* ----------------------------------------------------------------------
			unpack n lines from Atom section of data file
			call style-specific routine to parse line
			------------------------------------------------------------------------- */

			void Atom::data_atoms(int n, char *buf)
			{
			int m,imagedata,xptr,iptr;
			double xdata[3],lamda[3],sublo[3],subhi[3];
			double *coord;
			char *next;

			next = strchr(buf,'\n');
			*next = '\0';
			int nwords = count_words(buf);
			*next = '\n';

			if (nwords != avec->size_data_atom && nwords != avec->size_data_atom + 3)
			error->all("Incorrect atom format in data file");

			char *values = new char[nwords];

			// set bounds for my proc
			// if periodic and I am lo/hi proc, adjust bounds by EPSILON
			// insures all data atoms will be owned even with round-off

			int triclinic = domain->triclinic;
			if (triclinic == 0) {
			sublo[0] = domain->sublo[0]; subhi[0] = domain->subhi[0];
			sublo[1] = domain->sublo[1]; subhi[1] = domain->subhi[1];
			sublo[2] = domain->sublo[2]; subhi[2] = domain->subhi[2];
			} else {
			sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
			sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
			sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
			}

			if (domain->xperiodic) {
			if (comm->myloc[0] == 0) sublo[0] -= EPSILON;
			if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += EPSILON;
			}
			if (domain->yperiodic) {
			if (comm->myloc[1] == 0) sublo[1] -= EPSILON;
			if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += EPSILON;
			}
			if (domain->zperiodic) {
			if (comm->myloc[2] == 0) sublo[2] -= EPSILON;
			if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += EPSILON;
			}

			// xptr = which word in line starts xyz coords
			// iptr = which word in line starts ix,iy,iz image flags

			xptr = avec->xcol_data - 1;
			int imageflag = 0;
			if (nwords > avec->size_data_atom) imageflag = 1;
			if (imageflag) iptr = nwords - 3;

			// loop over lines of atom data
			// tokenize the line into values
			// extract xyz coords and image flags
			// remap atom into simulation box
			// if atom is in my sub-domain, unpack its values

			for (int i = 0; i < n; i++) {
			next = strchr(buf,'\n');

			values[0] = strtok(buf," \t\n\r\f");
			for (m = 1; m < nwords; m++)
			values[m] = strtok(NULL," \t\n\r\f");

			if (imageflag)
			imagedata = ((atoi(values[iptr+2]) + 512 & 1023) << 20) \|
			((atoi(values[iptr+1]) + 512 & 1023) << 10) \|
			(atoi(values[iptr]) + 512 & 1023);
			else imagedata = (512 << 20) \| (512 << 10) \| 512;

			xdata[0] = atof(values[xptr]);
			xdata[1] = atof(values[xptr+1]);
			xdata[2] = atof(values[xptr+2]);
			domain->remap(xdata,imagedata);
			if (triclinic) {
			domain->x2lamda(xdata,lamda);
			coord = lamda;
			} else coord = xdata;

			if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
			coord[1] >= sublo[1] && coord[1] < subhi[1] &&
			coord[2] >= sublo[2] && coord[2] < subhi[2])
			avec->data_atom(xdata,imagedata,values);

			buf = next + 1;
			}

			delete [] values;
			}

			/* ----------------------------------------------------------------------
			unpack n lines from Velocity section of data file
			check that atom IDs are > 0 and <= map_tag_max
			call style-specific routine to parse line
			------------------------------------------------------------------------- */

			void Atom::data_vels(int n, char *buf)
			{
			int j,m,tagdata;
			char *next;

			next = strchr(buf,'\n');
			*next = '\0';
			int nwords = count_words(buf);
			*next = '\n';

			if (nwords != avec->size_data_vel)
			error->all("Incorrect velocity format in data file");

			char *values = new char[nwords];

			// loop over lines of atom velocities
			// tokenize the line into values
			// if I own atom tag, unpack its values

			for (int i = 0; i < n; i++) {
			next = strchr(buf,'\n');

			values[0] = strtok(buf," \t\n\r\f");
			for (j = 1; j < nwords; j++)
			values[j] = strtok(NULL," \t\n\r\f");

			tagdata = atoi(values[0]);
			if (tagdata <= 0 \|\| tagdata > map_tag_max)
			error->one("Invalid atom ID in Velocities section of data file");
			if ((m = map(tagdata)) >= 0) avec->data_vel(m,&values[1]);

			buf = next + 1;
			}

			delete [] values;
			}

			/* ----------------------------------------------------------------------
			check that atom IDs are > 0 and <= map_tag_max
			------------------------------------------------------------------------- */

			void Atom::data_bonds(int n, char *buf)
			{
			int m,tmp,itype,atom1,atom2;
			char *next;
			int newton_bond = force->newton_bond;

			for (int i = 0; i < n; i++) {
			next = strchr(buf,'\n');
			*next = '\0';
			sscanf(buf,"%d %d %d %d",&tmp,&itype,&atom1,&atom2);
			if (atom1 <= 0 \|\| atom1 > map_tag_max \|\|
			atom2 <= 0 \|\| atom2 > map_tag_max)
			error->one("Invalid atom ID in Bonds section of data file");
			if (itype <= 0 \|\| itype > nbondtypes)
			error->one("Invalid bond type in Bonds section of data file");
			if ((m = map(atom1)) >= 0) {
			bond_type[m][num_bond[m]] = itype;
			bond_atom[m][num_bond[m]] = atom2;
			num_bond[m]++;
			}
			if (newton_bond == 0) {
			if ((m = map(atom2)) >= 0) {
			bond_type[m][num_bond[m]] = itype;
			bond_atom[m][num_bond[m]] = atom1;
			num_bond[m]++;
			}
			}
			buf = next + 1;
			}
			}

			/* ----------------------------------------------------------------------
			check that atom IDs are > 0 and <= map_tag_max
			------------------------------------------------------------------------- */

			void Atom::data_angles(int n, char *buf)
			{
			int m,tmp,itype,atom1,atom2,atom3;
			char *next;
			int newton_bond = force->newton_bond;

			for (int i = 0; i < n; i++) {
			next = strchr(buf,'\n');
			*next = '\0';
			sscanf(buf,"%d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3);
			if (atom1 <= 0 \|\| atom1 > map_tag_max \|\|
			atom2 <= 0 \|\| atom2 > map_tag_max \|\|
			atom3 <= 0 \|\| atom3 > map_tag_max)
			error->one("Invalid atom ID in Angles section of data file");
			if (itype <= 0 \|\| itype > nangletypes)
			error->one("Invalid angle type in Angles section of data file");
			if ((m = map(atom2)) >= 0) {
			angle_type[m][num_angle[m]] = itype;
			angle_atom1[m][num_angle[m]] = atom1;
			angle_atom2[m][num_angle[m]] = atom2;
			angle_atom3[m][num_angle[m]] = atom3;
			num_angle[m]++;
			}
			if (newton_bond == 0) {
			if ((m = map(atom1)) >= 0) {
			angle_type[m][num_angle[m]] = itype;
			angle_atom1[m][num_angle[m]] = atom1;
			angle_atom2[m][num_angle[m]] = atom2;
			angle_atom3[m][num_angle[m]] = atom3;
			num_angle[m]++;
			}
			if ((m = map(atom3)) >= 0) {
			angle_type[m][num_angle[m]] = itype;
			angle_atom1[m][num_angle[m]] = atom1;
			angle_atom2[m][num_angle[m]] = atom2;
			angle_atom3[m][num_angle[m]] = atom3;
			num_angle[m]++;
			}
			}
			buf = next + 1;
			}
			}

			/* ----------------------------------------------------------------------
			check that atom IDs are > 0 and <= map_tag_max
			------------------------------------------------------------------------- */

			void Atom::data_dihedrals(int n, char *buf)
			{
			int m,tmp,itype,atom1,atom2,atom3,atom4;
			char *next;
			int newton_bond = force->newton_bond;

			for (int i = 0; i < n; i++) {
			next = strchr(buf,'\n');
			*next = '\0';
			sscanf(buf,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
			if (atom1 <= 0 \|\| atom1 > map_tag_max \|\|
			atom2 <= 0 \|\| atom2 > map_tag_max \|\|
			atom3 <= 0 \|\| atom3 > map_tag_max \|\|
			atom4 <= 0 \|\| atom4 > map_tag_max)
			error->one("Invalid atom ID in Dihedrals section of data file");
			if (itype <= 0 \|\| itype > ndihedraltypes)
			error->one("Invalid dihedral type in Dihedrals section of data file");
			if ((m = map(atom2)) >= 0) {
			dihedral_type[m][num_dihedral[m]] = itype;
			dihedral_atom1[m][num_dihedral[m]] = atom1;
			dihedral_atom2[m][num_dihedral[m]] = atom2;
			dihedral_atom3[m][num_dihedral[m]] = atom3;
			dihedral_atom4[m][num_dihedral[m]] = atom4;
			num_dihedral[m]++;
			}
			if (newton_bond == 0) {
			if ((m = map(atom1)) >= 0) {
			dihedral_type[m][num_dihedral[m]] = itype;
			dihedral_atom1[m][num_dihedral[m]] = atom1;
			dihedral_atom2[m][num_dihedral[m]] = atom2;
			dihedral_atom3[m][num_dihedral[m]] = atom3;
			dihedral_atom4[m][num_dihedral[m]] = atom4;
			num_dihedral[m]++;
			}
			if ((m = map(atom3)) >= 0) {
			dihedral_type[m][num_dihedral[m]] = itype;
			dihedral_atom1[m][num_dihedral[m]] = atom1;
			dihedral_atom2[m][num_dihedral[m]] = atom2;
			dihedral_atom3[m][num_dihedral[m]] = atom3;
			dihedral_atom4[m][num_dihedral[m]] = atom4;
			num_dihedral[m]++;
			}
			if ((m = map(atom4)) >= 0) {
			dihedral_type[m][num_dihedral[m]] = itype;
			dihedral_atom1[m][num_dihedral[m]] = atom1;
			dihedral_atom2[m][num_dihedral[m]] = atom2;
			dihedral_atom3[m][num_dihedral[m]] = atom3;
			dihedral_atom4[m][num_dihedral[m]] = atom4;
			num_dihedral[m]++;
			}
			}
			buf = next + 1;
			}
			}

			/* ----------------------------------------------------------------------
			check that atom IDs are > 0 and <= map_tag_max
			------------------------------------------------------------------------- */

			void Atom::data_impropers(int n, char *buf)
			{
			int m,tmp,itype,atom1,atom2,atom3,atom4;
			char *next;
			int newton_bond = force->newton_bond;

			for (int i = 0; i < n; i++) {
			next = strchr(buf,'\n');
			*next = '\0';
			sscanf(buf,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
			if (atom1 <= 0 \|\| atom1 > map_tag_max \|\|
			atom2 <= 0 \|\| atom2 > map_tag_max \|\|
			atom3 <= 0 \|\| atom3 > map_tag_max \|\|
			atom4 <= 0 \|\| atom4 > map_tag_max)
			error->one("Invalid atom ID in Impropers section of data file");
			if (itype <= 0 \|\| itype > nimpropertypes)
			error->one("Invalid improper type in Impropers section of data file");
			if ((m = map(atom2)) >= 0) {
			improper_type[m][num_improper[m]] = itype;
			improper_atom1[m][num_improper[m]] = atom1;
			improper_atom2[m][num_improper[m]] = atom2;
			improper_atom3[m][num_improper[m]] = atom3;
			improper_atom4[m][num_improper[m]] = atom4;
			num_improper[m]++;
			}
			if (newton_bond == 0) {
			if ((m = map(atom1)) >= 0) {
			improper_type[m][num_improper[m]] = itype;
			improper_atom1[m][num_improper[m]] = atom1;
			improper_atom2[m][num_improper[m]] = atom2;
			improper_atom3[m][num_improper[m]] = atom3;
			improper_atom4[m][num_improper[m]] = atom4;
			num_improper[m]++;
			}
			if ((m = map(atom3)) >= 0) {
			improper_type[m][num_improper[m]] = itype;
			improper_atom1[m][num_improper[m]] = atom1;
			improper_atom2[m][num_improper[m]] = atom2;
			improper_atom3[m][num_improper[m]] = atom3;
			improper_atom4[m][num_improper[m]] = atom4;
			num_improper[m]++;
			}
			if ((m = map(atom4)) >= 0) {
			improper_type[m][num_improper[m]] = itype;
			improper_atom1[m][num_improper[m]] = atom1;
			improper_atom2[m][num_improper[m]] = atom2;
			improper_atom3[m][num_improper[m]] = atom3;
			improper_atom4[m][num_improper[m]] = atom4;
			num_improper[m]++;
			}
			}
			buf = next + 1;
			}
			}

			/* ----------------------------------------------------------------------
			allocate arrays of length ntypes
			only done after ntypes is set
			------------------------------------------------------------------------- */

			void Atom::allocate_type_arrays()
			{
			if (avec->mass_type) {
			mass = new double[ntypes+1];
			mass_setflag = new int[ntypes+1];
			for (int itype = 1; itype <= ntypes; itype++) mass_setflag[itype] = 0;
			}
			if (avec->shape_type) {
			memory->create(shape,ntypes+1,3,"atom:shape");
			shape_setflag = new int[ntypes+1];
			for (int itype = 1; itype <= ntypes; itype++) shape_setflag[itype] = 0;
			}
			if (avec->dipole_type) {
			dipole = new double[ntypes+1];
			dipole_setflag = new int[ntypes+1];
			for (int itype = 1; itype <= ntypes; itype++) dipole_setflag[itype] = 0;
			}
			}

			/* ----------------------------------------------------------------------
			set a mass and flag it as set
			called from reading of data file
			------------------------------------------------------------------------- */

			void Atom::set_mass(const char *str)
			{
			if (mass == NULL) error->all("Cannot set mass for this atom style");

			int itype;
			double mass_one;
			int n = sscanf(str,"%d %lg",&itype,&mass_one);
			if (n != 2) error->all("Invalid mass line in data file");

			if (itype < 1 \|\| itype > ntypes) error->all("Invalid type for mass set");

			mass[itype] = mass_one;
			mass_setflag[itype] = 1;

			if (mass[itype] <= 0.0) error->all("Invalid mass value");
			}

			/* ----------------------------------------------------------------------
			set a mass and flag it as set
			called from EAM pair routine
			------------------------------------------------------------------------- */

			void Atom::set_mass(int itype, double value)
			{
			if (mass == NULL) error->all("Cannot set mass for this atom style");
			if (itype < 1 \|\| itype > ntypes) error->all("Invalid type for mass set");

			mass[itype] = value;
			mass_setflag[itype] = 1;

			if (mass[itype] <= 0.0) error->all("Invalid mass value");
			}

			/* ----------------------------------------------------------------------
			set one or more masses and flag them as set
			called from reading of input script
			------------------------------------------------------------------------- */

			void Atom::set_mass(int narg, char **arg)
			{
			if (mass == NULL) error->all("Cannot set mass for this atom style");

			int lo,hi;
			force->bounds(arg[0],ntypes,lo,hi);
			if (lo < 1 \|\| hi > ntypes) error->all("Invalid type for mass set");

			for (int itype = lo; itype <= hi; itype++) {
			mass[itype] = atof(arg[1]);
			mass_setflag[itype] = 1;

			if (mass[itype] <= 0.0) error->all("Invalid mass value");
			}
			}

			/* ----------------------------------------------------------------------
			set all masses as read in from restart file
			------------------------------------------------------------------------- */

			void Atom::set_mass(double *values)
			{
			for (int itype = 1; itype <= ntypes; itype++) {
			mass[itype] = values[itype];
			mass_setflag[itype] = 1;
			}
			}

			/* ----------------------------------------------------------------------
			check that all masses have been set
			------------------------------------------------------------------------- */

			void Atom::check_mass()
			{
			if (mass == NULL) return;
			for (int itype = 1; itype <= ntypes; itype++)
			if (mass_setflag[itype] == 0) error->all("All masses are not set");
			}

			/* ----------------------------------------------------------------------
			set particle shape and flag it as set
			called from reading of data file
			------------------------------------------------------------------------- */

			void Atom::set_shape(const char *str)
			{
			if (shape == NULL) error->all("Cannot set shape for this atom style");

			int itype;
			double a,b,c;
			int n = sscanf(str,"%d %lg %lg %lg",&itype,&a,&b,&c);
			if (n != 4) error->all("Invalid shape line in data file");

			if (itype < 1 \|\| itype > ntypes) error->all("Invalid type for shape set");

			// store shape as radius, though specified as diameter

			shape[itype][0] = 0.5*a;
			shape[itype][1] = 0.5*b;
			shape[itype][2] = 0.5*c;
			shape_setflag[itype] = 1;

			if (shape[itype][0] < 0.0 \|\| shape[itype][1] < 0.0 \|\|
			shape[itype][2] < 0.0)
			error->all("Invalid shape value");
			if (shape[itype][0] > 0.0 \|\| shape[itype][1] > 0.0 \|\|
			shape[itype][2] > 0.0) {
			if (shape[itype][0] == 0.0 \|\| shape[itype][1] == 0.0 \|\|
			shape[itype][2] == 0.0)
			error->all("Invalid shape value");
			}
			}

			/* ----------------------------------------------------------------------
			set one or more particle shapes and flag them as set
			called from reading of input script
			------------------------------------------------------------------------- */

			void Atom::set_shape(int narg, char **arg)
			{
			if (shape == NULL) error->all("Cannot set shape for this atom style");

			int lo,hi;
			force->bounds(arg[0],ntypes,lo,hi);
			if (lo < 1 \|\| hi > ntypes)
			error->all("Invalid type for shape set");

			// store shape as radius, though specified as diameter

			for (int itype = lo; itype <= hi; itype++) {
			shape[itype][0] = 0.5*atof(arg[1]);
			shape[itype][1] = 0.5*atof(arg[2]);
			shape[itype][2] = 0.5*atof(arg[3]);
			shape_setflag[itype] = 1;

			if (shape[itype][0] < 0.0 \|\| shape[itype][1] < 0.0 \|\|
			shape[itype][2] < 0.0)
			error->all("Invalid shape value");
			if (shape[itype][0] > 0.0 \|\| shape[itype][1] > 0.0 \|\|
			shape[itype][2] > 0.0) {
			if (shape[itype][0] == 0.0 \|\| shape[itype][1] == 0.0 \|\|
			shape[itype][2] == 0.0)
			error->all("Invalid shape value");
			}
			}
			}

			/* ----------------------------------------------------------------------
			set all particle shapes as read in from restart file
			------------------------------------------------------------------------- */

			void Atom::set_shape(double **values)
			{
			for (int itype = 1; itype <= ntypes; itype++) {
			shape[itype][0] = values[itype][0];
			shape[itype][1] = values[itype][1];
			shape[itype][2] = values[itype][2];
			shape_setflag[itype] = 1;
			}
			}

			/* ----------------------------------------------------------------------
			check that all particle shapes have been set
			------------------------------------------------------------------------- */

			void Atom::check_shape()
			{
			if (shape == NULL) return;
			for (int itype = 1; itype <= ntypes; itype++)
			if (shape_setflag[itype] == 0) error->all("All shapes are not set");
			}

			/* ----------------------------------------------------------------------
			set a dipole moment and flag it as set
			called from reading of data file
			------------------------------------------------------------------------- */

			void Atom::set_dipole(const char *str)
			{
			if (dipole == NULL) error->all("Cannot set dipole for this atom style");

			int itype;
			double dipole_one;
			int n = sscanf(str,"%d %lg",&itype,&dipole_one);
			if (n != 2) error->all("Invalid dipole line in data file");

			dipole[itype] = dipole_one;
			dipole_setflag[itype] = 1;

			if (dipole[itype] < 0.0) error->all("Invalid dipole value");
			}

			/* ----------------------------------------------------------------------
			set one or more dipole moments and flag them as set
			called from reading of input script
			------------------------------------------------------------------------- */

			void Atom::set_dipole(int narg, char **arg)
			{
			if (dipole == NULL) error->all("Cannot set dipole for this atom style");

			int lo,hi;
			force->bounds(arg[0],ntypes,lo,hi);
			if (lo < 1 \|\| hi > ntypes) error->all("Invalid type for dipole set");

			for (int itype = lo; itype <= hi; itype++) {
			dipole[itype] = atof(arg[1]);
			dipole_setflag[itype] = 1;

			if (dipole[itype] < 0.0) error->all("Invalid dipole value");
			}
			}

			/* ----------------------------------------------------------------------
			set all dipole moments as read in from restart file
			------------------------------------------------------------------------- */

			void Atom::set_dipole(double *values)
			{
			for (int itype = 1; itype <= ntypes; itype++) {
			dipole[itype] = values[itype];
			dipole_setflag[itype] = 1;
			}
			}

			/* ----------------------------------------------------------------------
			check that all dipole moments have been set
			------------------------------------------------------------------------- */

			void Atom::check_dipole()
			{
			if (dipole == NULL) return;
			for (int itype = 1; itype <= ntypes; itype++)
			if (dipole_setflag[itype] == 0)
			error->all("All dipole moments are not set");
			}

			/* ----------------------------------------------------------------------
			reorder owned atoms so those in firstgroup appear first
			called by comm->exchange() if atom_modify first group is set
			only owned atoms exist at this point, no ghost atoms
			------------------------------------------------------------------------- */

			void Atom::first_reorder()
			{
			// insure there is one extra atom location at end of arrays for swaps

			if (nlocal == nmax) avec->grow(0);

			// loop over owned atoms
			// nfirst = index of first atom not in firstgroup
			// when find firstgroup atom out of place, swap it with atom nfirst

			int bitmask = group->bitmask[firstgroup];
			nfirst = 0;
			while (nfirst < nlocal && mask[nfirst] & bitmask) nfirst++;

			for (int i = 0; i < nlocal; i++) {
			if (mask[i] & bitmask && i > nfirst) {
			avec->copy(i,nlocal);
			avec->copy(nfirst,i);
			avec->copy(nlocal,nfirst);
			while (nfirst < nlocal && mask[nfirst] & bitmask) nfirst++;
			}
			}
			}

			/* ----------------------------------------------------------------------
			perform spatial sort of atoms within my sub-domain
			always called between comm->exchange() and comm->borders()
			don't have to worry about clearing/setting atom->map since done in comm
			------------------------------------------------------------------------- */

			void Atom::sort()
			{
			int i,m,n,ix,iy,iz,ibin,empty;

			// re-setup sort bins if needed

			if (domain->box_change) setup_sort_bins();
			if (nbins == 1) return;

			// reallocate per-atom vectors if needed

			if (nlocal > maxnext) {
			memory->destroy(next);
			memory->destroy(permute);
			maxnext = atom->nmax;
			memory->create(next,maxnext,"atom:next");
			memory->create(permute,maxnext,"atom:permute");
			}

			// insure there is one extra atom location at end of arrays for swaps

			if (nlocal == nmax) avec->grow(0);

			// bin atoms in reverse order so linked list will be in forward order

			for (i = 0; i < nbins; i++) binhead[i] = -1;

			for (i = nlocal-1; i >= 0; i--) {
			ix = static_cast<int> ((x[i][0]-bboxlo[0])*bininvx);
			iy = static_cast<int> ((x[i][1]-bboxlo[1])*bininvy);
			iz = static_cast<int> ((x[i][2]-bboxlo[2])*bininvz);
			ix = MAX(ix,0);
			iy = MAX(iy,0);
			iz = MAX(iz,0);
			ix = MIN(ix,nbinx-1);
			iy = MIN(iy,nbiny-1);
			iz = MIN(iz,nbinz-1);
			ibin = iznbinynbinx + iy*nbinx + ix;
			next[i] = binhead[ibin];
			binhead[ibin] = i;
			}

			// permute = desired permutation of atoms
			// permute[I] = J means Ith new atom will be Jth old atom

			n = 0;
			for (m = 0; m < nbins; m++) {
			i = binhead[m];
			while (i >= 0) {
			permute[n++] = i;
			i = next[i];
			}
			}

			// current = current permutation, just reuse next vector
			// current[I] = J means Ith current atom is Jth old atom

			int *current = next;
			for (i = 0; i < nlocal; i++) current[i] = i;

			// reorder local atom list, when done, current = permute
			// perform "in place" using copy() to extra atom location at end of list
			// inner while loop processes one cycle of the permutation
			// copy before inner-loop moves an atom to end of atom list
			// copy after inner-loop moves atom at end of list back into list
			// empty = location in atom list that is currently empty

			for (i = 0; i < nlocal; i++) {
			if (current[i] == permute[i]) continue;
			avec->copy(i,nlocal);
			empty = i;
			while (permute[empty] != i) {
			avec->copy(permute[empty],empty);
			empty = current[empty] = permute[empty];
			}
			avec->copy(nlocal,empty);
			current[empty] = permute[empty];
			}

			// sanity check that current = permute

			//int flag = 0;
			//for (i = 0; i < nlocal; i++)
			// if (current[i] != permute[i]) flag = 1;
			//int flagall;
			//MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
			//if (flagall) error->all("Atom sort did not operate correctly");

			// set next timestep for sorting to take place

			nextsort = (update->ntimestep/sortfreq)*sortfreq + sortfreq;
			}

			/* ----------------------------------------------------------------------
			setup bins for spatial sorting of atoms
			------------------------------------------------------------------------- */

			void Atom::setup_sort_bins()
			{
			// binsize = user setting or 1/2 of neighbor cutoff
			// neighbor cutoff can be 0.0

			double binsize;
			if (userbinsize > 0.0) binsize = userbinsize;
			else binsize = 0.5 * neighbor->cutneighmax;
			if (binsize == 0.0) error->all("Atom sorting has bin size = 0.0");

			double bininv = 1.0/binsize;

			// nbin xyz = local bins
			// bbox lo/hi = bounding box of my sub-domain

			if (domain->triclinic)
			domain->bbox(domain->sublo_lamda,domain->subhi_lamda,bboxlo,bboxhi);
			else {
			bboxlo[0] = domain->sublo[0];
			bboxlo[1] = domain->sublo[1];
			bboxlo[2] = domain->sublo[2];
			bboxhi[0] = domain->subhi[0];
			bboxhi[1] = domain->subhi[1];
			bboxhi[2] = domain->subhi[2];
			}

			nbinx = static_cast<int> ((bboxhi[0]-bboxlo[0]) * bininv);
			nbiny = static_cast<int> ((bboxhi[1]-bboxlo[1]) * bininv);
			nbinz = static_cast<int> ((bboxhi[2]-bboxlo[2]) * bininv);
			if (domain->dimension == 2) nbinz = 1;

			if (nbinx == 0) nbinx = 1;
			if (nbiny == 0) nbiny = 1;
			if (nbinz == 0) nbinz = 1;

			bininvx = nbinx / (bboxhi[0]-bboxlo[0]);
			bininvy = nbiny / (bboxhi[1]-bboxlo[1]);
			bininvz = nbinz / (bboxhi[2]-bboxlo[2]);

			if (1.0nbinxnbiny*nbinz > INT_MAX)
			error->one("Too many atom sorting bins");

			nbins = nbinxnbinynbinz;

			// reallocate per-bin memory if needed

			if (nbins > maxbin) {
			memory->destroy(binhead);
			maxbin = nbins;
			memory->create(binhead,maxbin,"atom:binhead");
			}
			}

			/* ----------------------------------------------------------------------
			register a callback to a fix so it can manage atom-based arrays
			happens when fix is created
			flag = 0 for grow, 1 for restart
			------------------------------------------------------------------------- */

			void Atom::add_callback(int flag)
			{
			int ifix;

			// find the fix
			// if find NULL ptr:
			// it's this one, since it is being replaced and has just been deleted
			// at this point in re-creation
			// if don't find NULL ptr:
			// i is set to nfix = new one currently being added at end of list

			for (ifix = 0; ifix < modify->nfix; ifix++)
			if (modify->fix[ifix] == NULL) break;

			// add callback to lists, reallocating if necessary

			if (flag == 0) {
			if (nextra_grow == nextra_grow_max) {
			nextra_grow_max += DELTA;
			memory->grow(extra_grow,nextra_grow_max,"atom:extra_grow");
			}
			extra_grow[nextra_grow] = ifix;
			nextra_grow++;
			} else if (flag == 1) {
			if (nextra_restart == nextra_restart_max) {
			nextra_restart_max += DELTA;
			memory->grow(extra_restart,nextra_restart_max,"atom:extra_restart");
			}
			extra_restart[nextra_restart] = ifix;
			nextra_restart++;
			}
			}

			/* ----------------------------------------------------------------------
			unregister a callback to a fix
			happens when fix is deleted, called by its destructor
			flag = 0 for grow, 1 for restart
			------------------------------------------------------------------------- */

			void Atom::delete_callback(const char *id, int flag)
			{
			int ifix;
			for (ifix = 0; ifix < modify->nfix; ifix++)
			if (strcmp(id,modify->fix[ifix]->id) == 0) break;

			// compact the list of callbacks

			if (flag == 0) {
			int match;
			for (match = 0; match < nextra_grow; match++)
			if (extra_grow[match] == ifix) break;
			for (int i = match; i < nextra_grow-1; i++)
			extra_grow[i] = extra_grow[i+1];
			nextra_grow--;

			} else if (flag == 1) {
			int match;
			for (match = 0; match < nextra_grow; match++)
			if (extra_restart[match] == ifix) break;
			for (int i = ifix; i < nextra_restart-1; i++)
			extra_restart[i] = extra_restart[i+1];
			nextra_restart--;
			}
			}

			/* ----------------------------------------------------------------------
			decrement ptrs in callback lists to fixes beyond the deleted ifix
			happens after fix is deleted
			------------------------------------------------------------------------- */

			void Atom::update_callback(int ifix)
			{
			for (int i = 0; i < nextra_grow; i++)
			if (extra_grow[i] > ifix) extra_grow[i]--;
			for (int i = 0; i < nextra_restart; i++)
			if (extra_restart[i] > ifix) extra_restart[i]--;
			}

			/* ----------------------------------------------------------------------
			return a pointer to a named internal variable
			if don't recognize name, return NULL
			customize by adding names
			------------------------------------------------------------------------- */

			void Atom::extract(char name)
			{
			if (strcmp(name,"id") == 0) return (void *) tag;
			if (strcmp(name,"type") == 0) return (void *) type;
			if (strcmp(name,"x") == 0) return (void *) x;
			if (strcmp(name,"v") == 0) return (void *) v;
			if (strcmp(name,"f") == 0) return (void *) f;
			if (strcmp(name,"mass") == 0) return (void *) mass;
			if (strcmp(name,"rmass") == 0) return (void *) rmass;

			return NULL;
			}

			/* ----------------------------------------------------------------------
			return # of bytes of allocated memory
			call to avec tallies per-atom vectors
			add in global to local mapping storage
			------------------------------------------------------------------------- */

			double Atom::memory_usage()
			{
			memlength = DELTA_MEMSTR;
			memory->create(memstr,memlength,"atom:memstr");
			memstr[0] = '\0';

			double bytes = avec->memory_usage();
			if (map_style == 1)
			bytes += map_tag_max * sizeof(int);
			else if (map_style == 2) {
			bytes += map_nbucket*sizeof(int);
			bytes += map_nhash*sizeof(HashElem);
			}

			memory->destroy(memstr);
			return bytes;
			}

			/* ----------------------------------------------------------------------
			accumulate per-atom vec names in memstr, padded by spaces
			return 1 if padded str is not already in memlist, else 0
			------------------------------------------------------------------------- */

			int Atom::memcheck(const char *str)
			{
			int n = strlen(str) + 3;
			char *padded = new char[n];
			strcpy(padded," ");
			strcat(padded,str);
			strcat(padded," ");

			if (strstr(memstr,padded)) {
			delete [] padded;
			return 0;
			}

			if (strlen(memstr) + n >= memlength) {
			memlength += DELTA_MEMSTR;
			memory->grow(memstr,memlength,"atom:memstr");
			}

			strcat(memstr,padded);
			delete [] padded;
			return 1;
			}

lammps/src/atom.cpp8dad49156d20lammm-master-deprecated

atom.cppView Options

lammps/src/atom.cpp
8dad49156d20lammm-master-deprecated

atom.cpp
View Options