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lammps/src/atom.h
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atom.h
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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.
------------------------------------------------------------------------- */
#ifndef ATOM_H
#define ATOM_H
#include "pointers.h"
namespace LAMMPS_NS {
class Atom : protected Pointers {
public:
char *atom_style;
class AtomVec *avec;
// atom counts
double natoms; // total # of atoms in system, could be 0
int nlocal,nghost; // # of owned and ghost atoms on this proc
int nmax; // max # of owned+ghost in arrays on this proc
int tag_enable; // 0/1 if atom ID tags are defined
int molecular; // 0 = atomic, 1 = molecular system
int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
int nbonds,nangles,ndihedrals,nimpropers;
int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
// per-atom arrays
// customize by adding new array
int *tag,*type,*mask,*image;
double **x,**v,**f;
int *molecule;
double *q,**mu;
double **xphi,**quat,**omega,**angmom,**torque;
double *radius,*density,*rmass,*vfrac;
int maxspecial;
int **nspecial,**special;
int *num_bond;
int **bond_type;
int **bond_atom;
int *num_angle;
int **angle_type;
int **angle_atom1,**angle_atom2,**angle_atom3;
int *num_dihedral;
int **dihedral_type;
int **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
int *num_improper;
int **improper_type;
int **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
// per-atom array existence flags
// customize by adding new flag
int molecule_flag;
int q_flag,mu_flag;
int xphi_flag,quat_flag,omega_flag,angmom_flag,torque_flag;
int radius_flag,density_flag,rmass_flag,vfrac_flag;
// extra peratom info in restart file destined for fix & diag
double **extra;
// per-type arrays
double *mass,**shape,*dipole;
int *mass_setflag,*shape_setflag,*dipole_setflag;
// callback ptrs for atom arrays managed by fix classes
int nextra_grow,nextra_restart; // # of callbacks of each type
int *extra_grow,*extra_restart; // index of fix to callback to
int nextra_grow_max,nextra_restart_max; // size of callback lists
int nextra_store;
int map_style; // default or user-specified style of map
// 0 = none, 1 = array, 2 = hash
// functions
Atom(class LAMMPS *);
~Atom();
void create_avec(char *, int, char **);
class AtomVec *new_avec(char *, int, char **);
void init();
int style_match(char *);
void modify_params(int, char **);
void tag_extend();
int tag_consecutive();
int parse_data(char *);
int count_words(char *);
void data_atoms(int, char *);
void data_vels(int, char *);
void data_bonds(int, char *);
void data_angles(int, char *);
void data_dihedrals(int, char *);
void data_impropers(int, char *);
void allocate_type_arrays();
void set_mass(char *);
void set_mass(int, double);
void set_mass(int, char **);
void set_mass(double *);
void check_mass();
void set_shape(char *);
void set_shape(int, char **);
void set_shape(double **);
void check_shape();
void set_dipole(char *);
void set_dipole(int, char **);
void set_dipole(double *);
void check_dipole();
void add_callback(int);
void delete_callback(char *, int);
void update_callback(int);
int memory_usage();
int memcheck(const char *);
// functions for global to local ID mapping
// map lookup function inlined for efficiency
inline int map(int global) {
if (map_style == 1) return map_array[global];
else return map_find_hash(global);
};
void map_init();
void map_clear();
void map_set();
void map_one(int, int);
void map_delete();
int map_find_hash(int);
private:
// data for global to local ID mapping
int map_tag_max;
int *map_array;
struct HashElem {
int global; // key to search on = global ID
int local; // value associated with key = local index
int next; // next entry in this bucket, -1 if last
};
int map_nhash; // # of entries hash table can hold
int map_nused; // # of actual entries in hash table
int map_free; // ptr to 1st unused entry in hash table
int map_nbucket; // # of hash buckets
int *map_bucket; // ptr to 1st entry in each bucket
HashElem *map_hash; // hash table
int *primes; // table of prime #s for hashing
int nprimes; // # of primes
int memlength; // allocated size of memstr
char *memstr; // string of array names already counted
};
}
#endif
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