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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 LMP_ATOM_H
#define LMP_ATOM_H
#include "pointers.h"
namespace LAMMPS_NS {
class Atom : protected Pointers {
public:
char *atom_style;
class AtomVec *avec;
// atom counts
bigint natoms; // total # of atoms in system, could be 0
// natoms may not be current if atoms lost
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
bigint nbonds,nangles,ndihedrals,nimpropers;
int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
int extra_bond_per_atom;
int firstgroup; // store atoms in this group first, -1 if unset
int nfirst; // # of atoms in first group on this proc
char *firstgroupname; // group-ID to store first, NULL if unset
// per-atom arrays
// customize by adding new array
int *tag,*type,*mask,*image;
double **x,**v,**f;
int *molecule;
double *q,**mu;
double **omega,**angmom,**torque;
double *radius,*rmass,*vfrac,*s0;
double **x0;
int *ellipsoid,*line,*tri;
int *spin;
double *eradius,*ervel,*erforce,*ervelforce;
double *cs,*csforce,*vforce;
int *etag;
double *rho, *drho;
double *e, *de;
double **vest;
double *cv;
int **nspecial; // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs
int **special; // IDs of 1-2,1-3,1-4 neighs of each atom
int maxspecial; // special[nlocal][maxspecial]
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;
// atom style and per-atom array existence flags
// customize by adding new flag
int sphere_flag,ellipsoid_flag,line_flag,tri_flag,peri_flag,electron_flag;
int wavepacket_flag,sph_flag;
int molecule_flag,q_flag,mu_flag;
int rmass_flag,radius_flag,omega_flag,torque_flag,angmom_flag;
int vfrac_flag,spin_flag,eradius_flag,ervel_flag,erforce_flag;
int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag;
int rho_flag,e_flag,cv_flag,vest_flag;
// extra peratom info in restart file destined for fix & diag
double **extra;
// per-type arrays
double *mass;
int *mass_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
// spatial sorting of atoms
int sortfreq; // sort atoms every this many steps, 0 = off
bigint nextsort; // next timestep to sort on
// functions
Atom(class LAMMPS *);
~Atom();
void settings(class Atom *);
void create_avec(const char *, int, char **, char *suffix = NULL);
class AtomVec *new_avec(const char *, int, char **, char *, int &);
void init();
void setup();
class AtomVec *style_match(const char *);
void modify_params(int, char **);
void tag_extend();
int tag_consecutive();
int parse_data(const char *);
int count_words(const char *);
void data_atoms(int, char *);
void data_vels(int, char *);
void data_bonus(int, char *, class AtomVec *);
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(const char *);
void set_mass(int, double);
void set_mass(int, char **);
void set_mass(double *);
void check_mass();
int radius_consistency(int, double &);
int shape_consistency(int, double &, double &, double &);
void first_reorder();
void sort();
void add_callback(int);
void delete_callback(const char *, int);
void update_callback(int);
void *extract(char *);
inline int* get_map_array() {return map_array;};
inline int get_map_size() {return map_tag_max+1;};
bigint 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:
// 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
// spatial sorting of atoms
int nbins; // # of sorting bins
int nbinx,nbiny,nbinz; // bins in each dimension
int maxbin; // max # of bins
int maxnext; // max size of next,permute
int *binhead; // 1st atom in each bin
int *next; // next atom in bin
int *permute; // permutation vector
double userbinsize; // requested sort bin size
double bininvx,bininvy,bininvz; // inverse actual bin sizes
double bboxlo[3],bboxhi[3]; // bounding box of my sub-domain
int memlength; // allocated size of memstr
char *memstr; // string of array names already counted
void setup_sort_bins();
};
}
#endif
/* ERROR/WARNING messages:
E: Invalid atom style
The choice of atom style is unknown.
E: Could not find atom_modify first group ID
Self-explanatory.
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Atom_modify map command after simulation box is defined
The atom_modify map command cannot be used after a read_data,
read_restart, or create_box command.
E: Atom_modify sort and first options cannot be used together
Self-explanatory.
E: Cannot create an atom map unless atoms have IDs
The simulation requires a mapping from global atom IDs to local atoms,
but the atoms that have been defined have no IDs.
E: Incorrect atom format in data file
Number of values per atom line in the data file is not consistent with
the atom style.
E: Incorrect velocity format in data file
Each atom style defines a format for the Velocity section
of the data file. The read-in lines do not match.
E: Invalid atom ID in Velocities section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Incorrect bonus data format in data file
See the read_data doc page for a description of how various kinds of
bonus data must be formatted for certain atom styles.
E: Invalid atom ID in Bonus section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Invalid atom ID in Bonds section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Invalid bond type in Bonds section of data file
Bond type must be positive integer and within range of specified bond
types.
E: Invalid atom ID in Angles section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Invalid angle type in Angles section of data file
Angle type must be positive integer and within range of specified angle
types.
E: Invalid atom ID in Dihedrals section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Invalid dihedral type in Dihedrals section of data file
Dihedral type must be positive integer and within range of specified
dihedral types.
E: Invalid atom ID in Impropers section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Invalid improper type in Impropers section of data file
Improper type must be positive integer and within range of specified
improper types.
E: Cannot set mass for this atom style
This atom style does not support mass settings for each atom type.
Instead they are defined on a per-atom basis in the data file.
E: Invalid mass line in data file
Self-explanatory.
E: Invalid type for mass set
Mass command must set a type from 1-N where N is the number of atom
types.
E: Invalid mass value
Self-explanatory.
E: All masses are not set
For atom styles that define masses for each atom type, all masses must
be set in the data file or by the mass command before running a
simulation. They must also be set before using the velocity
command.
E: Atom sort did not operate correctly
This is an internal LAMMPS error. Please report it to the
developers.
E: Atom sorting has bin size = 0.0
The neighbor cutoff is being used as the bin size, but it is zero.
Thus you must explicitly list a bin size in the atom_modify sort
command or turn off sorting.
E: Too many atom sorting bins
This is likely due to an immense simulation box that has blown up
to a large size.
*/

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