/* -*- c++ -*- ---------------------------------------------------------- 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 = standard molecular system, // 2 = molecule template 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,extra_angle_per_atom; int extra_dihedral_per_atom,extra_improper_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 tagint *tag; int *type,*mask; imageint *image; double **x,**v,**f; tagint *molecule; int *molindex,*molatom; double *q,**mu; double **omega,**angmom,**torque; double *radius,*rmass; int *ellipsoid,*line,*tri,*body; // PERI package double *vfrac,*s0; double **x0; // USER-EFF and USER-AWPMD packages int *spin; double *eradius,*ervel,*erforce,*ervelforce; double *cs,*csforce,*vforce; int *etag; // USER-SPH package double *rho,*drho,*e,*de,*cv; double **vest; int **nspecial; // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs tagint **special; // IDs of 1-2,1-3,1-4 neighs of each atom int maxspecial; // special[nlocal][maxspecial] int *num_bond; int **bond_type; tagint **bond_atom; int *num_angle; int **angle_type; tagint **angle_atom1,**angle_atom2,**angle_atom3; int *num_dihedral; int **dihedral_type; tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4; int *num_improper; int **improper_type; tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4; // custom arrays used by fix property/atom int **ivector; double **dvector; char **iname,**dname; int nivector,ndvector; // used by USER-CUDA to flag used per-atom arrays unsigned int datamask; unsigned int datamask_ext; // atom style and per-atom array existence flags // customize by adding new flag int sphere_flag,ellipsoid_flag,line_flag,tri_flag,body_flag; int peri_flag,electron_flag; int ecp_flag; int wavepacket_flag,sph_flag; int molecule_flag,molindex_flag,molatom_flag; int 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; // variables for offsetting molecule template ids int type_offset; int bond_offset; int angle_offset; int di_offset; int imp_offset; int autospecial_mode; // Peridynamics scale factor, used by dump cfg double pdscale; // molecule templates // each template can be a set of consecutive molecules // each with same ID (stored in molecules) // 1st molecule in template stores nset = # in set int nmolecule; class Molecule **molecules; // 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,nextra_border; // # of callbacks of each type int *extra_grow,*extra_restart,*extra_border; // index of fix to callback to int nextra_grow_max,nextra_restart_max; // size of callback lists int nextra_border_max; int nextra_store; int map_style; // style of atom map: 0=none, 1=array, 2=hash int map_user; // user selected style = same 0,1,2 tagint map_tag_max; // max atom ID that map() is setup for // spatial sorting of atoms int sortfreq; // sort atoms every this many steps, 0 = off bigint nextsort; // next timestep to sort on // indices of atoms with same ID int *sametag; // sametag[I] = next atom with same ID, -1 if no more // functions Atom(class LAMMPS *); ~Atom(); void settings(class Atom *); void create_avec(const char *, int, char **, int); class AtomVec *new_avec(const char *, int, int &); void init(); void setup(); class AtomVec *style_match(const char *); void modify_params(int, char **); void tag_check(); void tag_extend(); int tag_consecutive(); int parse_data(const char *); int count_words(const char *); void deallocate_topology(); void data_atoms(int, char *); void data_vels(int, char *); void data_bonds(int, char *, int *); void data_angles(int, char *, int *); void data_dihedrals(int, char *, int *); void data_impropers(int, char *, int *); void data_bonus(int, char *, class AtomVec *); void data_bodies(int, char *, class AtomVecBody *); virtual 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 add_molecule(int, char **); int find_molecule(char *); void add_molecule_atom(class Molecule *, int, int, tagint); void first_reorder(); virtual void sort(); void add_callback(int); void delete_callback(const char *, int); void update_callback(int); int find_custom(char *, int &); int add_custom(char *, int); void remove_custom(int, int); virtual void sync_modify(ExecutionSpace, unsigned int, unsigned 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 // return -1 if no map defined inline int map(tagint global) { if (map_style == 1) return map_array[global]; else if (map_style == 2) return map_find_hash(global); else return -1; }; void map_init(int check = 1); void map_clear(); void map_set(); void map_one(tagint, int); int map_style_set(); void map_delete(); int map_find_hash(tagint); protected: // global to local ID mapping int *map_array; // direct map via array that holds map_tag_max int map_maxarray; // allocated size of map_array (1 larger than this) struct HashElem { // hashed map tagint 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 max_same; // allocated size of sametag // 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(); int next_prime(int); }; } #endif /* ERROR/WARNING messages: E: Atom IDs must be used for molecular systems Atom IDs are used to identify and find partner atoms in bonds. E: Unknown atom style UNDOCUMENTED 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 id command after simulation box is defined The atom_modify id command cannot be used after a read_data, read_restart, or create_box command. 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: Atom ID is negative Self-explanatory. E: Atom ID is too big The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL setting in your Makefile. See Section_start 2.2 of the manual for more details. E: Atom ID is zero Either all atoms IDs must be zero or none of them. E: Not all atom IDs are 0 Either all atoms IDs must be zero or none of them. E: New atom IDs exceed maximum allowed ID See the setting for tagint in the src/lmptype.h file. 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: 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: 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 Bodies section of data file Atom IDs must be positive integers and within range of defined atoms. 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: Reuse of molecule template ID The template IDs must be unique. 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. U: Invalid atom style The choice of atom style is unknown. */