/* ---------------------------------------------------------------------- This is the ██╗ ██╗ ██████╗ ██████╗ ██████╗ ██╗ ██╗████████╗███████╗ ██║ ██║██╔════╝ ██╔════╝ ██╔════╝ ██║ ██║╚══██╔══╝██╔════╝ ██║ ██║██║ ███╗██║ ███╗██║ ███╗███████║ ██║ ███████╗ ██║ ██║██║ ██║██║ ██║██║ ██║██╔══██║ ██║ ╚════██║ ███████╗██║╚██████╔╝╚██████╔╝╚██████╔╝██║ ██║ ██║ ███████║ ╚══════╝╚═╝ ╚═════╝ ╚═════╝ ╚═════╝ ╚═╝ ╚═╝ ╚═╝ ╚══════╝® DEM simulation engine, released by DCS Computing Gmbh, Linz, Austria http://www.dcs-computing.com, office@dcs-computing.com LIGGGHTS® is part of CFDEM®project: http://www.liggghts.com | http://www.cfdem.com Core developer and main author: Christoph Kloss, christoph.kloss@dcs-computing.com LIGGGHTS® is open-source, distributed under the terms of the GNU Public License, version 2 or later. It is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. You should have received a copy of the GNU General Public License along with LIGGGHTS®. If not, see http://www.gnu.org/licenses . See also top-level README and LICENSE files. LIGGGHTS® and CFDEM® are registered trade marks of DCS Computing GmbH, the producer of the LIGGGHTS® software and the CFDEM®coupling software See http://www.cfdem.com/terms-trademark-policy for details. ------------------------------------------------------------------------- Contributing author and copyright for this file: This file is from LAMMPS 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. ------------------------------------------------------------------------- */ #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; tagint *image; double **x,**v,**f; int *molecule; double *q,**mu; double **omega,**angmom,**torque; double *radius,*rmass,*vfrac,*s0; double *density; double **x0; int *ellipsoid,*line,*tri,*body; int *spin; double *eradius,*ervel,*erforce,*ervelforce; double *cs,*csforce,*vforce; int *etag; double *rho, *drho; double *p; double *e, *de; double **vest; double *cv; //Superquadric bonus----------------------------------- double **shape, **blockiness; //half axes and blockiness parameters double **inertia, *volume, *area; //components Ix, Iy, Iz double **quaternion; //quaternion of current orientation //------------------------------------------------------ // USR-SMD double *contact_radius; double **smd_data_9; double **smd_stress; double *eff_plastic_strain; double *eff_plastic_strain_rate; double *damage; int smd_flag; int contact_radius_flag; int smd_data_9_flag; int smd_stress_flag; int x0_flag; int eff_plastic_strain_flag; int eff_plastic_strain_rate_flag; int damage_flag; int *shapetype; 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; double ***bond_hist; 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; // custom arrays used by fix property/atom int **ivector; double **dvector; double ***darray; char **iname,**dname,**daname; int nivector,ndvector, ndarray; // 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 superquadric_flag; int convex_hull_flag; int peri_flag,electron_flag; int ecp_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; int density_flag; int p_flag; int n_bondhist; int radvary_flag; int shapetype_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,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; // default or user-specified style of map // 0 = none, 1 = array, 2 = hash int 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 **, char *suffix = NULL); class AtomVec *new_avec(const 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 tag_max(); 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_bodies(int, char *, class AtomVecBody *); 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); bool has_callback(const char *, int); int find_custom(char *, int &); int add_custom(char *, int); void remove_custom(int, int); void *extract(const char *, int &); void *extract(const char * _id) { int a = 0; return extract(_id,a); } 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 *); inline class Properties* get_properties() { return properties; } // functions for global to local ID mapping // map lookup function inlined for efficiency // return -1 if no map defined inline int map(int 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(); 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_array; // direct map of length map_tag_max + 1 int smax; // max size of sametag 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 // 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 size_t memlength; // allocated size of memstr char *memstr; // string of array names already counted void setup_sort_bins(); int next_prime(int); class Properties *properties; }; } #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: 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 Bodies 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. */