226 lines
8.2 KiB
C++
226 lines
8.2 KiB
C++
/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifndef LMP_ATOM_VEC_H
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#define LMP_ATOM_VEC_H
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#include "pointers.h" // IWYU pragma: export
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#include <vector>
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namespace LAMMPS_NS {
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class AtomVec : protected Pointers {
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public:
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enum { PER_ATOM = 0, PER_TYPE = 1 };
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int molecular; // 0 = atomic, 1 = molecular system, 2 = molecular template system
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int bonds_allow, angles_allow; // 1 if bonds, angles are used
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int dihedrals_allow, impropers_allow; // 1 if dihedrals, impropers used
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int mass_type; // 1 if per-type masses
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int dipole_type; // 1 if per-type dipole moments
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int forceclearflag; // 1 if has forceclear() method
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int comm_x_only; // 1 if only exchange x in forward comm
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int comm_f_only; // 1 if only exchange f in reverse comm
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int size_forward; // # of values per atom in comm
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int size_reverse; // # in reverse comm
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int size_border; // # in border comm
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int size_velocity; // # of velocity based quantities
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int size_data_atom; // number of values in Atom line
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int size_data_vel; // number of values in Velocity line
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int xcol_data; // column (1-N) where x is in Atom line
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int maxexchange; // max size of exchanged atom
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// only needs to be set if size > BUFEXTRA
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int bonus_flag; // 1 if stores bonus data
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int size_forward_bonus; // # in forward bonus comm
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int size_border_bonus; // # in border bonus comm
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int size_restart_bonus_one; // # in restart bonus comm
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int size_data_bonus; // number of values in Bonus line
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class Molecule **onemols; // list of molecules for style template
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int nset; // # of molecules in list
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int kokkosable; // 1 if atom style is KOKKOS-enabled
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int nargcopy; // copy of command-line args for atom_style command
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char **argcopy; // used when AtomVec is realloced (restart,replicate)
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// additional list of peratom fields operated on by different methods
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// set or created by child styles
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std::vector<std::string> fields_grow, fields_copy, fields_comm, fields_comm_vel;
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std::vector<std::string> fields_reverse, fields_border, fields_border_vel;
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std::vector<std::string> fields_exchange, fields_restart, fields_create;
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std::vector<std::string> fields_data_atom, fields_data_vel;
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// methods
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AtomVec(class LAMMPS *);
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~AtomVec() override;
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void store_args(int, char **);
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virtual void process_args(int, char **);
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virtual void init();
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virtual void force_clear(int, size_t) {}
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virtual bigint roundup(bigint);
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virtual void grow(int);
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virtual void grow_pointers() {}
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virtual void copy(int, int, int);
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virtual void copy_bonus(int, int, int) {}
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virtual void clear_bonus() {}
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virtual int pack_comm(int, int *, double *, int, int *);
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virtual int pack_comm_vel(int, int *, double *, int, int *);
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virtual void unpack_comm(int, int, double *);
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virtual void unpack_comm_vel(int, int, double *);
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virtual int pack_comm_bonus(int, int *, double *) { return 0; }
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virtual void unpack_comm_bonus(int, int, double *) {}
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virtual int pack_reverse(int, int, double *);
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virtual void unpack_reverse(int, int *, double *);
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virtual int pack_border(int, int *, double *, int, int *);
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virtual int pack_border_vel(int, int *, double *, int, int *);
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virtual void unpack_border(int, int, double *);
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virtual void unpack_border_vel(int, int, double *);
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virtual int pack_border_bonus(int, int *, double *) { return 0; }
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virtual int unpack_border_bonus(int, int, double *) { return 0; }
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virtual int pack_exchange(int, double *);
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virtual int unpack_exchange(double *);
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virtual int pack_exchange_bonus(int, double *) { return 0; }
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virtual int unpack_exchange_bonus(int, double *) { return 0; }
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virtual int size_restart();
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virtual int pack_restart(int, double *);
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virtual int unpack_restart(double *);
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virtual void pack_restart_pre(int) {}
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virtual void pack_restart_post(int) {}
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virtual void unpack_restart_init(int) {}
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virtual int size_restart_bonus() { return 0; }
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virtual int pack_restart_bonus(int, double *) { return 0; }
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virtual int unpack_restart_bonus(int, double *) { return 0; }
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virtual void create_atom(int, double *);
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virtual void create_atom_post(int) {}
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virtual void data_atom(double *, imageint, const std::vector<std::string> &,
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std::string &);
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virtual void data_atom_post(int) {}
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virtual void data_atom_bonus(int, const std::vector<std::string> &) {}
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virtual void data_body(int, int, int, int *, double *) {}
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virtual void data_bonds_post(int, int, tagint, tagint, tagint) {}
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virtual void pack_data(double **);
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virtual void write_data(FILE *, int, double **);
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virtual void pack_data_pre(int) {}
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virtual void pack_data_post(int) {}
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virtual void data_vel(int, const std::vector<std::string> &);
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virtual void pack_vel(double **);
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virtual void write_vel(FILE *, int, double **);
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virtual int pack_bond(tagint **);
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virtual void write_bond(FILE *, int, tagint **, int);
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virtual int pack_angle(tagint **);
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virtual void write_angle(FILE *, int, tagint **, int);
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virtual int pack_dihedral(tagint **);
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virtual void write_dihedral(FILE *, int, tagint **, int);
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virtual int pack_improper(tagint **);
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virtual void write_improper(FILE *, int, tagint **, int);
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virtual int pack_data_bonus(double *, int) { return 0; }
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virtual void write_data_bonus(FILE *, int, double *, int) {}
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virtual void read_data_general_to_restricted(int, int);
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virtual void write_data_restricted_to_general();
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virtual void write_data_restore_restricted();
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virtual int property_atom(const std::string &) { return -1; }
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virtual void pack_property_atom(int, double *, int, int) {}
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virtual double memory_usage();
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virtual double memory_usage_bonus() { return 0; }
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protected:
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int nmax; // local copy of atom->nmax
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int deform_vremap; // local copy of domain properties
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int deform_groupbit;
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double *h_rate;
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tagint *tag; // peratom fields common to all styles
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int *type, *mask;
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imageint *image;
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double **x, **v, **f;
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// copies of original unrotated fields for write_data for general triclinic
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double **x_hold;
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double **v_hold, **omega_hold, **angmom_hold;
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// standard list of peratom fields always operated on by different methods
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// common to all styles, so not listed in field strings
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static const std::vector<std::string> default_grow, default_copy, default_comm, default_comm_vel;
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static const std::vector<std::string> default_reverse, default_border, default_border_vel;
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static const std::vector<std::string> default_exchange, default_restart, default_create;
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static const std::vector<std::string> default_data_atom, default_data_vel;
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struct Method {
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std::vector<void *> pdata;
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std::vector<int> datatype;
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std::vector<int> cols;
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std::vector<int *> maxcols;
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std::vector<int> collength;
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std::vector<void *> plength;
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std::vector<int> index;
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void resize(int nfield);
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};
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Method mgrow, mcopy;
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Method mcomm, mcomm_vel, mreverse, mborder, mborder_vel, mexchange, mrestart;
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Method mcreate, mdata_atom, mdata_vel;
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int ngrow, ncopy;
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int ncomm, ncomm_vel, nreverse, nborder, nborder_vel, nexchange, nrestart;
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int ncreate, ndata_atom, ndata_vel;
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// thread info for fields that are duplicated over threads
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// used by fields in grow() and memory_usage()
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bool *threads;
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// local methods
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void grow_nmax();
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int grow_nmax_bonus(int);
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void setup_fields();
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int process_fields(const std::vector<std::string> &, const std::vector<std::string> &, Method *);
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void init_method(int, Method *);
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};
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} // namespace LAMMPS_NS
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#endif
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