227 lines
7.3 KiB
C++
227 lines
7.3 KiB
C++
/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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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namespace LAMMPS_NS {
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class AtomVec : protected Pointers {
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public:
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int molecular; // 0 = atomic, 1 = molecular 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 size_data_bonus; // number of values in Bonus 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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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 by child styles
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char *fields_grow,*fields_copy;
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char *fields_comm,*fields_comm_vel,*fields_reverse;
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char *fields_border,*fields_border_vel;
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char *fields_exchange,*fields_restart;
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char *fields_create,*fields_data_atom,*fields_data_vel;
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// methods
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AtomVec(class LAMMPS *);
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virtual ~AtomVec();
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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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void grow(int);
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void copy(int, int, int);
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void clear_bonus() {}
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int pack_comm(int, int *, double *, int, int *);
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int pack_comm_vel(int, int *, double *, int, int *);
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void unpack_comm(int, int, double *);
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void unpack_comm_vel(int, int, double *);
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int pack_reverse(int, int, double *);
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void unpack_reverse(int, int *, double *);
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int pack_border(int, int *, double *, int, int *);
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int pack_border_vel(int, int *, double *, int, int *);
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void unpack_border(int, int, double *);
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void unpack_border_vel(int, int, double *);
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int pack_exchange(int, double *);
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int unpack_exchange(double *);
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int size_restart();
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virtual void pack_restart_pre(int) {}
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int pack_restart(int, double *);
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virtual void pack_restart_post(int) {}
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int unpack_restart(double *);
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virtual void unpack_restart_init(int) {}
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void create_atom(int, double *);
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virtual void create_atom_post(int) {}
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void data_atom(double *, imageint, char **);
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virtual void data_atom_post(int) {}
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void data_atom_bonus(int, char **) {}
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void data_vel(int, char **);
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virtual void pack_data_pre(int) {}
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void pack_data(double **);
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virtual void pack_data_post(int) {}
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int pack_data_hybrid(int, double *) {return 0;}
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void write_data(FILE *, int, double **);
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void pack_vel(double **);
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void write_vel(FILE *, int, double **);
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int pack_bond(tagint **);
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void write_bond(FILE *, int, tagint **, int);
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int pack_angle(tagint **);
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void write_angle(FILE *, int, tagint **, int);
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int pack_dihedral(tagint **);
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void write_dihedral(FILE *, int, tagint **, int);
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int pack_improper(tagint **);
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void write_improper(FILE *, int, tagint **, int);
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int property_atom(char *) {return -1;}
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void pack_property_atom(int, double *, int, int) {}
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bigint memory_usage();
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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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// 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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const char *default_grow,*default_copy;
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const char *default_comm,*default_comm_vel,*default_reverse;
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const char *default_border,*default_border_vel;
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const char *default_exchange,*default_restart;
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const char *default_create,*default_data_atom,*default_data_vel;
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struct Method {
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void **pdata;
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int *datatype;
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int *cols;
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int **maxcols;
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int *collength;
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void **plength;
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int *index;
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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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int nthreads;
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int *threads;
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// union data struct for packing 32-bit and 64-bit ints into double bufs
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// this avoids aliasing issues by having 2 pointers (double,int)
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// to same buf memory
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// constructor for 32-bit int prevents compiler
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// from possibly calling the double constructor when passed an int
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// copy to a double *buf:
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// buf[m++] = ubuf(foo).d, where foo is a 32-bit or 64-bit int
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// copy from a double *buf:
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// foo = (int) ubuf(buf[m++]).i;, where (int) or (tagint) match foo
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// the cast prevents compiler warnings about possible truncation
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union ubuf {
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double d;
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int64_t i;
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ubuf(double arg) : d(arg) {}
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ubuf(int64_t arg) : i(arg) {}
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ubuf(int arg) : i(arg) {}
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};
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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(char *, const char *, Method *);
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void create_method(int, Method *);
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void init_method(Method *);
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void destroy_method(Method *);
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};
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}
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#endif
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/* ERROR/WARNING messages:
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E: Invalid atom_style command
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Self-explanatory.
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E: KOKKOS package requires a kokkos enabled atom_style
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Self-explanatory.
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E: Per-processor system is too big
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The number of owned atoms plus ghost atoms on a single
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processor must fit in 32-bit integer.
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E: Invalid atom type in Atoms section of data file
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Atom types must range from 1 to specified # of types.
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*/
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