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atom_vec.h
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atom_vec.h
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/* -*- 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_VEC_H
#define LMP_ATOM_VEC_H
#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
class AtomVec : protected Pointers {
public:
int molecular; // 0 = atomic, 1 = molecular system
int bonds_allow,angles_allow; // 1 if bonds, angles are used
int dihedrals_allow,impropers_allow; // 1 if dihedrals, impropers used
int mass_type; // 1 if per-type masses
int dipole_type; // 1 if per-type dipole moments
int forceclearflag; // 1 if has forceclear() method
int comm_x_only; // 1 if only exchange x in forward comm
int comm_f_only; // 1 if only exchange f in reverse comm
int size_forward; // # of values per atom in comm
int size_reverse; // # in reverse comm
int size_border; // # in border comm
int size_velocity; // # of velocity based quantities
int size_data_atom; // number of values in Atom line
int size_data_vel; // number of values in Velocity line
int size_data_bonus; // number of values in Bonus line
int xcol_data; // column (1-N) where x is in Atom line
class Molecule **onemols; // list of molecules for style template
int nset; // # of molecules in list
int kokkosable; // 1 if atom style is KOKKOS-enabled
int nargcopy; // copy of command-line args for atom_style command
char **argcopy; // used when AtomVec is realloced (restart,replicate)
AtomVec(class LAMMPS *);
virtual ~AtomVec();
void store_args(int, char **);
virtual void process_args(int, char **);
virtual void init();
virtual void grow(int) = 0;
virtual void grow_reset() = 0;
virtual void copy(int, int, int) = 0;
virtual void clear_bonus() {}
virtual void force_clear(int, size_t) {}
virtual int pack_comm(int, int *, double *, int, int *) = 0;
virtual int pack_comm_vel(int, int *, double *, int, int *) = 0;
virtual int pack_comm_hybrid(int, int *, double *) {return 0;}
virtual void unpack_comm(int, int, double *) = 0;
virtual void unpack_comm_vel(int, int, double *) = 0;
virtual int unpack_comm_hybrid(int, int, double *) {return 0;}
virtual int pack_reverse(int, int, double *) = 0;
virtual int pack_reverse_hybrid(int, int, double *) {return 0;}
virtual void unpack_reverse(int, int *, double *) = 0;
virtual int unpack_reverse_hybrid(int, int *, double *) {return 0;}
virtual int pack_border(int, int *, double *, int, int *) = 0;
virtual int pack_border_vel(int, int *, double *, int, int *) = 0;
virtual int pack_border_hybrid(int, int *, double *) {return 0;}
virtual void unpack_border(int, int, double *) = 0;
virtual void unpack_border_vel(int, int, double *) = 0;
virtual int unpack_border_hybrid(int, int, double *) {return 0;}
virtual int pack_exchange(int, double *) = 0;
virtual int unpack_exchange(double *) = 0;
virtual int size_restart() = 0;
virtual int pack_restart(int, double *) = 0;
virtual int unpack_restart(double *) = 0;
virtual void create_atom(int, double *) = 0;
virtual void data_atom(double *, imageint, char **) = 0;
virtual void data_atom_bonus(int, char **) {}
virtual int data_atom_hybrid(int, char **) {return 0;}
virtual void data_vel(int, char **);
virtual int data_vel_hybrid(int, char **) {return 0;}
virtual void pack_data(double **) = 0;
virtual int pack_data_hybrid(int, double *) {return 0;}
virtual void write_data(FILE *, int, double **) = 0;
virtual int write_data_hybrid(FILE *, double *) {return 0;}
virtual void pack_vel(double **);
virtual int pack_vel_hybrid(int, double *) {return 0;}
virtual void write_vel(FILE *, int, double **);
virtual int write_vel_hybrid(FILE *, double *) {return 0;}
int pack_bond(tagint **);
void write_bond(FILE *, int, tagint **, int);
int pack_angle(tagint **);
void write_angle(FILE *, int, tagint **, int);
void pack_dihedral(tagint **);
void write_dihedral(FILE *, int, tagint **, int);
void pack_improper(tagint **);
void write_improper(FILE *, int, tagint **, int);
virtual int property_atom(char *) {return -1;}
virtual void pack_property_atom(int, double *, int, int) {}
virtual bigint memory_usage() = 0;
protected:
int nmax; // local copy of atom->nmax
int deform_vremap; // local copy of domain properties
int deform_groupbit;
double *h_rate;
// union data struct for packing 32-bit and 64-bit ints into double bufs
// this avoids aliasing issues by having 2 pointers (double,int)
// to same buf memory
// constructor for 32-bit int prevents compiler
// from possibly calling the double constructor when passed an int
// copy to a double *buf:
// buf[m++] = ubuf(foo).d, where foo is a 32-bit or 64-bit int
// copy from a double *buf:
// foo = (int) ubuf(buf[m++]).i;, where (int) or (tagint) match foo
// the cast prevents compiler warnings about possible truncation
union ubuf {
double d;
int64_t i;
ubuf(double arg) : d(arg) {}
ubuf(int64_t arg) : i(arg) {}
ubuf(int arg) : i(arg) {}
};
void grow_nmax();
int grow_nmax_bonus(int);
};
}
#endif
/* ERROR/WARNING messages:
E: Invalid atom_style command
Self-explanatory.
E: KOKKOS package requires a kokkos enabled atom_style
Self-explanatory.
*/

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