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102 lines (78 loc) · 2.82 KB
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/* ----------------------------------------------------------------------
miniMD is a simple, parallel molecular dynamics (MD) code. miniMD is
an MD microapplication in the Mantevo project at Sandia National
Laboratories ( http://www.mantevo.org ). The primary
authors of miniMD are Steve Plimpton (sjplimp@sandia.gov), Paul Crozier
(pscrozi@sandia.gov) and Christian Trott (crtrott@sandia.gov).
Copyright (2008) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This library is free software; you
can redistribute it and/or modify it under the terms of the GNU Lesser
General Public License as published by the Free Software Foundation;
either version 3 of the License, or (at your option) any later
version.
This library 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. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this software; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
USA. See also: http://www.gnu.org/licenses/lgpl.txt .
For questions, contact Paul S. Crozier (pscrozi@sandia.gov) or
Christian Trott (crtrott@sandia.gov).
Please read the accompanying README and LICENSE files.
---------------------------------------------------------------------- */
#ifndef ATOM_H
#define ATOM_H
#include "threadData.h"
#include "types.h"
class Neighbor;
struct Box
{
MMD_float xprd, yprd, zprd;
MMD_float xlo, xhi;
MMD_float ylo, yhi;
MMD_float zlo, zhi;
};
class Atom
{
public:
int natoms;
int nlocal, nghost;
int nmax;
MMD_float *x;
MMD_float *v;
MMD_float *f;
int ntypes;
int *type;
MMD_float *xold;
ThreadData *threads;
MMD_float virial, mass;
int comm_size, reverse_size, border_size;
struct Box box;
Atom(int ntypes_);
~Atom();
void addatom(MMD_float, MMD_float, MMD_float, MMD_float, MMD_float, MMD_float);
void pbc();
void growarray();
void growarray_sync();
void copy(int, int);
void pack_comm(int, int *, MMD_float *, const int *);
void unpack_comm(int, int, MMD_float *);
void self_comm(int, int *, int, const int *);
void pack_reverse(int, int, MMD_float *);
void unpack_reverse(int, int *, MMD_float *);
int pack_border(int, MMD_float *, int *);
int unpack_border(int, MMD_float *);
int pack_exchange(int, MMD_float *);
int unpack_exchange(int, MMD_float *);
int skip_exchange(MMD_float *);
void sort(Neighbor &neighbor);
private:
MMD_float *x_copy;
MMD_float *v_copy;
int * type_copy;
int copy_size;
};
#endif