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neigh_list.h
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neigh_list.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_NEIGH_LIST_H
#define LMP_NEIGH_LIST_H
#include "pointers.h"
#include "my_page.h"
namespace LAMMPS_NS {
class NeighList : protected Pointers {
public:
int index; // index of which neigh list it is
// needed when a class invokes it directly
// also indexes the request it came from
int buildflag; // 1 if pair_build invoked every reneigh
int growflag; // 1 if stores atom-based arrays & pages
int stencilflag; // 1 if stores stencil arrays
int ghostflag; // 1 if it stores neighbors of ghosts
// data structs to store neighbor pairs I,J and associated values
int inum; // # of I atoms neighbors are stored for
int gnum; // # of ghost atoms neighbors are stored for
int *ilist; // local indices of I atoms
int *numneigh; // # of J neighbors for each I atom
int **firstneigh; // ptr to 1st J int value of each I atom
double **firstdouble; // ptr to 1st J double value of each I atom
int pgsize; // size of each page
int oneatom; // max size for one atom
int dnum; // # of doubles per neighbor, 0 if none
MyPage<int> *ipage; // pages of neighbor indices
MyPage<double> *dpage; // pages of neighbor doubles, if dnum > 0
bigint last_build; // timestep of last build for occasional lists
// atom types to skip when building list
// iskip,ijskip are just ptrs to corresponding request
int *iskip; // iskip[i] = 1 if atoms of type I are not in list
int **ijskip; // ijskip[i][j] = 1 if pairs of type I,J are not in list
// settings and pointers for related neighbor lists and fixes
NeighList *listgranhistory; // point at list storing shear history
class FixShearHistory *fix_history; // fix that stores history info
int respamiddle; // 1 if this respaouter has middle list
NeighList *listinner; // me = respaouter, point to respainner
NeighList *listmiddle; // me = respaouter, point to respamiddle
NeighList *listfull; // me = half list, point to full I derive from
NeighList *listcopy; // me = copy list, point to list I copy from
NeighList *listskip; // me = skip list, point to list I skip from
// USER-DPD package and Shardlow Splitting Algorithm (SSA) support
int ssaflag; // 1 if the list has the ndxAIR_ssa array
uint16_t (*ndxAIR_ssa)[8]; // for each atom, last neighbor index of each AIR
int *bins_ssa; // index of next atom in each bin
int maxbin_ssa; // size of bins_ssa array
int *binhead_ssa; // index of 1st local atom in each bin
int *gbinhead_ssa; // index of 1st ghost atom in each bin
int maxhead_ssa; // size of binhead_ssa and gbinhead_ssa arrays
// stencils of bin indices for neighbor finding
int maxstencil; // max size of stencil
int nstencil; // # of bins in stencil
int *stencil; // list of bin offsets
int **stencilxyz; // bin offsets in xyz dims
int maxstencil_multi; // max sizes of stencils
int *nstencil_multi; // # bins in each type-based multi stencil
int **stencil_multi; // list of bin offsets in each stencil
double **distsq_multi; // sq distances to bins in each stencil
NeighList(class LAMMPS *);
virtual ~NeighList();
void setup_pages(int, int, int); // setup page data structures
void grow(int); // grow maxlocal
void stencil_allocate(int, int); // allocate stencil arrays
void copy_skip_info(int *, int **); // copy skip info from a neigh request
void print_attributes(); // debug routine
int get_maxlocal() {return maxatoms;}
bigint memory_usage();
protected:
int maxatoms; // size of allocated atom arrays
};
}
#endif

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