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neighbor.h
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rLAMMPS lammps
neighbor.h
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/* ----------------------------------------------------------------------
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_NEIGHBOR_H
#define LMP_NEIGHBOR_H
#include "pointers.h"
namespace
LAMMPS_NS
{
class
Neighbor
:
protected
Pointers
{
public:
int
style
;
// 0,1,2 = nsq, bin, multi
int
every
;
// build every this many steps
int
delay
;
// delay build for this many steps
int
dist_check
;
// 0 = always build, 1 = only if 1/2 dist
int
ago
;
// how many steps ago neighboring occurred
int
pgsize
;
// size of neighbor page
int
oneatom
;
// max # of neighbors for one atom
int
includegroup
;
// only build pairwise lists for this group
double
skin
;
// skin distance
double
cutneighmin
;
// min neighbor cutoff for all type pairs
double
cutneighmax
;
// max neighbor cutoff for all type pairs
double
*
cuttype
;
// for each type, max neigh cut w/ others
int
ncalls
;
// # of times build has been called
int
ndanger
;
// # of dangerous builds
int
nrequest
;
// requests for pairwise neighbor lists
class
NeighRequest
**
requests
;
// from Pair, Fix, Compute, Command classes
int
maxrequest
;
int
old_style
;
// previous run info to avoid
int
old_nrequest
;
// re-creation of pairwise neighbor lists
class
NeighRequest
**
old_requests
;
int
nlist
;
// pairwise neighbor lists
class
NeighList
**
lists
;
int
nbondlist
;
// list of bonds to compute
int
**
bondlist
;
int
nanglelist
;
// list of angles to compute
int
**
anglelist
;
int
ndihedrallist
;
// list of dihedrals to compute
int
**
dihedrallist
;
int
nimproperlist
;
// list of impropers to compute
int
**
improperlist
;
Neighbor
(
class
LAMMPS
*
);
~
Neighbor
();
void
init
();
int
request
(
void
*
);
// another class requests a neighbor list
void
print_lists_of_lists
();
// debug print out
int
decide
();
// decide whether to build or not
int
check_distance
();
// check max distance moved since last build
void
setup_bins
();
// setup bins based on box and cutoff
void
build
();
// create all neighbor lists (pair,bond)
void
build_one
(
int
);
// create a single neighbor list
void
set
(
int
,
char
**
);
// set neighbor style and skin distance
void
modify_params
(
int
,
char
**
);
// modify parameters that control builds
double
memory_usage
();
private:
int
me
,
nprocs
;
int
maxlocal
;
// size of atom-based NeighList arrays
int
maxbond
,
maxangle
,
maxdihedral
,
maximproper
;
// size of bond lists
int
build_once
;
// 1 if only build lists once per run
int
must_check
;
// 1 if must check other classes to reneigh
int
restart_check
;
// 1 if restart enabled, 0 if no
int
fix_check
;
// # of fixes that induce reneigh
int
*
fixchecklist
;
// which fixes to check
double
**
cutneighsq
;
// neighbor cutneigh sq for each type pair
double
cutneighmaxsq
;
// cutneighmax squared
double
*
cuttypesq
;
// cuttype squared
double
triggersq
;
// trigger = build when atom moves this dist
double
**
xhold
;
// atom coords at last neighbor build
int
maxhold
;
// size of xhold array
int
nbinx
,
nbiny
,
nbinz
;
// # of global bins
int
*
bins
;
// ptr to next atom in each bin
int
maxbin
;
// size of bins array
int
*
binhead
;
// ptr to 1st atom in each bin
int
maxhead
;
// size of binhead array
int
mbins
;
// # of local bins and offset
int
mbinx
,
mbiny
,
mbinz
;
int
mbinxlo
,
mbinylo
,
mbinzlo
;
int
binsizeflag
;
// user-chosen bin size
double
binsize_user
;
double
binsizex
,
binsizey
,
binsizez
;
// actual bin sizes and inverse sizes
double
bininvx
,
bininvy
,
bininvz
;
int
sx
,
sy
,
sz
,
smax
;
// bin stencil extents
int
dimension
;
// 2/3 for 2d/3d
int
triclinic
;
// 0 if domain is orthog, 1 if triclinic
int
newton_pair
;
// 0 if newton off, 1 if on for pairwise
double
*
bboxlo
,
*
bboxhi
;
// copy of full domain bounding box
double
inner
[
2
],
middle
[
2
];
// rRESPA cutoffs for extra lists
double
cut_inner_sq
;
// outer cutoff for inner neighbor list
double
cut_middle_sq
;
// outer cutoff for middle neighbor list
double
cut_middle_inside_sq
;
// inner cutoff for middle neighbor list
int
special_flag
[
4
];
// flags for 1-2, 1-3, 1-4 neighbors
int
exclude
;
// 0 if no type/group exclusions, 1 if yes
int
nex_type
;
// # of entries in type exclusion list
int
maxex_type
;
// max # in type list
int
*
ex1_type
,
*
ex2_type
;
// pairs of types to exclude
int
**
ex_type
;
// 2d array of excluded type pairs
int
nex_group
;
// # of entries in group exclusion list
int
maxex_group
;
// max # in group list
int
*
ex1_group
,
*
ex2_group
;
// pairs of group #'s to exclude
int
*
ex1_bit
,
*
ex2_bit
;
// pairs of group bits to exclude
int
nex_mol
;
// # of entries in molecule exclusion list
int
maxex_mol
;
// max # in molecule list
int
*
ex_mol_group
;
// molecule group #'s to exclude
int
*
ex_mol_bit
;
// molecule group bits to exclude
int
nblist
,
nglist
,
nslist
;
// # of pairwise neigh lists of various kinds
int
*
blist
;
// lists to build every reneighboring
int
*
glist
;
// lists to grow atom arrays every reneigh
int
*
slist
;
// lists to grow stencil arrays every reneigh
void
bin_atoms
();
// bin all atoms
double
bin_distance
(
int
,
int
,
int
);
// distance between binx
int
coord2bin
(
double
*
);
// mapping atom coord to a bin
int
find_special
(
int
,
int
);
// look for special neighbor
int
exclusion
(
int
,
int
,
int
,
int
,
int
*
,
int
*
);
// test for pair exclusion
void
choose_build
(
int
,
class
NeighRequest
*
);
void
choose_stencil
(
int
,
class
NeighRequest
*
);
// pairwise build functions
typedef
void
(
Neighbor
::*
PairPtr
)(
class
NeighList
*
);
PairPtr
*
pair_build
;
void
half_nsq_no_newton
(
class
NeighList
*
);
void
half_nsq_newton
(
class
NeighList
*
);
void
half_bin_no_newton
(
class
NeighList
*
);
void
half_bin_newton
(
class
NeighList
*
);
void
half_bin_newton_tri
(
class
NeighList
*
);
void
half_multi_no_newton
(
class
NeighList
*
);
void
half_multi_newton
(
class
NeighList
*
);
void
half_multi_newton_tri
(
class
NeighList
*
);
void
full_nsq
(
class
NeighList
*
);
void
full_bin
(
class
NeighList
*
);
void
full_multi
(
class
NeighList
*
);
void
half_from_full_no_newton
(
class
NeighList
*
);
void
half_from_full_newton
(
class
NeighList
*
);
void
skip_from
(
class
NeighList
*
);
void
skip_from_granular
(
class
NeighList
*
);
void
skip_from_respa
(
class
NeighList
*
);
void
copy_from
(
class
NeighList
*
);
void
granular_nsq_no_newton
(
class
NeighList
*
);
void
granular_nsq_newton
(
class
NeighList
*
);
void
granular_bin_no_newton
(
class
NeighList
*
);
void
granular_bin_newton
(
class
NeighList
*
);
void
granular_bin_newton_tri
(
class
NeighList
*
);
void
respa_nsq_no_newton
(
class
NeighList
*
);
void
respa_nsq_newton
(
class
NeighList
*
);
void
respa_bin_no_newton
(
class
NeighList
*
);
void
respa_bin_newton
(
class
NeighList
*
);
void
respa_bin_newton_tri
(
class
NeighList
*
);
// pairwise stencil creation functions
typedef
void
(
Neighbor
::*
StencilPtr
)(
class
NeighList
*
,
int
,
int
,
int
);
StencilPtr
*
stencil_create
;
void
stencil_half_bin_2d_no_newton
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_half_bin_3d_no_newton
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_half_bin_2d_newton
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_half_bin_3d_newton
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_half_bin_2d_newton_tri
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_half_bin_3d_newton_tri
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_half_multi_2d_no_newton
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_half_multi_3d_no_newton
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_half_multi_2d_newton
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_half_multi_3d_newton
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_half_multi_2d_newton_tri
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_half_multi_3d_newton_tri
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_full_bin_2d
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_full_bin_3d
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_full_multi_2d
(
class
NeighList
*
,
int
,
int
,
int
);
void
stencil_full_multi_3d
(
class
NeighList
*
,
int
,
int
,
int
);
// topology build functions
typedef
void
(
Neighbor
::*
BondPtr
)();
// ptrs to topology build functions
BondPtr
bond_build
;
// ptr to bond list functions
void
bond_all
();
// bond list with all bonds
void
bond_partial
();
// exclude certain bonds
BondPtr
angle_build
;
// ptr to angle list functions
void
angle_all
();
// angle list with all angles
void
angle_partial
();
// exclude certain angles
BondPtr
dihedral_build
;
// ptr to dihedral list functions
void
dihedral_all
();
// dihedral list with all dihedrals
void
dihedral_partial
();
// exclude certain dihedrals
BondPtr
improper_build
;
// ptr to improper list functions
void
improper_all
();
// improper list with all impropers
void
improper_partial
();
// exclude certain impropers
};
}
#endif
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