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tsoc
openmm
Commits
c7f6cd3a
Commit
c7f6cd3a
authored
Sep 24, 2008
by
Peter Eastman
Browse files
Attempting to fix incorrect file capitalization introduced by Windows
parent
04ea8ce9
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platforms/reference/src/SimTKReference/ReferenceNeighborList.h
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platforms/reference/src/SimTKReference/ReferenceNeighborList.h
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04ea8ce9
#ifndef OPENMM_REFERENCE_NEIGHBORLIST_H_
#define OPENMM_REFERENCE_NEIGHBORLIST_H_
#include "../SimTKUtilities/SimTKOpenMMRealType.h"
#include <set>
#include <vector>
namespace
OpenMM
{
typedef
RealOpenMM
**
AtomLocationList
;
typedef
unsigned
int
AtomIndex
;
typedef
std
::
pair
<
AtomIndex
,
AtomIndex
>
AtomPair
;
typedef
std
::
vector
<
AtomPair
>
NeighborList
;
// Ridiculous O(n^2) version of neighbor list
// for pedagogical purposes and simplicity
// parameter neighborList is automatically clear()ed before
// neighbors are added
void
computeNeighborListNaive
(
NeighborList
&
neighborList
,
int
nAtoms
,
const
AtomLocationList
&
atomLocations
,
const
std
::
vector
<
std
::
set
<
int
>
>&
exclusions
,
const
RealOpenMM
*
periodicBoxSize
,
double
maxDistance
,
double
minDistance
=
0.0
,
bool
reportSymmetricPairs
=
false
);
// O(n) neighbor list method using voxel hash data structure
// parameter neighborList is automatically clear()ed before
// neighbors are added
void
computeNeighborListVoxelHash
(
NeighborList
&
neighborList
,
int
nAtoms
,
const
AtomLocationList
&
atomLocations
,
const
std
::
vector
<
std
::
set
<
int
>
>&
exclusions
,
const
RealOpenMM
*
periodicBoxSize
,
double
maxDistance
,
double
minDistance
=
0.0
,
bool
reportSymmetricPairs
=
false
);
}
// namespace OpenMM
#endif // OPENMM_REFERENCE_NEIGHBORLIST_H_
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