stormm::energy::ForwardExclusionMask Class Reference

This exclusion mask relies on the reality that, in most topologies, the bulk of one atom's exclusions will be found within the next 32 atoms listed in the topology. If an atom excludes other atoms beyond this range, a separate index records the position at which this happens and provides either an index into a list of additional atoms or, if possible, the index of one other reference index in the topology followed by a second mask of 32 atoms which indicate exclusions relative to the reference index. To keep the list as compact as possible, the exclusion mask only considers "forward" exclusions, meaning excluded atoms with higher index than the one for which the mask is made. There is no double-counting: if atom 1 excludes atom 5, then atom 5 does not note an exclusion of atom 1. More...

#include <forward_exclusionmask.h>

Public Member Functions
int	getAtomCount () const
	Get the number of atoms in the system.
int	getPrimaryMaskCount () const
	Get the number of unique primary masks that the system requires to store all of its non-bonded exclusions.
int	getExtendedMaskCount () const
	Get the number of primary masks that involve a half-mask extension rather than a reference to a full list of additional secondary masks.
int	getSecondaryMaskCount () const
	Get the number of secondary masks that the system requires to store all of its non-bonded exclusions.
int	getTotalExclusionsCount () const
	Get the total number of exclusions by counting all the checked bits and accounting for excluded reference atoms.
uint2	getPrimaryMask (int index) const
	Get an atom's primary mask.
std::vector< uint2 >	getSecondaryMasks (int start, int length) const
	Get all secondary masks associated with an atom. Each presents the exclusions for a cluster of atoms following some reference atom.
const ForwardExclusionMaskReader	data (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the collection of this object's pointers and critical constants.
bool	testExclusion (int atom_i, int atom_j) const
	Test whether a pair of atoms is an exclusion or not.
	ForwardExclusionMask (const AtomGraph *ag_in=nullptr)
	The constructor requires a topology and creates a blank object if given nullptr.
	ForwardExclusionMask (const AtomGraph &ag_in)
	ForwardExclusionMask (const ForwardExclusionMask &original)=default
	The default copy and move constructors as well as the copy and move assignment operator will suffice for this object, which has no POINTER-kind Hybrid objects among its members.
	ForwardExclusionMask (ForwardExclusionMask &&original)=default
ForwardExclusionMask &	operator= (const ForwardExclusionMask &other)=default
ForwardExclusionMask &	operator= (ForwardExclusionMask &&other)=default

Detailed Description

This exclusion mask relies on the reality that, in most topologies, the bulk of one atom's exclusions will be found within the next 32 atoms listed in the topology. If an atom excludes other atoms beyond this range, a separate index records the position at which this happens and provides either an index into a list of additional atoms or, if possible, the index of one other reference index in the topology followed by a second mask of 32 atoms which indicate exclusions relative to the reference index. To keep the list as compact as possible, the exclusion mask only considers "forward" exclusions, meaning excluded atoms with higher index than the one for which the mask is made. There is no double-counting: if atom 1 excludes atom 5, then atom 5 does not note an exclusion of atom 1.

Member Function Documentation

data()

const ForwardExclusionMaskReader stormm::energy::ForwardExclusionMask::data

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get the collection of this object's pointers and critical constants.

Parameters

tier	Level at which to get the data pointers (host CPU or GPU device)

getPrimaryMask()

uint2 stormm::energy::ForwardExclusionMask::getPrimaryMask

(

int

index

)

const

Get an atom's primary mask.

Parameters

index

Topological index of the atom of interest

getSecondaryMasks()

std::vector< uint2 > stormm::energy::ForwardExclusionMask::getSecondaryMasks	(	int	start,
		int	length ) const

Get all secondary masks associated with an atom. Each presents the exclusions for a cluster of atoms following some reference atom.

Parameters

start	The index of the first secondary mask to read
length	The number of secondary masks to read

testExclusion()

bool stormm::energy::ForwardExclusionMask::testExclusion	(	int	atom_i,
		int	atom_j ) const

Test whether a pair of atoms is an exclusion or not.

Parameters

atom_i	The first atom
atom_j	The second atom (if atom_j < atom_i, the function will make a recursive call with atom_i and atom_j reversed)

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The documentation for this class was generated from the following files:

• src/Potential/forward_exclusionmask.h
• src/Potential/forward_exclusionmask.cpp