A functor to handle lennard-jones interactions between two particles (molecules). More...

#include <LJFunctor.h>

Inheritance diagram for mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >:

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Collaboration diagram for mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >:

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Public Member Functions
	LJFunctor ()=delete
	Deleted default constructor.

	LJFunctor (double cutoff)
	Constructor for Functor with mixing disabled.

	LJFunctor (double cutoff, ParticlePropertiesLibrary< double, size_t > &particlePropertiesLibrary)
	Constructor for Functor with mixing active.

std::string	getName () final
	Returns name of functor.

bool	isRelevantForTuning () final
	Specifies whether the functor should be considered for the auto-tuning process.

bool	allowsNewton3 () final
	Specifies whether the functor is capable of Newton3-like functors.

bool	allowsNonNewton3 () final
	Specifies whether the functor is capable of non-Newton3-like functors.

void	AoSFunctor (Particle_T &i, Particle_T &j, bool newton3) final
	PairwiseFunctor for arrays of structures (AoS).

void	SoAFunctorSingle (autopas::SoAView< SoAArraysType > soa, bool newton3) final
	PairwiseFunctor for structure of arrays (SoA)

void	SoAFunctorPair (autopas::SoAView< SoAArraysType > soa1, autopas::SoAView< SoAArraysType > soa2, const bool newton3) final
	PairwiseFunctor for structure of arrays (SoA)

void	SoAFunctorVerlet (autopas::SoAView< SoAArraysType > soa, const size_t indexFirst, const std::vector< size_t, autopas::AlignedAllocator< size_t > > &neighborList, bool newton3) final
	PairwiseFunctor for structure of arrays (SoA) for neighbor lists.

void	setParticleProperties (SoAFloatPrecision epsilon24, SoAFloatPrecision sigmaSquared)
	Sets the particle properties constants for this functor.

void	initTraversal () final
	Reset the global values.

void	endTraversal (bool newton3) final
	Accumulates global values, e.g.

double	getPotentialEnergy ()
	Get the potential Energy.

double	getVirial ()
	Get the virial.

size_t	getNumFLOPs () const override
	Gets the number of useful FLOPs.

double	getHitRate () const override
	Get the hit rate.

Public Member Functions inherited from autopas::PairwiseFunctor< Particle_T, CRTP_T >
	PairwiseFunctor (double cutoff)
	Constructor.

virtual void	AoSFunctor (Particle_T &i, Particle_T &j, bool newton3)
	PairwiseFunctor for arrays of structures (AoS).

virtual void	SoAFunctorSingle (SoAView< SoAArraysType > soa, bool newton3)
	PairwiseFunctor for structure of arrays (SoA)

virtual void	SoAFunctorVerlet (SoAView< SoAArraysType > soa, const size_t indexFirst, const std::vector< size_t, AlignedAllocator< size_t > > &neighborList, bool newton3)
	PairwiseFunctor for structure of arrays (SoA) for neighbor lists.

virtual void	SoAFunctorPair (SoAView< SoAArraysType > soa1, SoAView< SoAArraysType > soa2, bool newton3)
	PairwiseFunctor for structure of arrays (SoA)

Public Member Functions inherited from autopas::Functor< Particle_T, CRTP_T >
	Functor (double cutoff)
	Constructor.

virtual void	initTraversal ()
	This function is called at the start of each traversal.

virtual void	endTraversal (bool newton3)
	This function is called at the end of each traversal.

template<class ParticleCell >
void	SoALoader (ParticleCell &cell, SoA< SoAArraysType > &soa, size_t offset, bool skipSoAResize)
	Copies the AoS data of the given cell in the given soa.

template<typename ParticleCell >
void	SoAExtractor (ParticleCell &cell, SoA< SoAArraysType > &soa, size_t offset)
	Copies the data stored in the soa back into the cell.

virtual bool	allowsNewton3 ()=0
	Specifies whether the functor is capable of Newton3-like functors.

virtual bool	allowsNonNewton3 ()=0
	Specifies whether the functor is capable of non-Newton3-like functors.

virtual bool	isRelevantForTuning ()=0
	Specifies whether the functor should be considered for the auto-tuning process.

virtual std::string	getName ()=0
	Returns name of functor.

double	getCutoff () const
	Getter for the functor's cutoff.

virtual size_t	getNumFLOPs () const
	Get the number of FLOPs.

virtual double	getHitRate () const
	Get the hit rate.

Static Public Member Functions
static constexpr auto	getNeededAttr ()
	Get attributes needed for computation.

static constexpr auto	getNeededAttr (std::false_type)
	Get attributes needed for computation without N3 optimization.

static constexpr auto	getComputedAttr ()
	Get attributes computed by this functor.

static constexpr bool	getMixing ()

Static Public Member Functions inherited from autopas::Functor< Particle_T, CRTP_T >
static constexpr std::array< typename Particle_T::AttributeNames, 0 >	getNeededAttr ()
	Get attributes needed for computation.

static constexpr std::array< typename Particle_T::AttributeNames, 0 >	getNeededAttr (std::false_type)
	Get attributes needed for computation without N3 optimization.

static constexpr std::array< typename Particle_T::AttributeNames, 0 >	getComputedAttr ()
	Get attributes computed by this functor.

Additional Inherited Members
Public Types inherited from autopas::PairwiseFunctor< Particle_T, CRTP_T >
using	SoAArraysType = typename Particle_T::SoAArraysType
	Structure of the SoAs defined by the particle.

Public Types inherited from autopas::Functor< Particle_T, CRTP_T >
using	SoAArraysType = typename Particle_T::SoAArraysType
	Structure of the SoAs defined by the particle.

using	Functor_T = CRTP_T
	Make the Implementation type template publicly available.

Detailed Description

template<class Particle_T, bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>
class mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >

A functor to handle lennard-jones interactions between two particles (molecules).

This functor assumes that duplicated calculations are always happening, which is characteristic for a Full-Shell scheme.

Template Parameters

Particle_T	The type of particle.
applyShift	Switch for the lj potential to be truncated shifted.
useMixing	Switch for the functor to be used with multiple particle types. If set to false, _epsilon and _sigma need to be set and the constructor with PPL can be omitted.
useNewton3	Switch for the functor to support newton3 on, off or both. See FunctorN3Modes for possible values.
calculateGlobals	Defines whether the global values are to be calculated (energy, virial).
countFLOPs	counts FLOPs and hitrate
relevantForTuning	Whether or not the auto-tuner should consider this functor.

Constructor & Destructor Documentation

◆ LJFunctor() [1/2]

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::LJFunctor ( double cutoff )

inlineexplicit

Constructor for Functor with mixing disabled.

When using this functor it is necessary to call setParticleProperties() to set internal constants because it does not use a particle properties library.

Note: Only to be used with mixing == false.

Parameters

cutoff

◆ LJFunctor() [2/2]

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::LJFunctor	(	double	cutoff,
		ParticlePropertiesLibrary< double, size_t > &	particlePropertiesLibrary
	)

inlineexplicit

Constructor for Functor with mixing active.

This functor takes a ParticlePropertiesLibrary to look up (mixed) properties like sigma, epsilon and shift.

Parameters

cutoff
particlePropertiesLibrary

Member Function Documentation

◆ allowsNewton3()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

bool mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::allowsNewton3 ( )

inlinefinalvirtual

Specifies whether the functor is capable of Newton3-like functors.

If the functor provides an interface to soa or aos functions that utilize Newton's third law of motion (actio = reactio) to reduce the computational complexity this function should return true. If this is not the case this function should return false.

Returns: true if and only if this functor provides an interface to Newton3-like functions.

Implements autopas::Functor< Particle_T, CRTP_T >.

◆ allowsNonNewton3()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

bool mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::allowsNonNewton3 ( )

inlinefinalvirtual

Specifies whether the functor is capable of non-Newton3-like functors.

If the functor provides an interface to soa or aos functions that do not utilize Newton's third law of motion (actio = reactio) this function should return true. If this is not the case this function should return false.

Returns: true if and only if this functor provides an interface to functions that do not utilize Newton3.

Implements autopas::Functor< Particle_T, CRTP_T >.

◆ AoSFunctor()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

void mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::AoSFunctor	(	Particle_T &	i,
		Particle_T &	j,
		bool	newton3
	)

inlinefinalvirtual

PairwiseFunctor for arrays of structures (AoS).

This functor should calculate the forces or any other pair-wise interaction between two particles. This should include a cutoff check if needed!

Parameters

i	Particle i
j	Particle j
newton3	defines whether or whether not to use newton 3

Reimplemented from autopas::PairwiseFunctor< Particle_T, CRTP_T >.

◆ endTraversal()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

void mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::endTraversal ( bool newton3 )

inlinefinalvirtual

Accumulates global values, e.g.

potential energy and virial.

Parameters

newton3

Reimplemented from autopas::Functor< Particle_T, CRTP_T >.

◆ getComputedAttr()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

static constexpr auto mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::getComputedAttr ( )

inlinestaticconstexpr

Get attributes computed by this functor.

Returns: Attributes computed by this functor.

Todo:: C++20: make this function virtual

◆ getHitRate()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

double mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::getHitRate ( ) const

inlineoverridevirtual

Get the hit rate.

Implementation required if FLOPLogger used.

If derived class provides no implementation, the FLOPLogger interprets the default NaN output as invalid and leaves "Not Implemented" in the log.

Returns: (number of kernel calls) / (number of distance calculations)

Reimplemented from autopas::Functor< Particle_T, CRTP_T >.

◆ getMixing()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

static constexpr bool mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::getMixing ( )

inlinestaticconstexpr

Returns: useMixing

◆ getName()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

std::string mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::getName ( )

inlinefinalvirtual

Returns name of functor.

Intended for use with the iteration logger, to differentiate between calls to computeInteractions using different functors in the logs.

Returns: name of functor.

Implements autopas::Functor< Particle_T, CRTP_T >.

◆ getNeededAttr() [1/2]

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

static constexpr auto mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::getNeededAttr ( )

inlinestaticconstexpr

Get attributes needed for computation.

Returns: Attributes needed for computation.

Todo:: C++20: make this function virtual

◆ getNeededAttr() [2/2]

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

static constexpr auto mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::getNeededAttr ( std::false_type )

inlinestaticconstexpr

Get attributes needed for computation without N3 optimization.

Returns: Attributes needed for computation.

Todo:: C++20: make this function virtual

◆ getNumFLOPs()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

size_t mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::getNumFLOPs ( ) const

inlineoverridevirtual

Gets the number of useful FLOPs.

For the distance squared calculation, this is:

Displacement: 3
DistanceSquared in each dimension: 3
DistanceSquared Total: 2
Total: 8

For the force kernel, this is:

inverse distance squared: 1 (assume division is 1 FLOP)
lj2: 1
lj6: 2
lj12: 1
lj12m6: 1
scalar factor: 3
force: 3
accumulate force on mol i: 3
accumulate force on mol j if n3: 3
Total: 15 without n3, 18 with n3

For the globals calculation, this is:

virial: 3
potential: 1, or 2 with shift
accumulation: 4 without n3, 8 with n3
Total: 8 or 9 without n3, 12 or 13 with n3

Caveats:

This function is supposed to return useful FLOPs, e.g. without counting masked vector instructions. You could also argue that, strictly speaking, we redundantly calculate forces and globals twice in the newton3 case on a owned/halo boundary. This function does not treat such "redundant" calculations as useless. Similarly, this function does not treat halo-halo interactions as redundant useless calculations.

Returns: number of FLOPs since initTraversal() is called.

Reimplemented from autopas::Functor< Particle_T, CRTP_T >.

◆ getPotentialEnergy()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

double mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::getPotentialEnergy ( )

inline

Get the potential Energy.

Returns: the potential Energy

◆ getVirial()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

double mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::getVirial ( )

inline

Get the virial.

Returns

◆ initTraversal()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

void mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::initTraversal ( )

inlinefinalvirtual

Reset the global values.

Will set the global values to zero to prepare for the next iteration.

Reimplemented from autopas::Functor< Particle_T, CRTP_T >.

◆ isRelevantForTuning()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

bool mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::isRelevantForTuning ( )

inlinefinalvirtual

Specifies whether the functor should be considered for the auto-tuning process.

Returns: true if and only if this functor is relevant for auto-tuning.

Implements autopas::Functor< Particle_T, CRTP_T >.

◆ setParticleProperties()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

void mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::setParticleProperties	(	SoAFloatPrecision	epsilon24,
		SoAFloatPrecision	sigmaSquared
	)

inline

Sets the particle properties constants for this functor.

This is only necessary if no particlePropertiesLibrary is used.

Parameters

epsilon24
sigmaSquared

◆ SoAFunctorPair()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

void mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::SoAFunctorPair	(	autopas::SoAView< SoAArraysType >	soa1,
		autopas::SoAView< SoAArraysType >	soa2,
		const bool	newton3
	)

inlinefinalvirtual

PairwiseFunctor for structure of arrays (SoA)

This functor should calculate the forces or any other pair-wise interaction between all particles of soa1 and soa2. This should include a cutoff check if needed!

Parameters

soa1	First structure of arrays.
soa2	Second structure of arrays.
newton3	defines whether or whether not to use newton 3

Reimplemented from autopas::PairwiseFunctor< Particle_T, CRTP_T >.

◆ SoAFunctorSingle()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

void mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::SoAFunctorSingle	(	autopas::SoAView< SoAArraysType >	soa,
		bool	newton3
	)

inlinefinalvirtual

PairwiseFunctor for structure of arrays (SoA)

This functor should calculate the forces or any other pair-wise interaction between all particles in an soa. This should include a cutoff check if needed!

Parameters

soa	Structure of arrays
newton3	defines whether or whether not to use newton 3 This functor will always use a newton3 like traversal of the soa.

Reimplemented from autopas::PairwiseFunctor< Particle_T, CRTP_T >.

◆ SoAFunctorVerlet()

template<class Particle_T , bool applyShift = false, bool useMixing = false, autopas::FunctorN3Modes useNewton3 = autopas::FunctorN3Modes::Both, bool calculateGlobals = false, bool countFLOPs = false, bool relevantForTuning = true>

void mdLib::LJFunctor< Particle_T, applyShift, useMixing, useNewton3, calculateGlobals, countFLOPs, relevantForTuning >::SoAFunctorVerlet	(	autopas::SoAView< SoAArraysType >	soa,
		const size_t	indexFirst,
		const std::vector< size_t, autopas::AlignedAllocator< size_t > > &	neighborList,
		bool	newton3
	)

inlinefinalvirtual

PairwiseFunctor for structure of arrays (SoA) for neighbor lists.

This functor should calculate the forces or any other pair-wise interaction between the particle in the SoA with index indexFirst and all particles with indices in the neighborList. This should include a cutoff check if needed!

Parameters

soa	Structure of arrays
indexFirst	The index of the first particle for each interaction
neighborList	The list of neighbors
newton3	defines whether or whether not to use newton 3

Note: If you want to parallelize this by openmp, please ensure that there are no dependencies, i.e. introduce colors!

Reimplemented from autopas::PairwiseFunctor< Particle_T, CRTP_T >.

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

/github/workspace/applicationLibrary/molecularDynamics/molecularDynamicsLibrary/LJFunctor.h

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ LJFunctor() [1/2]

◆ LJFunctor() [2/2]

Member Function Documentation

◆ allowsNewton3()

◆ allowsNonNewton3()

◆ AoSFunctor()

◆ endTraversal()

◆ getComputedAttr()

◆ getHitRate()

◆ getMixing()

◆ getName()

◆ getNeededAttr() [1/2]

◆ getNeededAttr() [2/2]

◆ getNumFLOPs()

◆ getPotentialEnergy()

◆ getVirial()

◆ initTraversal()

◆ isRelevantForTuning()

◆ setParticleProperties()

◆ SoAFunctorPair()

◆ SoAFunctorSingle()

◆ SoAFunctorVerlet()