Standard multi-site LJ molecules. More...

#include <MultisiteMoleculeLJ.h>

Inheritance diagram for mdLib::MultisiteMoleculeLJ:

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Collaboration diagram for mdLib::MultisiteMoleculeLJ:

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Public Types
enum	AttributeNames : int { ptr , id , posX , posY , posZ , velocityX , velocityY , velocityZ , forceX , forceY , forceZ , oldForceX , oldForceY , oldForceZ , quaternion0 , quaternion1 , quaternion2 , quaternion3 , angularVelX , angularVelY , angularVelZ , torqueX , torqueY , torqueZ , typeId , ownershipState }
	Enums used as ids for accessing and creating a dynamically sized SoA.

using	SoAArraysType = typename autopas::utils::SoAType< MultisiteMoleculeLJ *, size_t, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, size_t, autopas::OwnershipState >::Type
	The type for the SoA storage.

Public Types inherited from mdLib::MoleculeLJ
enum	AttributeNames : int { ptr , id , posX , posY , posZ , velocityX , velocityY , velocityZ , forceX , forceY , forceZ , oldForceX , oldForceY , oldForceZ , typeId , ownershipState }
	Enums used as ids for accessing and creating a dynamically sized SoA.

using	SoAArraysType = typename autopas::utils::SoAType< MoleculeLJ *, size_t, double, double, double, double, double, double, double, double, double, double, double, double, size_t, autopas::OwnershipState >::Type
	The type for the SoA storage.

Public Types inherited from autopas::ParticleBase< floatType, idType >
enum	AttributeNames : int { ptr , id , posX , posY , posZ , forceX , forceY , forceZ , ownershipState }
	Enums used as ids for accessing and creating a dynamically sized SoA.

using	ParticleSoAFloatPrecision = floatType
	Floating Point Type used for this particle.

using	ParticleIdType = idType
	Id Type used for this particle.

using	SoAArraysType = typename autopas::utils::SoAType< ParticleBase< floatType, idType > *, idType, floatType, floatType, floatType, floatType, floatType, floatType, OwnershipState >::Type
	The type for the soa storage.

Public Member Functions
	MultisiteMoleculeLJ (std::array< double, 3 > r, std::array< double, 3 > v, std::array< double, 4 > q, std::array< double, 3 > angularVel, unsigned long moleculeId, unsigned long typeId=0)
	Constructor of the MultisiteMoleculeLJ Class.

	~MultisiteMoleculeLJ () override=default
	Destructor of the MultisiteMoleculeLJ class.

template<AttributeNames attribute, std::enable_if_t< attribute==AttributeNames::ptr, bool > = true>
constexpr std::tuple_element< attribute, SoAArraysType >::type::value_type	get ()
	Non-const getter for the pointer of this object.

template<AttributeNames attribute, std::enable_if_t< attribute !=AttributeNames::ptr, bool > = true>
constexpr std::tuple_element< attribute, SoAArraysType >::type::value_type	get () const
	Getter, which allows access to an attribute using the corresponding attribute name (defined in AttributeNames).

template<AttributeNames attribute>
constexpr void	set (typename std::tuple_element< attribute, SoAArraysType >::type::value_type value)
	Setter, which allows set an attribute using the corresponding attribute name (defined in AttributeNames).

const std::array< double, 4 > &	getQuaternion () const
	Get the quaternion defining rotation.

void	setQuaternion (const std::array< double, 4 > &q)
	Set the quaternion defining rotation.

const std::array< double, 3 > &	getAngularVel () const
	Get the angular velocity.

void	setAngularVel (const std::array< double, 3 > &angularVel)
	Set the angular velocity.

void	addAngularVel (const std::array< double, 3 > &angularVel)
	Adds given angular velocity to the particle's angular velocity.

const std::array< double, 3 > &	getTorque () const
	Get the torque.

void	setTorque (const std::array< double, 3 > &torque)
	Set the torque.

void	addTorque (const std::array< double, 3 > &torque)
	Adds given torque to the particle's torque.

void	subTorque (const std::array< double, 3 > &torque)
	Subracts given torque to the particle's torque.

std::string	toString () const override
	Creates a string containing all data of the particle.

Public Member Functions inherited from mdLib::MoleculeLJ
	MoleculeLJ (const std::array< double, 3 > &pos, const std::array< double, 3 > &v, unsigned long moleculeId, unsigned long typeId=0)
	Constructor of lennard jones molecule with initialization of typeID.

template<AttributeNames attribute, std::enable_if_t< attribute==AttributeNames::ptr, bool > = true>
constexpr std::tuple_element< attribute, SoAArraysType >::type::value_type	get ()
	Non-const getter for the pointer of this object.

template<AttributeNames attribute, std::enable_if_t< attribute !=AttributeNames::ptr, bool > = true>
constexpr std::tuple_element< attribute, SoAArraysType >::type::value_type	get () const
	Getter, which allows access to an attribute using the corresponding attribute name (defined in AttributeNames).

template<AttributeNames attribute>
constexpr void	set (typename std::tuple_element< attribute, SoAArraysType >::type::value_type value)
	Setter, which allows set an attribute using the corresponding attribute name (defined in AttributeNames).

const std::array< double, 3 > &	getOldF () const
	Get the old force.

void	setOldF (const std::array< double, 3 > &oldForce)
	Set old force.

size_t	getTypeId () const
	Get TypeId.

void	setTypeId (size_t typeId)
	Set the type id of the Molecule.

std::string	toString () const override
	Creates a string containing all data of the particle.

Public Member Functions inherited from autopas::ParticleBase< floatType, idType >
	ParticleBase (const std::array< double, 3 > &r, const std::array< double, 3 > &v, idType id, OwnershipState ownershipState=OwnershipState::owned)
	Constructor of the Particle class.

virtual	~ParticleBase ()=default
	Destructor of ParticleBase class.

bool	operator== (const ParticleBase &rhs) const
	Equality operator for ParticleBase class.

bool	operator!= (const ParticleBase &rhs) const
	Not-Equals operator for ParticleBase class.

const std::array< double, 3 > &	getF () const
	get the force acting on the particle

void	setF (const std::array< double, 3 > &f)
	Set the force acting on the particle.

void	addF (const std::array< double, 3 > &f)
	Add a partial force to the force acting on the particle.

void	subF (const std::array< double, 3 > &f)
	Substract a partial force from the force acting on the particle.

idType	getID () const
	Get the id of the particle.

void	setID (idType id)
	Set the id of the particle.

const std::array< double, 3 > &	getR () const
	Get the position of the particle.

void	setR (const std::array< double, 3 > &r)
	Set the position of the particle.

bool	setRDistanceCheck (const std::array< double, 3 > &r, double maxDistSquared)
	Add a distance vector to the position of the particle and check if the distance between the old and new position is less than a given max distance.

void	addR (const std::array< double, 3 > &r)
	Add a distance vector to the position of the particle.

bool	addRDistanceCheck (const std::array< double, 3 > &r, double maxDistSquared)
	Add a distance vector to the position of the particle and check if the distance between the old and new position is less than a given max distance.

const std::array< double, 3 > &	getV () const
	Get the velocity of the particle.

void	setV (const std::array< double, 3 > &v)
	Set the velocity of the particle.

void	addV (const std::array< double, 3 > &v)
	Add a vector to the current velocity of the particle.

virtual std::string	toString () const
	Creates a string containing all data of the particle.

bool	isOwned () const
	Defines whether the particle is owned by the current AutoPas object (aka (MPI-)process)

bool	isHalo () const
	Defines whether the particle is a halo particle, i.e., not owned by the current AutoPas object (aka (MPI-)process)

bool	isDummy () const
	Returns whether the particle is a dummy particle.

OwnershipState	getOwnershipState () const
	Returns the particle's ownership state.

void	setOwnershipState (OwnershipState ownershipState)
	Set the OwnershipState to the given value.

template<AttributeNames attribute, std::enable_if_t< attribute==AttributeNames::ptr, bool > = true>
constexpr std::tuple_element< attribute, SoAArraysType >::type::value_type	get ()
	Non-const getter for the pointer of this object.

template<AttributeNames attribute, std::enable_if_t< attribute !=AttributeNames::ptr, bool > = true>
constexpr std::tuple_element< attribute, SoAArraysType >::type::value_type	get () const
	Getter, which allows access to an attribute using the corresponding attribute name (defined in AttributeNames).

template<AttributeNames attribute>
constexpr void	set (typename std::tuple_element< attribute, SoAArraysType >::type::value_type value)
	Setter, which allows set an attribute using the corresponding attribute name (defined in AttributeNames).

Protected Attributes
std::array< double, 4 >	_q {}
	Rotational direction of particle as quaternion.

std::array< double, 3 >	_angularVel {}
	Angular velocity of the particle.

std::array< double, 3 >	_torque {}
	Torque applied to particle.

Protected Attributes inherited from mdLib::MoleculeLJ
size_t	_typeId = 0
	Molecule type id.

std::array< double, 3 >	_oldF = {0., 0., 0.}
	Old Force of the particle experiences as 3D vector.

Protected Attributes inherited from autopas::ParticleBase< floatType, idType >
std::array< floatType, 3 >	_r
	Particle position as 3D coordinates.

std::array< floatType, 3 >	_v
	Particle velocity as 3D vector.

std::array< floatType, 3 >	_f
	Force the particle experiences as 3D vector.

idType	_id
	Particle id.

OwnershipState	_ownershipState
	Defines the state of the ownership of the particle.

Detailed Description

Standard multi-site LJ molecules.

The molecule is treated as a single particle for the purposes of cutoffs and containers, with a quaternion for angular direction, a 3D vector-array for angular velocity, and a vectors of site positions relative to the center of mass and angular direction.

Member Typedef Documentation

◆ SoAArraysType

using mdLib::MultisiteMoleculeLJ::SoAArraysType = typename autopas::utils::SoAType< MultisiteMoleculeLJ *, size_t, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, size_t, autopas::OwnershipState >::Type

The type for the SoA storage.

Note: The attribute owned is of type float but treated as a bool. This means it shall always only take values 0.0 (=false) or 1.0 (=true). The reason for this is the easier use of the value in calculations (See LJFunctor "energyFactor")

Constructor & Destructor Documentation

◆ MultisiteMoleculeLJ()

mdLib::MultisiteMoleculeLJ::MultisiteMoleculeLJ	(	std::array< double, 3 >	r,
		std::array< double, 3 >	v,
		std::array< double, 4 >	q,
		std::array< double, 3 >	angularVel,
		unsigned long	moleculeId,
		unsigned long	typeId = `0`
	)

Constructor of the MultisiteMoleculeLJ Class.

Parameters

r	Position of the particle.
v	Velocity of the particle.
q	Quaternion defining rotation of particle.
angularVel	Rotational velocity of the particle.
moleculeId	Id of the particle.
typeId	Id of the type of the particle. Used in conjunction with ParticlePropertiesLibrary to access molecular information such as site types and relative site positions.

Member Function Documentation

◆ addAngularVel()

void mdLib::MultisiteMoleculeLJ::addAngularVel ( const std::array< double, 3 > & angularVel )

Adds given angular velocity to the particle's angular velocity.

Parameters

angularVel angular velocity to be added

◆ addTorque()

void mdLib::MultisiteMoleculeLJ::addTorque ( const std::array< double, 3 > & torque )

Adds given torque to the particle's torque.

Parameters

torque torque to be added

◆ get() [1/2]

template<AttributeNames attribute, std::enable_if_t< attribute==AttributeNames::ptr, bool > = true>

constexpr std::tuple_element< attribute, SoAArraysType >::type::value_type mdLib::MultisiteMoleculeLJ::get ( )

inlineconstexpr

Non-const getter for the pointer of this object.

Template Parameters

attribute Attribute name.

Returns: this.

◆ get() [2/2]

template<AttributeNames attribute, std::enable_if_t< attribute !=AttributeNames::ptr, bool > = true>

constexpr std::tuple_element< attribute, SoAArraysType >::type::value_type mdLib::MultisiteMoleculeLJ::get ( ) const

inlineconstexpr

Getter, which allows access to an attribute using the corresponding attribute name (defined in AttributeNames).

Template Parameters

attribute Attribute name.

Returns: Value of the requested attribute.

Note: The value of owned is return as floating point number (true = 1.0, false = 0.0).; Moving this function to the .cpp leads to undefined references

◆ getAngularVel()

const std::array< double, 3 > & mdLib::MultisiteMoleculeLJ::getAngularVel ( ) const

Get the angular velocity.

Returns: angular velocity

◆ getQuaternion()

const std::array< double, 4 > & mdLib::MultisiteMoleculeLJ::getQuaternion ( ) const

Get the quaternion defining rotation.

Returns: quaternion defining rotation

◆ getTorque()

const std::array< double, 3 > & mdLib::MultisiteMoleculeLJ::getTorque ( ) const

Get the torque.

Returns: torque

◆ set()

template<AttributeNames attribute>

constexpr void mdLib::MultisiteMoleculeLJ::set ( typename std::tuple_element< attribute, SoAArraysType >::type::value_type value )

inlineconstexpr

Setter, which allows set an attribute using the corresponding attribute name (defined in AttributeNames).

Template Parameters

attribute Attribute name.

Parameters

value New value of the requested attribute.

Note: The value of owned is extracted from a floating point number (true = 1.0, false = 0.0).; Moving this function to the .cpp leads to undefined references

◆ setAngularVel()

void mdLib::MultisiteMoleculeLJ::setAngularVel ( const std::array< double, 3 > & angularVel )

Set the angular velocity.

Parameters

angularVel

◆ setQuaternion()

void mdLib::MultisiteMoleculeLJ::setQuaternion ( const std::array< double, 4 > & q )

Set the quaternion defining rotation.

Parameters

q	quaternion defining rotation

◆ setTorque()

void mdLib::MultisiteMoleculeLJ::setTorque ( const std::array< double, 3 > & torque )

Set the torque.

Parameters

torque

◆ subTorque()

void mdLib::MultisiteMoleculeLJ::subTorque ( const std::array< double, 3 > & torque )

Subracts given torque to the particle's torque.

Parameters

torque torque to be subtracted

◆ toString()

std::string mdLib::MultisiteMoleculeLJ::toString ( ) const

overridevirtual

Creates a string containing all data of the particle.

Returns: String representation.

Reimplemented from mdLib::MoleculeLJ.

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

/github/workspace/applicationLibrary/molecularDynamics/molecularDynamicsLibrary/MultisiteMoleculeLJ.h
/github/workspace/applicationLibrary/molecularDynamics/molecularDynamicsLibrary/MultisiteMoleculeLJ.cpp

Public Types

Public Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ SoAArraysType

Constructor & Destructor Documentation

◆ MultisiteMoleculeLJ()

Member Function Documentation

◆ addAngularVel()

◆ addTorque()

◆ get() [1/2]

◆ get() [2/2]

◆ getAngularVel()

◆ getQuaternion()

◆ getTorque()

◆ set()

◆ setAngularVel()

◆ setQuaternion()

◆ setTorque()

◆ subTorque()

◆ toString()