A particle class for use with ItoSolvers, i.e. drifting Brownian walkers. More...

#include <CD_ItoParticle.H>

Inheritance diagram for ItoParticle:

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Collaboration diagram for ItoParticle:

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Public Member Functions
	ItoParticle ()
	Default constructor – user should subsequently set the variables or call define.

	ItoParticle (const Real a_weight, const RealVect &a_position, const RealVect &a_velocity=RealVect::Zero, const Real a_diffusion=0.0, const Real a_mobility=1.0, const Real a_energy=0.0)
	Constructor. This calls the define function.

	ItoParticle (const ItoParticle &a_other)
	Copy constructor. Copies all fields.

virtual	~ItoParticle ()
	Destructor (deallocates runtime memory storage)

void	define (const Real a_weight, const RealVect &a_position, const RealVect &a_velocity=RealVect::Zero, const Real a_diffusion=0.0, const Real a_mobility=1.0, const Real a_energy=0.0)
	Full define function.

Real &	weight ()
	Get particle weight.

const Real &	weight () const
	Get particle weight.

Real &	diffusion ()
	Get particle diffusion coefficient.

const Real &	diffusion () const
	Get particle diffusion coefficient.

Real &	mobility ()
	Get mobility coefficient.

const Real &	mobility () const
	Get mobility coefficient.

Real &	energy ()
	Get average particle energy.

const Real &	energy () const
	Get average particle energy.

RealVect &	oldPosition ()
	Get the old particle position.

const RealVect &	oldPosition () const
	Get the old particle position.

RealVect &	velocity ()
	Get the particle velocity.

const RealVect &	velocity () const
	Get the particle velocity.

Real	totalEnergy () const
	Get the total energy.

Real	conductivity () const
	Get the particle conductivity.

Real	diffusivity () const
	Get the particle diffusivity.

Real &	tmpReal ()
	Return scratch scalar storage.

const Real &	tmpReal () const
	Return scratch scalar storage.

RealVect &	tmpVect ()
	Return scratch RealVect storage.

const RealVect &	tmpVect () const
	Return scratch RealVect storage.

virtual int	H5size () const
	Function that is used when writing particles to HDF5.

virtual void	H5linearOut (void *const a_buffer) const
	Linearize the checkpointed Real components onto a buffer workable by HDF5.

virtual void	H5linearIn (const void *const a_buffer)
	Delinearize the buffer onto the checkpointed real components in the particle class.

Public Member Functions inherited from GenericParticle< 5, 3 >
	GenericParticle ()
	Default constructor – initializes everything to zero.

	GenericParticle (const GenericParticle< M, N > &a_other)
	Copy constructor. Copies all fields.

virtual	~GenericParticle ()
	Destructor (deallocates runtime memory storage)

const int32_t &	particleID () const noexcept
	Get the particle ID.

int32_t &	particleID () noexcept
	Get the particle ID.

const int32_t &	rankID () const noexcept
	Get the MPI rank ID.

int32_t &	rankID () noexcept
	Get the MPI rank ID.

RealVect &	position ()
	Get the particle position.

const RealVect &	position () const
	Get the particle position.

const std::array< Real, M > &	getReals () const noexcept
	Get the M scalars.

std::array< Real, M > &	getReals () noexcept
	Get the M scalars.

const std::array< RealVect, N > &	getVects () const noexcept
	Get the N vectors.

std::array< RealVect, N > &	getVects () noexcept
	Get the N vectors.

Real &	real ()
	Get one of the scalars.

const Real &	real () const
	Get one of the scalars.

RealVect &	vect ()
	Get one of the RealVects.

const RealVect &	vect () const
	Get one of the RealVects.

bool	operator== (const GenericParticle< M, N > &a_other) const
	Comparison operator with other particle.

bool	operator!= (const GenericParticle< M, N > &a_other) const
	Comparison operator with other particle.

bool	operator< (const GenericParticle< M, N > &a_other) const noexcept
	Particle comparison operator. Returns lexicographical ordering.

virtual int	size () const
	Returns the size, in number of bytes, of a flat representation of the data in this object.

virtual void	linearOut (void *const a_buffer) const
	Write a linear binary representation of the internal data. Assumes that sufficient memory for the buffer has already been allocated by the caller.

virtual void	linearIn (const void *const a_buffer)
	Read a linear binary representation of the internal data. Assumes that the buffer has the correct data.

Static Public Attributes
static std::vector< std::string >	s_realVariables = {"weight", "mobility", "diffusion", "energy", "tmpReal"}
	Naming convention for scalar fields.

static std::vector< std::string >	s_vectVariables = {"oldPos", "velocity", "tmpVect"}
	Naming convention for vector fields.

Additional Inherited Members
Protected Attributes inherited from GenericParticle< 5, 3 >
int32_t	m_particleID
	Particle ID.

int32_t	m_rankID
	MPI rank owning this particle.

RealVect	m_position
	Particle position.

std::array< Real, M >	m_scalars
	Scalar storage array.

std::array< RealVect, N >	m_vectors
	vector storage array

Detailed Description

A particle class for use with ItoSolvers, i.e. drifting Brownian walkers.

This class is used to encapsulate the requirements for running an ItoSolver. This computational particle contains position, weight, velocity, as well as a diffusion coefficient, a mobility, energy, and previous particle position. These are stored as follows:

m_scalars[0] => weight m_scalars[1] => mobility m_scalars[2] => diffusion m_scalars[3] => energy m_scalars[4] => Temp storage. m_vectors[0] => oldPosition m_vectors[1] => velocity m_vectors[3] => Temp storage.

Constructor & Destructor Documentation

◆ ItoParticle() [1/3]

ItoParticle::ItoParticle ( )

inline

Default constructor – user should subsequently set the variables or call define.

Note: If the user has called setNumRuntimeScalars/Vectors then will allocate runtime buffers

◆ ItoParticle() [2/3]

ItoParticle::ItoParticle	(	const Real	a_weight,
		const RealVect &	a_position,
		const RealVect &	a_velocity = `RealVect::Zero`,
		const Real	a_diffusion = `0.0`,
		const Real	a_mobility = `1.0`,
		const Real	a_energy = `0.0`
	)

inline

Constructor. This calls the define function.

Parameters

[in]	a_weight	Particle weight
[in]	a_position	Particle position
[in]	a_velocity	Particle velocity
[in]	a_diffusion	Particle diffusion coefficient
[in]	a_mobility	Particle mobility coefficient
[in]	a_energy	Particle average energy

Note: If the user has called setNumRuntimeScalars/Vectors then will allocate runtime buffers

◆ ItoParticle() [3/3]

ItoParticle::ItoParticle ( const ItoParticle & a_other )

inline

Copy constructor. Copies all fields.

Parameters

[in] a_other Other particle.

Member Function Documentation

◆ conductivity()

Real ItoParticle::conductivity ( ) const

inline

Get the particle conductivity.

Returns: Returns m_weight * m_mobility

◆ define()

void ItoParticle::define	(	const Real	a_weight,
		const RealVect &	a_position,
		const RealVect &	a_velocity = `RealVect::Zero`,
		const Real	a_diffusion = `0.0`,
		const Real	a_mobility = `1.0`,
		const Real	a_energy = `0.0`
	)

inline

Full define function.

Parameters

[in]	a_weight	Particle weight
[in]	a_position	Particle position
[in]	a_velocity	Particle velocity
[in]	a_diffusion	Particle diffusion coefficient
[in]	a_mobility	Particle mobility coefficient
[in]	a_energy	Particle average energy

◆ diffusion() [1/2]

Real & ItoParticle::diffusion ( )

inline

Get particle diffusion coefficient.

Returns: m_diffusion

◆ diffusion() [2/2]

const Real & ItoParticle::diffusion ( ) const

inline

Get particle diffusion coefficient.

Returns: m_diffusion

◆ diffusivity()

Real ItoParticle::diffusivity ( ) const

inline

Get the particle diffusivity.

Returns: Returns m_weight * m_diffusion

◆ energy() [1/2]

Real & ItoParticle::energy ( )

inline

Get average particle energy.

Returns: m_energy

◆ energy() [2/2]

const Real & ItoParticle::energy ( ) const

inline

Get average particle energy.

Returns: m_energy

◆ H5linearIn()

void ItoParticle::H5linearIn ( const void *const a_buffer )

inlinevirtual

Delinearize the buffer onto the checkpointed real components in the particle class.

Ignores the particleID and rankID, so we can directly plug into Chombo's HDF5 API.

Parameters

[in] a_buffer Pointer to memory block

Reimplemented from GenericParticle< 5, 3 >.

◆ H5linearOut()

void ItoParticle::H5linearOut ( void *const a_buffer ) const

inlinevirtual

Linearize the checkpointed Real components onto a buffer workable by HDF5.

Ignores the particleID and rankID, so we can directly plug into Chombo's HDF5 API.

Parameters

[in] a_buffer Pointer to memory block

Reimplemented from GenericParticle< 5, 3 >.

◆ H5size()

int ItoParticle::H5size ( ) const

inlinevirtual

Function that is used when writing particles to HDF5.

This ignores the particleID and rankID, so we can directory plug into Chombo's HDF5 APIs.

Reimplemented from GenericParticle< 5, 3 >.

◆ mobility() [1/2]

Real & ItoParticle::mobility ( )

inline

Get mobility coefficient.

Returns: m_mobility

◆ mobility() [2/2]

const Real & ItoParticle::mobility ( ) const

inline

Get mobility coefficient.

Returns: m_mobility

◆ oldPosition() [1/2]

RealVect & ItoParticle::oldPosition ( )

inline

Get the old particle position.

Returns: m_oldPosition.

◆ oldPosition() [2/2]

const RealVect & ItoParticle::oldPosition ( ) const

inline

Get the old particle position.

Returns: m_oldPosition.

◆ totalEnergy()

Real ItoParticle::totalEnergy ( ) const

inline

Get the total energy.

Returns: Returns m_weight * m_energy

◆ velocity() [1/2]

RealVect & ItoParticle::velocity ( )

inline

Get the particle velocity.

Returns: m_velocity

◆ velocity() [2/2]

const RealVect & ItoParticle::velocity ( ) const

inline

Get the particle velocity.

Returns: m_velocity

◆ weight() [1/2]

Real & ItoParticle::weight ( )

inline

Get particle weight.

Returns: m_weight

◆ weight() [2/2]

const Real & ItoParticle::weight ( ) const

inline

Get particle weight.

Returns: m_weight

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

Source/ItoDiffusion/CD_ItoParticle.H
Source/ItoDiffusion/CD_ItoParticle.cpp
Source/ItoDiffusion/CD_ItoParticleImplem.H

Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ItoParticle() [1/3]

◆ ItoParticle() [2/3]

◆ ItoParticle() [3/3]

Member Function Documentation

◆ conductivity()

◆ define()

◆ diffusion() [1/2]

◆ diffusion() [2/2]

◆ diffusivity()

◆ energy() [1/2]

◆ energy() [2/2]

◆ H5linearIn()

◆ H5linearOut()

◆ H5size()

◆ mobility() [1/2]

◆ mobility() [2/2]

◆ oldPosition() [1/2]

◆ oldPosition() [2/2]

◆ totalEnergy()

◆ velocity() [1/2]

◆ velocity() [2/2]

◆ weight() [1/2]

◆ weight() [2/2]