Inheritance diagram for molecule:

Collaboration diagram for molecule:

Classes
class	constantProperties
	Class to hold molecule constant properties. More...

class	iNew
	Factory class to read-construct particles used for. More...

class	trackingData
	Class used to pass tracking data to the trackToFace function. More...

Public Types
enum	specialTypes { SPECIAL_TETHERED = -1, SPECIAL_FROZEN = -2, NOT_SPECIAL = 0, SPECIAL_USER = 1 }

Public Member Functions
	molecule (const polyMesh &mesh, const barycentric &coordinates, const label celli, const label tetFacei, const label tetPti, const tensor &Q, const vector &v, const vector &a, const vector &pi, const vector &tau, const vector &specialPosition, const constantProperties &constProps, const label special, const label id)
	Construct from components. More...

	molecule (const polyMesh &mesh, const vector &position, const label celli, const tensor &Q, const vector &v, const vector &a, const vector &pi, const vector &tau, const vector &specialPosition, const constantProperties &constProps, const label special, const label id)
	Construct from a position and a cell, searching for the rest of the. More...

	molecule (const polyMesh &mesh, Istream &is, bool readFields=true)
	Construct from Istream. More...

autoPtr< particle >	clone () const
	Construct and return a clone. More...

bool	move (trackingData &, const scalar trackTime)

virtual void	transformProperties (const tensor &T)
	Transform the physical properties of the particle. More...

virtual void	transformProperties (const vector &separation)
	Transform the physical properties of the particle. More...

void	setSitePositions (const constantProperties &constProps)

void	setSiteSizes (label size)

const tensor &	Q () const

tensor &	Q ()

const vector &	v () const

vector &	v ()

const vector &	a () const

vector &	a ()

const vector &	pi () const

vector &	pi ()

const vector &	tau () const

vector &	tau ()

const List< vector > &	siteForces () const

List< vector > &	siteForces ()

const List< vector > &	sitePositions () const

List< vector > &	sitePositions ()

const vector &	specialPosition () const

vector &	specialPosition ()

scalar	potentialEnergy () const

scalar &	potentialEnergy ()

const tensor &	rf () const

tensor &	rf ()

label	special () const

bool	tethered () const

label	id () const

bool	hitPatch (const polyPatch &, trackingData &td, const label patchi, const scalar trackFraction, const tetIndices &tetIs)
	Overridable function to handle the particle hitting a patch. More...

void	hitProcessorPatch (const processorPolyPatch &, trackingData &td)
	Overridable function to handle the particle hitting a processorPatch. More...

void	hitWallPatch (const wallPolyPatch &, trackingData &td, const tetIndices &)
	Overridable function to handle the particle hitting a wallPatch. More...

void	hitPatch (const polyPatch &, trackingData &td)
	Overridable function to handle the particle hitting a polyPatch. More...

Public Member Functions inherited from particle< Type >
	TypeName ("particle")
	Runtime type information. More...

	particle (const polyMesh &mesh, const barycentric &coordinates, const label celli, const label tetFacei, const label tetPti)
	Construct from components. More...

	particle (const polyMesh &mesh, const vector &position, const label celli)
	Construct from a position and a cell, searching for the rest of the. More...

	particle (const polyMesh &mesh, Istream &, bool readFields=true)
	Construct from Istream. More...

	particle (const particle &p)
	Construct as a copy. More...

	particle (const particle &p, const polyMesh &mesh)
	Construct as a copy with refernce to a new mesh. More...

virtual	~particle ()
	Destructor. More...

label	getNewParticleID () const
	Get unique particle creation id. More...

const polyMesh &	mesh () const
	Return the mesh database. More...

const barycentric &	coordinates () const
	Return current particle coordinates. More...

label	cell () const
	Return current cell particle is in. More...

label	tetFace () const
	Return current tet face particle is in. More...

label	tetPt () const
	Return current tet face particle is in. More...

label	face () const
	Return current face particle is on otherwise -1. More...

scalar	stepFraction () const
	Return the fraction of time-step completed. More...

scalar &	stepFraction ()
	Return the fraction of time-step completed. More...

label	origProc () const
	Return the originating processor ID. More...

label &	origProc ()
	Return the originating processor ID. More...

label	origId () const
	Return the particle ID on the originating processor. More...

label &	origId ()
	Return the particle ID on the originating processor. More...

Pair< scalar >	stepFractionSpan () const
	Return the step fraction change within the overall time-step. More...

scalar	currentTimeFraction () const
	Return the current fraction within the timestep. This differs. More...

tetIndices	currentTetIndices () const
	Return the indices of the current tet that the. More...

barycentricTensor	currentTetTransform () const
	Return the current tet transformation tensor. More...

vector	normal () const
	Return the normal of the tri on tetFacei_ for the. More...

vector	oldNormal () const
	Return the normal of the tri on tetFacei_ for the. More...

bool	onFace () const
	Is the particle on a face? More...

bool	onInternalFace () const
	Is the particle on an internal face? More...

bool	onBoundaryFace () const
	Is the particle on a boundary face? More...

label	patch () const
	Return the index of patch that the particle is on. More...

vector	position () const
	Return current particle position. More...

scalar	track (const vector &displacement, const scalar fraction)
	Track along the displacement for a given fraction of the overall. More...

scalar	trackToFace (const vector &displacement, const scalar fraction)
	As particle::track, but also stops on internal faces. More...

scalar	trackToTri (const vector &displacement, const scalar fraction, label &tetTriI)
	As particle::trackToFace, but also stops on tet triangles. On. More...

scalar	trackToStationaryTri (const vector &displacement, const scalar fraction, label &tetTriI)
	As particle::trackToTri, but for stationary meshes. More...

scalar	trackToMovingTri (const vector &displacement, const scalar fraction, label &tetTriI)
	As particle::trackToTri, but for moving meshes. More...

template<class TrackData >
void	trackToFace (const vector &displacement, const scalar fraction, TrackData &td)
	As non-templated particle::trackToFace, but with additional. More...

void	constrainToMeshCentre ()
	Set the constrained components of the particle position to the. More...

void	patchData (vector &n, vector &U) const
	Get the normal and velocity of the current patch location. More...

virtual scalar	wallImpactDistance (const vector &n) const
	The nearest distance to a wall that. More...

template<class TrackData >
void	prepareForParallelTransfer (const label patchi, TrackData &td)
	Convert global addressing to the processor patch. More...

template<class TrackData >
void	correctAfterParallelTransfer (const label patchi, TrackData &td)
	Convert processor patch addressing to the global equivalents. More...

void	prepareForInteractionListReferral (const vectorTensorTransform &transform)
	Break the topology and store the particle position so that the. More...

void	correctAfterInteractionListReferral (const label celli)
	Correct the topology after referral. The particle may still be. More...

label	procTetPt (const polyMesh &procMesh, const label procCell, const label procTetFace) const
	Return the tet point approproate for decomposition or reconstruction. More...

void	autoMap (const vector &position, const mapPolyMesh &mapper)
	Map after a topology change. More...

void	writePosition (Ostream &) const
	Write the particle position and cell. More...

Static Public Member Functions
static void	readFields (Cloud< molecule > &mC)

static void	writeFields (const Cloud< molecule > &mC)

Static Public Member Functions inherited from particle< Type >
static string	propertyList ()

template<class CloudType >
static void	readFields (CloudType &c)
	Read the fields associated with the owner cloud. More...

template<class CloudType >
static void	writeFields (const CloudType &c)
	Write the fields associated with the owner cloud. More...

Friends
class	Cloud< molecule >

Ostream &	operator<< (Ostream &, const molecule &)

Additional Inherited Members
Static Public Attributes inherited from particle< Type >
static string	propertyList_ = Foam::particle::propertyList()
	String representation of properties. More...

static label	particleCount_ = 0
	Cumulative particle counter - used to provode unique ID. More...

Protected Member Functions inherited from particle< Type >
template<class TrackData >
void	hitFace (TrackData &td)
	Overridable function to handle the particle hitting a face. More...

template<class TrackData >
bool	hitPatch (const polyPatch &, TrackData &td, const label patchi, const scalar trackFraction, const tetIndices &tetIs)
	Overridable function to handle the particle hitting a. More...

template<class TrackData >
void	hitWedgePatch (const wedgePolyPatch &, TrackData &td)
	Overridable function to handle the particle hitting a wedgePatch. More...

template<class TrackData >
void	hitSymmetryPlanePatch (const symmetryPlanePolyPatch &, TrackData &td)
	Overridable function to handle the particle hitting a. More...

template<class TrackData >
void	hitSymmetryPatch (const symmetryPolyPatch &, TrackData &td)
	Overridable function to handle the particle hitting a. More...

template<class TrackData >
void	hitCyclicPatch (const cyclicPolyPatch &, TrackData &td)
	Overridable function to handle the particle hitting a cyclicPatch. More...

template<class TrackData >
void	hitCyclicAMIPatch (const cyclicAMIPolyPatch &, TrackData &td, const vector &direction)
	Overridable function to handle the particle hitting a cyclicAMIPatch. More...

template<class TrackData >
void	hitProcessorPatch (const processorPolyPatch &, TrackData &td)
	Overridable function to handle the particle hitting a. More...

template<class TrackData >
void	hitWallPatch (const wallPolyPatch &, TrackData &td, const tetIndices &tetIs)
	Overridable function to handle the particle hitting a wallPatch. More...

template<class TrackData >
void	hitPatch (const polyPatch &, TrackData &td)
	Overridable function to handle the particle hitting a. More...

Detailed Description

Foam::molecule.

Source files

Definition at line 64 of file molecule.H.

Member Enumeration Documentation

◆ specialTypes

enum specialTypes

Enumerator
SPECIAL_TETHERED
SPECIAL_FROZEN
NOT_SPECIAL
SPECIAL_USER

Definition at line 80 of file molecule.H.

Constructor & Destructor Documentation

◆ molecule() [1/3]

molecule	(	const polyMesh &	mesh,
		const barycentric &	coordinates,
		const label	celli,
		const label	tetFacei,
		const label	tetPti,
		const tensor &	Q,
		const vector &	v,
		const vector &	a,
		const vector &	pi,
		const vector &	tau,
		const vector &	specialPosition,
		const constantProperties &	constProps,
		const label	special,
		const label	id
	)

inline

Construct from components.

Definition at line 221 of file moleculeI.H.

References molecule::setSitePositions().

Referenced by molecule::clone(), molecule::constantProperties::constantProperties(), and molecule::iNew::operator()().

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◆ molecule() [2/3]

molecule	(	const polyMesh &	mesh,
		const vector &	position,
		const label	celli,
		const tensor &	Q,
		const vector &	v,
		const vector &	a,
		const vector &	pi,
		const vector &	tau,
		const vector &	specialPosition,
		const constantProperties &	constProps,
		const label	special,
		const label	id
	)

inline

Construct from a position and a cell, searching for the rest of the.

required topology

Definition at line 258 of file moleculeI.H.

References Foam::abort(), Foam::FatalError, FatalErrorInFunction, Foam::findIndex(), forAll, molecule::id(), Foam::mag(), Foam::nl, molecule::setSitePositions(), List< T >::setSize(), molecule::constantProperties::siteIds(), and List< T >::size().

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◆ molecule() [3/3]

molecule	(	const polyMesh &	mesh,
		Istream &	is,
		bool	readFields = `true`
	)

Construct from Istream.

Definition at line 41 of file moleculeIO.C.

References IOstream::check(), IOstream::format(), Istream::read(), Foam::readLabel(), and readScalar.

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Member Function Documentation

◆ clone()

autoPtr<particle> clone ( ) const

inlinevirtual

Construct and return a clone.

Reimplemented from particle< Type >.

Definition at line 283 of file molecule.H.

References molecule::molecule().

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◆ move()

bool move	(	molecule::trackingData &	td,
		const scalar	trackTime
	)

Definition at line 68 of file molecule.C.

References Foam::abort(), particle< Type >::TrackingData< CloudType >::cloud(), moleculeCloud::constProps(), f(), Foam::FatalError, FatalErrorInFunction, forAll, particle< Type >::TrackingData< CloudType >::keepParticle, molecule::trackingData::part(), R, s(), molecule::setSitePositions(), particle< Type >::stepFraction(), particle< Type >::TrackingData< CloudType >::switchProcessor, Tensor< Cmpt >::T(), particle< Type >::trackToFace(), Vector< Cmpt >::x(), Vector< Cmpt >::y(), and Foam::Zero.

Referenced by molecule::iNew::operator()().

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◆ transformProperties() [1/2]

void transformProperties ( const tensor & T )

virtual

Transform the physical properties of the particle.

according to the given transformation tensor

Reimplemented from particle< Type >.

Definition at line 184 of file molecule.C.

References particle< Type >::position(), Foam::transform(), and particle< Type >::transformProperties().

Referenced by molecule::iNew::operator()().

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◆ transformProperties() [2/2]

void transformProperties ( const vector & separation )

virtual

Transform the physical properties of the particle.

according to the given separation vector

Reimplemented from particle< Type >.

Definition at line 206 of file molecule.C.

References molecule::SPECIAL_TETHERED, and particle< Type >::transformProperties().

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◆ setSitePositions()

void setSitePositions ( const constantProperties & constProps )

Definition at line 219 of file molecule.C.

References particle< Type >::position(), and molecule::constantProperties::siteReferencePositions().

Referenced by molecule::molecule(), molecule::move(), and molecule::iNew::operator()().

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◆ setSiteSizes()

void setSiteSizes ( label size )

Definition at line 225 of file molecule.C.

References molecule::hitPatch(), and List< T >::setSize().

Referenced by molecule::iNew::operator()().

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◆ Q() [1/2]

const Foam::tensor & Q ( ) const

inline

Definition at line 501 of file moleculeI.H.

Referenced by molecule::constantProperties::constantProperties(), molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ Q() [2/2]

Foam::tensor & Q ( )

inline

Definition at line 507 of file moleculeI.H.

◆ v() [1/2]

const Foam::vector & v ( ) const

inline

Definition at line 513 of file moleculeI.H.

Referenced by molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ v() [2/2]

Foam::vector & v ( )

inline

Definition at line 519 of file moleculeI.H.

◆ a() [1/2]

const Foam::vector & a ( ) const

inline

Definition at line 525 of file moleculeI.H.

Referenced by molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ a() [2/2]

Foam::vector & a ( )

inline

Definition at line 531 of file moleculeI.H.

◆ pi() [1/2]

const Foam::vector & pi ( ) const

inline

Definition at line 537 of file moleculeI.H.

Referenced by molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ pi() [2/2]

Foam::vector & pi ( )

inline

Definition at line 543 of file moleculeI.H.

◆ tau() [1/2]

const Foam::vector & tau ( ) const

inline

Definition at line 549 of file moleculeI.H.

Referenced by molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ tau() [2/2]

Foam::vector & tau ( )

inline

Definition at line 555 of file moleculeI.H.

◆ siteForces() [1/2]

const Foam::List< Foam::vector > & siteForces ( ) const

inline

Definition at line 561 of file moleculeI.H.

Referenced by molecule::iNew::operator()().

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◆ siteForces() [2/2]

Foam::List< Foam::vector > & siteForces ( )

inline

Definition at line 567 of file moleculeI.H.

◆ sitePositions() [1/2]

const Foam::List< Foam::vector > & sitePositions ( ) const

inline

Definition at line 573 of file moleculeI.H.

Referenced by molecule::iNew::operator()().

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◆ sitePositions() [2/2]

Foam::List< Foam::vector > & sitePositions ( )

inline

Definition at line 579 of file moleculeI.H.

◆ specialPosition() [1/2]

const Foam::vector & specialPosition ( ) const

inline

Definition at line 585 of file moleculeI.H.

Referenced by molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ specialPosition() [2/2]

Foam::vector & specialPosition ( )

inline

Definition at line 591 of file moleculeI.H.

◆ potentialEnergy() [1/2]

Foam::scalar potentialEnergy ( ) const

inline

Definition at line 597 of file moleculeI.H.

Referenced by molecule::iNew::operator()().

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◆ potentialEnergy() [2/2]

Foam::scalar & potentialEnergy ( )

inline

Definition at line 603 of file moleculeI.H.

◆ rf() [1/2]

const Foam::tensor & rf ( ) const

inline

Definition at line 609 of file moleculeI.H.

Referenced by molecule::iNew::operator()().

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◆ rf() [2/2]

Foam::tensor & rf ( )

inline

Definition at line 615 of file moleculeI.H.

◆ special()

Foam::label special ( ) const

inline

Definition at line 621 of file moleculeI.H.

Referenced by molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ tethered()

bool tethered ( ) const

inline

Definition at line 627 of file moleculeI.H.

References molecule::SPECIAL_TETHERED.

Referenced by molecule::iNew::operator()().

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◆ id()

Foam::label id ( ) const

inline

Definition at line 633 of file moleculeI.H.

Referenced by molecule::molecule(), molecule::iNew::operator()(), molecule::readFields(), and molecule::writeFields().

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◆ hitPatch() [1/2]

bool hitPatch	(	const polyPatch &	,
		trackingData &	td,
		const label	patchi,
		const scalar	trackFraction,
		const tetIndices &	tetIs
	)

Overridable function to handle the particle hitting a patch.

Executed before other patch-hitting functions

Definition at line 234 of file molecule.C.

References molecule::hitProcessorPatch().

Referenced by molecule::hitWallPatch(), molecule::iNew::operator()(), and molecule::setSiteSizes().

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◆ hitProcessorPatch()

void hitProcessorPatch	(	const processorPolyPatch &	,
		trackingData &	td
	)

Overridable function to handle the particle hitting a processorPatch.

Definition at line 247 of file molecule.C.

References molecule::hitWallPatch(), and particle< Type >::TrackingData< CloudType >::switchProcessor.

Referenced by molecule::hitPatch(), and molecule::iNew::operator()().

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◆ hitWallPatch()

void hitWallPatch	(	const wallPolyPatch &	wpp,
		trackingData &	td,
		const tetIndices &	tetIs
	)

Overridable function to handle the particle hitting a wallPatch.

Definition at line 257 of file molecule.C.

References molecule::hitPatch(), Foam::mag(), particle< Type >::normal(), and nw.

Referenced by molecule::hitProcessorPatch(), and molecule::iNew::operator()().

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◆ hitPatch() [2/2]

void hitPatch	(	const polyPatch &	,
		trackingData &	td
	)

Overridable function to handle the particle hitting a polyPatch.

Definition at line 279 of file molecule.C.

References particle< Type >::TrackingData< CloudType >::keepParticle.

◆ readFields()

void readFields ( Cloud< molecule > & mC )

static

Definition at line 94 of file moleculeIO.C.

References molecule::a(), Cloud< ParticleType >::checkFieldIOobject(), Cloud< ParticleType >::fieldIOobject(), forAllIter, molecule::id(), IOobject::MUST_READ, molecule::pi(), molecule::Q(), particle< Type >::readFields(), Cloud< ParticleType >::size(), molecule::special(), molecule::specialPosition(), molecule::tau(), and molecule::v().

Referenced by moleculeCloud::moleculeCloud(), and molecule::iNew::operator()().

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◆ writeFields()

void writeFields ( const Cloud< molecule > & mC )

static

Definition at line 150 of file moleculeIO.C.

References molecule::a(), Foam::endl(), Cloud< ParticleType >::fieldIOobject(), forAllConstIter(), molecule::id(), Foam::Info, moleculeCloud::mesh(), IOobject::name(), IOobject::NO_READ, molecule::pi(), cloud::prefix, molecule::Q(), Cloud< ParticleType >::size(), molecule::special(), molecule::specialPosition(), molecule::tau(), objectRegistry::time(), Time::timePath(), molecule::v(), particle< Type >::writeFields(), and moleculeCloud::writeXYZ().

Referenced by molecule::iNew::operator()().

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Friends And Related Function Documentation

◆ Cloud< molecule >

friend class Cloud< molecule >

friend

Definition at line 233 of file molecule.H.

◆ operator<<

Ostream& operator<<	(	Ostream &	,
		const molecule &
	)

friend

Referenced by molecule::iNew::operator()().

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

src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C

Classes

Public Types

Public Member Functions

Static Public Member Functions

Friends

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ specialTypes

Constructor & Destructor Documentation

◆ molecule() [1/3]

◆ molecule() [2/3]

◆ molecule() [3/3]

Member Function Documentation

◆ clone()

◆ move()

◆ transformProperties() [1/2]

◆ transformProperties() [2/2]

◆ setSitePositions()

◆ setSiteSizes()

◆ Q() [1/2]

◆ Q() [2/2]

◆ v() [1/2]

◆ v() [2/2]

◆ a() [1/2]

◆ a() [2/2]

◆ pi() [1/2]

◆ pi() [2/2]

◆ tau() [1/2]

◆ tau() [2/2]

◆ siteForces() [1/2]

◆ siteForces() [2/2]

◆ sitePositions() [1/2]

◆ sitePositions() [2/2]

◆ specialPosition() [1/2]

◆ specialPosition() [2/2]

◆ potentialEnergy() [1/2]

◆ potentialEnergy() [2/2]

◆ rf() [1/2]

◆ rf() [2/2]

◆ special()

◆ tethered()

◆ id()

◆ hitPatch() [1/2]

◆ hitProcessorPatch()

◆ hitWallPatch()

◆ hitPatch() [2/2]

◆ readFields()

◆ writeFields()

Friends And Related Function Documentation

◆ Cloud< molecule >

◆ operator<<