Inheritance diagram for molecule:

Collaboration diagram for molecule:

Classes
class	constantProperties
	Class to hold molecule constant properties. 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 vector &position, const label celli, label &nLocateBoundaryHits, 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 (Istream &is, bool readFields=true)
	Construct from Istream. More...

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

bool	move (moleculeCloud &, trackingData &)

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

void	setSitePositions (const polyMesh &mesh, 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

void	hitWallPatch (moleculeCloud &cloud, trackingData &td)
	Overridable function to handle the particle hitting a wallPatch. More...

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

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

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

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

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

virtual	~particle ()
	Destructor. More...

label	getNewParticleIndex () const
	Get unique particle creation id. 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...

label &	face ()
	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...

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

vector	normal (const polyMesh &mesh) 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 polyMesh &mesh) const
	Is the particle on an internal face? More...

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

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

vector	position (const polyMesh &mesh) const
	Return current particle position. More...

void	reset (const scalar stepFraction)
	Set the step fraction and clear the behind data in preparation. More...

bool	locate (const polyMesh &mesh, const vector &position, label celli)
	Locate the particle at the given position. More...

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

scalar	trackToCell (const polyMesh &mesh, const vector &displacement, const scalar fraction)
	As particle::track, but stops when a new cell is reached. More...

scalar	trackToFace (const polyMesh &mesh, const vector &displacement, const scalar fraction)
	As particle::track, but stops when a face is hit. More...

template<class TrackCloudType >
void	hitFace (const vector &displacement, const scalar fraction, TrackCloudType &cloud, trackingData &td)
	Hit the current face. If the current face is internal than this. More...

template<class TrackCloudType >
scalar	trackToAndHitFace (const vector &displacement, const scalar fraction, TrackCloudType &cloud, trackingData &td)
	Convenience function. Combines trackToFace and hitFace. More...

vector	deviationFromMeshCentre (const polyMesh &mesh) const
	Get the displacement from the mesh centre. Used to correct the. More...

void	patchData (const polyMesh &mesh, vector &normal, vector &displacement) const
	Get the normal and displacement of the current patch location. More...

template<class TrackCloudType >
void	prepareForParallelTransfer (TrackCloudType &, trackingData &)
	Make changes prior to a parallel transfer. Runs either. More...

template<class TrackCloudType >
void	correctAfterParallelTransfer (TrackCloudType &, trackingData &)
	Make changes following a parallel transfer. Runs either. More...

void	prepareForProcessorTransfer (trackingData &td)
	Make changes prior to a transfer across a processor boundary. More...

void	correctAfterProcessorTransfer (trackingData &td)
	Make changes following a transfer across a processor boundary. More...

void	prepareForNonConformalCyclicTransfer (const polyMesh &mesh, const label sendToPatch, const label sendToPatchFace, const vector &sendToPosition)
	Make changes prior to a transfer across a non conformal cyclic. More...

void	correctAfterNonConformalCyclicTransfer (const polyMesh &mesh, const label sendToPatch, labelList &patchNLocateBoundaryHits)
	Make changes following a transfer across a non conformal cyclic. More...

template<class TrackCloudType >
bool	hitPatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a patch. More...

template<class TrackCloudType >
void	hitWedgePatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a wedgePatch. More...

template<class TrackCloudType >
void	hitSymmetryPlanePatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a. More...

template<class TrackCloudType >
void	hitSymmetryPatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a. More...

template<class TrackCloudType >
void	hitCyclicPatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a. More...

template<class TrackCloudType >
bool	hitNonConformalCyclicPatch (const vector &displacement, const scalar fraction, const label patchi, TrackCloudType &cloud, trackingData &td)
	Overridable function to handle the particle hitting an. More...

template<class TrackCloudType >
void	hitProcessorPatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a. More...

template<class TrackCloudType >
void	hitWallPatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a wallPatch. More...

template<class TrackCloudType >
void	hitBasicPatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a basic. More...

void	prepareForInteractionListReferral (const polyMesh &mesh, const transformer &transform)
	Break the topology and store the cartesian position so that the. More...

void	correctAfterInteractionListReferral (const polyMesh &mesh, const label celli)
	Correct the topology after referral. Locates the particle. More...

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

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

template<class TrackCloudType >
Foam::scalar	trackToAndHitFace (const vector &displacement, const scalar fraction, TrackCloudType &cloud, trackingData &td)

Static Public Member Functions
static autoPtr< molecule >	New (Istream &is)
	Construct from Istream and return. More...

static void	readFields (lagrangian::Cloud< molecule > &mC)

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

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

static autoPtr< particle >	New (Istream &is)
	Construct from Istream and return. More...

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

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

Friends
class	lagrangian::Cloud< molecule >

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

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

static label	particleCount = 0
	Cumulative particle counter - used to provide unique ID. More...

static const bool	instantaneous = false
	Particles are not instantaneous by default. More...

Detailed Description

Foam::molecule.

Source files

Definition at line 65 of file molecule.H.

Member Enumeration Documentation

◆ specialTypes

enum specialTypes

Enumerator
SPECIAL_TETHERED
SPECIAL_FROZEN
NOT_SPECIAL
SPECIAL_USER

Definition at line 81 of file molecule.H.

Constructor & Destructor Documentation

◆ molecule() [1/2]

molecule	(	const polyMesh &	mesh,
		const vector &	position,
		const label	celli,
		label &	nLocateBoundaryHits,
		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 222 of file moleculeI.H.

References mesh, and molecule::setSitePositions().

Referenced by molecule::clone(), and molecule::New().

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◆ molecule() [2/2]

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

Construct from Istream.

Definition at line 40 of file moleculeIO.C.

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

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Member Function Documentation

◆ clone()

autoPtr<particle> clone ( ) const

inlinevirtual

Construct and return a clone.

Reimplemented from particle.

Definition at line 284 of file molecule.H.

References molecule::molecule().

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◆ New()

static autoPtr<molecule> New ( Istream & is )

inlinestatic

Construct from Istream and return.

Definition at line 290 of file molecule.H.

References molecule::molecule().

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◆ move()

bool move	(	moleculeCloud &	cloud,
		trackingData &	td
	)

Definition at line 68 of file molecule.C.

References Foam::abort(), TimeState::deltaTValue(), f(), Foam::FatalError, FatalErrorInFunction, forAll, particle::trackingData::keepParticle, molecule::constantProperties::linearMolecule(), molecule::constantProperties::mass(), particle::trackingData::mesh, molecule::constantProperties::momentOfInertia(), molecule::trackingData::part(), molecule::constantProperties::pointMolecule(), Foam::R(), s(), particle::trackingData::sendToProc, molecule::constantProperties::siteReferencePositions(), objectRegistry::time(), and Foam::Zero.

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◆ transformProperties()

void transformProperties ( const transformer & )

virtual

Transform the physical properties of the particle.

according to the given transformation tensor

Reimplemented from particle.

Definition at line 190 of file molecule.C.

References Foam::transform(), dimensionSet::transform, and particle::transformProperties().

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◆ setSitePositions()

void setSitePositions	(	const polyMesh &	mesh,
		const constantProperties &	constProps
	)

Definition at line 217 of file molecule.C.

References mesh, Foam::tracking::position(), and molecule::constantProperties::siteReferencePositions().

Referenced by molecule::molecule().

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◆ setSiteSizes()

void setSiteSizes ( label size )

Definition at line 229 of file molecule.C.

◆ Q() [1/2]

const Foam::tensor & Q ( ) const

inline

Definition at line 467 of file moleculeI.H.

Referenced by molecule::constantProperties::constantProperties().

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◆ Q() [2/2]

Foam::tensor & Q ( )

inline

Definition at line 473 of file moleculeI.H.

◆ v() [1/2]

const Foam::vector & v ( ) const

inline

Definition at line 479 of file moleculeI.H.

◆ v() [2/2]

Foam::vector & v ( )

inline

Definition at line 485 of file moleculeI.H.

◆ a() [1/2]

const Foam::vector & a ( ) const

inline

Definition at line 491 of file moleculeI.H.

◆ a() [2/2]

Foam::vector & a ( )

inline

Definition at line 497 of file moleculeI.H.

◆ pi() [1/2]

const Foam::vector & pi ( ) const

inline

Definition at line 503 of file moleculeI.H.

◆ pi() [2/2]

Foam::vector & pi ( )

inline

Definition at line 509 of file moleculeI.H.

◆ tau() [1/2]

const Foam::vector & tau ( ) const

inline

Definition at line 515 of file moleculeI.H.

◆ tau() [2/2]

Foam::vector & tau ( )

inline

Definition at line 521 of file moleculeI.H.

◆ siteForces() [1/2]

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

inline

Definition at line 527 of file moleculeI.H.

◆ siteForces() [2/2]

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

inline

Definition at line 533 of file moleculeI.H.

◆ sitePositions() [1/2]

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

inline

Definition at line 539 of file moleculeI.H.

◆ sitePositions() [2/2]

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

inline

Definition at line 545 of file moleculeI.H.

◆ specialPosition() [1/2]

const Foam::vector & specialPosition ( ) const

inline

Definition at line 551 of file moleculeI.H.

◆ specialPosition() [2/2]

Foam::vector & specialPosition ( )

inline

Definition at line 557 of file moleculeI.H.

◆ potentialEnergy() [1/2]

Foam::scalar potentialEnergy ( ) const

inline

Definition at line 563 of file moleculeI.H.

◆ potentialEnergy() [2/2]

Foam::scalar & potentialEnergy ( )

inline

Definition at line 569 of file moleculeI.H.

◆ rf() [1/2]

const Foam::tensor & rf ( ) const

inline

Definition at line 575 of file moleculeI.H.

◆ rf() [2/2]

Foam::tensor & rf ( )

inline

Definition at line 581 of file moleculeI.H.

◆ special()

Foam::label special ( ) const

inline

Definition at line 587 of file moleculeI.H.

◆ tethered()

bool tethered ( ) const

inline

Definition at line 593 of file moleculeI.H.

◆ id()

Foam::label id ( ) const

inline

Definition at line 599 of file moleculeI.H.

◆ hitWallPatch()

void hitWallPatch	(	moleculeCloud &	cloud,
		trackingData &	td
	)

Overridable function to handle the particle hitting a wallPatch.

Definition at line 237 of file molecule.C.

References particle::trackingData::mesh.

◆ readFields()

void readFields ( lagrangian::Cloud< molecule > & mC )

static

Definition at line 89 of file moleculeIO.C.

References Cloud< ParticleType >::checkFieldIOobject(), Cloud< ParticleType >::fieldIOobject(), forAllIter, IOobject::MUST_READ, Foam::constant::mathematical::pi(), particle::readFields(), Cloud< ParticleType >::size(), tau, and Foam::vtkWriteOps::write().

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

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◆ writeFields()

void writeFields ( const lagrangian::Cloud< molecule > & mC )

static

Definition at line 145 of file moleculeIO.C.

References Foam::endl(), Cloud< ParticleType >::fieldIOobject(), forAllConstIter, Foam::Info, moleculeCloud::mesh(), IOobject::name(), IOobject::NO_READ, Foam::constant::mathematical::pi(), cloud::prefix, Cloud< ParticleType >::size(), tau, objectRegistry::time(), Time::timePath(), regIOobject::write(), Foam::vtkWriteOps::write(), particle::writeFields(), and moleculeCloud::writeXYZ().

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Friends And Related Function Documentation

◆ lagrangian::Cloud< molecule >

friend class lagrangian::Cloud< molecule >

friend

Definition at line 252 of file molecule.H.

◆ operator<<

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

friend

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

src/lagrangian/molecularDynamics/molecule/molecule.H
src/lagrangian/molecularDynamics/molecule/molecule.C
src/lagrangian/molecularDynamics/molecule/moleculeI.H
src/lagrangian/molecularDynamics/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() [1/2]

◆ molecule() [2/2]

Member Function Documentation

◆ clone()

◆ New()

◆ move()

◆ transformProperties()

◆ 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()

◆ hitWallPatch()

◆ readFields()

◆ writeFields()

Friends And Related Function Documentation

◆ lagrangian::Cloud< molecule >

◆ operator<<