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 vector &position, 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, 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 vector &position, const label celli, const label tetFacei, const label tetPtI)
	Construct from components. More...

	particle (const polyMesh &mesh, const vector &position, const label celli, bool doCellFacePt=true)
	Construct from components, tetFacei_ and tetPtI_ are not. 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 vector &	position () const
	Return current particle position. More...

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

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

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

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

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

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

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

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

tetPointRef	currentTet () const
	Return the geometry of the current tet that the. 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...

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

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

bool	softImpact () const
	Return the impact model to be used, soft or hard (default). More...

scalar	currentTime () const
	Return the particle current time. More...

void	initCellFacePt ()
	Check the stored cell value (setting if necessary) and. More...

bool	onBoundary () const
	Is the particle on the boundary/(or outside the domain)? More...

bool	internalFace (const label facei) const
	Is this global face an internal face? More...

bool	boundaryFace (const label facei) const
	Is this global face a boundary face? More...

label	patch (const label facei) const
	Which patch is particle on. More...

label	patchFace (const label patchi, const label facei) const
	Which face of this patch is this particle on. More...

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

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

label	origProc () const
	Return const access to the originating processor id. More...

label &	origProc ()
	Return the originating processor id for manipulation. More...

label	origId () const
	Return const access to the particle id on originating processor. More...

label &	origId ()
	Return the particle id on originating processor for manipulation. More...

template<class TrackData >
label	track (const vector &endPosition, TrackData &td)
	Track particle to end of trajectory. More...

template<class TrackData >
scalar	trackToFace (const vector &endPosition, TrackData &td)
	Track particle to a given position and returns 1.0 if the. More...

label	faceInterpolation () const
	Return the index of the face to be used in the interpolation. 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	writePosition (Ostream &) const
	Write the particle position and cell. More...

template<class TrackData >
Foam::label	track (const vector &endPosition, TrackData &td)

template<class TrackData >
Foam::scalar	trackToFace (const vector &endPosition, TrackData &td)

Public Member Functions inherited from DLListBase::link
	link ()
	Null construct. More...

bool	registered () const
	Check if the link is registered with the DLListBase. More...

void	deregister ()
	Deregister the link after removal. 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
Public Attributes inherited from DLListBase::link
link *	prev_
	Pointer to next entry in list. More...

link *	next_

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...

static const scalar	trackingCorrectionTol = 1e-5
	Fraction of distance to tet centre to move a particle to. More...

static const scalar	lambdaDistanceToleranceCoeff = 1e3*SMALL
	Fraction of the cell volume to use in determining tolerance values. More...

static const scalar	minStepFractionTol = 1e5*SMALL
	Minimum stepFraction tolerance. More...

Protected Member Functions inherited from particle< Type >
void	findTris (const vector &position, DynamicList< label > &faceList, const tetPointRef &tet, const FixedList< vector, 4 > &tetAreas, const FixedList< label, 4 > &tetPlaneBasePtIs, const scalar tol) const
	Find the tet tri faces between position and tet centre. More...

scalar	tetLambda (const vector &from, const vector &to, const label triI, const vector &tetArea, const label tetPlaneBasePtI, const label celli, const label tetFacei, const label tetPtI, const scalar tol) const
	Find the lambda value for the line to-from across the. More...

scalar	movingTetLambda (const vector &from, const vector &to, const label triI, const vector &tetArea, const label tetPlaneBasePtI, const label celli, const label tetFacei, const label tetPtI, const scalar tol) const
	Find the lambda value for a moving tri face. More...

void	tetNeighbour (label triI)
	Modify the tet owner data by crossing triI. More...

void	crossEdgeConnectedFace (const label &celli, label &tetFacei, label &tetPtI, const edge &e)
	Cross the from the given face across the given edge of the. More...

template<class CloudType >
void	hitWallFaces (const CloudType &td, const vector &from, const vector &to, scalar &lambdaMin, tetIndices &closestTetIs)

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...

Protected Attributes inherited from particle< Type >
const polyMesh &	mesh_
	Reference to the polyMesh database. More...

vector	position_
	Position of particle. More...

label	celli_
	Index of the cell it is in. More...

label	facei_
	Face index if the particle is on a face otherwise -1. More...

scalar	stepFraction_
	Fraction of time-step completed. More...

label	tetFacei_
	Index of the face that owns the decomposed tet that the. More...

label	tetPtI_
	Index of the point on the face that defines the decomposed. More...

label	origProc_
	Originating processor id. More...

label	origId_
	Local particle id on originating processor. More...

Detailed Description

Foam::molecule.

Source files

Definition at line 64 of file molecule.H.

Member Enumeration Documentation

enum specialTypes

Enumerator
SPECIAL_TETHERED
SPECIAL_FROZEN
NOT_SPECIAL
SPECIAL_USER

Definition at line 80 of file molecule.H.

Constructor & Destructor Documentation

molecule	(	const polyMesh &	mesh,
		const vector &	position,
		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 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().

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

Here is the call graph for this function:

Here is the caller graph for this function:

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.

Here is the call graph for this function:

Member Function Documentation

autoPtr<particle> clone ( ) const

inlinevirtual

Construct and return a clone.

Reimplemented from particle< Type >.

Definition at line 265 of file molecule.H.

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

Here is the call graph for this function:

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, Foam::min(), molecule::trackingData::part(), particle< Type >::position(), 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()().

Here is the call graph for this function:

Here is the caller graph for this function:

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 192 of file molecule.C.

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

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

Here is the call graph for this function:

Here is the caller graph for this function:

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 214 of file molecule.C.

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

Here is the call graph for this function:

void setSitePositions ( const constantProperties & constProps )

Definition at line 227 of file molecule.C.

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

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

Here is the call graph for this function:

Here is the caller graph for this function:

void setSiteSizes ( label size )

Definition at line 233 of file molecule.C.

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

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

Here is the call graph for this function:

Here is the caller graph for this function:

const Foam::tensor & Q ( ) const

inline

Definition at line 466 of file moleculeI.H.

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

Here is the caller graph for this function:

Foam::tensor & Q ( )

inline

Definition at line 472 of file moleculeI.H.

const Foam::vector & v ( ) const

inline

Definition at line 478 of file moleculeI.H.

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

Here is the caller graph for this function:

Foam::vector & v ( )

inline

Definition at line 484 of file moleculeI.H.

const Foam::vector & a ( ) const

inline

Definition at line 490 of file moleculeI.H.

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

Here is the caller graph for this function:

Foam::vector & a ( )

inline

Definition at line 496 of file moleculeI.H.

const Foam::vector & pi ( ) const

inline

Definition at line 502 of file moleculeI.H.

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

Here is the caller graph for this function:

Foam::vector & pi ( )

inline

Definition at line 508 of file moleculeI.H.

const Foam::vector & tau ( ) const

inline

Definition at line 514 of file moleculeI.H.

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

Here is the caller graph for this function:

Foam::vector & tau ( )

inline

Definition at line 520 of file moleculeI.H.

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

inline

Definition at line 526 of file moleculeI.H.

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

Here is the caller graph for this function:

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

inline

Definition at line 532 of file moleculeI.H.

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

inline

Definition at line 538 of file moleculeI.H.

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

Here is the caller graph for this function:

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

inline

Definition at line 544 of file moleculeI.H.

const Foam::vector & specialPosition ( ) const

inline

Definition at line 550 of file moleculeI.H.

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

Here is the caller graph for this function:

Foam::vector & specialPosition ( )

inline

Definition at line 556 of file moleculeI.H.

Foam::scalar potentialEnergy ( ) const

inline

Definition at line 562 of file moleculeI.H.

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

Here is the caller graph for this function:

Foam::scalar & potentialEnergy ( )

inline

Definition at line 568 of file moleculeI.H.

const Foam::tensor & rf ( ) const

inline

Definition at line 574 of file moleculeI.H.

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

Here is the caller graph for this function:

Foam::tensor & rf ( )

inline

Definition at line 580 of file moleculeI.H.

Foam::label special ( ) const

inline

Definition at line 586 of file moleculeI.H.

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

Here is the caller graph for this function:

bool tethered ( ) const

inline

Definition at line 592 of file moleculeI.H.

References molecule::SPECIAL_TETHERED.

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

Here is the caller graph for this function:

Foam::label id ( ) const

inline

Definition at line 598 of file moleculeI.H.

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

Here is the caller graph for this function:

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 242 of file molecule.C.

References molecule::hitProcessorPatch().

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

Here is the call graph for this function:

Here is the caller graph for this function:

void hitProcessorPatch	(	const processorPolyPatch &	,
		trackingData &	td
	)

Overridable function to handle the particle hitting a processorPatch.

Definition at line 255 of file molecule.C.

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

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

Here is the call graph for this function:

Here is the caller graph for this function:

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

Overridable function to handle the particle hitting a wallPatch.

Definition at line 265 of file molecule.C.

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

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

Here is the call graph for this function:

Here is the caller graph for this function:

void hitPatch	(	const polyPatch &	,
		trackingData &	td
	)

Overridable function to handle the particle hitting a polyPatch.

Definition at line 287 of file molecule.C.

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

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()().

Here is the call graph for this function:

Here is the caller graph for this function:

void writeFields ( const Cloud< molecule > & mC )

static

Definition at line 148 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()().

Here is the call graph for this function:

Here is the caller graph for this function:

Friends And Related Function Documentation

friend class Cloud< molecule >

friend

Definition at line 233 of file molecule.H.

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

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation