#include <molecule/molecule.H>

Detailed Description

Foam::molecule.

Source files

Definition at line 57 of file molecule.H.

Inheritance diagram for molecule:

Collaboration diagram for molecule:

List of all members.

Classes
class	constantProperties
	Class to hold molecule constant properties. More...
class	trackData
	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 Cloud< molecule > &c, 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 components.
	molecule (const Cloud< molecule > &c, Istream &is, bool readFields=true)
	Construct from Istream.
autoPtr< molecule >	clone () const
	Construct and return a clone.
bool	move (trackData &)
void	transformProperties (const tensor &T)
	Transform the physical properties of the particle.
void	transformProperties (const vector &separation)
	Transform the physical properties of the particle.
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 &, molecule::trackData &td, const label patchI)
	Overridable function to handle the particle hitting a patch.
bool	hitPatch (const polyPatch &p, int &td, const label patchI)
	Overridable function to handle the particle hitting a patch.
void	hitProcessorPatch (const processorPolyPatch &, molecule::trackData &td)
	Overridable function to handle the particle hitting a processorPatch.
void	hitProcessorPatch (const processorPolyPatch &, int &)
	Overridable function to handle the particle hitting a processorPatch.
void	hitWallPatch (const wallPolyPatch &, molecule::trackData &td)
	Overridable function to handle the particle hitting a wallPatch.
void	hitWallPatch (const wallPolyPatch &, int &)
	Overridable function to handle the particle hitting a wallPatch.
void	hitPatch (const polyPatch &, molecule::trackData &td)
	Overridable function to handle the particle hitting a polyPatch.
void	hitPatch (const polyPatch &, int &)
	Overridable function to handle the particle hitting a polyPatch.
Public Member Functions inherited from Particle< molecule >
	TypeName ("Particle")
	Runtime type information.
	Particle (const Cloud< molecule > &, const vector &position, const label celli)
	Construct from components.
	Particle (const Cloud< molecule > &, Istream &, bool readFields=true)
	Construct from Istream.
	Particle (const Particle &p)
	Construct as a copy.
virtual	~Particle ()
	Destructor.
bool	inCell () const
	Return true if particle is in cell.
bool	inCell (const vector &position, const label celli, const scalar stepFraction) const
	Return true if position is in cell i.
const vector &	position () const
	Return current particle position.
vector &	position ()
	Return current particle position.
label &	cell ()
	Return current cell particle is in.
label	cell () const
	Return current cell particle is in.
label	face () const
	Return current face particle is on otherwise -1.
const Cloud< molecule > &	cloud () const
	Return reference to the particle cloud.
bool	softImpact () const
	Return the impact model to be used, soft or hard (default).
scalar	currentTime () const
	Return the particle current time.
bool	onBoundary () const
	Is the particle on the boundary/(or outside the domain)?
label	patch (const label facei) const
	Which patch is particle on.
label	patchFace (const label patchi, const label facei) const
	Which face of this patch is this particle on.
scalar	wallImpactDistance (const vector &n) const
	The nearest distance to a wall that.
scalar &	stepFraction ()
	Return the fraction of time-step completed.
scalar	stepFraction () const
	Return the fraction of time-step completed.
label	origProc () const
	Return the originating processor id.
label	origId () const
	Return the particle id on originating processor.
label	track (const vector &endPosition, TrackData &td)
	Track particle to end of trajectory.
label	track (const vector &endPosition)
	Calls the templated track with dummy TrackData.
scalar	trackToFace (const vector &endPosition, TrackData &td)
	Track particle to a given position and returns 1.0 if the.
scalar	trackToFace (const vector &endPosition)
	Calls the templated trackToFace with dummy TrackData.
label	faceInterpolation () const
	Return the index of the face to be used in the interpolation.
void	write (Ostream &os, bool writeFields) const
	Write the particle data.

Static Public Member Functions
static void	readFields (Cloud< molecule > &mC)
	Read the fields associated with the owner cloud.
static void	writeFields (const Cloud< molecule > &mC)
	Write the fields associated with the owner cloud.

Friends
class	Cloud< molecule >
Ostream &	operator<< (Ostream &, const molecule &)

Additional Inherited Members
Static Public Attributes inherited from Particle< molecule >
static string	propHeader
	String representation of properties.
Protected Member Functions inherited from Particle< molecule >
scalar	lambda (const vector &from, const vector &to, const label facei, const scalar stepFraction) const
	Return the 'lambda' value for the position, p, on the face,.
scalar	lambda (const vector &from, const vector &to, const label facei) const
	Return the 'lambda' value for the position, p, on the face,.
void	findFaces (const vector &position, DynamicList< label > &faceList) const
	Find the faces between position and cell centre.
void	findFaces (const vector &position, const label celli, const scalar stepFraction, DynamicList< label > &faceList) const
	Find the faces between position and cell centre.
bool	hitPatch (const polyPatch &, TrackData &td, const label patchI)
	Overridable function to handle the particle hitting a patch.
void	hitPatch (const polyPatch &, TrackData &td)
	Overridable function to handle the particle hitting a.
void	hitWedgePatch (const wedgePolyPatch &, TrackData &td)
	Overridable function to handle the particle hitting a wedgePatch.
void	hitSymmetryPatch (const symmetryPolyPatch &, TrackData &td)
	Overridable function to handle the particle hitting a.
void	hitCyclicPatch (const cyclicPolyPatch &, TrackData &td)
	Overridable function to handle the particle hitting a cyclicPatch.
void	hitProcessorPatch (const processorPolyPatch &, TrackData &td)
	Overridable function to handle the particle hitting a.
void	hitWallPatch (const wallPolyPatch &, TrackData &td)
	Overridable function to handle the particle hitting a wallPatch.
virtual void	transformPosition (const tensor &T)
	Transform the position the particle.
void	prepareForParallelTransfer (const label patchi, TrackData &td)
	Convert global addressing to the processor patch.
void	correctAfterParallelTransfer (const label patchi, TrackData &td)
	Convert processor patch addressing to the global equivalents.
Protected Attributes inherited from Particle< molecule >
const Cloud< molecule > &	cloud_
	Reference to the particle cloud.
vector	position_
	Position of particle.
label	celli_
	Index of the cell it is in.
label	facei_
	Face index if the particle is on a face otherwise -1.
scalar	stepFraction_
	Fraction of time-step completed.
label	origProc_
	Originating processor id.
label	origId_
	Local particle id on originating processor.

Member Enumeration Documentation

enum specialTypes

Enumerator:

SPECIAL_TETHERED
SPECIAL_FROZEN
NOT_SPECIAL
SPECIAL_USER

Definition at line 68 of file molecule.H.

Constructor & Destructor Documentation

molecule	(	const Cloud< molecule > &	c,
		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 components.

Definition at line 221 of file moleculeI.H.

References molecule::setSitePositions().

Referenced by molecule::clone().

molecule	(	const Cloud< molecule > &	c,
		Istream &	is,
		bool	readFields = `true`
	)

Construct from Istream.

Definition at line 33 of file moleculeIO.C.

References readScalar.

Member Function Documentation

autoPtr<molecule> clone ( ) const

inline

Construct and return a clone.

Reimplemented from Particle< molecule >.

Definition at line 259 of file molecule.H.

References molecule::molecule().

bool move ( molecule::trackData & td )

void transformProperties ( const tensor & T )

virtual

Transform the physical properties of the particle.

according to the given transformation tensor

Reimplemented from Particle< molecule >.

Definition at line 210 of file molecule.C.

void transformProperties ( const vector & separation )

virtual

Transform the physical properties of the particle.

according to the given separation vector

Reimplemented from Particle< molecule >.

Definition at line 220 of file molecule.C.

void setSitePositions ( const constantProperties & constProps )

Definition at line 229 of file molecule.C.

References molecule::constantProperties::siteReferencePositions().

Referenced by molecule::molecule().

void setSiteSizes ( label size )

Definition at line 235 of file molecule.C.

const Foam::tensor & Q ( ) const

inline

Definition at line 479 of file moleculeI.H.

Referenced by molecule::constantProperties::constantProperties(), and molecule::readFields().

Foam::tensor & Q ( )

inline

Definition at line 485 of file moleculeI.H.

const Foam::vector & v ( ) const

inline

Definition at line 491 of file moleculeI.H.

Referenced by molecule::readFields().

Foam::vector & v ( )

inline

Definition at line 497 of file moleculeI.H.

const Foam::vector & a ( ) const

inline

Definition at line 503 of file moleculeI.H.

Referenced by molecule::readFields().

Foam::vector & a ( )

inline

Definition at line 509 of file moleculeI.H.

const Foam::vector & pi ( ) const

inline

Definition at line 515 of file moleculeI.H.

Referenced by molecule::readFields().

Foam::vector & pi ( )

inline

Definition at line 521 of file moleculeI.H.

const Foam::vector & tau ( ) const

inline

Definition at line 527 of file moleculeI.H.

Referenced by molecule::readFields().

Foam::vector & tau ( )

inline

Definition at line 533 of file moleculeI.H.

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

inline

Definition at line 539 of file moleculeI.H.

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

inline

Definition at line 545 of file moleculeI.H.

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

inline

Definition at line 551 of file moleculeI.H.

Referenced by referredCellList::referMolecules().

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

inline

Definition at line 557 of file moleculeI.H.

const Foam::vector & specialPosition ( ) const

inline

Definition at line 563 of file moleculeI.H.

Referenced by molecule::readFields().

Foam::vector & specialPosition ( )

inline

Definition at line 569 of file moleculeI.H.

Foam::scalar potentialEnergy ( ) const

inline

Definition at line 575 of file moleculeI.H.

Foam::scalar & potentialEnergy ( )

inline

Definition at line 581 of file moleculeI.H.

const Foam::tensor & rf ( ) const

inline

Definition at line 587 of file moleculeI.H.

Foam::tensor & rf ( )

inline

Definition at line 593 of file moleculeI.H.

Foam::label special ( ) const

inline

Definition at line 599 of file moleculeI.H.

Referenced by molecule::readFields().

bool tethered ( ) const

inline

Definition at line 605 of file moleculeI.H.

References molecule::SPECIAL_TETHERED.

Foam::label id ( ) const

inline

Definition at line 611 of file moleculeI.H.

Referenced by molecule::readFields(), and referredCellList::referMolecules().

bool hitPatch	(	const polyPatch &	,
		molecule::trackData &	td,
		const label	patchI
	)

Overridable function to handle the particle hitting a patch.

Executed before other patch-hitting functions

Definition at line 244 of file molecule.C.

bool hitPatch	(	const polyPatch &	p,
		int &	td,
		const label	patchI
	)

Overridable function to handle the particle hitting a patch.

Executed before other patch-hitting functions without trackData

Definition at line 255 of file molecule.C.

void hitProcessorPatch	(	const processorPolyPatch &	,
		molecule::trackData &	td
	)

Overridable function to handle the particle hitting a processorPatch.

Definition at line 266 of file molecule.C.

References Particle< ParticleType >::trackData::switchProcessor.

void hitProcessorPatch	(	const processorPolyPatch &	,
		int &
	)

Overridable function to handle the particle hitting a processorPatch.

without trackData

Definition at line 276 of file molecule.C.

void hitWallPatch	(	const wallPolyPatch &	wpp,
		molecule::trackData &	td
	)

Overridable function to handle the particle hitting a wallPatch.

Definition at line 284 of file molecule.C.

References polyPatch::faceAreas(), Foam::mag(), and polyPatch::whichFace().

void hitWallPatch	(	const wallPolyPatch &	,
		int &
	)

Overridable function to handle the particle hitting a wallPatch.

without trackData

Definition at line 303 of file molecule.C.

void hitPatch	(	const polyPatch &	,
		molecule::trackData &	td
	)

Overridable function to handle the particle hitting a polyPatch.

Definition at line 311 of file molecule.C.

References Particle< ParticleType >::trackData::keepParticle.

void hitPatch	(	const polyPatch &	,
		int &
	)

Overridable function to handle the particle hitting a polyPatch.

without trackData

Definition at line 321 of file molecule.C.

void readFields ( Cloud< molecule > & c )

static

Read the fields associated with the owner cloud.

Reimplemented from Particle< molecule >.

Definition at line 100 of file moleculeIO.C.

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

Referenced by moleculeCloud::moleculeCloud().

void writeFields ( const Cloud< molecule > & c )

static

Write the fields associated with the owner cloud.

Reimplemented from Particle< molecule >.

Definition at line 154 of file moleculeIO.C.

References Cloud< ParticleType >::fieldIOobject(), forAllConstIter, moleculeCloud::mesh(), IOobject::NO_READ, Foam::mathematicalConstant::pi(), Cloud< ParticleType >::size(), objectRegistry::time(), Time::timePath(), regIOobject::write(), Particle< ParticleType >::writeFields(), and moleculeCloud::writeXYZ().

Friends And Related Function Documentation

friend class Cloud< molecule >

friend

Definition at line 229 of file molecule.H.

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

friend

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

Detailed Description

Classes

Public Types

Public Member Functions

Static Public Member Functions

Friends

Additional Inherited Members

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation