Inheritance diagram for moleculeCloud:

Collaboration diagram for moleculeCloud:

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Public Member Functions
	moleculeCloud (const polyMesh &mesh, const potential &pot, bool readFields=true)
	Construct given mesh and potential references. More...

	moleculeCloud (const polyMesh &mesh, const potential &pot, const IOdictionary &mdInitialiseDict, bool readFields=true)
	Construct given mesh, potential and mdInitialiseDict. More...

void	evolve ()
	Evolve the molecules (move, calculate forces, control state etc) More...

void	calculateForce ()

void	applyConstraintsAndThermostats (const scalar targetTemperature, const scalar measuredTemperature)

const polyMesh &	mesh () const

const potential &	pot () const

const List< DynamicList< molecule * > > &	cellOccupancy () const

const InteractionLists< molecule > &	il () const

const List< molecule::constantProperties >	constProps () const

const molecule::constantProperties &	constProps (label id) const

Random &	rndGen ()

void	writeXYZ (const fileName &fName) const
	Write molecule sites in XYZ format. More...

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

	Cloud (const polyMesh &mesh, const IDLList< ParticleType > &particles)
	Construct from mesh and a list of particles. More...

	Cloud (const polyMesh &mesh, const word &cloudName, const IDLList< ParticleType > &particles)
	Construct from mesh, cloud name, and a list of particles. More...

	Cloud (const polyMesh &mesh, const bool checkClass=true)
	Construct from mesh by reading from file. More...

	Cloud (const polyMesh &pMesh, const word &cloudName, const bool checkClass=true)
	Construct from mesh by reading from file with given cloud instance. More...

const polyMesh &	pMesh () const
	Return the polyMesh reference. More...

label	size () const

DynamicList< label > &	labels ()

label	nTrackingRescues () const
	Return nTrackingRescues. More...

void	trackingRescue () const
	Increment the nTrackingRescues counter. More...

const PackedBoolList &	cellHasWallFaces () const
	Whether each cell has any wall faces (demand driven data) More...

virtual bool	hasWallImpactDistance () const
	Switch to specify if particles of the cloud can return. More...

const const_iterator	begin () const

const const_iterator	cbegin () const

const const_iterator	end () const

const const_iterator	cend () const

iterator	begin ()

iterator	end ()

void	clear ()

void	addParticle (ParticleType *pPtr)
	Transfer particle to cloud. More...

void	deleteParticle (ParticleType &)
	Remove particle from cloud and delete. More...

void	cloudReset (const Cloud< ParticleType > &c)
	Reset the particles. More...

template<class TrackData >
void	move (TrackData &td, const scalar trackTime)
	Move the particles. More...

template<class TrackData >
void	autoMap (TrackData &td, const mapPolyMesh &)
	Remap the cells of particles corresponding to the. More...

IOobject	fieldIOobject (const word &fieldName, const IOobject::readOption r) const
	Helper to construct IOobject for field and current time. More...

template<class DataType >
void	checkFieldIOobject (const Cloud< ParticleType > &c, const IOField< DataType > &data) const
	Check lagrangian data field. More...

template<class DataType >
void	checkFieldFieldIOobject (const Cloud< ParticleType > &c, const CompactIOField< Field< DataType >, DataType > &data) const
	Check lagrangian data fieldfield. More...

virtual void	readFields ()
	Read the field data for the cloud of particles. Dummy at. More...

virtual void	writeFields () const
	Write the field data for the cloud of particles Dummy at. More...

virtual bool	writeObject (IOstream::streamFormat fmt, IOstream::versionNumber ver, IOstream::compressionType cmp) const
	Write using given format, version and compression. More...

void	writePositions () const
	Write positions to <cloudName>_positions.obj file. More...

Private Member Functions
void	buildConstProps ()

void	setSiteSizesAndPositions ()

void	buildCellOccupancy ()
	Determine which molecules are in which cells. More...

void	calculatePairForce ()

void	evaluatePair (molecule &molI, molecule &molJ)

bool	evaluatePotentialLimit (molecule &molI, molecule &molJ) const

void	calculateTetherForce ()

void	calculateExternalForce ()

void	removeHighEnergyOverlaps ()

void	initialiseMolecules (const IOdictionary &mdInitialiseDict)

void	createMolecule (const point &position, label cell, label tetFace, label tetPt, label id, bool tethered, scalar temperature, const vector &bulkVelocity)

label	nSites () const

vector	equipartitionLinearVelocity (scalar temperature, scalar mass)

vector	equipartitionAngularMomentum (scalar temperature, const molecule::constantProperties &cP)

	moleculeCloud (const moleculeCloud &)
	Disallow default bitwise copy construct. More...

void	operator= (const moleculeCloud &)
	Disallow default bitwise assignment. More...

Private Attributes
const polyMesh &	mesh_

const potential &	pot_

List< DynamicList< molecule * > >	cellOccupancy_

InteractionLists< molecule >	il_

List< molecule::constantProperties >	constPropList_

Random	rndGen_

Additional Inherited Members
Public Types inherited from Cloud
typedef ParticleType	particleType

typedef IDLList< ParticleType >::iterator	iterator

typedef IDLList< ParticleType >::const_iterator	const_iterator

Static Public Attributes inherited from Cloud
static word	cloudPropertiesName
	Name of cloud properties dictionary. More...

Detailed Description

Source files

Definition at line 56 of file moleculeCloud.H.

Constructor & Destructor Documentation

◆ moleculeCloud() [1/3]

moleculeCloud ( const moleculeCloud & )

private

Disallow default bitwise copy construct.

◆ moleculeCloud() [2/3]

moleculeCloud	(	const polyMesh &	mesh,
		const potential &	pot,
		bool	readFields = `true`
	)

Construct given mesh and potential references.

Definition at line 1103 of file moleculeCloud.C.

References molecule::readFields().

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◆ moleculeCloud() [3/3]

moleculeCloud	(	const polyMesh &	mesh,
		const potential &	pot,
		const IOdictionary &	mdInitialiseDict,
		bool	readFields = `true`
	)

Construct given mesh, potential and mdInitialiseDict.

Definition at line 1133 of file moleculeCloud.C.

References clear(), and molecule::readFields().

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Member Function Documentation

◆ buildConstProps()

void buildConstProps ( )

private

Definition at line 41 of file moleculeCloud.C.

References Foam::abort(), constProp(), Foam::endl(), Foam::FatalError, FatalErrorInFunction, Foam::findIndex(), forAll, Foam::Info, dictionary::lookup(), IOobject::MUST_READ_IF_MODIFIED, Foam::nl, IOobject::NO_WRITE, List::size(), and dictionary::subDict().

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◆ setSiteSizesAndPositions()

void setSiteSizesAndPositions ( )

private

Definition at line 96 of file moleculeCloud.C.

References forAllIter, and molecule::constantProperties::nSites().

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◆ buildCellOccupancy()

void buildCellOccupancy ( )

private

Determine which molecules are in which cells.

Definition at line 109 of file moleculeCloud.C.

References forAll, and forAllIter.

◆ calculatePairForce()

void calculatePairForce ( )

private

Definition at line 128 of file moleculeCloud.C.

References cellOccupancy, forAll, forAllIter, UPstream::nonBlocking, and UPstream::nRequests().

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◆ evaluatePair()

void evaluatePair	(	molecule &	molI,
		molecule &	molJ
	)

inlineprivate

◆ evaluatePotentialLimit()

bool evaluatePotentialLimit	(	molecule &	molI,
		molecule &	molJ
	)		const

inlineprivate

Definition at line 156 of file moleculeCloudI.H.

References pairPotentialList::electrostatic(), molecule::constantProperties::electrostaticSites(), Foam::endl(), pairPotential::energy(), pairPotentialList::energy(), forAll, molecule::id(), Foam::mag(), Foam::magSqr(), molecule::constantProperties::pairPotentialSites(), pairPotentialList::rCutMaxSqr(), pairPotentialList::rCutSqr(), pairPotentialList::rMin(), pairPotential::rMin(), molecule::constantProperties::siteCharges(), molecule::constantProperties::siteIds(), molecule::sitePositions(), and WarningInFunction.

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◆ calculateTetherForce()

void calculateTetherForce ( )

private

Definition at line 216 of file moleculeCloud.C.

References tetherPotentialList::energy(), forAllIter, and tetherPotentialList::force().

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◆ calculateExternalForce()

void calculateExternalForce ( )

private

Definition at line 243 of file moleculeCloud.C.

References forAllIter.

◆ removeHighEnergyOverlaps()

void removeHighEnergyOverlaps ( )

private

Definition at line 252 of file moleculeCloud.C.

References DynamicList::append(), cellOccupancy, Foam::endl(), Foam::findIndex(), forAll, forAllIter, molecule::id(), Foam::Info, Foam::nl, UPstream::nonBlocking, UPstream::nRequests(), particle< Type >::origId(), UPstream::parRun(), Foam::reduce(), and Foam::tab.

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◆ initialiseMolecules()

void initialiseMolecules ( const IOdictionary & mdInitialiseDict )

private

Definition at line 476 of file moleculeCloud.C.

References Foam::abort(), Foam::cos(), Foam::det(), Foam::endl(), Foam::FatalError, FatalErrorInFunction, Foam::findIndex(), forAll, dictionary::found(), Foam::Info, Foam::inv(), dictionary::lookup(), molecule::constantProperties::mass(), n, zone::name(), Foam::nl, Vector< scalar >::one, p, phi, Foam::constant::mathematical::pi(), Foam::pow(), psi, R, Foam::readScalar(), Foam::sign(), Foam::sin(), List::size(), dictionary::subDict(), WarningInFunction, Vector< Cmpt >::x(), Vector< Cmpt >::y(), and Vector< Cmpt >::z().

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◆ createMolecule()

void createMolecule	(	const point &	position,
		label	cell,
		label	tetFace,
		label	tetPt,
		label	id,
		bool	tethered,
		scalar	temperature,
		const vector &	bulkVelocity
	)