Inheritance diagram for moleculeCloud:

Collaboration diagram for moleculeCloud:

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< ParticleType >
	TypeName ("Cloud")
	Runtime type information. More...

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

virtual label	nParcels () const
	Return the number of particles in the cloud. More...

DynamicList< label > &	labels () const
	Return temporary addressing. More...

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

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

void	deleteLostParticles ()
	Remove lost particles from cloud and delete. More...

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

template<class TrackCloudType >
void	move (TrackCloudType &cloud, typename ParticleType::trackingData &td, const scalar trackTime)
	Move the particles. More...

void	autoMap (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...

template<class Type >
bool	readStoreFile (const IOobject &io, const IOobject &ioNew) const
	Helper function to store a cloud field on its registry. More...

void	readFromFiles (objectRegistry &obr, const wordRes &selectFields) const
	Read from files into objectRegistry. More...

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

virtual bool	writeObject (IOstreamOption streamOpt, const bool valid) const
	Write using stream options. More...

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

void	storeGlobalPositions () const
	Call this before a topology change. More...

Additional Inherited Members
Public Types inherited from Cloud< ParticleType >
typedef ParticleType	particleType

typedef ParticleType	parcelType
	Parcels are just particles. More...

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

Protected Attributes inherited from Cloud< ParticleType >
cloud::geometryType	geometryType_
	Geometry type. More...

Detailed Description

Source files

Definition at line 58 of file moleculeCloud.H.

Constructor & Destructor Documentation

◆ moleculeCloud() [1/2]

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

Construct given mesh and potential references.

Definition at line 1042 of file moleculeCloud.C.

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

Here is the call graph for this function:

◆ moleculeCloud() [2/2]

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

Construct given mesh, potential and mdInitialiseDict.

Definition at line 1072 of file moleculeCloud.C.

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

Here is the call graph for this function:

Member Function Documentation

◆ evolve()

void evolve ( )

Evolve the molecules (move, calculate forces, control state etc)

Definition at line 1101 of file moleculeCloud.C.

References Cloud< ParticleType >::move().

Here is the call graph for this function:

◆ calculateForce()

void calculateForce ( )

Definition at line 1119 of file moleculeCloud.C.

References molecule::potentialEnergy(), molecule::rf(), molecule::siteForces(), and Foam::Zero.

Here is the call graph for this function:

◆ applyConstraintsAndThermostats()

void applyConstraintsAndThermostats	(	const scalar	targetTemperature,
		const scalar	measuredTemperature
	)

Definition at line 1142 of file moleculeCloud.C.

References Foam::endl(), Foam::Info, Foam::max(), Foam::nl, molecule::pi(), Foam::sqrt(), and molecule::v().

Here is the call graph for this function:

◆ mesh()

const Foam::polyMesh & mesh ( ) const

inline

Definition at line 343 of file moleculeCloudI.H.

Referenced by molecule::writeFields().

Here is the caller graph for this function:

◆ pot()

const Foam::potential & pot ( ) const

inline

Definition at line 349 of file moleculeCloudI.H.

◆ cellOccupancy()

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

inline

Definition at line 356 of file moleculeCloudI.H.

◆ il()

const Foam::InteractionLists< Foam::molecule > & il ( ) const

inline

Definition at line 363 of file moleculeCloudI.H.

◆ constProps() [1/2]

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

inline

Definition at line 370 of file moleculeCloudI.H.

◆ constProps() [2/2]

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

inline

Definition at line 377 of file moleculeCloudI.H.

◆ rndGen()

Foam::Random & rndGen ( )

inline

Definition at line 383 of file moleculeCloudI.H.

◆ writeXYZ()

void writeXYZ ( const fileName & fName ) const

Write molecule sites in XYZ format.

Definition at line 1170 of file moleculeCloud.C.

References forAll, molecule::id(), Foam::nl, os(), molecule::constantProperties::siteIds(), molecule::sitePositions(), Vector< Cmpt >::x(), Vector< Cmpt >::y(), and Vector< Cmpt >::z().

Referenced by molecule::writeFields().

Here is the call graph for this function:

Here is the caller graph for this function:

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

src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ moleculeCloud() [1/2]

◆ moleculeCloud() [2/2]

Member Function Documentation

◆ evolve()

◆ calculateForce()

◆ applyConstraintsAndThermostats()

◆ mesh()

◆ pot()

◆ cellOccupancy()

◆ il()

◆ constProps() [1/2]

◆ constProps() [2/2]

◆ rndGen()

◆ writeXYZ()