Inheritance diagram for molecule:

Collaboration diagram for molecule:

Classes
class	constantProperties

class	iNew

class	trackingData

Public Types
enum	specialTypes { SPECIAL_TETHERED = -1, SPECIAL_FROZEN = -2, NOT_SPECIAL = 0, SPECIAL_USER = 1 }

Public Member Functions
	molecule (const polyMesh &mesh, const barycentric &coordinates, 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)

	molecule (const polyMesh &mesh, 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)

	molecule (const polyMesh &mesh, Istream &is, bool readFields=true, bool newFormat=true)

autoPtr< particle >	clone () const

bool	move (moleculeCloud &, trackingData &, const scalar trackTime)

virtual void	transformProperties (const tensor &T)

virtual void	transformProperties (const vector &separation)

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 (moleculeCloud &cloud, trackingData &td)

void	hitProcessorPatch (moleculeCloud &cloud, trackingData &td)

void	hitWallPatch (moleculeCloud &cloud, trackingData &td)

Public Member Functions inherited from particle< Type >
	TypeName ("particle")

	particle (const polyMesh &mesh, const barycentric &coordinates, const label celli, const label tetFacei, const label tetPti)

	particle (const polyMesh &mesh, const vector &position, const label celli=-1)

	particle (const polyMesh &mesh, const vector &position, const label celli, const label tetFacei, const label tetPti, const bool doLocate=true)

	particle (const polyMesh &mesh, Istream &, bool readFields=true, bool newFormat=true)

	particle (const particle &p)

	particle (const particle &p, const polyMesh &mesh)

virtual	~particle ()=default

label	getNewParticleID () const

const polyMesh &	mesh () const

const barycentric &	coordinates () const

label	cell () const

label &	cell ()

label	tetFace () const

label &	tetFace ()

label	tetPt () const

label &	tetPt ()

label	face () const

label &	face ()

scalar	stepFraction () const

scalar &	stepFraction ()

label	origProc () const

label &	origProc ()

label	origId () const

label &	origId ()

Pair< scalar >	stepFractionSpan () const

scalar	currentTimeFraction () const

tetIndices	currentTetIndices () const

barycentricTensor	currentTetTransform () const

vector	normal () const

bool	onFace () const

bool	onInternalFace () const

bool	onBoundaryFace () const

label	patch () const

vector	position () const

void	reset ()

scalar	track (const vector &displacement, const scalar fraction)

scalar	trackToFace (const vector &displacement, const scalar fraction)

scalar	trackToTri (const vector &displacement, const scalar fraction, label &tetTriI)

scalar	trackToStationaryTri (const vector &displacement, const scalar fraction, label &tetTriI)

scalar	trackToMovingTri (const vector &displacement, const scalar fraction, label &tetTriI)

template<class TrackCloudType >
void	hitFace (const vector &direction, TrackCloudType &cloud, trackingData &td)

template<class TrackCloudType >
void	trackToAndHitFace (const vector &direction, const scalar fraction, TrackCloudType &cloud, trackingData &td)

vector	deviationFromMeshCentre () const

void	patchData (vector &n, vector &U) const

void	prepareForParallelTransfer ()

void	correctAfterParallelTransfer (const label patchi, trackingData &td)

void	prepareForInteractionListReferral (const vectorTensorTransform &transform)

void	correctAfterInteractionListReferral (const label celli)

label	procTetPt (const polyMesh &procMesh, const label procCell, const label procTetFace) const

void	autoMap (const vector &position, const mapPolyMesh &mapper)

void	relocate (const point &position, const label celli=-1)

void	writeProperties (Ostream &os, const wordRes &filters, const word &delim, const bool namesOnly) const

void	writeCoordinates (Ostream &os) const

virtual void	writePosition (Ostream &os) const

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 Type >
static void	writePropertyName (Ostream &os, const word &name, const word &delim)

template<class Type >
static void	writeProperty (Ostream &os, const word &name, const Type &value, const bool nameOnly, const word &delim, const wordRes &filters=wordRes::null())

template<class Type >
static void	writeProperty (Ostream &os, const word &name, const Field< Type > &values, const bool nameOnly, const word &delim, const wordRes &filters=wordRes::null())

template<class TrackCloudType >
static void	readFields (TrackCloudType &c)

template<class TrackCloudType >
static void	writeFields (const TrackCloudType &c)

template<class CloudType >
static void	readObjects (CloudType &c, const objectRegistry &obr)

template<class CloudType >
static void	writeObjects (const CloudType &c, objectRegistry &obr)

Static Public Attributes
static const std::size_t	sizeofFields

Static Public Attributes inherited from particle< Type >
static string	propertyList_ = Foam::particle::propertyList()

static label	particleCount_ = 0

static bool	writeLagrangianCoordinates = true

static bool	writeLagrangianPositions

Friends
class	Cloud< molecule >

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

Additional Inherited Members
Protected Member Functions inherited from particle< Type >
template<class TrackCloudType >
bool	hitPatch (TrackCloudType &, trackingData &)

template<class TrackCloudType >
void	hitWedgePatch (TrackCloudType &, trackingData &)

template<class TrackCloudType >
void	hitSymmetryPlanePatch (TrackCloudType &, trackingData &)

template<class TrackCloudType >
void	hitSymmetryPatch (TrackCloudType &, trackingData &)

template<class TrackCloudType >
void	hitCyclicPatch (TrackCloudType &, trackingData &)

template<class TrackCloudType >
void	hitCyclicAMIPatch (TrackCloudType &, trackingData &, const vector &)

template<class TrackCloudType >
void	hitCyclicACMIPatch (TrackCloudType &, trackingData &, const vector &)

template<class TrackCloudType >
void	hitProcessorPatch (TrackCloudType &, trackingData &)

template<class TrackCloudType >
void	hitWallPatch (TrackCloudType &, trackingData &)

Detailed Description

Foam::molecule.

Source files

Definition at line 63 of file molecule.H.

Member Enumeration Documentation

◆ specialTypes

enum specialTypes

Enumerator
SPECIAL_TETHERED
SPECIAL_FROZEN
NOT_SPECIAL
SPECIAL_USER

Definition at line 77 of file molecule.H.

Constructor & Destructor Documentation

◆ molecule() [1/3]

molecule	(	const polyMesh &	mesh,
		const barycentric &	coordinates,
		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

Definition at line 219 of file moleculeI.H.

References molecule::setSitePositions().

Referenced by molecule::clone().

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◆ molecule() [2/3]

molecule	(	const polyMesh &	mesh,
		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

Definition at line 256 of file moleculeI.H.

References molecule::setSitePositions().

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◆ molecule() [3/3]

molecule	(	const polyMesh &	mesh,
		Istream &	is,
		bool	readFields = `true`,
		bool	newFormat = `true`
	)

Definition at line 37 of file moleculeIO.C.

References Istream::beginRawRead(), IOstream::check(), IOstream::checkLabelSize(), IOstream::checkScalarSize(), Istream::endRawRead(), IOstreamOption::format(), FUNCTION_NAME, Istream::read(), Foam::readFields(), and Foam::readRawLabel().

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Member Function Documentation

◆ clone()

autoPtr<particle> clone ( ) const

inlinevirtual

Reimplemented from particle< Type >.

Definition at line 282 of file molecule.H.

References molecule::molecule().

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◆ move()

bool move	(	moleculeCloud &	cloud,
		trackingData &	td,
		const scalar	trackTime
	)

Definition at line 64 of file molecule.C.

References Foam::abort(), f(), Foam::FatalError, FatalErrorInFunction, forAll, particle< Type >::trackingData::keepParticle, molecule::constantProperties::linearMolecule(), molecule::constantProperties::mass(), molecule::constantProperties::momentOfInertia(), molecule::trackingData::part(), molecule::constantProperties::pointMolecule(), R, s, molecule::constantProperties::siteReferencePositions(), particle< Type >::trackingData::switchProcessor, and Foam::Zero.

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◆ transformProperties() [1/2]

void transformProperties ( const tensor & T )

virtual

Reimplemented from particle< Type >.

Definition at line 184 of file molecule.C.

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

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◆ transformProperties() [2/2]

void transformProperties ( const vector & separation )

virtual

Reimplemented from particle< Type >.

Definition at line 206 of file molecule.C.

References particle< Type >::transformProperties().

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◆ setSitePositions()

void setSitePositions ( const constantProperties & constProps )

Definition at line 219 of file molecule.C.

References molecule::constantProperties::siteReferencePositions().

Referenced by molecule::molecule().

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◆ setSiteSizes()

void setSiteSizes ( label size )

Definition at line 225 of file molecule.C.

◆ Q() [1/2]

Foam::tensor & Q ( ) const

inline

Definition at line 502 of file moleculeI.H.

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

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◆ Q() [2/2]

tensor& Q ( )

inline

◆ v() [1/2]

Foam::vector & v ( ) const

inline

Definition at line 514 of file moleculeI.H.

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

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◆ v() [2/2]

vector& v ( )

inline

◆ a() [1/2]

Foam::vector & a ( ) const

inline

Definition at line 526 of file moleculeI.H.

Referenced by molecule::readFields().

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◆ a() [2/2]

vector& a ( )

inline

◆ pi() [1/2]

Foam::vector & pi ( ) const

inline

Definition at line 538 of file moleculeI.H.

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

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◆ pi() [2/2]

vector& pi ( )

inline

◆ tau() [1/2]

Foam::vector & tau ( ) const

inline

Definition at line 550 of file moleculeI.H.

Referenced by molecule::readFields().

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◆ tau() [2/2]

vector& tau ( )

inline

◆ siteForces() [1/2]

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

inline

Definition at line 562 of file moleculeI.H.

Referenced by moleculeCloud::calculateForce().

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◆ siteForces() [2/2]

List<vector>& siteForces ( )

inline

◆ sitePositions() [1/2]

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

inline

Definition at line 574 of file moleculeI.H.

Referenced by moleculeCloud::writeXYZ().

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◆ sitePositions() [2/2]

List<vector>& sitePositions ( )

inline

◆ specialPosition() [1/2]

Foam::vector & specialPosition ( ) const

inline

Definition at line 586 of file moleculeI.H.

Referenced by molecule::readFields().

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◆ specialPosition() [2/2]

vector& specialPosition ( )

inline

◆ potentialEnergy() [1/2]

Foam::scalar & potentialEnergy ( ) const

inline

Definition at line 598 of file moleculeI.H.

Referenced by moleculeCloud::calculateForce().

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◆ potentialEnergy() [2/2]

scalar& potentialEnergy ( )

inline

◆ rf() [1/2]

Foam::tensor & rf ( ) const

inline

Definition at line 610 of file moleculeI.H.

Referenced by moleculeCloud::calculateForce().

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◆ rf() [2/2]

tensor& rf ( )

inline

◆ special()

Foam::label special ( ) const

inline

Definition at line 622 of file moleculeI.H.

Referenced by molecule::readFields().

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◆ tethered()

bool tethered ( ) const

inline

Definition at line 628 of file moleculeI.H.

References molecule::SPECIAL_TETHERED.

◆ id()

Foam::label id ( ) const

inline

Definition at line 634 of file moleculeI.H.

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

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◆ hitPatch()

bool hitPatch	(	moleculeCloud &	cloud,
		trackingData &	td
	)

Definition at line 233 of file molecule.C.

◆ hitProcessorPatch()

void hitProcessorPatch	(	moleculeCloud &	cloud,
		trackingData &	td
	)

Definition at line 239 of file molecule.C.

References particle< Type >::trackingData::switchProcessor.

◆ hitWallPatch()

void hitWallPatch	(	moleculeCloud &	cloud,
		trackingData &	td
	)

Definition at line 245 of file molecule.C.

◆ readFields()

void readFields ( Cloud< molecule > & mC )

static

Definition at line 104 of file moleculeIO.C.

References molecule::a(), Cloud::checkFieldIOobject(), Cloud::fieldIOobject(), molecule::id(), IOobject::MUST_READ, molecule::pi(), molecule::Q(), particle< Type >::readFields(), molecule::special(), molecule::specialPosition(), molecule::tau(), and molecule::v().

Referenced by moleculeCloud::moleculeCloud().

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◆ writeFields()

void writeFields ( const Cloud< molecule > & mC )

static

Definition at line 159 of file moleculeIO.C.

References Foam::endl(), Cloud::fieldIOobject(), Foam::Info, moleculeCloud::mesh(), IOobject::NO_READ, Foam::constant::mathematical::pi(), cloud::prefix, objectRegistry::time(), Time::timePath(), particle< Type >::writeFields(), and moleculeCloud::writeXYZ().

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Friends And Related Function Documentation

◆ Cloud< molecule >

friend class Cloud< molecule >

friend

Definition at line 231 of file molecule.H.

◆ operator<<

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

friend

Member Data Documentation

◆ sizeofFields

const std::size_t sizeofFields

static

Definition at line 70 of file molecule.H.

Referenced by Foam::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

Static Public Attributes

Friends

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ specialTypes

Constructor & Destructor Documentation

◆ molecule() [1/3]

◆ molecule() [2/3]

◆ molecule() [3/3]

Member Function Documentation

◆ clone()

◆ move()

◆ transformProperties() [1/2]

◆ transformProperties() [2/2]

◆ 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()

◆ hitPatch()

◆ hitProcessorPatch()

◆ hitWallPatch()

◆ readFields()

◆ writeFields()

Friends And Related Function Documentation

◆ Cloud< molecule >

◆ operator<<

Member Data Documentation

◆ sizeofFields