#include <molecule.H>

Inheritance diagram for molecule:

Collaboration diagram for molecule:

Classes
class	constantProperties
	Class to hold molecule constant properties. More...
class	trackingData
	Class used to pass tracking data to the trackToFace function. More...
class	iNew
	Factory class to read-construct particles (for parallel transfer). 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 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)
	Construct from components.
	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)
	Construct from a position and a cell, searching for the rest of the.
	molecule (const polyMesh &mesh, Istream &is, bool readFields=true, bool newFormat=true)
	Construct from Istream.
virtual autoPtr< particle >	clone () const
	Return a clone.
bool	move (moleculeCloud &, trackingData &, const scalar trackTime)
virtual void	transformProperties (const tensor &T)
	Transform the physical properties of the particle.
virtual 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 (moleculeCloud &cloud, trackingData &td)
	Overridable function to handle the particle hitting a patch.
void	hitProcessorPatch (moleculeCloud &cloud, trackingData &td)
	Overridable function to handle the particle hitting a processorPatch.
void	hitWallPatch (moleculeCloud &cloud, trackingData &td)
	Overridable function to handle the particle hitting a wallPatch.
Public Member Functions inherited from particle< Type >
	TypeName ("particle")
	Runtime type information.
	particle (const polyMesh &mesh, const barycentric &coordinates, const label celli, const label tetFacei, const label tetPti)
	Construct from components.
	particle (const polyMesh &mesh, const vector &position, const label celli=-1)
	Construct from a position and a cell.
	particle (const polyMesh &mesh, const vector &position, const label celli, const label tetFacei, const label tetPti, const bool doLocate=true)
	Construct from position components.
	particle (const polyMesh &mesh, Istream &, const bool readFields=true, const bool newFormat=true, const bool doLocate=true)
	Construct from Istream.
	particle (const particle &p, const polyMesh &mesh)
	Construct as a copy with reference to a mesh.
	particle (const particle &p)
	Copy construct.
virtual	~particle ()=default
	Destructor.
label	getNewParticleID () const
	Get unique particle creation id.
const polyMesh &	mesh () const noexcept
	Return the mesh database.
const barycentric &	coordinates () const noexcept
	Return current particle coordinates.
label	cell () const noexcept
	Return current cell particle is in.
label &	cell () noexcept
	Return current cell particle is in for manipulation.
label	tetFace () const noexcept
	Return current tet face particle is in.
label &	tetFace () noexcept
	Return current tet face particle is in for manipulation.
label	tetPt () const noexcept
	Return current tet face particle is in.
label &	tetPt () noexcept
	Return current tet face particle is in for manipulation.
label	face () const noexcept
	Return current face particle is on otherwise -1.
label &	face () noexcept
	Return current face particle is on for manipulation.
scalar	stepFraction () const noexcept
	Return the fraction of time-step completed.
scalar &	stepFraction () noexcept
	Return the fraction of time-step completed.
label	origProc () const noexcept
	Return the originating processor ID.
label &	origProc () noexcept
	Return the originating processor ID.
label	origId () const noexcept
	Return the particle ID on the originating processor.
label &	origId () noexcept
	Return the particle ID on the originating processor.
Pair< scalar >	stepFractionSpan () const
	Return the step fraction change within the overall time-step.
scalar	currentTimeFraction () const
	Return the current fraction within the timestep. This differs.
tetIndices	currentTetIndices () const noexcept
	Return indices of the current tet that the particle occupies.
barycentricTensor	currentTetTransform () const
	Return the current tet transformation tensor.
vector	normal () const
	The (unit) normal of the tri on tetFacei_ for the current tet.
bool	onFace () const noexcept
	Is the particle on a face?
bool	onInternalFace () const noexcept
	Is the particle on an internal face?
bool	onBoundaryFace () const noexcept
	Is the particle on a boundary face?
label	patch () const
	Return the index of patch that the particle is on.
vector	position () const
	Return current particle position.
void	reset ()
	Reset particle data.
scalar	track (const vector &displacement, const scalar fraction)
	Track along the displacement for a given fraction of the overall.
scalar	trackToFace (const vector &displacement, const scalar fraction)
	As particle::track, but also stops on internal faces.
scalar	trackToTri (const vector &displacement, const scalar fraction, label &tetTriI)
	As particle::trackToFace, but also stops on tet triangles. On.
scalar	trackToStationaryTri (const vector &displacement, const scalar fraction, label &tetTriI)
	As particle::trackToTri, but for stationary meshes.
scalar	trackToMovingTri (const vector &displacement, const scalar fraction, label &tetTriI)
	As particle::trackToTri, but for moving meshes.
template<class TrackCloudType>
void	hitFace (const vector &direction, TrackCloudType &cloud, trackingData &td)
	Hit the current face. If the current face is internal than this.
template<class TrackCloudType>
void	trackToAndHitFace (const vector &direction, const scalar fraction, TrackCloudType &cloud, trackingData &td)
	Convenience function. Combines trackToFace and hitFace.
vector	deviationFromMeshCentre () const
	Get the displacement from the mesh centre. Used to correct the.
void	patchData (vector &n, vector &U) const
	Get the normal and velocity of the current patch location.
void	prepareForParallelTransfer ()
	Convert global addressing to the processor patch local equivalents.
void	correctAfterParallelTransfer (const label patchi, trackingData &td)
	Convert processor patch addressing to the global equivalents.
void	prepareForInteractionListReferral (const vectorTensorTransform &transform)
	Break the topology and store the particle position so that the.
void	correctAfterInteractionListReferral (const label celli)
	Correct the topology after referral. The particle may still be.
label	procTetPt (const polyMesh &procMesh, const label procCell, const label procTetFace) const
	Return the tet point appropriate for decomposition or reconstruction.
void	autoMap (const vector &position, const mapPolyMesh &mapper)
	Map after a topology change.
void	relocate (const point &position, const label celli=-1)
	Set the addressing based on the provided position.
void	writeProperties (Ostream &os, const wordRes &filters, const word &delim, const bool namesOnly) const
	Write individual particle properties to stream.
void	writeCoordinates (Ostream &os) const
	Write the particle barycentric coordinates and cell info.
virtual void	writePosition (Ostream &os) const
	Write the particle position and cell id.
Public Member Functions inherited from DLListBase::link
	link () noexcept=default
	Default construct.
bool	registered () const noexcept
	Node registered (linked) in a list?
void	deregister () noexcept
	Deregister the node (after removal).

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 Derived>
static autoPtr< particle >	Clone (const Derived &p)
	Clone a particle.
template<class Derived>
static autoPtr< particle >	Clone (const Derived &p, const polyMesh &mesh)
	Clone a particle with a mesh reference.
template<class Type>
static void	writePropertyName (Ostream &os, const word &name, const word &delim)
	Write the name representation to stream.
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())
	Write a named particle property to stream, optionally filtered based on its name.
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())
	Write a named particle property list to stream, optionally filtered based on its name.
template<class TrackCloudType>
static void	readFields (TrackCloudType &c)
	Read the fields associated with the owner cloud.
template<class TrackCloudType>
static void	writeFields (const TrackCloudType &c)
	Write the fields associated with the owner cloud.
template<class CloudType>
static void	readObjects (CloudType &c, const objectRegistry &obr)
	Read particle fields as objects from the obr registry.
template<class CloudType>
static void	writeObjects (const CloudType &c, objectRegistry &obr)
	Write particle fields as objects into the obr registry.

Static Public Attributes
static const std::size_t	sizeofFields
	Size in bytes of the fields.
Static Public Attributes inherited from particle< Type >
static string	propertyList_ = Foam::particle::propertyList()
	String representation of properties.
static label	particleCount_ = 0
	Cumulative particle counter - used to provide unique ID.
static bool	writeLagrangianCoordinates = true
	Write particle coordinates file (v1712 and later) Default is true.
static bool	writeLagrangianPositions
	Write particle positions file (v1706 format and earlier) Default is true (disable in etc/controlDict).

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

Additional Inherited Members
Public Attributes inherited from DLListBase::link
link *	prev_ = nullptr
	Pointer to prev entry in list.
link *	next_ = nullptr
	Pointer to next entry in list.
Protected Member Functions inherited from particle< Type >
void	readData (Istream &is, point &position, const bool readFields, const bool newFormat, const bool doLocate)
	Read particle from stream. Optionally (for old format) return.
template<class TrackCloudType>
bool	hitPatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a patch.
template<class TrackCloudType>
void	hitWedgePatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a wedgePatch.
template<class TrackCloudType>
void	hitSymmetryPlanePatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a.
template<class TrackCloudType>
void	hitSymmetryPatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a symmetryPatch.
template<class TrackCloudType>
void	hitCyclicPatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a cyclicPatch.
template<class TrackCloudType>
void	hitCyclicAMIPatch (TrackCloudType &, trackingData &, const vector &)
	Overridable function to handle the particle hitting a cyclicAMIPatch.
template<class TrackCloudType>
void	hitCyclicACMIPatch (TrackCloudType &, trackingData &, const vector &)
	Overridable function to handle the particle hitting a.
template<class TrackCloudType>
void	hitProcessorPatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a processorPatch.
template<class TrackCloudType>
void	hitWallPatch (TrackCloudType &, trackingData &)
	Overridable function to handle the particle hitting a wallPatch.
template<class TrackCloudType>
void	hitBoundaryFace (const vector &direction, TrackCloudType &cloud, trackingData &td)
	Dispatch function for boundary face interaction. Calls one of.

Detailed Description

Foam::molecule.

Source files

Definition at line 62 of file molecule.H.

Member Enumeration Documentation

◆ specialTypes

enum specialTypes

Enumerator
SPECIAL_TETHERED
SPECIAL_FROZEN
NOT_SPECIAL
SPECIAL_USER

Definition at line 78 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

Construct from components.

Definition at line 218 of file moleculeI.H.

References a(), particle< Type >::coordinates(), id(), particle< Type >::mesh(), particle< Type >::particle(), pi(), Q(), setSitePositions(), special(), specialPosition(), tau(), v(), and Foam::Zero.

Referenced by Cloud< molecule >, operator<<, readFields(), and writeFields().

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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

Construct from a position and a cell, searching for the rest of the.

required topology

Definition at line 255 of file moleculeI.H.

References a(), id(), particle< Type >::mesh(), particle< Type >::particle(), pi(), particle< Type >::position(), Q(), setSitePositions(), special(), specialPosition(), tau(), v(), and Foam::Zero.

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◆ molecule() [3/3]

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

Construct from Istream.

Definition at line 36 of file moleculeIO.C.

References IOstreamOption::ASCII, IOstream::check(), IOstream::fatalCheckNativeSizes(), IOstreamOption::format(), FUNCTION_NAME, particle< Type >::mesh(), particle< Type >::particle(), Istream::read(), readFields(), sizeofFields, and Foam::Zero.

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Member Function Documentation

◆ clone()

virtual autoPtr< particle > clone ( ) const

inlinevirtual

Return a clone.

Reimplemented from particle< Type >.

Definition at line 298 of file molecule.H.

References particle< Type >::Clone().

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◆ move()

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

Definition at line 63 of file molecule.C.

References Foam::abort(), f(), Foam::FatalError, FatalErrorInFunction, forAll, molecule::constantProperties::linearMolecule(), molecule::constantProperties::mass(), molecule::constantProperties::momentOfInertia(), molecule::constantProperties::pointMolecule(), R, s(), setSitePositions(), molecule::constantProperties::siteReferencePositions(), particle< Type >::stepFraction(), td(), particle< Type >::trackToAndHitFace(), and Foam::Zero.

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◆ transformProperties() [1/2]

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 184 of file molecule.C.

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

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◆ transformProperties() [2/2]

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 206 of file molecule.C.

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

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◆ setSitePositions()

void setSitePositions ( const constantProperties & constProps )

Definition at line 219 of file molecule.C.

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

Referenced by molecule(), molecule(), and move().

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◆ setSiteSizes()

void setSiteSizes ( label size )

Definition at line 225 of file molecule.C.

◆ Q() [1/2]

const Foam::tensor & Q ( ) const

inline

Definition at line 502 of file moleculeI.H.

Referenced by Cloud< molecule >, molecule::constantProperties::constantProperties(), molecule(), molecule(), readFields(), and writeFields().

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◆ Q() [2/2]

Foam::tensor & Q ( )

inline

Definition at line 508 of file moleculeI.H.

◆ v() [1/2]

const Foam::vector & v ( ) const

inline

Definition at line 514 of file moleculeI.H.

Referenced by moleculeCloud::applyConstraintsAndThermostats(), Cloud< molecule >, molecule(), molecule(), readFields(), and writeFields().

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◆ v() [2/2]

Foam::vector & v ( )

inline

Definition at line 520 of file moleculeI.H.

◆ a() [1/2]

const Foam::vector & a ( ) const

inline

Definition at line 526 of file moleculeI.H.

Referenced by Cloud< molecule >, molecule(), molecule(), readFields(), and writeFields().

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◆ a() [2/2]

Foam::vector & a ( )

inline

Definition at line 532 of file moleculeI.H.

◆ pi() [1/2]

const Foam::vector & pi ( ) const

inline

Definition at line 538 of file moleculeI.H.

Referenced by moleculeCloud::applyConstraintsAndThermostats(), Cloud< molecule >, molecule(), molecule(), readFields(), and writeFields().

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◆ pi() [2/2]

Foam::vector & pi ( )

inline

Definition at line 544 of file moleculeI.H.

◆ tau() [1/2]

const Foam::vector & tau ( ) const

inline

Definition at line 550 of file moleculeI.H.

Referenced by Cloud< molecule >, molecule(), molecule(), readFields(), and writeFields().

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◆ tau() [2/2]

Foam::vector & tau ( )

inline

Definition at line 556 of file moleculeI.H.

◆ siteForces() [1/2]

const 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]

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

inline

Definition at line 568 of file moleculeI.H.

◆ sitePositions() [1/2]

const 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]

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

inline

Definition at line 580 of file moleculeI.H.

◆ specialPosition() [1/2]

const Foam::vector & specialPosition ( ) const

inline

Definition at line 586 of file moleculeI.H.

Referenced by Cloud< molecule >, molecule(), molecule(), readFields(), and writeFields().

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◆ specialPosition() [2/2]

Foam::vector & specialPosition ( )

inline

Definition at line 592 of file moleculeI.H.

◆ 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]

Foam::scalar & potentialEnergy ( )

inline

Definition at line 604 of file moleculeI.H.

◆ rf() [1/2]

const Foam::tensor & rf ( ) const

inline

Definition at line 610 of file moleculeI.H.

Referenced by moleculeCloud::calculateForce().

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◆ rf() [2/2]

Foam::tensor & rf ( )

inline

Definition at line 616 of file moleculeI.H.

◆ special()

Foam::label special ( ) const

inline

Definition at line 622 of file moleculeI.H.

Referenced by Cloud< molecule >, molecule(), molecule(), readFields(), and writeFields().

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◆ tethered()

bool tethered ( ) const

inline

Definition at line 628 of file moleculeI.H.

References SPECIAL_TETHERED.

◆ id()

Foam::label id ( ) const

inline

Definition at line 634 of file moleculeI.H.

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

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◆ hitPatch()

bool hitPatch	(	moleculeCloud &	cloud,
		trackingData &	td )

Overridable function to handle the particle hitting a patch.

Executed before other patch-hitting functions

Definition at line 233 of file molecule.C.

◆ hitProcessorPatch()

void hitProcessorPatch	(	moleculeCloud &	cloud,
		trackingData &	td )

Overridable function to handle the particle hitting a processorPatch.

Definition at line 239 of file molecule.C.

References td().

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◆ hitWallPatch()

void hitWallPatch	(	moleculeCloud &	cloud,
		trackingData &	td )

Overridable function to handle the particle hitting a wallPatch.

Definition at line 245 of file molecule.C.

References particle< Type >::normal().

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◆ readFields()

void readFields ( Cloud< molecule > & mC )

static

Definition at line 88 of file moleculeIO.C.

References a(), Cloud< ParticleType >::checkFieldIOobject(), id(), molecule(), IOobjectOption::MUST_READ, objectRegistry::newIOobject(), pi(), pi(), Q(), particle< Type >::readFields(), HashTable< T, Key, Hash >::size(), special(), specialPosition(), tau(), and v().

Referenced by Cloud< molecule >, molecule(), moleculeCloud::moleculeCloud(), and moleculeCloud::moleculeCloud().

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◆ writeFields()

void writeFields ( const Cloud< molecule > & mC )

static

Definition at line 147 of file moleculeIO.C.

References a(), Foam::endl(), id(), Foam::Info, Foam::isA(), moleculeCloud::mesh(), molecule(), IOobject::name(), objectRegistry::newIOobject(), IOobjectOption::NO_READ, pi(), pi(), cloud::prefix, Q(), HashTable< T, Key, Hash >::size(), special(), specialPosition(), tau(), objectRegistry::time(), Time::timePath(), v(), regIOobject::write(), particle< Type >::writeFields(), and moleculeCloud::writeXYZ().

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◆ Cloud< molecule >

friend class Cloud< molecule >

friend

Definition at line 233 of file molecule.H.

References a(), particle< Type >::coordinates(), particle< Type >::mesh(), molecule(), pi(), particle< Type >::position(), Q(), readFields(), special(), specialPosition(), tau(), and v().

◆ operator<<

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

friend

References molecule().

Member Data Documentation

◆ sizeofFields

const std::size_t sizeofFields

static

Size in bytes of the fields.

Definition at line 71 of file molecule.H.

Referenced by molecule(), and 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 Symbol Documentation

◆ Cloud< molecule >

◆ operator<<

Member Data Documentation

◆ sizeofFields