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 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...

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

	cloud (const objectRegistry &, const word &cloudName="")
	Construct for the given objectRegistry and named cloud instance. More...

virtual	~cloud ()
	Destructor. More...

virtual void	autoMap (const mapPolyMesh &)
	Remap the cells of particles corresponding to the. More...

Public Member Functions inherited from objectRegistry
	TypeName ("objectRegistry")
	Declare type name for this IOobject. More...

	objectRegistry (const Time &db, const label nIoObjects=128)
	Construct the time objectRegistry given an initial estimate. More...

	objectRegistry (const IOobject &io, const label nIoObjects=128)
	Construct a sub-registry given an IObject to describe the registry. More...

virtual	~objectRegistry ()
	Destructor. More...

const Time &	time () const
	Return time. More...

const objectRegistry &	parent () const
	Return the parent objectRegistry. More...

virtual const fileName &	dbDir () const
	Local directory path of this objectRegistry relative to the time. More...

wordList	names () const
	Return the list of names of the IOobjects. More...

wordList	sortedNames () const
	Return the sorted list of names of the IOobjects. More...

wordList	names (const word &className) const
	Return the list of names of IOobjects of given class name. More...

wordList	sortedNames (const word &className) const
	Return the sorted list of names of IOobjects of given class name. More...

template<class Type >
wordList	names () const
	Return the list of names of the IOobjects of given type. More...

template<class Type >
wordList	names (const wordRe &name) const
	Return the list of objects whose name matches the input regExp. More...

template<class Type >
wordList	names (const wordReList &name) const
	Return the list of objects whose name matches the input regExp. More...

const objectRegistry &	subRegistry (const word &name, const bool forceCreate=false) const
	Lookup and return a const sub-objectRegistry. Optionally create. More...

template<class Type >
HashTable< const Type * >	lookupClass (const bool strict=false) const
	Lookup and return all objects of the given Type. More...

template<class Type >
HashTable< Type * >	lookupClass (const bool strict=false)
	Lookup and return all objects of the given Type. More...

template<class Type >
bool	foundObject (const word &name) const
	Is the named Type found? More...

template<class Type >
const Type &	lookupObject (const word &name) const
	Lookup and return the object of the given Type. More...

label	getEvent () const
	Return new event number. More...

virtual void	rename (const word &newName)
	Rename. More...

bool	checkIn (regIOobject &) const
	Add an regIOobject to registry. More...

bool	checkOut (regIOobject &) const
	Remove an regIOobject from registry. More...

virtual bool	modified () const
	Return true if any of the object's files have been modified. More...

void	readModifiedObjects ()
	Read the objects that have been modified. More...

virtual bool	readIfModified ()
	Read object if modified. More...

virtual bool	writeData (Ostream &) const
	writeData function required by regIOobject but not used More...

template<class Type >
Foam::wordList	names () const

template<class Type >
Foam::wordList	names (const wordRe &name) const

template<class Type >
Foam::wordList	names (const wordReList &patterns) const

template<class Type >
Foam::HashTable< const Type * >	lookupClass (const bool strict) const

template<class Type >
Foam::HashTable< Type * >	lookupClass (const bool strict)

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

	regIOobject (const IOobject &, const bool isTime=false)
	Construct from IOobject. Optional flag for if IOobject is the. More...

	regIOobject (const regIOobject &)
	Construct as copy. More...

	regIOobject (const regIOobject &, bool registerCopy)
	Construct as copy, transferring registry registration to copy. More...

	regIOobject (const word &newName, const regIOobject &, bool registerCopy)
	Construct as copy with new name, transfering registry registration. More...

	regIOobject (const IOobject &, const regIOobject &)
	Construct as copy with new IO parameters. More...

virtual	~regIOobject ()
	Destructor. More...

bool	checkIn ()
	Add object to registry. More...

bool	checkOut ()
	Remove object from registry. More...

bool	ownedByRegistry () const
	Is this object owned by the registry? More...

void	store ()
	Transfer ownership of this object to its registry. More...

void	release ()
	Release ownership of this object from its registry. More...

label	eventNo () const
	Event number at last update. More...

label &	eventNo ()
	Event number at last update. More...

bool	upToDate (const regIOobject &) const
	Return true if up-to-date with respect to given object. More...

bool	upToDate (const regIOobject &, const regIOobject &) const
	Return true if up-to-date with respect to given objects. More...

bool	upToDate (const regIOobject &, const regIOobject &, const regIOobject &) const
	Return true if up-to-date with respect to given objects. More...

bool	upToDate (const regIOobject &, const regIOobject &, const regIOobject &, const regIOobject &) const
	Return true if up-to-date with respect to given objects. More...

void	setUpToDate ()
	Set up to date (obviously) More...

Istream &	readStream (const word &)
	Return Istream and check object type against that given. More...

void	close ()
	Close Istream. More...

virtual bool	readData (Istream &)
	Virtual readData function. More...

virtual bool	read ()
	Read object. More...

label	watchIndex () const
	Return file-monitoring handle. More...

label &	watchIndex ()
	Return file-monitoring handle. More...

virtual bool	write () const
	Write using setting from DB. More...

void	operator= (const IOobject &)

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

	IOobject (const word &name, const fileName &instance, const objectRegistry &registry, readOption r=NO_READ, writeOption w=NO_WRITE, bool registerObject=true)
	Construct from name, instance, registry, io options. More...

	IOobject (const word &name, const fileName &instance, const fileName &local, const objectRegistry &registry, readOption r=NO_READ, writeOption w=NO_WRITE, bool registerObject=true)
	Construct from name, instance, local, registry, io options. More...

	IOobject (const fileName &path, const objectRegistry &registry, readOption r=NO_READ, writeOption w=NO_WRITE, bool registerObject=true)
	Construct from path, registry, io options. More...

Foam::autoPtr< IOobject >	clone () const
	Clone. More...

virtual	~IOobject ()
	Destructor. More...

const Time &	time () const
	Return time. More...

const objectRegistry &	db () const
	Return the local objectRegistry. More...

const word &	name () const
	Return name. More...

const word &	headerClassName () const
	Return name of the class name read from header. More...

string &	note ()
	Return non-constant access to the optional note. More...

const string &	note () const
	Return the optional note. More...

bool &	registerObject ()
	Register object created from this IOobject with registry if true. More...

bool	registerObject () const
	Register object created from this IOobject with registry if true. More...

readOption	readOpt () const

readOption &	readOpt ()

writeOption	writeOpt () const

writeOption &	writeOpt ()

word	group () const
	Return group (extension part of name) More...

word	member () const
	Return member (name without the extension) More...

const fileName &	rootPath () const

const fileName &	caseName () const

const fileName &	instance () const

fileName &	instance ()

const fileName &	local () const

fileName	path () const
	Return complete path. More...

fileName	path (const word &instance, const fileName &local="") const
	Return complete path with alternative instance and local. More...

fileName	objectPath () const
	Return complete path + object name. More...

fileName	filePath () const
	Return complete path + object name if the file exists. More...

bool	readHeader (Istream &)
	Read header. More...

bool	headerOk ()
	Read and check header info. More...

bool	writeHeader (Ostream &) const
	Write header. More...

bool	writeHeader (Ostream &, const word &objectType) const
	Write header. Allow override of type. More...

bool	good () const

bool	bad () const

InfoProxy< IOobject >	info () const
	Return info proxy. More...

void	operator= (const IOobject &)

template<class Name >
Foam::word	groupName (Name name, const word &group)

Public Member Functions inherited from HashTable< regIOobject * >
bool	set (const word &, const regIOobject *&newElmt)
	Assign a new hashedEntry, overwriting existing entries. More...

	HashTable (const label size=128)
	Construct given initial table size. More...

	HashTable (Istream &, const label size=128)
	Construct from Istream. More...

	HashTable (const HashTable< regIOobject *, word, string::hash > &)
	Construct as copy. More...

	HashTable (const Xfer< HashTable< regIOobject *, word, string::hash >> &)
	Construct by transferring the parameter contents. More...

	~HashTable ()
	Destructor. More...

label	capacity () const
	The size of the underlying table. More...

label	size () const
	Return number of elements in table. More...

bool	empty () const
	Return true if the hash table is empty. More...

bool	found (const word &) const
	Return true if hashedEntry is found in table. More...

iterator	find (const word &)
	Find and return an iterator set at the hashedEntry. More...

const_iterator	find (const word &) const
	Find and return an const_iterator set at the hashedEntry. More...

List< word >	toc () const
	Return the table of contents. More...

List< word >	sortedToc () const
	Return the table of contents as a sorted list. More...

Ostream &	printInfo (Ostream &) const
	Print information. More...

bool	insert (const word &, const regIOobject *&newElmt)
	Insert a new hashedEntry. More...

bool	erase (const iterator &)
	Erase a hashedEntry specified by given iterator. More...

bool	erase (const word &)
	Erase a hashedEntry specified by the given key. More...

label	erase (const UList< word > &)
	Remove entries given by the listed keys from this HashTable. More...

label	erase (const HashTable< AnyType, word, AnyHash > &)
	Remove entries given by the given keys from this HashTable. More...

void	resize (const label newSize)
	Resize the hash table for efficiency. More...

void	clear ()
	Clear all entries from table. More...

void	clearStorage ()
	Clear the table entries and the table itself. More...

void	shrink ()
	Shrink the allocated table to approx. twice number of elements. More...

void	transfer (HashTable< regIOobject *, word, string::hash > &)
	Transfer the contents of the argument table into this table. More...

Xfer< HashTable< regIOobject *, word, string::hash > >	xfer ()
	Transfer contents to the Xfer container. More...

regIOobject *&	operator[] (const word &)
	Find and return a hashedEntry. More...

const regIOobject *&	operator[] (const word &) const
	Find and return a hashedEntry. More...

regIOobject *&	operator() (const word &)
	Find and return a hashedEntry, create it null if not present. More...

void	operator= (const HashTable< regIOobject *, word, string::hash > &)
	Assignment. More...

bool	operator== (const HashTable< regIOobject *, word, string::hash > &) const
	Equality. Hash tables are equal if the keys and values are equal. More...

bool	operator!= (const HashTable< regIOobject *, word, string::hash > &) const
	The opposite of the equality operation. Takes linear time. More...

iterator	begin ()
	Iterator set to the beginning of the HashTable. More...

const_iterator	begin () const
	const_iterator set to the beginning of the HashTable More...

const_iterator	cbegin () const
	const_iterator set to the beginning of the HashTable More...

Public Member Functions inherited from HashTableCore
	HashTableCore ()
	Construct null. More...

	ClassName ("HashTable")
	Define template name and debug. More...

Public Member Functions inherited from IDLList< ParticleType >
	IDLList ()
	Null construct. More...

	IDLList (const ParticleType &a)
	Construct given initial T. More...

	IDLList (Istream &is, const INew &inewt)
	Construct from Istream using given Istream constructor class. More...

	IDLList (Istream &is)
	Construct from Istream. More...

	IDLList (const IDLList< ParticleType > &idll, const CloneArg &cloneArg)
	Copy constructor with additional argument for clone. More...

Public Member Functions inherited from ILList< DLListBase, ParticleType >
	ILList ()
	Null construct. More...

	ILList (ParticleType *a)
	Construct given initial T. More...

	ILList (Istream &)
	Construct from Istream. More...

	ILList (const ILList< DLListBase, ParticleType > &)
	Construct as copy. More...

	ILList (const ILList< DLListBase, ParticleType > &lst, const CloneArg &cloneArg)
	Copy constructor with additional argument for clone. More...

	ILList (Istream &, const INew &)
	Construct from Istream using given Istream constructor class. More...

	~ILList ()
	Destructor. More...

bool	eraseHead ()
	Remove the head element specified from the list and delete it. More...

bool	erase (ParticleType *p)
	Remove the specified element from the list and delete it. More...

void	clear ()
	Clear the contents of the list. More...

void	transfer (ILList< DLListBase, ParticleType > &)
	Transfer the contents of the argument into this List. More...

void	operator= (const ILList< DLListBase, ParticleType > &)

Public Member Functions inherited from UILList< DLListBase, ParticleType >
	UILList ()
	Null construct. More...

	UILList (ParticleType *a)
	Construct given initial T. More...

	UILList (const UILList< DLListBase, ParticleType > &)
	Construct as copy. More...

ParticleType *	first ()
	Return the first entry. More...

const ParticleType *	first () const
	Return the first entry. More...

ParticleType *	last ()
	Return the last entry. More...

const ParticleType *	last () const
	Return the last entry. More...

ParticleType *	removeHead ()
	Remove and return head. More...

ParticleType *	remove (ParticleType *p)
	Remove and return element. More...

ParticleType *	remove (iterator &it)
	Remove and return specified by iterator. More...

void	operator= (const UILList< DLListBase, ParticleType > &)

iterator	begin ()

const_iterator	begin () const

const iterator &	end ()

const const_iterator &	end () const

const_iterator	cbegin () const

const const_iterator &	cend () const

const_reverse_iterator	crbegin () const

const const_reverse_iterator &	crend () const

const_reverse_iterator	rbegin () const

const const_reverse_iterator &	rend () const

bool	operator== (const UILList< DLListBase, ParticleType > &) const
	Equality operation on ULists of the same type. More...

bool	operator!= (const UILList< DLListBase, ParticleType > &) const
	The opposite of the equality operation. Takes linear time. More...

Public Member Functions inherited from DLListBase
	DLListBase ()
	Null construct. More...

	DLListBase (link *)
	Construct given initial entry. More...

	~DLListBase ()
	Destructor. More...

label	size () const
	Return number of elements in list. More...

bool	empty () const
	Return true if the list is empty. More...

link *	first ()
	Return first entry. More...

const link *	first () const
	Return const access to first entry. More...

link *	last ()
	Return last entry. More...

const link *	last () const
	Return const access to last entry. More...

void	insert (link *)
	Add at head of list. More...

void	append (link *)
	Add at tail of list. More...

bool	swapUp (link *)
	Swap this element with the one above unless it is at the top. More...

bool	swapDown (link *)
	Swap this element with the one below unless it is at the bottom. More...

link *	removeHead ()
	Remove and return head. More...

link *	remove (link *)
	Remove and return element. More...

link *	remove (iterator &)

link *	replace (link oldLink, link newLink)
	Replace oldLink with newLink and return element. More...

link *	replace (iterator &oldIter, link *newLink)
	Replace oldIter with newLink and return element. More...

void	clear ()
	Clear the list. More...

void	transfer (DLListBase &)
	Transfer the contents of the argument into this List. More...

iterator	begin ()

const iterator &	end ()

const_iterator	cbegin () const

const const_iterator &	cend () const

const_iterator	begin () const

const const_iterator &	end () const

const_reverse_iterator	crbegin () const

const const_reverse_iterator &	crend () const

const_reverse_iterator	rbegin () const

const const_reverse_iterator &	rend () const

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

typedef IDLList< ParticleType >::iterator	iterator

typedef IDLList< ParticleType >::const_iterator	const_iterator

Public Types inherited from regIOobject
enum	fileCheckTypes { timeStamp, timeStampMaster, inotify, inotifyMaster }
	Types of communications. More...

Public Types inherited from IOobject
enum	objectState { GOOD, BAD }
	Enumeration defining the valid states of an IOobject. More...

enum	readOption { MUST_READ, MUST_READ_IF_MODIFIED, READ_IF_PRESENT, NO_READ }
	Enumeration defining the read options. More...

enum	writeOption { AUTO_WRITE = 0, NO_WRITE = 1 }
	Enumeration defining the write options. More...

Public Types inherited from HashTable< regIOobject * >
typedef regIOobject *	value_type
	Type of values the HashTable contains. More...

typedef regIOobject *&	reference
	Type that can be used for storing into HashTable::value_type. More...

typedef const regIOobject *&	const_reference
	Type that can be used for storing into constant. More...

typedef label	size_type
	The type that can represent the size of a HashTable. More...

Public Types inherited from UILList< DLListBase, ParticleType >
typedef ParticleType	value_type
	Type of values the DLList contains. More...

typedef ParticleType &	reference
	Type that can be used for storing into DLList::value_type. More...

typedef const ParticleType &	const_reference
	Type that can be used for storing into constant. More...

typedef label	size_type
	The type that can represent the size of a DLList. More...

typedef DLListBase::iterator	LListBase_iterator

typedef DLListBase::const_iterator	LListBase_const_iterator

Static Public Member Functions inherited from regIOobject
template<class Type >
static Type &	store (Type *)
	Transfer ownership of the given object pointer to its registry. More...

template<class Type >
static Type &	store (autoPtr< Type > &)
	Transfer ownership of the given object pointer to its registry. More...

Static Public Member Functions inherited from IOobject
static bool	fileNameComponents (const fileName &path, fileName &instance, fileName &local, word &name)
	Split path into instance, local, name components. More...

template<class Name >
static word	groupName (Name name, const word &group)

template<class Stream >
static Stream &	writeBanner (Stream &os, bool noHint=false)
	Write the standard OpenFOAM file/dictionary banner. More...

template<class Stream >
static Stream &	writeDivider (Stream &os)
	Write the standard file section divider. More...

template<class Stream >
static Stream &	writeEndDivider (Stream &os)
	Write the standard end file divider. More...

Static Public Member Functions inherited from HashTableCore
static label	canonicalSize (const label)
	Return a canonical (power-of-two) size. More...

static iteratorEnd	cend ()
	iteratorEnd set to beyond the end of any HashTable More...

static iteratorEnd	end ()
	iteratorEnd set to beyond the end of any HashTable More...

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

Static Public Attributes inherited from cloud
static const word	prefix
	The prefix to local: lagrangian. More...

static word	defaultName
	The default cloud name: defaultCloud. More...

Static Public Attributes inherited from regIOobject
static const NamedEnum< fileCheckTypes, 4 >	fileCheckTypesNames

static int	fileModificationSkew

static fileCheckTypes	fileModificationChecking

Static Public Attributes inherited from HashTableCore
static const label	maxTableSize
	Maximum allowable table size. More...

Protected Member Functions inherited from IOobject
Istream *	objectStream ()
	Construct and return an IFstream for the object. More...

Istream *	objectStream (const fileName &)
	Construct and return an IFstream for the object given the. More...

void	setBad (const string &)
	Set the object state to bad. More...

Static Protected Attributes inherited from regIOobject
static bool	masterOnlyReading = false
	To flag master-only reading of objects. More...