moleculeCloud Class Reference
Inheritance diagram for moleculeCloud:
Collaboration diagram for moleculeCloud:

Public Member Functions

 TypeName ("moleculeCloud")
 Runtime type information. More...
 
 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...
 
 moleculeCloud (const moleculeCloud &)=delete
 Disallow default bitwise copy construction. More...
 
void evolve ()
 Evolve the molecules (move, calculate forces, control state etc) More...
 
void calculateForce ()
 
void applyConstraintsAndThermostats (const scalar targetTemperature, const scalar measuredTemperature)
 
const polyMeshmesh () const
 
const potentialpot () const
 
const List< DynamicList< molecule * > > & cellOccupancy () const
 
const InteractionLists< molecule > & il () const
 
const List< molecule::constantPropertiesconstProps () const
 
const molecule::constantPropertiesconstProps (label id) const
 
randomGeneratorrndGen ()
 
distributions::standardNormalstdNormal ()
 
void writeXYZ (const fileName &fName) const
 Write molecule sites in XYZ format. More...
 
void operator= (const moleculeCloud &)=delete
 Disallow default bitwise assignment. More...
 
- Public Member Functions inherited from Cloud< molecule >
const labelListpatchNbrProc () const
 Map from patch index to the neighbouring processor index. More...
 
const labelListpatchNbrProcPatch () const
 Map from patch index to the corresponding patch index on the. More...
 
const labelListListpatchNonConformalCyclicPatches () const
 Return map from patch index to connected non-conformal cyclics. More...
 
 Cloud (const polyMesh &mesh, const word &cloudName, const IDLList< molecule > &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 polyMeshpMesh () const
 Return the polyMesh reference. More...
 
label size () const
 Return the number of particles in the cloud. More...
 
bool cpuLoad () const
 Return true to cache per-cell CPU load. More...
 
const const_iterator begin () const
 
iterator begin ()
 
const const_iterator cbegin () const
 
const const_iterator end () const
 
iterator end ()
 
const const_iterator cend () const
 
void clear ()
 
void addParticle (molecule *pPtr)
 Transfer particle to cloud. More...
 
void deleteParticle (molecule &)
 Remove particle from cloud and delete. More...
 
void deleteLostParticles ()
 Remove lost particles from cloud and delete. More...
 
void cloudReset (const Cloud< molecule > &c)
 Reset the particles. More...
 
void changeTimeStep ()
 Change the particles' state from the end of the previous time. More...
 
void move (TrackCloudType &cloud, typename ParticleType::trackingData &td)
 Move the particles. More...
 
virtual void topoChange (const polyTopoChangeMap &)
 Update topology using the given map. More...
 
virtual void mapMesh (const polyMeshMap &)
 Update from another mesh using the given map. More...
 
virtual void distribute (const polyDistributionMap &)
 Redistribute or update using the given distribution map. More...
 
IOobject fieldIOobject (const word &fieldName, const IOobject::readOption r) const
 Helper to construct IOobject for field and current time. More...
 
void checkFieldIOobject (const Cloud< molecule > &c, const IOField< DataType > &data) const
 Check lagrangian data field. More...
 
void checkFieldFieldIOobject (const Cloud< molecule > &c, const CompactIOField< Field< DataType >> &data) const
 Check lagrangian data fieldfield. 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 bool write=true) const
 Write using given format, version and compression. More...
 
void writePositions () const
 Write positions to <cloudName>_positions.obj file. More...
 
void storeGlobalPositions () const
 Call this before a topology change. Stores the particles global. More...
 
- Public Member Functions inherited from cloud
 TypeName ("cloud")
 Runtime type information. More...
 
 cloud (const objectRegistry &, const word &cloudName=defaultName)
 Construct for the given objectRegistry and named cloud instance. More...
 
 cloud (const cloud &)=delete
 Disallow default bitwise copy construction. More...
 
virtual ~cloud ()
 Destructor. More...
 
void operator= (const cloud &)=delete
 Disallow default bitwise assignment. 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...
 
 objectRegistry (objectRegistry &&)=default
 Move constructor. More...
 
 objectRegistry (const objectRegistry &)=delete
 Disallow default bitwise copy construction. More...
 
virtual ~objectRegistry ()
 Destructor. More...
 
const Timetime () const
 Return time. More...
 
const objectRegistryparent () const
 Return the parent objectRegistry. More...
 
virtual const fileNamedbDir () const
 Local directory path of this objectRegistry relative to the time. More...
 
fileName path (const word &instance, const fileName &local="") const
 Return complete path with alternative instance and local. More...
 
wordList toc (const word &className) const
 Return the list of names of IOobjects of given class name. More...
 
wordList sortedToc (const word &className) const
 Return the sorted list of names of IOobjects of given class name. More...
 
template<class Type >
wordList toc () const
 Return the list of names of the IOobjects of given type. More...
 
template<class Type >
wordList toc (const wordRe &name) const
 Return the list of objects whose name matches the input regExp. More...
 
template<class Type >
wordList toc (const wordReList &name) const
 Return the list of objects whose name matches the input regExp. More...
 
const objectRegistrysubRegistry (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 in registry. More...
 
template<class Type >
const Type & lookupObject (const word &name) const
 Lookup and return the object of the given Type and name. More...
 
template<class Type >
Type & lookupObjectRef (const word &name) const
 Lookup and return the object reference of the given Type. More...
 
template<class Type >
bool foundType (const word &group=word::null) const
 Is the Type in registry. More...
 
template<class Type >
const Type & lookupType (const word &group=word::null) const
 Lookup and return the object of the given Type. More...
 
label getEvent () const
 Return new event number. More...
 
const objectRegistrythisDb () const
 Return the object registry. 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...
 
void clear ()
 Remove all regIOobject owned by the registry. More...
 
void addTemporaryObject (const word &name) const
 Add the given name to the set of temporary objects to cache. More...
 
bool cacheTemporaryObject (const word &name) const
 Return true if given name is in the cacheTemporaryObjects set. More...
 
template<class Object >
bool cacheTemporaryObject (Object &ob) const
 Cache the given object. More...
 
void resetCacheTemporaryObject (const regIOobject &ob) const
 Reset the cache state of the given object. More...
 
bool checkCacheTemporaryObjects () const
 Check that all objects in the cacheTemporaryObjects set. More...
 
virtual bool modified () const
 Return true if any of the object's files have been modified. More...
 
virtual bool dependenciesModified () const
 Cache pointers to objects who's dependencies have been modified. More...
 
virtual bool readIfModified ()
 Read object if modified. More...
 
virtual bool read ()
 Read dependent objects. More...
 
void readModifiedObjects ()
 Read the objects that have been modified. More...
 
void printToc (Ostream &os) const
 Print the list of object names and their type. More...
 
virtual bool writeData (Ostream &) const
 writeData function required by regIOobject but not used More...
 
void operator= (const objectRegistry &)=delete
 Disallow default bitwise assignment. More...
 
template<class Type >
Foam::wordList toc () const
 
template<class Type >
Foam::wordList toc (const wordRe &name) const
 
template<class Type >
Foam::wordList toc (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)
 
fileName path () const
 Return complete path. More...
 
- 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 &)
 Copy constructor. More...
 
 regIOobject (const regIOobject &&)
 Move constructor. More...
 
 regIOobject (const regIOobject &, bool registerCopy)
 Copy constructor, transferring registry registration to copy. More...
 
 regIOobject (const word &newName, const regIOobject &, bool registerCopy)
 Copy constructor with new name, transferring registry registration. More...
 
 regIOobject (const IOobject &, const regIOobject &)
 Copy constructor with new IO parameters. More...
 
virtual ~regIOobject ()
 Destructor. More...
 
virtual bool global () const
 Return true if object is global, i.e. same for all processors. More...
 
virtual bool globalFile () const
 Return true if object is global, i.e. same for all processors. More...
 
const fileNamecaseName () const
 
fileName path () const
 Return complete path. More...
 
fileName objectPath () const
 Return complete path + object name. More...
 
fileName filePath () const
 Return complete path + object name if the file exists. More...
 
bool checkIn ()
 Add object to registry. More...
 
bool checkOut ()
 Remove object from registry. More...
 
void addWatch ()
 Add file watch on object (if registered and READ_IF_MODIFIED) More...
 
bool registered () const
 Is this object registered with the 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...
 
labeleventNo ()
 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...
 
bool headerOk ()
 Read and check header info. More...
 
IstreamreadStream (const word &, const bool read=true)
 Return Istream and check object type against that given. More...
 
void close ()
 Close Istream. More...
 
virtual bool readData (Istream &)
 Virtual readData function. More...
 
const labelListwatchIndices () const
 Return file-monitoring handles. More...
 
labelListwatchIndices ()
 Return file-monitoring handles. More...
 
virtual bool write (const bool write=true) const
 Write using setting from DB. More...
 
void operator= (const IOobject &)
 Assign to IOobject. More...
 
void operator= (const regIOobject &)=delete
 Disallow default assignment. More...
 
const fileNamecaseName (const bool global) const
 
fileName path (const bool global) const
 Return complete path including the processor sub-directory. More...
 
fileName objectPath (const bool global) const
 Return complete path + object name including the processor. More...
 
fileName filePath (const word &typeName, const bool global) const
 Return complete path + object name if the file exists. More...
 
- 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...
 
 IOobject (const IOobject &io, const objectRegistry &registry)
 Construct from copy resetting registry. More...
 
 IOobject (const IOobject &io, const word &name)
 Construct from copy resetting name. More...
 
 IOobject (const IOobject &io)=default
 Copy constructor. More...
 
autoPtr< IOobjectclone () const
 Clone. More...
 
autoPtr< IOobjectclone (const objectRegistry &registry) const
 Clone resetting registry. More...
 
virtual ~IOobject ()
 Destructor. More...
 
const Timetime () const
 Return time. More...
 
const objectRegistrydb () const
 Return the local objectRegistry. More...
 
const wordname () const
 Return name. More...
 
const wordheaderClassName () const
 Return name of the class name read from header. More...
 
wordheaderClassName ()
 Return name of the class name read from header. More...
 
stringnote ()
 Return non-constant access to the optional note. More...
 
const stringnote () 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
 
readOptionreadOpt ()
 
writeOption writeOpt () const
 
writeOptionwriteOpt ()
 
word group () const
 Return group (extension part of name) More...
 
word member () const
 Return member (name without the extension) More...
 
const fileNamerootPath () const
 
const fileNamecaseName (const bool global) const
 
fileNameinstance () const
 Return the instance directory, constant, system, <time> etc. More...
 
void updateInstance () const
 If the instance is a time directory update to the current time. More...
 
const fileNamelocal () const
 
fileName path (const bool global) const
 Return complete path including the processor sub-directory. More...
 
fileName objectPath (const bool global) const
 Return complete path + object name including the processor. More...
 
fileName relativePath () const
 Return the path relative to the case directory. More...
 
fileName relativeObjectPath () const
 Return complete relativePath + object name. More...
 
fileName filePath (const word &typeName, const bool global) const
 Return complete path + object name if the file exists. More...
 
bool readHeader (Istream &)
 Read header. More...
 
bool headerOk ()
 Read header of local object without type-checking. More...
 
template<class Type >
void warnNoRereading () const
 Helper: warn that type does not support re-reading. 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< IOobjectinfo () 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)
 Set a new hashedEntry, overwriting existing entries. More...
 
void set (const HashTable< regIOobject *, word, string::hash > &)
 Insert all the entries from the given HashTable,. More...
 
 HashTable (const label size=128)
 Construct given initial table size. More...
 
 HashTable (Istream &, const label size=128)
 Construct from Istream. More...
 
 HashTable (const UList< word > &keyList, const UList< regIOobject * > &elmtList)
 Construct from a list of keys and list of elements. More...
 
 HashTable (const HashTable< regIOobject *, word, string::hash > &)
 Copy constructor. More...
 
 HashTable (HashTable< regIOobject *, word, string::hash > &&)
 Move constructor. More...
 
 HashTable (std::initializer_list< Tuple2< word, regIOobject * >>)
 Construct from an initialiser list. 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< wordtoc () const
 Return the table of contents. More...
 
List< wordsortedToc () const
 Return the table of contents as a sorted list. More...
 
List< const_iteratorsorted () const
 Return a sorted list of constant iterators. More...
 
OstreamprintInfo (Ostream &) const
 Print information. More...
 
bool insert (const word &, const regIOobject * &newElmt)
 Insert a new hashedEntry. More...
 
void insert (const HashTable< regIOobject *, word, string::hash > &)
 Insert all the entries from the given HashTable. 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...
 
Foam::label erase (const HashTable< AnyType, word, AnyHash > &rhs)
 
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...
 
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 operator. More...
 
void operator= (HashTable< regIOobject *, word, string::hash > &&)
 Move assignment operator. More...
 
void operator= (std::initializer_list< Tuple2< word, regIOobject * >>)
 Assignment to an initialiser list. 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 ILList< LListBase, T >
 ILList ()
 Null construct. More...
 
 ILList (T *a)
 Construct given initial T. More...
 
 ILList (Istream &)
 Construct from Istream. More...
 
 ILList (const ILList< LListBase, T > &)
 Copy constructor. More...
 
 ILList (ILList< LListBase, T > &&)
 Move constructor. More...
 
template<class CloneArg >
 ILList (const ILList< LListBase, T > &lst, const CloneArg &cloneArg)
 Copy constructor with additional argument for clone. More...
 
template<class INew >
 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 (T *p)
 Remove the specified element from the list and delete it. More...
 
void clear ()
 Clear the contents of the list. More...
 
void transfer (ILList< LListBase, T > &)
 Transfer the contents of the argument into this List. More...
 
void operator= (const ILList< LListBase, T > &)
 Assignment operator. More...
 
void operator= (ILList< LListBase, T > &&)
 Move assignment operator. More...
 
- Public Member Functions inherited from UILList< LListBase, T >
 UILList ()
 Null construct. More...
 
 UILList (T *a)
 Construct given initial T. More...
 
 UILList (const UILList< LListBase, T > &)
 Copy constructor. More...
 
 UILList (UILList< LListBase, T > &&)
 Move constructor. More...
 
Tfirst ()
 Return the first entry. More...
 
const Tfirst () const
 Return the first entry. More...
 
Tlast ()
 Return the last entry. More...
 
const Tlast () const
 Return the last entry. More...
 
TremoveHead ()
 Remove and return head. More...
 
Tremove (T *p)
 Remove and return element. More...
 
Tremove (iterator &it)
 Remove and return specified by iterator. More...
 
void operator= (const UILList< LListBase, T > &)
 Assignment operator. More...
 
void operator= (UILList< LListBase, T > &&)
 Move assignment operator. More...
 
iterator begin ()
 
const iteratorend ()
 
const_iterator cbegin () const
 
const const_iteratorcend () const
 
const_iterator begin () const
 
const const_iteratorend () const
 
const_reverse_iterator crbegin () const
 
const const_reverse_iteratorcrend () const
 
const_reverse_iterator rbegin () const
 
const const_reverse_iteratorrend () const
 
bool operator== (const UILList< LListBase, T > &) const
 Equality operation on ULists of the same type. More...
 
bool operator!= (const UILList< LListBase, T > &) const
 The opposite of the equality operation. Takes linear time. More...
 

Additional Inherited Members

- Public Types inherited from Cloud< molecule >
typedef molecule particleType
 
typedef IDLList< molecule >::value_type value_type
 
typedef IDLList< molecule >::iterator iterator
 
typedef IDLList< molecule >::const_iterator const_iterator
 
- 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...
 
enum  fileCheckTypes { timeStamp , timeStampMaster , inotify , inotifyMaster }
 Enumeration defining the file checking options. More...
 
- Public Types inherited from HashTable< regIOobject * >
typedef regIOobjectvalue_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< LListBase, T >
typedef T value_type
 Type of values the DLList contains. More...
 
typedef Treference
 Type that can be used for storing into DLList::value_type. More...
 
typedef const Tconst_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 LListBase::iterator LListBase_iterator
 
typedef LListBase::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)
 
static word group (const word &name)
 Return group (extension part of name) More...
 
static word member (const word &name)
 Return member (name without the extension) More...
 
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< molecule >
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 float fileModificationSkew
 
- Static Public Attributes inherited from IOobject
static constexpr const char * foamFile = "FoamFile"
 Keyword for the FoamFile header sub-dictionary. More...
 
static const NamedEnum< fileCheckTypes, 4 > fileCheckTypesNames
 
static fileCheckTypes fileModificationChecking
 Type of file modification checking. More...
 
- Static Public Attributes inherited from HashTableCore
static const label maxTableSize
 Maximum allowable table size. More...
 
- Protected Member Functions inherited from regIOobject
bool readHeaderOk (const IOstream::streamFormat defaultFormat, const word &typeName)
 Read header, check readOpt flags and read data if necessary. More...
 
- Protected Member Functions inherited from IOobject
void setBad (const string &)
 Set the object state to bad. More...
 
template<class Type >
bool typeHeaderOk (const bool checkType)
 Read header using typeGlobalFile to find file. More...
 

Detailed Description

Source files

Definition at line 57 of file moleculeCloud.H.

Constructor & Destructor Documentation

◆ moleculeCloud() [1/3]

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

Construct given mesh and potential references.

Definition at line 1070 of file moleculeCloud.C.

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

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◆ moleculeCloud() [2/3]

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

Construct given mesh, potential and mdInitialiseDict.

Definition at line 1101 of file moleculeCloud.C.

References Cloud< molecule >::clear(), molecule::readFields(), and Foam::readFields().

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◆ moleculeCloud() [3/3]

moleculeCloud ( const moleculeCloud )
delete

Disallow default bitwise copy construction.

Member Function Documentation

◆ TypeName()

TypeName ( "moleculeCloud"  )

Runtime type information.

◆ evolve()

void evolve ( )

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

Definition at line 1132 of file moleculeCloud.C.

References Cloud< ParticleType >::move(), molecule::trackingData::part(), molecule::trackingData::tpLinearTrack, molecule::trackingData::tpRotationalTrack, molecule::trackingData::tpVelocityHalfStep0, and molecule::trackingData::tpVelocityHalfStep1.

Referenced by main().

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◆ calculateForce()

void calculateForce ( )

Definition at line 1152 of file moleculeCloud.C.

References forAllIter, and Foam::Zero.

Referenced by moleculeCloud::moleculeCloud().

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◆ applyConstraintsAndThermostats()

void applyConstraintsAndThermostats ( const scalar  targetTemperature,
const scalar  measuredTemperature 
)

Definition at line 1174 of file moleculeCloud.C.

References Foam::endl(), forAllIter, Foam::Info, Foam::max(), Foam::nl, and Foam::sqrt().

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◆ mesh()

const Foam::polyMesh & mesh ( ) const
inline

Definition at line 341 of file moleculeCloudI.H.

Referenced by molecule::writeFields().

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◆ pot()

const Foam::potential & pot ( ) const
inline

Definition at line 347 of file moleculeCloudI.H.

◆ cellOccupancy()

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

Definition at line 354 of file moleculeCloudI.H.

◆ il()

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

Definition at line 361 of file moleculeCloudI.H.

◆ constProps() [1/2]

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

Definition at line 368 of file moleculeCloudI.H.

◆ constProps() [2/2]

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

Definition at line 375 of file moleculeCloudI.H.

◆ rndGen()

Foam::randomGenerator & rndGen ( )
inline

Definition at line 381 of file moleculeCloudI.H.

◆ stdNormal()

Foam::distributions::standardNormal & stdNormal ( )
inline

Definition at line 387 of file moleculeCloudI.H.

◆ writeXYZ()

void writeXYZ ( const fileName fName) const

Write molecule sites in XYZ format.

Definition at line 1203 of file moleculeCloud.C.

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

Referenced by molecule::writeFields().

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◆ operator=()

void operator= ( const moleculeCloud )
delete

Disallow default bitwise assignment.


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