Public Member Functions | |
| moleculeCloud (const polyMesh &mesh, const potential &pot, bool readFields=true) | |
| Construct given mesh and potential references. More... | |
| moleculeCloud (const polyMesh &mesh, const potential &pot, const IOdictionary &mdInitialiseDict, bool readFields=true) | |
| Construct given mesh, potential and mdInitialiseDict. More... | |
| void | evolve () |
| Evolve the molecules (move, calculate forces, control state etc) More... | |
| void | calculateForce () |
| void | applyConstraintsAndThermostats (const scalar targetTemperature, const scalar measuredTemperature) |
| const polyMesh & | mesh () const |
| const potential & | pot () const |
| const List< DynamicList< molecule * > > & | cellOccupancy () const |
| const InteractionLists< molecule > & | il () const |
| const List< molecule::constantProperties > | constProps () const |
| const molecule::constantProperties & | constProps (label id) const |
| Random & | rndGen () |
| void | writeXYZ (const fileName &fName) const |
| Write molecule sites in XYZ format. More... | |
 Public Member Functions inherited from Cloud< ParticleType > | |
| TypeName ("Cloud") | |
| Runtime type information. More... | |
| Cloud (const polyMesh &mesh, const word &cloudName, const IDLList< ParticleType > &particles) | |
| Construct from mesh and a list of particles. More... | |
| Cloud (const polyMesh &pMesh, const word &cloudName, const bool checkClass=true) | |
| Construct from mesh by reading from file with given cloud instance. More... | |
| const polyMesh & | pMesh () const |
| Return the polyMesh reference. More... | |
| virtual label | nParcels () const |
| Return the number of particles in the cloud. More... | |
| DynamicList< label > & | labels () const |
| Return temporary addressing. More... | |
| void | addParticle (ParticleType *pPtr) |
| Transfer particle to cloud. More... | |
| void | deleteParticle (ParticleType &p) |
| Remove particle from cloud and delete. More... | |
| void | deleteLostParticles () |
| Remove lost particles from cloud and delete. More... | |
| void | cloudReset (const Cloud< ParticleType > &c) |
| Reset the particles. More... | |
| template<class TrackCloudType > | |
| void | move (TrackCloudType &cloud, typename ParticleType::trackingData &td, const scalar trackTime) |
| Move the particles. More... | |
| void | autoMap (const mapPolyMesh &) |
| Remap the cells of particles corresponding to the. More... | |
| IOobject | fieldIOobject (const word &fieldName, const IOobject::readOption r) const |
| Helper to construct IOobject for field and current time. More... | |
| template<class DataType > | |
| void | checkFieldIOobject (const Cloud< ParticleType > &c, const IOField< DataType > &data) const |
| Check lagrangian data field. More... | |
| template<class DataType > | |
| void | checkFieldFieldIOobject (const Cloud< ParticleType > &c, const CompactIOField< Field< DataType >, DataType > &data) const |
| Check lagrangian data fieldfield. More... | |
| virtual void | writeFields () const |
| Write the field data for the cloud of particles Dummy at. More... | |
| virtual bool | writeObject (IOstreamOption streamOpt, const bool valid) const |
| Write using stream options. More... | |
| void | writePositions () const |
| Write positions to <cloudName>_positions.obj file. More... | |
| void | storeGlobalPositions () const |
| Call this before a topology change. More... | |
Additional Inherited Members | |
| Public Types inherited from Cloud< ParticleType > | |
| typedef ParticleType | particleType |
| typedef ParticleType | parcelType |
| Parcels are just particles. More... | |
| Static Public Attributes inherited from Cloud< ParticleType > | |
| static word | cloudPropertiesName |
| Name of cloud properties dictionary. More... | |
| Protected Attributes inherited from Cloud< ParticleType > | |
| cloud::geometryType | geometryType_ |
| Geometry type. More... | |
Definition at line 58 of file moleculeCloud.H.
| moleculeCloud | ( | const polyMesh & | mesh, |
| const potential & | pot, | ||
| bool | readFields = true |
||
| ) |
Construct given mesh and potential references.
Definition at line 1042 of file moleculeCloud.C.
References Foam::readFields(), and molecule::readFields().
| moleculeCloud | ( | const polyMesh & | mesh, |
| const potential & | pot, | ||
| const IOdictionary & | mdInitialiseDict, | ||
| bool | readFields = true |
||
| ) |
Construct given mesh, potential and mdInitialiseDict.
Definition at line 1072 of file moleculeCloud.C.
References clear(), Foam::readFields(), and molecule::readFields().
| void evolve | ( | ) |
Evolve the molecules (move, calculate forces, control state etc)
Definition at line 1101 of file moleculeCloud.C.
References Cloud< ParticleType >::move().
| void calculateForce | ( | ) |
Definition at line 1119 of file moleculeCloud.C.
References molecule::potentialEnergy(), molecule::rf(), molecule::siteForces(), and Foam::Zero.
| void applyConstraintsAndThermostats | ( | const scalar | targetTemperature, |
| const scalar | measuredTemperature | ||
| ) |
Definition at line 1142 of file moleculeCloud.C.
References Foam::endl(), Foam::Info, Foam::max(), Foam::nl, molecule::pi(), Foam::sqrt(), and molecule::v().
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inline |
Definition at line 343 of file moleculeCloudI.H.
Referenced by molecule::writeFields().
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Definition at line 349 of file moleculeCloudI.H.
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Definition at line 356 of file moleculeCloudI.H.
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Definition at line 363 of file moleculeCloudI.H.
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Definition at line 370 of file moleculeCloudI.H.
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Definition at line 377 of file moleculeCloudI.H.
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Definition at line 383 of file moleculeCloudI.H.
| void writeXYZ | ( | const fileName & | fName | ) | const |
Write molecule sites in XYZ format.
Definition at line 1170 of file moleculeCloud.C.
References forAll, molecule::id(), Foam::nl, molecule::constantProperties::siteIds(), molecule::sitePositions(), Vector< Cmpt >::x(), Vector< Cmpt >::y(), and Vector< Cmpt >::z().
Referenced by molecule::writeFields().
1.8.17 