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38 #ifndef moleculeCloud_H
39 #define moleculeCloud_H
61 public Cloud<molecule>
80 void buildConstProps();
82 void setSiteSizesAndPositions();
85 void buildCellOccupancy();
87 void calculatePairForce();
89 inline void evaluatePair
95 inline bool evaluatePotentialLimit
101 void calculateTetherForce();
103 void calculateExternalForce();
105 void removeHighEnergyOverlaps();
107 void initialiseMolecules
114 const point& position,
119 const vector& bulkVelocity
122 label nSites()
const;
124 inline vector equipartitionLinearVelocity
130 inline vector equipartitionAngularMomentum
174 const scalar targetTemperature,
175 const scalar measuredTemperature
IOdictionary is derived from dictionary and IOobject to give the dictionary automatic IO functionalit...
const List< DynamicList< molecule * > > & cellOccupancy() const
const InteractionLists< molecule > & il() const
A class for handling file names.
Mesh consisting of general polyhedral cells.
const List< molecule::constantProperties > constProps() const
Builds direct interaction list, specifying which local (real) cells are potentially in range of each ...
void evolve()
Evolve the molecules (move, calculate forces, control state etc)
const polyMesh & mesh() const
void writeXYZ(const fileName &fName) const
Write molecule sites in XYZ format.
void readFields(const typename GeoFieldType::Mesh &mesh, const IOobjectList &objects, const wordHashSet &selectedFields, LIFOStack< regIOobject * > &storedObjects)
Read the selected GeometricFields of the templated type.
const potential & pot() const
void applyConstraintsAndThermostats(const scalar targetTemperature, const scalar measuredTemperature)
A 1D array of objects of type <T>, where the size of the vector is known and used for subscript bound...
Base cloud calls templated on particle type.
Class to hold molecule constant properties.
A cell is defined as a list of faces with extra functionality.