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
void writeXYZ(const fileName &fName) const
Write molecule sites in XYZ format.
const InteractionLists< molecule > & il() const
A class for handling file names.
Builds direct interaction list, specifying which local (real) cells are potentially in range of each ...
Class to hold molecule constant properties.
void evolve()
Evolve the molecules (move, calculate forces, control state etc)
A 1D array of objects of type <T>, where the size of the vector is known and used for subscript bound...
IOdictionary is derived from dictionary and IOobject to give the dictionary automatic IO functionalit...
const List< DynamicList< molecule * > > & cellOccupancy() const
void applyConstraintsAndThermostats(const scalar targetTemperature, const scalar measuredTemperature)
Base cloud calls templated on particle type.
A Vector of values with scalar precision, where scalar is float/double depending on the compilation f...
const potential & pot() const
A cell is defined as a list of faces with extra functionality.
const List< molecule::constantProperties > constProps() const
Mesh consisting of general polyhedral cells.
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 polyMesh & mesh() const