36 #ifndef moleculeCloud_H 37 #define moleculeCloud_H 59 public Cloud<molecule>
81 void buildConstProps();
83 void setSiteSizesAndPositions();
86 void buildCellOccupancy();
88 void calculatePairForce();
90 inline void evaluatePair
96 inline bool evaluatePotentialLimit
102 void calculateTetherForce();
104 void calculateExternalForce();
106 void removeHighEnergyOverlaps();
108 void initialiseMolecules
115 const point& position,
120 const vector& bulkVelocity
123 label nSites()
const;
125 inline vector equipartitionLinearVelocity
131 inline vector equipartitionAngularMomentum
175 const scalar targetTemperature,
176 const scalar measuredTemperature
void writeXYZ(const fileName &fName) const
Write molecule sites in XYZ format.
const InteractionLists< molecule > & il() const
intWM_LABEL_SIZE_t label
A label is an int32_t or int64_t as specified by the pre-processor macro WM_LABEL_SIZE.
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 readFields(const typename GeoFieldType::Mesh &mesh, const IOobjectList &objects, const HashSet< word > &selectedFields, LIFOStack< regIOobject *> &storedObjects)
Read the selected GeometricFields of the specified type.
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)
Simple random number generator.
Base cloud calls templated on particle type.
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.
const polyMesh & mesh() const