36 #ifndef moleculeCloud_H 37 #define moleculeCloud_H 59 public Cloud<molecule>
78 void buildConstProps();
80 void setSiteSizesAndPositions();
83 void buildCellOccupancy();
85 void calculatePairForce();
87 inline void evaluatePair
93 inline bool evaluatePotentialLimit
99 void calculateTetherForce();
101 void calculateExternalForce();
103 void removeHighEnergyOverlaps();
105 void initialiseMolecules
112 const point& position,
117 const vector& bulkVelocity
120 label nSites()
const;
122 inline vector equipartitionLinearVelocity
128 inline vector equipartitionAngularMomentum
169 const scalar targetTemperature,
170 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)
void operator=(const moleculeCloud &)=delete
Disallow default bitwise assignment.
Base cloud calls templated on particle type.
moleculeCloud(const polyMesh &mesh, const potential &pot, bool readFields=true)
Construct given mesh and potential references.
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