ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.
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ProtoMol::SemiGenericTopology< TBoundaryConditions > Class Template Reference

#include <SemiGenericTopology.h>

Inheritance diagram for ProtoMol::SemiGenericTopology< TBoundaryConditions >:

ProtoMol::GenericTopology ProtoMol::Makeable ProtoMol::Topology< TBoundaryConditions, TCellManager > List of all members.

Public Types

typedef TBoundaryConditions BoundaryConditions

Public Member Functions

 SemiGenericTopology ()
 SemiGenericTopology (Real csf, const ExclusionType &e, const TBoundaryConditions &b)
virtual ~SemiGenericTopology ()
virtual std::vector< Parameter > getDefaults (const Vector3DBlock &positions) const
virtual Vector3D minimalDifference (const Vector3D &c1, const Vector3D &c2) const
virtual Vector3D minimalPosition (const Vector3D &c) const
virtual Real getVolume () const
virtual Real getVolume (const Vector3DBlock &positions) const
virtual void rescaleVolume (Real fac)
virtual void getBoundingbox (const Vector3DBlock &positions, Vector3D &minbb, Vector3D &maxbb) const
virtual void getBoundaryConditionsBox (Vector3D &minbb, Vector3D &maxbb) const
virtual bool checkMoleculePairDistances (const Vector3DBlock &positions) const
virtual void minimalImage (Vector3DBlock &positions)

Public Attributes

BoundaryConditions boundaryConditions

Detailed Description

template<class TBoundaryConditions>
class ProtoMol::SemiGenericTopology< TBoundaryConditions >

Introducing a semi-generic topology for the forces which do not depend on the cell manager

Member Typedef Documentation

template<class TBoundaryConditions>
typedef TBoundaryConditions ProtoMol::SemiGenericTopology< TBoundaryConditions >::BoundaryConditions
 

Constructor & Destructor Documentation

template<class TBoundaryConditions>
ProtoMol::SemiGenericTopology< TBoundaryConditions >::SemiGenericTopology (   )  [inline]
 

template<class TBoundaryConditions>
ProtoMol::SemiGenericTopology< TBoundaryConditions >::SemiGenericTopology (  Real  csf,
const ExclusionType &  e,
const TBoundaryConditions &  b
)  [inline]
 

template<class TBoundaryConditions>
virtual ProtoMol::SemiGenericTopology< TBoundaryConditions >::~SemiGenericTopology (   )  [inline, virtual]
 

Member Function Documentation

template<class TBoundaryConditions>
virtual bool ProtoMol::SemiGenericTopology< TBoundaryConditions >::checkMoleculePairDistances (  const Vector3DBlock &  positions  )  const [inline, virtual]
 

checks whether the plain distances between all atoms on each molecule are the same as with applying the boundary conditions. If true, there is no molecule, which is wrapped around.

Implements ProtoMol::GenericTopology.

template<class TBoundaryConditions>
virtual void ProtoMol::SemiGenericTopology< TBoundaryConditions >::getBoundaryConditionsBox (  Vector3D &  minbb,
Vector3D &  maxbb
)  const [inline, virtual]
 

returns the bounding box of the boundary conditions

Implements ProtoMol::GenericTopology.

template<class TBoundaryConditions>
virtual void ProtoMol::SemiGenericTopology< TBoundaryConditions >::getBoundingbox (  const Vector3DBlock &  positions,
Vector3D &  minbb,
Vector3D &  maxbb
)  const [inline, virtual]
 

computes the minimal bounding box of the positions taking into account of the boundary conditions

Implements ProtoMol::GenericTopology.

template<class TBoundaryConditions>
virtual std::vector<Parameter> ProtoMol::SemiGenericTopology< TBoundaryConditions >::getDefaults (  const Vector3DBlock &  positions  )  const [inline, virtual]
 

Returns possible default values for the parameters based on the positions.

Implements ProtoMol::GenericTopology.

template<class TBoundaryConditions>
virtual Real ProtoMol::SemiGenericTopology< TBoundaryConditions >::getVolume (  const Vector3DBlock &  positions  )  const [inline, virtual]
 

Actual volume of the simulation box or the particles.

Implements ProtoMol::GenericTopology.

template<class TBoundaryConditions>
virtual Real ProtoMol::SemiGenericTopology< TBoundaryConditions >::getVolume (   )  const [inline, virtual]
 

Volume by boundary conditions.

Implements ProtoMol::GenericTopology.

template<class TBoundaryConditions>
virtual Vector3D ProtoMol::SemiGenericTopology< TBoundaryConditions >::minimalDifference (  const Vector3D &  c1,
const Vector3D &  c2
)  const [inline, virtual]
 

Perform a minimal-image subtraction.

Implements ProtoMol::GenericTopology.

template<class TBoundaryConditions>
virtual void ProtoMol::SemiGenericTopology< TBoundaryConditions >::minimalImage (  Vector3DBlock &  positions  )  [inline, virtual]
 

translates all positions of a each molecule such that the plain distances between them yields and that the center of mass is inside the minimal image/basis cell. It may not work for molecules which are bigger then half of the simulation cell.

Implements ProtoMol::GenericTopology.

template<class TBoundaryConditions>
virtual Vector3D ProtoMol::SemiGenericTopology< TBoundaryConditions >::minimalPosition (  const Vector3D &  c  )  const [inline, virtual]
 

Find the position in the basis/original cell/image.

Implements ProtoMol::GenericTopology.

template<class TBoundaryConditions>
virtual void ProtoMol::SemiGenericTopology< TBoundaryConditions >::rescaleVolume (  Real  fac  )  [inline, virtual]
 

rescales the volume of the system cell/minimal image

Implements ProtoMol::GenericTopology.

Member Data Documentation

template<class TBoundaryConditions>
BoundaryConditions ProtoMol::SemiGenericTopology< TBoundaryConditions >::boundaryConditions
 

The documentation for this class was generated from the following file: Last update: . GNU GENERAL PUBLIC LICENSE, copyrighted by the University of Notre Dame and the University of Bergen, Norway.