ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.
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ProtoMol::EquilibriumMOLLYIntegrator Class Reference

#include <EquilibriumMOLLYIntegrator.h>

Inheritance diagram for ProtoMol::EquilibriumMOLLYIntegrator:

ProtoMol::MOLLYIntegrator ProtoMol::MTSIntegrator ProtoMol::StandardIntegrator ProtoMol::Integrator ProtoMol::Makeable List of all members.

Public Member Functions

 EquilibriumMOLLYIntegrator ()
 EquilibriumMOLLYIntegrator (int cycles, ForceGroup *overloadedForces, StandardIntegrator *nextIntegrator)
virtual ~EquilibriumMOLLYIntegrator ()
virtual void initialize (GenericTopology *topo, Vector3DBlock *positions, Vector3DBlock *velocities, ScalarStructure *energies)
virtual std::string getIdNoAlias () const

Static Public Attributes

const std::string keyword

Private Types

enum  { maxGDim = 4 }

Private Member Functions

virtual Vector3DBlock * doAveragingPositions ()
virtual void doMollification (Vector3DBlock *preprocessedPositions)
virtual MTSIntegrator * doMake (std::string &errMsg, const std::vector< Value > &values, ForceGroup *fg, StandardIntegrator *nextIntegrator) const
void luDcmp (Real(&m)[maxGDim][maxGDim], int dim, int(&index)[maxGDim], Real &d) const
void luBksb (Real(&m)[maxGDim][maxGDim], int dim, const int(&index)[maxGDim], Real(&b)[maxGDim]) const

Private Attributes

Vector3DBlock * myAveragedPositions
Real myMOLLYStepsize
std::vector< std::vector<
HydrogenBond > > 		myHydrogenConstraintGroups
std::vector< std::vector<
int > > 		myHydrogenAtomGroups

Member Enumeration Documentation

anonymous enum [private]
 

Enumeration values:
maxGDim 

Constructor & Destructor Documentation

ProtoMol::EquilibriumMOLLYIntegrator::EquilibriumMOLLYIntegrator (   ) 
 

ProtoMol::EquilibriumMOLLYIntegrator::EquilibriumMOLLYIntegrator (  int  cycles,
ForceGroup *  overloadedForces,
StandardIntegrator *  nextIntegrator
) 
 

ProtoMol::EquilibriumMOLLYIntegrator::~EquilibriumMOLLYIntegrator (   )  [virtual]
 

Member Function Documentation

Vector3DBlock * ProtoMol::EquilibriumMOLLYIntegrator::doAveragingPositions (   )  [private, virtual]
 

Implements ProtoMol::MOLLYIntegrator.

virtual MTSIntegrator* ProtoMol::EquilibriumMOLLYIntegrator::doMake (  std::string &  errMsg,
const std::vector< Value > &  values,
ForceGroup *  fg,
StandardIntegrator *  nextIntegrator
)  const [private, virtual]
 

Implements ProtoMol::MTSIntegrator.

void ProtoMol::EquilibriumMOLLYIntegrator::doMollification (  Vector3DBlock *  preprocessedPositions  )  [private, virtual]
 

Implements ProtoMol::MOLLYIntegrator.

virtual std::string ProtoMol::EquilibriumMOLLYIntegrator::getIdNoAlias (   )  const [inline, virtual]
 

Implements ProtoMol::Makeable.

void ProtoMol::EquilibriumMOLLYIntegrator::initialize (  GenericTopology *  topo,
Vector3DBlock *  positions,
Vector3DBlock *  velocities,
ScalarStructure *  energies
)  [virtual]
 

Set the integrator up. This method can be called at any time, and should perform any starting force evaluations the integrator needs in order to run correctly. The simulation data should be kept in the given structures.

Reimplemented from ProtoMol::MOLLYIntegrator.

void ProtoMol::EquilibriumMOLLYIntegrator::luBksb (  Real &  m[maxGDim][maxGDim],
int  dim,
const int &  index[maxGDim],
Real &  b[maxGDim]
)  const [private]
 

void ProtoMol::EquilibriumMOLLYIntegrator::luDcmp (  Real &  m[maxGDim][maxGDim],
int  dim,
int &  index[maxGDim],
Real &  d
)  const [private]
 

Member Data Documentation

const string ProtoMol::EquilibriumMOLLYIntegrator::keyword [static]
 

Vector3DBlock* ProtoMol::EquilibriumMOLLYIntegrator::myAveragedPositions [private]
 

std::vector<std::vector<int> > ProtoMol::EquilibriumMOLLYIntegrator::myHydrogenAtomGroups [private]
 

std::vector<std::vector<HydrogenBond> > ProtoMol::EquilibriumMOLLYIntegrator::myHydrogenConstraintGroups [private]
 

Real ProtoMol::EquilibriumMOLLYIntegrator::myMOLLYStepsize [private]
 

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