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

#include <ScalarStructure.h>

Inheritance diagram for ProtoMol::ScalarStructure:

ProtoMol::Proxy List of all members.

Public Types

enum  Index {
  FIRST = 0,
  COULOMB = FIRST,
  LENNARDJONES,
  BOND,
  ANGLE,
  DIHEDRAL,
  IMPROPER,
  OTHER,
  VIRIALXX,
  VIRIALXY,
  VIRIALXZ,
  VIRIALYX,
  VIRIALYY,
  VIRIALYZ,
  VIRIALZX,
  VIRIALZY,
  VIRIALZZ,
  MOLVIRIALXX,
  MOLVIRIALXY,
  MOLVIRIALXZ,
  MOLVIRIALYX,
  MOLVIRIALYY,
  MOLVIRIALYZ,
  MOLVIRIALZX,
  MOLVIRIALZY,
  MOLVIRIALZZ,
  COULOMB_DELTAMU,
  LENNARDJONES_DELTAMU,
  BOND_DELTAMU,
  ANGLE_DELTAMU,
  DIHEDRAL_DELTAMU,
  IMPROPER_DELTAMU,
  CQFLUCTUATION,
  DELTATIME,
  INTEGRATOR,
  LASTREDUCE,
  SHADOW = LASTREDUCE,
  LAST
}

Public Member Functions

 ScalarStructure ()
Real & operator[] (Index i)
Real operator[] (Index i) const
void clear ()
ScalarStructure & intoAdd (const ScalarStructure &e)
ScalarStructure & intoSubtract (const ScalarStructure &e)
Real potentialEnergy () const
Real pressure (Real volume) const
Real molecularPressure (Real volume) const
Real deltaMu () const
void addVirial (const Vector3D &force12, const Vector3D &diff)
void addMolVirial (const Vector3D &force12, const Vector3D &diff)
void addVirial (const Vector3D &force12, const Vector3D &diff, const Vector3D &comDiff)
bool molecularVirial () const
bool molecularVirial (bool doMolecularVirial)
bool output () const
bool output (bool doOutput)
bool virial () const
bool virial (bool doVirial)

Private Attributes

Real myTable [LAST-FIRST]
bool myDoVirial
bool myDoMolecularVirial
bool myDoOutput

Detailed Description

Container holding energies and all kind of scalar values of intreset. The values are kept in array of fixed size and in parallel environment the values are reduced from FIRST to LASTREDUCE.

Member Enumeration Documentation

enum ProtoMol::ScalarStructure::Index
 

Index of the array of relevant scalars.

Enumeration values:
FIRST 
COULOMB 
LENNARDJONES 
BOND 
ANGLE 
DIHEDRAL 
IMPROPER 
OTHER 
VIRIALXX 
VIRIALXY 
VIRIALXZ 
VIRIALYX 
VIRIALYY 
VIRIALYZ 
VIRIALZX 
VIRIALZY 
VIRIALZZ 
MOLVIRIALXX 
MOLVIRIALXY 
MOLVIRIALXZ 
MOLVIRIALYX 
MOLVIRIALYY 
MOLVIRIALYZ 
MOLVIRIALZX 
MOLVIRIALZY 
MOLVIRIALZZ 
COULOMB_DELTAMU  needed for iSG simulations
LENNARDJONES_DELTAMU  needed for iSG simulations
BOND_DELTAMU  needed for iSG simulations
ANGLE_DELTAMU  needed for iSG simulations
DIHEDRAL_DELTAMU  needed for iSG simulations
IMPROPER_DELTAMU  needed for iSG simulations
CQFLUCTUATION  needed for iSG simulations
DELTATIME  needed for iSG simulations
INTEGRATOR 
LASTREDUCE  Last value to be reduced in parallel environment, only internal purpose.
SHADOW 
LAST 

Constructor & Destructor Documentation

ProtoMol::ScalarStructure::ScalarStructure (   ) 
 

Member Function Documentation

void ProtoMol::ScalarStructure::addMolVirial (  const Vector3D &  force12,
const Vector3D &  diff
) 
 

Add molecular viral term for one force pair.

void ProtoMol::ScalarStructure::addVirial (  const Vector3D &  force12,
const Vector3D &  diff,
const Vector3D &  comDiff
) 
 

Add viral term for one force pair and molecular viral term for one force pair.

void ProtoMol::ScalarStructure::addVirial (  const Vector3D &  force12,
const Vector3D &  diff
) 
 

Add viral term for one force pair.

void ProtoMol::ScalarStructure::clear (   ) 
 

Clear all of the energies in this structure.

Real ProtoMol::ScalarStructure::deltaMu (   )  const [inline]
 

The chemical potential difference.

ScalarStructure & ProtoMol::ScalarStructure::intoAdd (  const ScalarStructure &  e  ) 
 

ScalarStructure & ProtoMol::ScalarStructure::intoSubtract (  const ScalarStructure &  e  ) 
 

Real ProtoMol::ScalarStructure::molecularPressure (  Real  volume  )  const [inline]
 

The Molecular pressure.

bool ProtoMol::ScalarStructure::molecularVirial (  bool  doMolecularVirial  ) 
 

bool ProtoMol::ScalarStructure::molecularVirial (   )  const [inline]
 

test if molecular virial tensor desired

Real ProtoMol::ScalarStructure::operator[] (  Index  i  )  const [inline]
 

Real& ProtoMol::ScalarStructure::operator[] (  Index  i  )  [inline]
 

bool ProtoMol::ScalarStructure::output (  bool  doOutput  ) 
 

bool ProtoMol::ScalarStructure::output (   )  const [inline]
 

test if output desired, can be used to suppress output

Real ProtoMol::ScalarStructure::potentialEnergy (   )  const [inline]
 

The potential energy.

Real ProtoMol::ScalarStructure::pressure (  Real  volume  )  const [inline]
 

The atomic pressure.

bool ProtoMol::ScalarStructure::virial (  bool  doVirial  ) 
 

bool ProtoMol::ScalarStructure::virial (   )  const [inline]
 

test if virial tensor desired

Member Data Documentation

bool ProtoMol::ScalarStructure::myDoMolecularVirial [private]
 

bool ProtoMol::ScalarStructure::myDoOutput [private]
 

bool ProtoMol::ScalarStructure::myDoVirial [private]
 

Real ProtoMol::ScalarStructure::myTable[LAST-FIRST] [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.