OpenMD  2.5
Molecular Dynamics in the Open
OpenMD::Globals Class Reference

#include <Globals.hpp>

Inheritance diagram for OpenMD::Globals:
OpenMD::DataHolder

Public Types

typedef std::pair< int, int > intPair
 

Public Member Functions

 Globals ()
 
virtual ~Globals ()
 
 DeclareParameter (ForceField, std::string)
 
 DeclareParameter (TargetTemp, RealType)
 
 DeclareParameter (Ensemble, std::string)
 
 DeclareParameter (Dt, RealType)
 
 DeclareParameter (RunTime, RealType)
 
 DeclareParameter (FinalConfig, std::string)
 
 DeclareParameter (SampleTime, RealType)
 
 DeclareParameter (ResetTime, RealType)
 
 DeclareParameter (StatusTime, RealType)
 
 DeclareParameter (CutoffRadius, RealType)
 
 DeclareParameter (SwitchingRadius, RealType)
 
 DeclareParameter (TempSet, bool)
 
 DeclareParameter (ThermalTime, RealType)
 
 DeclareParameter (UsePeriodicBoundaryConditions, bool)
 
 DeclareParameter (TargetPressure, RealType)
 
 DeclareParameter (UseAtomicVirial, bool)
 
 DeclareParameter (UseLongRangeCorrections, bool)
 
 DeclareParameter (TauThermostat, RealType)
 
 DeclareParameter (TauBarostat, RealType)
 
 DeclareParameter (ZconsTime, RealType)
 
 DeclareParameter (ZconsTol, RealType)
 
 DeclareParameter (ZconsForcePolicy, std::string)
 
 DeclareParameter (Seed, unsigned long int)
 
 DeclareParameter (UseInitalTime, bool)
 
 DeclareParameter (UseIntialExtendedSystemState, bool)
 
 DeclareParameter (OrthoBoxTolerance, RealType)
 
 DeclareParameter (ZconsGap, RealType)
 
 DeclareParameter (ZconsFixtime, RealType)
 
 DeclareParameter (ZconsUsingSMD, bool)
 
 DeclareParameter (UseThermodynamicIntegration, bool)
 
 DeclareParameter (ThermodynamicIntegrationLambda, RealType)
 
 DeclareParameter (ThermodynamicIntegrationK, RealType)
 
 DeclareParameter (ForceFieldVariant, std::string)
 
 DeclareParameter (ForceFieldFileName, std::string)
 
 DeclareParameter (SurfaceTension, RealType)
 
 DeclareParameter (PrintPressureTensor, bool)
 
 DeclareParameter (PrintHeatFlux, bool)
 
 DeclareParameter (TaggedAtomPair, intPair)
 
 DeclareParameter (PrintTaggedPairDistance, bool)
 
 DeclareParameter (ElectrostaticSummationMethod, std::string)
 
 DeclareParameter (ElectrostaticScreeningMethod, std::string)
 
 DeclareParameter (DampingAlpha, RealType)
 
 DeclareParameter (Dielectric, RealType)
 
 DeclareParameter (CutoffMethod, std::string)
 
 DeclareParameter (SwitchingFunctionType, std::string)
 
 DeclareParameter (CompressDumpFile, bool)
 
 DeclareParameter (OutputForceVector, bool)
 
 DeclareParameter (OutputParticlePotential, bool)
 
 DeclareParameter (OutputElectricField, bool)
 
 DeclareParameter (OutputFluctuatingCharges, bool)
 
 DeclareParameter (OutputSitePotential, bool)
 
 DeclareParameter (OutputDensity, bool)
 
 DeclareParameter (SkinThickness, RealType)
 
 DeclareParameter (StatFileFormat, std::string)
 
 DeclareParameter (StatFilePrecision, int)
 
 DeclareParameter (HydroPropFile, std::string)
 
 DeclareParameter (Viscosity, RealType)
 
 DeclareParameter (BeadSize, RealType)
 
 DeclareParameter (UseSphericalBoundaryConditions, bool)
 
 DeclareParameter (FrozenBufferRadius, RealType)
 
 DeclareParameter (LangevinBufferRadius, RealType)
 
 DeclareParameter (AccumulateBoxDipole, bool)
 
 DeclareParameter (AccumulateBoxQuadrupole, bool)
 
 DeclareParameter (NeighborListNeighbors, int)
 
 DeclareParameter (UseMultipleTemperatureMethod, bool)
 
 DeclareParameter (MTM_Ce, RealType)
 
 DeclareParameter (MTM_G, RealType)
 
 DeclareParameter (MTM_Io, RealType)
 
 DeclareParameter (MTM_Sigma, RealType)
 
 DeclareParameter (MTM_R, RealType)
 
 DeclareParameter (UseRestraints, bool)
 
 DeclareParameter (Restraint_file, std::string)
 
 DeclareParameter (HULL_Method, std::string)
 
 DeclareParameter (Alpha, RealType)
 
 DeclareAlterableParameter (MDfileVersion, int)
 
 DeclareParameter (UniformField, std::vector< RealType >)
 
 DeclareParameter (UniformGradientStrength, RealType)
 
 DeclareParameter (UniformGradientDirection1, std::vector< RealType >)
 
 DeclareParameter (UniformGradientDirection2, std::vector< RealType >)
 
 DeclareParameter (ElectricField, std::vector< RealType >)
 
 DeclareParameter (ConstraintTime, RealType)
 
 DeclareParameter (PotentialSelection, std::string)
 
bool addComponent (Component *comp)
 
bool addZConsStamp (ZConsStamp *zcons)
 
bool addRestraintStamp (RestraintStamp *rest)
 
bool addMoleculeStamp (MoleculeStamp *molStamp)
 
int getNComponents ()
 
std::vector< Component * > getComponents ()
 
ComponentgetComponentAt (int index)
 
int getNZconsStamps ()
 
std::vector< ZConsStamp * > getZconsStamps ()
 
ZConsStampgetZconsStampAt (int index)
 
int getNRestraintStamps ()
 
std::vector< RestraintStamp * > getRestraintStamps ()
 
RestraintStampgetRestraintStampAt (int index)
 
bool addFluctuatingChargeParameters (FluctuatingChargeParameters *flucqPars)
 
FluctuatingChargeParametersgetFluctuatingChargeParameters ()
 
bool addRNEMDParameters (RNEMDParameters *rnemdPars)
 
RNEMDParametersgetRNEMDParameters ()
 
bool addMinimizerParameters (MinimizerParameters *miniPars)
 
MinimizerParametersgetMinimizerParameters ()
 
virtual void validate ()
 
- Public Member Functions inherited from OpenMD::DataHolder
 DataHolder ()
 
virtual ~DataHolder ()
 
template<class T >
void assign (const std::string &keyword, T val)
 

Private Attributes

std::vector< Component * > components_
 
std::vector< ZConsStamp * > zconstraints_
 
std::vector< RestraintStamp * > restraints_
 
std::map< std::string, MoleculeStamp * > moleculeStamps_
 
std::pair< int, int > taggedAtomPair_
 
FluctuatingChargeParametersflucQpars_
 
RNEMDParametersrnemdPars_
 
MinimizerParametersminimizerPars_
 

Additional Inherited Members

- Protected Types inherited from OpenMD::DataHolder
typedef std::map< std::string, ParameterBase * > ParamMap
 
- Protected Attributes inherited from OpenMD::DataHolder
ParamMap parameters_
 
std::set< std::string > deprecatedKeywords_
 

Detailed Description

Definition at line 63 of file Globals.hpp.

Member Typedef Documentation

◆ intPair

typedef std::pair<int, int> OpenMD::Globals::intPair

Definition at line 65 of file Globals.hpp.

Constructor & Destructor Documentation

◆ Globals()

◆ ~Globals()

OpenMD::Globals::~Globals ( )
virtual

Member Function Documentation

◆ addComponent()

bool OpenMD::Globals::addComponent ( Component comp)

Definition at line 291 of file Globals.cpp.

References components_.

Referenced by MDTreeParser::componentblock().

◆ addFluctuatingChargeParameters()

bool OpenMD::Globals::addFluctuatingChargeParameters ( FluctuatingChargeParameters flucqPars)

Definition at line 306 of file Globals.cpp.

References flucQpars_.

Referenced by MDTreeParser::flucqblock(), and getRestraintStampAt().

◆ addMinimizerParameters()

bool OpenMD::Globals::addMinimizerParameters ( MinimizerParameters miniPars)

Definition at line 322 of file Globals.cpp.

References minimizerPars_.

Referenced by getRNEMDParameters(), and MDTreeParser::minimizerblock().

◆ addMoleculeStamp()

bool OpenMD::Globals::addMoleculeStamp ( MoleculeStamp molStamp)

Definition at line 330 of file Globals.cpp.

References moleculeStamps_.

Referenced by MDTreeParser::moleculeblock().

◆ addRestraintStamp()

bool OpenMD::Globals::addRestraintStamp ( RestraintStamp rest)

Definition at line 301 of file Globals.cpp.

References restraints_.

Referenced by MDTreeParser::restraintblock().

◆ addRNEMDParameters()

bool OpenMD::Globals::addRNEMDParameters ( RNEMDParameters rnemdPars)

Definition at line 314 of file Globals.cpp.

References rnemdPars_.

Referenced by getFluctuatingChargeParameters(), and MDTreeParser::rnemdblock().

◆ addZConsStamp()

bool OpenMD::Globals::addZConsStamp ( ZConsStamp zcons)

Definition at line 296 of file Globals.cpp.

References zconstraints_.

Referenced by MDTreeParser::zconstraintblock().

◆ DeclareAlterableParameter()

OpenMD::Globals::DeclareAlterableParameter ( MDfileVersion  ,
int   
)

◆ DeclareParameter() [1/81]

OpenMD::Globals::DeclareParameter ( ForceField  ,
std::string   
)

◆ DeclareParameter() [2/81]

OpenMD::Globals::DeclareParameter ( TargetTemp  ,
RealType   
)

◆ DeclareParameter() [3/81]

OpenMD::Globals::DeclareParameter ( Ensemble  ,
std::string   
)

◆ DeclareParameter() [4/81]

OpenMD::Globals::DeclareParameter ( Dt  ,
RealType   
)

◆ DeclareParameter() [5/81]

OpenMD::Globals::DeclareParameter ( RunTime  ,
RealType   
)

◆ DeclareParameter() [6/81]

OpenMD::Globals::DeclareParameter ( FinalConfig  ,
std::string   
)

◆ DeclareParameter() [7/81]

OpenMD::Globals::DeclareParameter ( SampleTime  ,
RealType   
)

◆ DeclareParameter() [8/81]

OpenMD::Globals::DeclareParameter ( ResetTime  ,
RealType   
)

◆ DeclareParameter() [9/81]

OpenMD::Globals::DeclareParameter ( StatusTime  ,
RealType   
)

◆ DeclareParameter() [10/81]

OpenMD::Globals::DeclareParameter ( CutoffRadius  ,
RealType   
)

◆ DeclareParameter() [11/81]

OpenMD::Globals::DeclareParameter ( SwitchingRadius  ,
RealType   
)

◆ DeclareParameter() [12/81]

OpenMD::Globals::DeclareParameter ( TempSet  ,
bool   
)

◆ DeclareParameter() [13/81]

OpenMD::Globals::DeclareParameter ( ThermalTime  ,
RealType   
)

◆ DeclareParameter() [14/81]

OpenMD::Globals::DeclareParameter ( UsePeriodicBoundaryConditions  ,
bool   
)

◆ DeclareParameter() [15/81]

OpenMD::Globals::DeclareParameter ( TargetPressure  ,
RealType   
)

◆ DeclareParameter() [16/81]

OpenMD::Globals::DeclareParameter ( UseAtomicVirial  ,
bool   
)

◆ DeclareParameter() [17/81]

OpenMD::Globals::DeclareParameter ( UseLongRangeCorrections  ,
bool   
)

◆ DeclareParameter() [18/81]

OpenMD::Globals::DeclareParameter ( TauThermostat  ,
RealType   
)

◆ DeclareParameter() [19/81]

OpenMD::Globals::DeclareParameter ( TauBarostat  ,
RealType   
)

◆ DeclareParameter() [20/81]

OpenMD::Globals::DeclareParameter ( ZconsTime  ,
RealType   
)

◆ DeclareParameter() [21/81]

OpenMD::Globals::DeclareParameter ( ZconsTol  ,
RealType   
)

◆ DeclareParameter() [22/81]

OpenMD::Globals::DeclareParameter ( ZconsForcePolicy  ,
std::string   
)

◆ DeclareParameter() [23/81]

OpenMD::Globals::DeclareParameter ( Seed  ,
unsigned long  int 
)

◆ DeclareParameter() [24/81]

OpenMD::Globals::DeclareParameter ( UseInitalTime  ,
bool   
)

◆ DeclareParameter() [25/81]

OpenMD::Globals::DeclareParameter ( UseIntialExtendedSystemState  ,
bool   
)

◆ DeclareParameter() [26/81]

OpenMD::Globals::DeclareParameter ( OrthoBoxTolerance  ,
RealType   
)

◆ DeclareParameter() [27/81]

OpenMD::Globals::DeclareParameter ( ZconsGap  ,
RealType   
)

◆ DeclareParameter() [28/81]

OpenMD::Globals::DeclareParameter ( ZconsFixtime  ,
RealType   
)

◆ DeclareParameter() [29/81]

OpenMD::Globals::DeclareParameter ( ZconsUsingSMD  ,
bool   
)

◆ DeclareParameter() [30/81]

OpenMD::Globals::DeclareParameter ( UseThermodynamicIntegration  ,
bool   
)

◆ DeclareParameter() [31/81]

OpenMD::Globals::DeclareParameter ( ThermodynamicIntegrationLambda  ,
RealType   
)

◆ DeclareParameter() [32/81]

OpenMD::Globals::DeclareParameter ( ThermodynamicIntegrationK  ,
RealType   
)

◆ DeclareParameter() [33/81]

OpenMD::Globals::DeclareParameter ( ForceFieldVariant  ,
std::string   
)

◆ DeclareParameter() [34/81]

OpenMD::Globals::DeclareParameter ( ForceFieldFileName  ,
std::string   
)

◆ DeclareParameter() [35/81]

OpenMD::Globals::DeclareParameter ( SurfaceTension  ,
RealType   
)

◆ DeclareParameter() [36/81]

OpenMD::Globals::DeclareParameter ( PrintPressureTensor  ,
bool   
)

◆ DeclareParameter() [37/81]

OpenMD::Globals::DeclareParameter ( PrintHeatFlux  ,
bool   
)

◆ DeclareParameter() [38/81]

OpenMD::Globals::DeclareParameter ( TaggedAtomPair  ,
intPair   
)

◆ DeclareParameter() [39/81]

OpenMD::Globals::DeclareParameter ( PrintTaggedPairDistance  ,
bool   
)

◆ DeclareParameter() [40/81]

OpenMD::Globals::DeclareParameter ( ElectrostaticSummationMethod  ,
std::string   
)

◆ DeclareParameter() [41/81]

OpenMD::Globals::DeclareParameter ( ElectrostaticScreeningMethod  ,
std::string   
)

◆ DeclareParameter() [42/81]

OpenMD::Globals::DeclareParameter ( DampingAlpha  ,
RealType   
)

◆ DeclareParameter() [43/81]

OpenMD::Globals::DeclareParameter ( Dielectric  ,
RealType   
)

◆ DeclareParameter() [44/81]

OpenMD::Globals::DeclareParameter ( CutoffMethod  ,
std::string   
)

◆ DeclareParameter() [45/81]

OpenMD::Globals::DeclareParameter ( SwitchingFunctionType  ,
std::string   
)

◆ DeclareParameter() [46/81]

OpenMD::Globals::DeclareParameter ( CompressDumpFile  ,
bool   
)

◆ DeclareParameter() [47/81]

OpenMD::Globals::DeclareParameter ( OutputForceVector  ,
bool   
)

◆ DeclareParameter() [48/81]

OpenMD::Globals::DeclareParameter ( OutputParticlePotential  ,
bool   
)

◆ DeclareParameter() [49/81]

OpenMD::Globals::DeclareParameter ( OutputElectricField  ,
bool   
)

◆ DeclareParameter() [50/81]

OpenMD::Globals::DeclareParameter ( OutputFluctuatingCharges  ,
bool   
)

◆ DeclareParameter() [51/81]

OpenMD::Globals::DeclareParameter ( OutputSitePotential  ,
bool   
)

◆ DeclareParameter() [52/81]

OpenMD::Globals::DeclareParameter ( OutputDensity  ,
bool   
)

◆ DeclareParameter() [53/81]

OpenMD::Globals::DeclareParameter ( SkinThickness  ,
RealType   
)

◆ DeclareParameter() [54/81]

OpenMD::Globals::DeclareParameter ( StatFileFormat  ,
std::string   
)

◆ DeclareParameter() [55/81]

OpenMD::Globals::DeclareParameter ( StatFilePrecision  ,
int   
)

◆ DeclareParameter() [56/81]

OpenMD::Globals::DeclareParameter ( HydroPropFile  ,
std::string   
)

◆ DeclareParameter() [57/81]

OpenMD::Globals::DeclareParameter ( Viscosity  ,
RealType   
)

◆ DeclareParameter() [58/81]

OpenMD::Globals::DeclareParameter ( BeadSize  ,
RealType   
)

◆ DeclareParameter() [59/81]

OpenMD::Globals::DeclareParameter ( UseSphericalBoundaryConditions  ,
bool   
)

◆ DeclareParameter() [60/81]

OpenMD::Globals::DeclareParameter ( FrozenBufferRadius  ,
RealType   
)

◆ DeclareParameter() [61/81]

OpenMD::Globals::DeclareParameter ( LangevinBufferRadius  ,
RealType   
)

◆ DeclareParameter() [62/81]

OpenMD::Globals::DeclareParameter ( AccumulateBoxDipole  ,
bool   
)

◆ DeclareParameter() [63/81]

OpenMD::Globals::DeclareParameter ( AccumulateBoxQuadrupole  ,
bool   
)

◆ DeclareParameter() [64/81]

OpenMD::Globals::DeclareParameter ( NeighborListNeighbors  ,
int   
)

◆ DeclareParameter() [65/81]

OpenMD::Globals::DeclareParameter ( UseMultipleTemperatureMethod  ,
bool   
)

◆ DeclareParameter() [66/81]

OpenMD::Globals::DeclareParameter ( MTM_Ce  ,
RealType   
)

◆ DeclareParameter() [67/81]

OpenMD::Globals::DeclareParameter ( MTM_G  ,
RealType   
)

◆ DeclareParameter() [68/81]

OpenMD::Globals::DeclareParameter ( MTM_Io  ,
RealType   
)

◆ DeclareParameter() [69/81]

OpenMD::Globals::DeclareParameter ( MTM_Sigma  ,
RealType   
)

◆ DeclareParameter() [70/81]

OpenMD::Globals::DeclareParameter ( MTM_R  ,
RealType   
)

◆ DeclareParameter() [71/81]

OpenMD::Globals::DeclareParameter ( UseRestraints  ,
bool   
)

◆ DeclareParameter() [72/81]

OpenMD::Globals::DeclareParameter ( Restraint_file  ,
std::string   
)

◆ DeclareParameter() [73/81]

OpenMD::Globals::DeclareParameter ( HULL_Method  ,
std::string   
)

◆ DeclareParameter() [74/81]

OpenMD::Globals::DeclareParameter ( Alpha  ,
RealType   
)

◆ DeclareParameter() [75/81]

OpenMD::Globals::DeclareParameter ( UniformField  ,
std::vector< RealType >   
)

◆ DeclareParameter() [76/81]

OpenMD::Globals::DeclareParameter ( UniformGradientStrength  ,
RealType   
)

◆ DeclareParameter() [77/81]

OpenMD::Globals::DeclareParameter ( UniformGradientDirection1  ,
std::vector< RealType >   
)

◆ DeclareParameter() [78/81]

OpenMD::Globals::DeclareParameter ( UniformGradientDirection2  ,
std::vector< RealType >   
)

◆ DeclareParameter() [79/81]

OpenMD::Globals::DeclareParameter ( ElectricField  ,
std::vector< RealType >   
)

◆ DeclareParameter() [80/81]

OpenMD::Globals::DeclareParameter ( ConstraintTime  ,
RealType   
)

◆ DeclareParameter() [81/81]

OpenMD::Globals::DeclareParameter ( PotentialSelection  ,
std::string   
)

◆ getComponentAt()

Component* OpenMD::Globals::getComponentAt ( int  index)
inline

Definition at line 162 of file Globals.hpp.

References components_.

◆ getComponents()

std::vector<Component*> OpenMD::Globals::getComponents ( )
inline

Definition at line 161 of file Globals.hpp.

References components_.

Referenced by main(), and OpenMD::SimInfo::SimInfo().

◆ getFluctuatingChargeParameters()

◆ getMinimizerParameters()

MinimizerParameters* OpenMD::Globals::getMinimizerParameters ( )
inline

Definition at line 179 of file Globals.hpp.

References minimizerPars_, and validate().

Referenced by main().

◆ getNComponents()

int OpenMD::Globals::getNComponents ( )
inline

Definition at line 160 of file Globals.hpp.

References components_.

◆ getNRestraintStamps()

int OpenMD::Globals::getNRestraintStamps ( )
inline

Definition at line 168 of file Globals.hpp.

References restraints_.

Referenced by OpenMD::RestraintForceManager::RestraintForceManager().

◆ getNZconsStamps()

int OpenMD::Globals::getNZconsStamps ( )
inline

◆ getRestraintStampAt()

RestraintStamp* OpenMD::Globals::getRestraintStampAt ( int  index)
inline

Definition at line 170 of file Globals.hpp.

References addFluctuatingChargeParameters(), and restraints_.

◆ getRestraintStamps()

std::vector<RestraintStamp*> OpenMD::Globals::getRestraintStamps ( )
inline

Definition at line 169 of file Globals.hpp.

References restraints_.

Referenced by OpenMD::RestraintForceManager::RestraintForceManager().

◆ getRNEMDParameters()

◆ getZconsStampAt()

ZConsStamp* OpenMD::Globals::getZconsStampAt ( int  index)
inline

Definition at line 166 of file Globals.hpp.

References zconstraints_.

◆ getZconsStamps()

std::vector<ZConsStamp*> OpenMD::Globals::getZconsStamps ( )
inline

◆ validate()

Member Data Documentation

◆ components_

std::vector<Component*> OpenMD::Globals::components_
private

◆ flucQpars_

FluctuatingChargeParameters* OpenMD::Globals::flucQpars_
private

◆ minimizerPars_

MinimizerParameters* OpenMD::Globals::minimizerPars_
private

Definition at line 191 of file Globals.hpp.

Referenced by addMinimizerParameters(), getMinimizerParameters(), Globals(), and ~Globals().

◆ moleculeStamps_

std::map<std::string, MoleculeStamp*> OpenMD::Globals::moleculeStamps_
private

Definition at line 187 of file Globals.hpp.

Referenced by addMoleculeStamp(), and validate().

◆ restraints_

std::vector<RestraintStamp*> OpenMD::Globals::restraints_
private

◆ rnemdPars_

RNEMDParameters* OpenMD::Globals::rnemdPars_
private

Definition at line 190 of file Globals.hpp.

Referenced by addRNEMDParameters(), getRNEMDParameters(), Globals(), and ~Globals().

◆ taggedAtomPair_

std::pair<int, int> OpenMD::Globals::taggedAtomPair_
private

Definition at line 188 of file Globals.hpp.

◆ zconstraints_

std::vector<ZConsStamp*> OpenMD::Globals::zconstraints_
private

The documentation for this class was generated from the following files: