ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.

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- a -

AbstractEnumType() : ProtoMol::AbstractEnumType< T, noCase >
Acceptor() : ProtoMol::PSF::Acceptor
accumulateEnergy() : ProtoMol::iSGLennardJonesTableForce, ProtoMol::iSGLennardJonesForce, ProtoMol::iSGIdealGasLennardJonesForce, ProtoMol::iSGIdealGasCoulombForce, ProtoMol::iSGCoulombForce, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::iSGCoulombEwaldRealForce, ProtoMol::MagneticDipoleForce, ProtoMol::LennardJonesTableForce, ProtoMol::LennardJonesForce, ProtoMol::GravitationForce, ProtoMol::CoulombMultiGridDirectTableForce< TKernel >, ProtoMol::CoulombMultiGridDirectForce< TKernel >, ProtoMol::CoulombForce, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::CoulombEwaldRealForce
accumulateNegTo() : ProtoMol::ReducedHessAngle
accumulateTo() : ProtoMol::ReducedHessAngle
add() : ProtoMol::ExclusionTable, ProtoMol::OutputCache, ProtoMol::Vector3D
addBond() : ProtoMol::AngleInfo
addDoKeyword() : ProtoMol::OutputScreen, ProtoMol::Output
addElement() : ProtoMol::Stack< T >
addExtendedForce() : ProtoMol::ForceGroup
addForce() : ProtoMol::WrapperMetaForce, ProtoMol::ForceGroup
addMetaForce() : ProtoMol::ForceGroup
addModifier() : ProtoMol::Integrator
addModifierAfterInitialize() : ProtoMol::iSGIntegrator, ProtoMol::STSIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::NoseNVTLeapfrogIntegrator, ProtoMol::Integrator
addModifierBeforeInitialize() : ProtoMol::iSGIntegrator, ProtoMol::MOLLYIntegrator, ProtoMol::Integrator
addMollyForce() : ProtoMol::ForceGroup
addMolVirial() : ProtoMol::ScalarStructure
addRandomForceToMyForce() : ProtoMol::BBKIntegrator
addSystemForce() : ProtoMol::ForceGroup
addToCache() : ProtoMol::OutputCollection
addToForceGroup() : ProtoMol::SystemForce, ProtoMol::MollyForce, ProtoMol::MetaForce, ProtoMol::Force, ProtoMol::ExtendedForce
addVirial() : ProtoMol::ScalarStructure
adjustAlias() : ProtoMol::Makeable
adjustWithDefaultParameters() : ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputScreen, ProtoMol::OutputPDBFramePos, ProtoMol::OutputPaulTrap, ProtoMol::OutputFile, ProtoMol::OutputDihedrals, ProtoMol::OutputDCDTrajectory, ProtoMol::Makeable
adoptMediForceModifier() : ProtoMol::Integrator
adoptOutput() : ProtoMol::OutputCollection
adoptPostDriftOrNextModifier() : ProtoMol::Integrator
adoptPostForceModifier() : ProtoMol::Integrator
adoptPostStepModifier() : ProtoMol::Integrator
adoptPreDriftOrNextModifier() : ProtoMol::Integrator
adoptPreForceModifier() : ProtoMol::Integrator
adoptPreStepModifier() : ProtoMol::Integrator
Angle() : ProtoMol::Angle, ProtoMol::PSF::Angle, ProtoMol::PAR::Angle, ProtoMol::iSGPAR::Angle
AngleIndex() : ProtoMol::BSplineMOLLYIntegrator::AngleIndex
AngleInfo() : ProtoMol::AngleInfo
angularMomentum() : ProtoMol::OutputCache
anterpolateCharge() : ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
anyExtendedForces() : ProtoMol::ForceGroup
anyForces() : ProtoMol::ForceGroup
anyMediForceModify() : ProtoMol::Integrator
anyMetaForces() : ProtoMol::ForceGroup
anyMollyForces() : ProtoMol::ForceGroup
anyPostDriftOrNextModify() : ProtoMol::Integrator
anyPostForceModify() : ProtoMol::Integrator
anyPostStepModify() : ProtoMol::Integrator
anyPreDriftOrNextModify() : ProtoMol::Integrator
anyPreForceModify() : ProtoMol::Integrator
anyPreStepModify() : ProtoMol::Integrator
anySystemForces() : ProtoMol::ForceGroup
Array() : ProtoMol::Array< T, N >
ArrayCellListStructure() : ProtoMol::ArrayCellListStructure
ArraySize() : ProtoMol::ArraySize< N >
ArraySizes() : ProtoMol::ArraySizes, ProtoMol::ArraySize< N >
Atom() : ProtoMol::PSF::Atom, ProtoMol::Atom
AtomType() : ProtoMol::TRANS::AtomType, ProtoMol::iSGPAR::AtomType, ProtoMol::AtomType
averagingPositions() : ProtoMol::MOLLYIntegrator

- b -

backward() : ProtoMol::Integrator, ProtoMol::FFTComplex, ProtoMol::FFTInternal
BankLennardJonesParameterTable() : ProtoMol::BankLennardJonesParameterTable
basisCell() : ProtoMol::ArrayCellListStructure
BBKIntegrator() : ProtoMol::BBKIntegrator
bcast() : ProtoMol::Parallel
bcastSlaves() : ProtoMol::Parallel
begin() : ProtoMol::ArrayCellListStructure, ProtoMol::OutputCollection, ProtoMol::Factory< Type >, ProtoMol::PPM, ProtoMol::PGM, ProtoMol::Configuration, ProtoMol::Array< T, N >, ProtoMol::Array< T, N >::RefArray< 1 >, ProtoMol::Array< T, N >::RefArray< N >, ProtoMol::Array< T, N >, ProtoMol::RefArray< T, 1 >, ProtoMol::RefArray< T, N >
blocksCorrection() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
Bond() : ProtoMol::Bond, ProtoMol::PSF::Bond, ProtoMol::PAR::Bond, ProtoMol::iSGPAR::Bond
BondIndex() : ProtoMol::BSplineMOLLYIntegrator::BondIndex
bottom() : ProtoMol::Integrator
boundingbox() : ProtoMol::Vector3DBlock
brent() : ProtoMol::OutputCache
brentMaxima() : ProtoMol::OutputCache
BSpline() : ProtoMol::BSpline
BSplineMOLLYIntegrator() : ProtoMol::BSplineMOLLYIntegrator
buildLatticeVectors() : ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions

- c -

C1SwitchingFunction() : ProtoMol::C1SwitchingFunction
C2SwitchingFunction() : ProtoMol::C2SwitchingFunction
calcAngle() : ProtoMol::iSGAngleSystemForce< TBoundaryConditions >, ProtoMol::AngleSystemForce< TBoundaryConditions >
calcAngleEnergy() : ProtoMol::iSGAngleSystemForce< TBoundaryConditions >, ProtoMol::AngleSystemForce< TBoundaryConditions >
calcBond() : ProtoMol::iSGBondSystemForce< TBoundaryConditions >, ProtoMol::BondSystemForce< TBoundaryConditions >
calcBondEnergy() : ProtoMol::iSGBondSystemForce< TBoundaryConditions >, ProtoMol::BondSystemForce< TBoundaryConditions >
calcError() : ProtoMol::ModifierMetaShake, ProtoMol::ModifierMetaRattleShake, ProtoMol::ModifierMetaRattle
calcHessiansBondsAnglesHBonds() : ProtoMol::BSplineMOLLYIntegrator
calcMOLLYForcesHalfKickOneDrift() : ProtoMol::BSplineMOLLYIntegrator
calcMOLLYForcesOneKickOneDrift() : ProtoMol::BSplineMOLLYIntegrator
calcShadow4() : ProtoMol::ShadowHMCIntegrator
calcShadow8() : ProtoMol::ShadowHMCIntegrator
calcTorsion() : ProtoMol::iSGMTorsionSystemForce< TBoundaryConditions >, ProtoMol::MTorsionSystemForce< TBoundaryConditions >
calcTorsionEnergy() : ProtoMol::iSGMTorsionSystemForce< TBoundaryConditions >, ProtoMol::MTorsionSystemForce< TBoundaryConditions >
calculateDissipativeAndRandomForces() : ProtoMol::DMDLeapfrogIntegrator
calculateDissipativeForces() : ProtoMol::DMDLeapfrogIntegrator
calculateForces() : ProtoMol::STSIntegrator, ProtoMol::StandardIntegrator
calculateMOLLYForcesBonded() : ProtoMol::BSplineMOLLYIntegrator
calculateMOLLYForcesHBonded() : ProtoMol::BSplineMOLLYIntegrator
calculateShadow() : ProtoMol::ShadowHMCIntegrator
CellListEnumerator() : ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
centerOfMass() : ProtoMol::OutputCache
check() : ProtoMol::ExclusionTable, ProtoMol::DebugPostConstraint, ProtoMol::DebugPreConstraint, ProtoMol::NotSameMoleculeConstraint, ProtoMol::SameMoleculeConstraint, ProtoMol::HBondConstraint, ProtoMol::NoConstraint, ProtoMol::ValueTraits< ValueType::Force >, ProtoMol::ValueTraits< ValueType::Integrator >, ProtoMol::ValueTraits< std::vector< Real > >, ProtoMol::ValueTraits< Vector3D >, ProtoMol::ValueTraits< bool >, ProtoMol::ValueTraits< Real >, ProtoMol::ValueTraits< unsigned int >, ProtoMol::ValueTraits< int >, ProtoMol::ValueTraits< std::string >
checkBoundaries() : ProtoMol::ArrayCellListStructure
checkForStageCompletion() : ProtoMol::ModifierISG
checkForTransformation() : ProtoMol::iSGIntegrator
checkMoleculePairDistances() : ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::GenericTopology
checkParameters() : ProtoMol::Makeable
checkParameterTypes() : ProtoMol::Makeable
checkReallyFast() : ProtoMol::ExclusionTable
cleanTemporaries() : ProtoMol::ExclusionTable
clear() : ProtoMol::XSC, ProtoMol::TRANS, ProtoMol::iSGGrid< TInterpolation >, ProtoMol::ExclusionTable, ProtoMol::FactoryBase< Type >, ProtoMol::XYZ, ProtoMol::Vector3DBlock, ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder, ProtoMol::ScalarStructure, ProtoMol::ReducedHessAngle, ProtoMol::PSF, ProtoMol::PPM, ProtoMol::PGM, ProtoMol::PDB, ProtoMol::PAR, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::iSGPAR, ProtoMol::Grid< TInterpolation >, ProtoMol::Array< T, N >
cleaR() : ProtoMol::Vector3DBlock
clearCache() : ProtoMol::OutputFile
client_alive() : ProtoMol::IMDElf
clone() : ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder
close() : ProtoMol::File, ProtoMol::OutputFile
coarseToFine() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
cohesive() : ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
CompareError() : ProtoMol::CompareForce::CompareError
CompareForce() : ProtoMol::CompareForce
ComplementSwitchingFunction() : ProtoMol::ComplementSwitchingFunction< TOriginalSwitchingFunction >
ConfigurationReader() : ProtoMol::ConfigurationReader
connect() : ProtoMol::IMDElf
Constraint() : ProtoMol::Bond::Constraint, ProtoMol::InputValue< TBase, type, constraint >
convert() : ProtoMol::ValueTraits< ValueType::Force >, ProtoMol::ValueTraits< ValueType::Integrator >, ProtoMol::ValueTraits< std::vector< Real > >, ProtoMol::ValueTraits< Vector3D >, ProtoMol::ValueTraits< bool >, ProtoMol::ValueTraits< Real >, ProtoMol::ValueTraits< unsigned int >, ProtoMol::ValueTraits< int >, ProtoMol::ValueTraits< std::string >, ProtoMol::Matrix3by3
convertFromJacobian() : ProtoMol::ReducedHessAngle
convertTest() : ProtoMol::ValueTraits< ValueType::Force >, ProtoMol::ValueTraits< ValueType::Integrator >, ProtoMol::ValueTraits< std::vector< Real > >, ProtoMol::ValueTraits< Vector3D >, ProtoMol::ValueTraits< bool >, ProtoMol::ValueTraits< Real >, ProtoMol::ValueTraits< unsigned int >, ProtoMol::ValueTraits< int >, ProtoMol::ValueTraits< std::string >
copy() : ProtoMol::Makeable, ProtoMol::Array< T, N >, ProtoMol::Array< T, N >::RefArray< 1 >, ProtoMol::Array< T, N >::RefArray< N >, ProtoMol::Array< T, N >, ProtoMol::RefArray< T, 1 >, ProtoMol::RefArray< T, N >
correction() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
correctionTerm() : ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
CoulombEwaldRealForce() : ProtoMol::CoulombEwaldRealForce
CoulombEwaldRealTableForce() : ProtoMol::CoulombEwaldRealTableForce
CoulombMultiGridDirectForce() : ProtoMol::CoulombMultiGridDirectForce< TKernel >
CoulombMultiGridDirectTableForce() : ProtoMol::CoulombMultiGridDirectTableForce< TKernel >
createRattleModifier() : ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::Integrator
createShakeModifier() : ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::Integrator
createTables() : ProtoMol::BankLennardJonesParameterTable
cross() : ProtoMol::Vector3D
CubicCellLocation() : ProtoMol::CubicCellLocation
CubicCellManager() : ProtoMol::CubicCellManager
cutoffSquared() : ProtoMol::UniversalSwitchingFunction, ProtoMol::ShiftSwitchingFunction, ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::CutoffSwitchingFunction, ProtoMol::ComplementSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction
CutoffSwitchingFunction() : ProtoMol::CutoffSwitchingFunction
Cycles() : ProtoMol::Cycles

- d -

- e -

e1() : ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
e1r() : ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
e2() : ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
e2r() : ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
e3() : ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
e3r() : ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
ElectricFieldSystemForce() : ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >
empty() : ProtoMol::ExclusionTable, ProtoMol::HelpTextFactory, ProtoMol::Factory< Type >, ProtoMol::ValueTraits< ValueType::Force >, ProtoMol::ValueTraits< ValueType::Integrator >, ProtoMol::ValueTraits< std::vector< Real > >, ProtoMol::ValueTraits< Vector3D >, ProtoMol::ValueTraits< bool >, ProtoMol::ValueTraits< Real >, ProtoMol::ValueTraits< unsigned int >, ProtoMol::ValueTraits< int >, ProtoMol::ValueTraits< std::string >, ProtoMol::Configuration, ProtoMol::Array< T, N >
enable() : ProtoMol::Modifier
enableBetaUpdate() : ProtoMol::ShadowHMCIntegrator
end() : ProtoMol::ArrayCellListStructure, ProtoMol::OutputCollection, ProtoMol::Factory< Type >, ProtoMol::PPM, ProtoMol::PGM, ProtoMol::Configuration, ProtoMol::Array< T, N >, ProtoMol::Array< T, N >::RefArray< 1 >, ProtoMol::Array< T, N >::RefArray< N >, ProtoMol::Array< T, N >, ProtoMol::RefArray< T, 1 >, ProtoMol::RefArray< T, N >
energy() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
Enum2ValueType() : ProtoMol::ValueEnum::Enum2ValueType< e >
epsilonEnergy() : ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
equal() : ProtoMol::Value
equalConstraint() : ProtoMol::Value
equalType() : ProtoMol::Value
equalTypeAndConstraint() : ProtoMol::Value
EquilibriumMOLLYIntegrator() : ProtoMol::EquilibriumMOLLYIntegrator
evaluate() : ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::iSGImproperSystemForce< TBoundaryConditions >, ProtoMol::iSGDihedralSystemForce< TBoundaryConditions >, ProtoMol::iSGBondSystemForce< TBoundaryConditions >, ProtoMol::iSGAngleSystemForce< TBoundaryConditions >, ProtoMol::HapticSystemForce, ProtoMol::SystemTimeForce, ProtoMol::SystemForce, ProtoMol::SystemCompareForce, ProtoMol::SphericalSystemForce, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >, ProtoMol::NonbondedSimpleFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::NonbondedFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedCutoffSystemForce< TCellManager, TOneAtomPair >, ProtoMol::NonbondedCutoffMollyForce< TCellManager, TOneAtomPair >, ProtoMol::MollyForce, ProtoMol::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, ProtoMol::ImproperSystemForce< TBoundaryConditions >, ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >, ProtoMol::FrictionExtendedForce, ProtoMol::ExternalMagneticFieldExtendedForce, ProtoMol::ExternalGravitationSystemForce, ProtoMol::ExtendedTimeForce, ProtoMol::ExtendedForce, ProtoMol::ExtendedCompareForce, ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >, ProtoMol::DihedralSystemForce< TBoundaryConditions >, ProtoMol::BondSystemForce< TBoundaryConditions >, ProtoMol::AngleSystemForce< TBoundaryConditions >, ProtoMol::ReducedHessAngle
evaluateExtendedForces() : ProtoMol::ForceGroup
evaluateMollyForces() : ProtoMol::ForceGroup
evaluateSystemForces() : ProtoMol::ForceGroup
ExclusionPair() : ProtoMol::ExclusionPair
ExclusionTable() : ProtoMol::ExclusionTable
execute() : ProtoMol::Modifier
ExtendedCompareForce() : ProtoMol::ExtendedCompareForce
ExtendedForce() : ProtoMol::ExtendedForce
ExtendedTimeForce() : ProtoMol::ExtendedTimeForce
ExternalGravitationSystemForce() : ProtoMol::ExternalGravitationSystemForce
ExternalMagneticFieldExtendedForce() : ProtoMol::ExternalMagneticFieldExtendedForce

- f -

Factory() : ProtoMol::Factory< Type >
FactoryBase() : ProtoMol::FactoryBase< Type >
fftBack() : ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
FFTComplex() : ProtoMol::FFTComplex
FFTComplexMPIFinalize() : ProtoMol::FFTComplex
FFTComplexMPIInit() : ProtoMol::FFTComplex
fftForward() : ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
FFTInternal() : ProtoMol::FFTInternal
File() : ProtoMol::File
finalize() : ProtoMol::Parallel, ProtoMol::OutputCollection, ProtoMol::Output
finalized() : ProtoMol::Parallel
find() : ProtoMol::ArrayCellListStructure, ProtoMol::Factory< Type >, ProtoMol::Configuration
find_free_port() : ProtoMol::IMDElf
findCell() : ProtoMol::CubicCellManager
findPeriodic() : ProtoMol::ArrayCellListStructure
fineToCoarse() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
first() : ProtoMol::Output, ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >::CellPair, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >::CellPair, ProtoMol::PairIntSorted
fitplane() : ProtoMol::Vector3DBlock
fluctuationLI() : ProtoMol::LangevinImpulseIntegrator
flushCache() : ProtoMol::OutputFile
Force() : ProtoMol::Force, ProtoMol::ValueEnum
ForceFactoryDetails() : ProtoMol::ForceFactoryDetails
ForceGroup() : ProtoMol::ForceGroup
forward() : ProtoMol::Integrator, ProtoMol::FFTComplex, ProtoMol::FFTInternal
friction() : ProtoMol::NoseNVTLeapfrogIntegrator
FrictionExtendedForce() : ProtoMol::FrictionExtendedForce

- g -

- h -

HapticSystemForce() : ProtoMol::HapticSystemForce
harmCalcTorsion() : ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >
HarmDihedralSystemForce() : ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >
Hbond() : ProtoMol::PAR::Hbond, ProtoMol::iSGPAR
height() : ProtoMol::PPM, ProtoMol::PGM
HelpTextFactory() : ProtoMol::HelpTextFactory
Hermite() : ProtoMol::Hermite
hessian() : ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction
HMCIntegrator() : ProtoMol::HMCIntegrator
Holder() : ProtoMol::Value::Holder< ValueTrait, Constraint >
hookup() : ProtoMol::IMDElf

- i -

iAmMaster() : ProtoMol::Parallel
iAmSlave() : ProtoMol::Parallel
identity() : ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3, ProtoMol::PSF::Atom
IMDElf() : ProtoMol::IMDElf
Improper() : ProtoMol::PSF::Improper, ProtoMol::PAR::Improper, ProtoMol::iSGPAR::Improper
ImpulseIntegrator() : ProtoMol::ImpulseIntegrator
incrCoord() : ProtoMol::UmbrellaIntegrator
indexBonds() : ProtoMol::ModifierISG
init() : ProtoMol::Parallel, ProtoMol::PaulTrapIntegrator, ProtoMol::BSplineMOLLYIntegrator, ProtoMol::ValueTraits< ValueType::Force >, ProtoMol::ValueTraits< ValueType::Integrator >, ProtoMol::ValueTraits< std::vector< Real > >, ProtoMol::ValueTraits< Vector3D >, ProtoMol::ValueTraits< bool >, ProtoMol::ValueTraits< Real >, ProtoMol::ValueTraits< unsigned int >, ProtoMol::ValueTraits< int >, ProtoMol::ValueTraits< std::string >, ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder
initialize() : ProtoMol::iSGIntegrator, ProtoMol::iSGOneAtomPairTwoFull< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::iSGOneAtomPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::iSGOneAtomPairFull< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::iSGOneAtomPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::iSGGrid< TInterpolation >, ProtoMol::CubicCellManager, ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >, ProtoMol::ArrayCellListStructure, ProtoMol::UmbrellaIntegrator, ProtoMol::STSIntegrator, ProtoMol::StandardIntegrator, ProtoMol::ShadowHMCIntegrator, ProtoMol::PLeapfrogIntegrator, ProtoMol::PaulTrapIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::NoseNVTLeapfrogIntegrator, ProtoMol::MTSIntegrator, ProtoMol::MOLLYIntegrator, ProtoMol::Modifier, ProtoMol::MCIntegrator, ProtoMol::LeapfrogIntegrator, ProtoMol::LangevinImpulseIntegrator, ProtoMol::Integrator, ProtoMol::ImpulseIntegrator, ProtoMol::HMCIntegrator, ProtoMol::EquilibriumMOLLYIntegrator, ProtoMol::DMDLeapfrogIntegrator, ProtoMol::DLMCIntegrator, ProtoMol::DihedralHMCIntegrator, ProtoMol::BSplineMOLLYIntegrator, ProtoMol::BBKIntegrator, ProtoMol::OutputCollection, ProtoMol::OutputCache, ProtoMol::Output, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >, ProtoMol::OneMollyPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond >, ProtoMol::OneMollyPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce >, ProtoMol::OneAtomPairTwoFull< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::OneAtomPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::OneAtomPairFull< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::OneAtomPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >, ProtoMol::FFTComplex, ProtoMol::FFTInternal, ProtoMol::Array< T, N >, ProtoMol::Array< T, N >::RefArray< 1 >, ProtoMol::Array< T, N >::RefArray< N >, ProtoMol::Array< T, N >, ProtoMol::RefArray< T, 1 >, ProtoMol::RefArray< T, N >
initialized() : ProtoMol::Parallel
initializeForces() : ProtoMol::StandardIntegrator
initializeModifiers() : ProtoMol::Integrator
InputPosVel() : ProtoMol::InputPosVel
InputValue() : ProtoMol::InputValue< TBase, type, constraint >
instance() : ProtoMol::Parallel, ProtoMol::HelpTextFactory, ProtoMol::Factory< Type >
Integrator() : ProtoMol::Integrator, ProtoMol::ValueEnum
IntegratorDefinition() : ProtoMol::IntegratorDefinition
IntegratorFactoryDetails() : ProtoMol::IntegratorFactoryDetails
IntegratorInput() : ProtoMol::IntegratorFactoryDetails::IntegratorInput
interpolateForce() : ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
Interpolation3D() : ProtoMol::iSGGrid< TInterpolation >::Interpolation3D, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >::Interpolation3D, ProtoMol::Grid< TInterpolation >::Interpolation3D
intoAdd() : ProtoMol::Vector3DBlock, ProtoMol::Vector3D, ProtoMol::ScalarStructure
intoAssign() : ProtoMol::Vector3DBlock
intoDivide() : ProtoMol::Vector3D
intoMultiply() : ProtoMol::Vector3D
intoSubtract() : ProtoMol::Vector3DBlock, ProtoMol::Vector3D, ProtoMol::ScalarStructure
intoWeighted() : ProtoMol::Vector3DBlock
intoWeightedAdd() : ProtoMol::Vector3DBlock, ProtoMol::Vector3D
intoWeightedSubtract() : ProtoMol::Vector3DBlock, ProtoMol::Vector3D
invert() : ProtoMol::Matrix3by3
isAccessible() : ProtoMol::File
isBarrier() : ProtoMol::Parallel
isDynamic() : ProtoMol::Parallel
isEnabled() : ProtoMol::Modifier
isExclusionAtom() : ProtoMol::AngleInfo
isforward() : ProtoMol::Integrator
iSGCoulombEwaldRealForce() : ProtoMol::iSGCoulombEwaldRealForce
iSGCoulombEwaldRealTableForce() : ProtoMol::iSGCoulombEwaldRealTableForce
iSGGrid() : ProtoMol::iSGGrid< TInterpolation >
iSGIdealGasLennardJonesForce() : ProtoMol::iSGIdealGasLennardJonesForce
iSGIntegrator() : ProtoMol::iSGIntegrator
iSGLennardJonesForce() : ProtoMol::iSGLennardJonesForce
iSGLennardJonesTableForce() : ProtoMol::iSGLennardJonesTableForce
iSGModifierPostForceChemostat() : ProtoMol::iSGModifierPostForceChemostat, ProtoMol::iSGIntegrator
iSGModifierPreForceChemostat() : ProtoMol::iSGModifierPreForceChemostat, ProtoMol::iSGIntegrator
iSGNonbondedFullEwaldSystemForce() : ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
iSGNonbondedPMEwaldSystemForce() : ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >
iSGOneAtomPair() : ProtoMol::iSGOneAtomPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >
iSGOneAtomPairFull() : ProtoMol::iSGOneAtomPairFull< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >
iSGOneAtomPairTwo() : ProtoMol::iSGOneAtomPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >
iSGOneAtomPairTwoFull() : ProtoMol::iSGOneAtomPairTwoFull< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >
iSGpar() : ProtoMol::OutputCache
iSGPARReader() : ProtoMol::iSGPARReader
isIdDefined() : ProtoMol::OutputScreen, ProtoMol::Output
isInnerAtom() : ProtoMol::AngleInfo
isInternal() : ProtoMol::ModifierISG, ProtoMol::iSGModifierPreForceChemostat, ProtoMol::iSGModifierPostForceChemostat, ProtoMol::ModifierUmbrella, ProtoMol::ModifierUpdateBetaAndPush, ProtoMol::ModifierUpdateBeta, ProtoMol::ModifierRemoveLinearMomentum, ProtoMol::ModifierRemoveAngularMomentum, ProtoMol::ModifierPreForceThermostat< TIntegrator >, ProtoMol::ModifierPreForceBarostat< TIntegrator >, ProtoMol::ModifierPostForceThermostat< TIntegrator >, ProtoMol::ModifierPostForceBarostat< TIntegrator >, ProtoMol::ModifierMollification, ProtoMol::ModifierMetaRattleShake, ProtoMol::ModifierIncrementTimestep, ProtoMol::ModifierFriction, ProtoMol::ModifierAveraging, ProtoMol::Modifier
isKeywordCharmm19() : ProtoMol::iSGPARReader, ProtoMol::PARReader
isKeywordCharmm28() : ProtoMol::iSGPARReader, ProtoMol::PARReader
isLittleEndian() : ProtoMol::Endian
isOrthogonal() : ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
isParallel() : ProtoMol::Parallel, ProtoMol::TimerStatistic, ProtoMol::FFTComplex
isSigma() : ProtoMol::Hermite, ProtoMol::Lagrange, ProtoMol::BSpline
istringstream() : std::istringstream
isVisited() : ProtoMol::AngleInfo

- k -

- l -

Lagrange() : ProtoMol::Lagrange
LangevinImpulseIntegrator() : ProtoMol::LangevinImpulseIntegrator
lap() : ProtoMol::Timer
LeapfrogIntegrator() : ProtoMol::LeapfrogIntegrator
LennardJonesParameters() : ProtoMol::LennardJonesParameters
LennardJonesParameterTable() : ProtoMol::LennardJonesParameterTable
LennardJonesTableForce() : ProtoMol::LennardJonesTableForce
less() : ProtoMol::Value
lessEqual() : ProtoMol::Value
level() : ProtoMol::Integrator
linearMomentum() : ProtoMol::OutputCache
listen() : ProtoMol::IMDElf
longRangeTerm() : ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >
luBksb() : ProtoMol::EquilibriumMOLLYIntegrator
luDcmp() : ProtoMol::EquilibriumMOLLYIntegrator

- m -

MagneticDipoleForce() : ProtoMol::MagneticDipoleForce
MagneticDipoleMirrorSystemForce() : ProtoMol::MagneticDipoleMirrorSystemForce< TBoundaryConditions >
make() : ProtoMol::iSGOneAtomPairTwoFull< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::iSGOneAtomPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::iSGOneAtomPairFull< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::iSGOneAtomPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::iSGLennardJonesTableForce, ProtoMol::iSGLennardJonesForce, ProtoMol::iSGIdealGasLennardJonesForce, ProtoMol::iSGIdealGasCoulombForce, ProtoMol::iSGCoulombForce, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::iSGCoulombEwaldRealForce, ProtoMol::VacuumBoundaryConditions, ProtoMol::UniversalSwitchingFunction, ProtoMol::ShiftSwitchingFunction, ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::PeriodicBoundaryConditions, ProtoMol::GenericTopology, ProtoMol::CutoffSwitchingFunction, ProtoMol::CubicCellManager, ProtoMol::ComplementSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction, ProtoMol::STSIntegrator, ProtoMol::NonStandardIntegrator, ProtoMol::MTSIntegrator, ProtoMol::TopologyFactoryDetails, ProtoMol::OutputFactoryDetails, ProtoMol::Output, ProtoMol::IntegratorFactoryDetails, ProtoMol::ForceFactoryDetails, ProtoMol::OneMollyPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond >, ProtoMol::OneMollyPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce >, ProtoMol::OneAtomPairTwoFull< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::OneAtomPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::OneAtomPairFull< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::OneAtomPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::MagneticDipoleForce, ProtoMol::LennardJonesTableForce, ProtoMol::LennardJonesForce, ProtoMol::GravitationForce, ProtoMol::Force, ProtoMol::CoulombMultiGridDirectTableForce< TKernel >, ProtoMol::CoulombMultiGridDirectForce< TKernel >, ProtoMol::CoulombForce, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::CoulombEwaldRealForce
MakeableDefinition() : ProtoMol::MakeableDefinition
makeCollection() : ProtoMol::OutputFactoryDetails
makeCompareForce() : ProtoMol::SystemForce, ProtoMol::Force, ProtoMol::ExtendedForce
makeTimeForce() : ProtoMol::SystemForce, ProtoMol::Force, ProtoMol::ExtendedForce
mass() : ProtoMol::OutputCache, ProtoMol::TRANS::AtomType, ProtoMol::PSF::Atom, ProtoMol::Molecule, ProtoMol::iSGPAR::AtomType, ProtoMol::AtomType
Matrix3by3() : ProtoMol::Matrix3by3
MCIntegrator() : ProtoMol::MCIntegrator
mediForceModify() : ProtoMol::Integrator
MetaForce() : ProtoMol::MetaForce
metropolisTest() : ProtoMol::MCIntegrator, ProtoMol::DihedralHMCIntegrator
minimalDifference() : ProtoMol::VacuumBoundaryConditions, ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::PeriodicBoundaryConditions, ProtoMol::GenericTopology
minimalImage() : ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::GenericTopology
minimalPosition() : ProtoMol::VacuumBoundaryConditions, ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::PeriodicBoundaryConditions, ProtoMol::GenericTopology
minimalTranslationDifference() : ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
minimalTranslationPosition() : ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
Modifier() : ProtoMol::Modifier
ModifierAveraging() : ProtoMol::ModifierAveraging, ProtoMol::MOLLYIntegrator
ModifierFriction() : ProtoMol::ModifierFriction, ProtoMol::NoseNVTLeapfrogIntegrator
ModifierIncrementTimestep() : ProtoMol::ModifierIncrementTimestep
ModifierISG() : ProtoMol::ModifierISG, ProtoMol::iSGIntegrator
ModifierMetaRattle() : ProtoMol::ModifierMetaRattle
ModifierMetaRattleShake() : ProtoMol::ModifierMetaRattleShake
ModifierMetaShake() : ProtoMol::ModifierMetaShake
ModifierMollification() : ProtoMol::ModifierMollification, ProtoMol::MOLLYIntegrator
ModifierNPTRattle() : ProtoMol::ModifierNPTRattle< TIntegrator >
ModifierNPTRattleDetails() : ProtoMol::ModifierNPTRattleDetails
ModifierNPTShake() : ProtoMol::ModifierNPTShake< TIntegrator >
ModifierNPTShakeDetails() : ProtoMol::ModifierNPTShakeDetails
ModifierNVTRattle() : ProtoMol::ModifierNVTRattle< TIntegrator >
ModifierNVTRattleDetails() : ProtoMol::ModifierNVTRattleDetails
ModifierNVTShake() : ProtoMol::ModifierNVTShake< TIntegrator >
ModifierNVTShakeDetails() : ProtoMol::ModifierNVTShakeDetails
ModifierPostForceBarostat() : ProtoMol::ModifierPostForceBarostat< TIntegrator >, ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator
ModifierPostForceThermostat() : ProtoMol::ModifierPostForceThermostat< TIntegrator >, ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
ModifierPreForceBarostat() : ProtoMol::ModifierPreForceBarostat< TIntegrator >, ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator
ModifierPreForceThermostat() : ProtoMol::ModifierPreForceThermostat< TIntegrator >, ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
ModifierRattle() : ProtoMol::ModifierRattle
ModifierRemoveAngularMomentum() : ProtoMol::ModifierRemoveAngularMomentum
ModifierRemoveLinearMomentum() : ProtoMol::ModifierRemoveLinearMomentum
ModifierShake() : ProtoMol::ModifierShake
ModifierUmbrella() : ProtoMol::ModifierUmbrella
ModifierUpdateBeta() : ProtoMol::ModifierUpdateBeta, ProtoMol::ShadowHMCIntegrator
ModifierUpdateBetaAndPush() : ProtoMol::ModifierUpdateBetaAndPush, ProtoMol::ShadowHMCIntegrator
modifyForces() : ProtoMol::iSGIntegrator
molecularKineticEnergy() : ProtoMol::OutputCache
molecularPressure() : ProtoMol::OutputCache, ProtoMol::ScalarStructure
molecularTemperature() : ProtoMol::OutputCache
molecularVirial() : ProtoMol::ScalarStructure
Molecule() : ProtoMol::Molecule
mollification() : ProtoMol::MOLLYIntegrator
MollyForce() : ProtoMol::MollyForce
MOLLYIntegrator() : ProtoMol::MOLLYIntegrator
MTSIntegrator() : ProtoMol::MTSIntegrator, ProtoMol::StandardIntegrator
MultiGrid() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
multiply() : ProtoMol::Vector3D
MyStreamer() : ProtoMol::Report::MyStreamer

- n -

Nbfix() : ProtoMol::PAR::Nbfix, ProtoMol::iSGPAR
next() : ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >, ProtoMol::Parallel, ProtoMol::STSIntegrator, ProtoMol::MTSIntegrator, ProtoMol::Integrator
nextMaster() : ProtoMol::Parallel
nextNewPair() : ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
Ngrp() : ProtoMol::PSF::Ngrp
Nonbonded() : ProtoMol::PSF::Nonbonded, ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
NonbondedCutoffForce() : ProtoMol::NonbondedCutoffForce< TCellManager, TOneAtomPair, TForce, TImplForce >
NonbondedCutoffMollyForce() : ProtoMol::NonbondedCutoffMollyForce< TCellManager, TOneAtomPair >
NonbondedCutoffSystemForce() : ProtoMol::NonbondedCutoffSystemForce< TCellManager, TOneAtomPair >
NonbondedFullEwaldSystemForce() : ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
NonbondedFullSystemForce() : ProtoMol::NonbondedFullSystemForce< TOneAtomPair >
NonbondedMultiGridSystemForce() : ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >
NonbondedPMEwaldSystemForce() : ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >
NonbondedSimpleFullSystemForce() : ProtoMol::NonbondedSimpleFullSystemForce< TOneAtomPair >
NonStandardIntegrator() : ProtoMol::NonStandardIntegrator
norm() : ProtoMol::Vector3D
normalize() : ProtoMol::Vector3D
normalized() : ProtoMol::Vector3D
normSquared() : ProtoMol::Vector3D
NoseNVTLeapfrogIntegrator() : ProtoMol::NoseNVTLeapfrogIntegrator
notSameCell() : ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
NPTVerletIntegrator() : ProtoMol::NPTVerletIntegrator
numberOfBlocks() : ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::iSGImproperSystemForce< TBoundaryConditions >, ProtoMol::iSGDihedralSystemForce< TBoundaryConditions >, ProtoMol::iSGBondSystemForce< TBoundaryConditions >, ProtoMol::iSGAngleSystemForce< TBoundaryConditions >, ProtoMol::TimeForce, ProtoMol::SphericalSystemForce, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >, ProtoMol::NonbondedSimpleFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::NonbondedFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedCutoffForce< TCellManager, TOneAtomPair, TForce, TImplForce >, ProtoMol::ImproperSystemForce< TBoundaryConditions >, ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >, ProtoMol::FrictionExtendedForce, ProtoMol::Force, ProtoMol::ExternalMagneticFieldExtendedForce, ProtoMol::ExternalGravitationSystemForce, ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >, ProtoMol::DihedralSystemForce< TBoundaryConditions >, ProtoMol::CompareForce, ProtoMol::BondSystemForce< TBoundaryConditions >, ProtoMol::AngleSystemForce< TBoundaryConditions >
numBonds() : ProtoMol::AngleInfo
NVTVerletIntegrator() : ProtoMol::NVTVerletIntegrator

- o -

ObjectDefinition() : ProtoMol::ObjectDefinition
ok() : ProtoMol::Parallel, ProtoMol::Value::Holder< ValueTrait, Constraint >
OneAtomPair() : ProtoMol::OneAtomPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >
OneAtomPairFull() : ProtoMol::OneAtomPairFull< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >
OneAtomPairTwo() : ProtoMol::OneAtomPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >
OneAtomPairTwoFull() : ProtoMol::OneAtomPairTwoFull< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >
OneMollyPair() : ProtoMol::OneMollyPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce >
OneMollyPairTwo() : ProtoMol::OneMollyPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond >
open() : ProtoMol::XSCWriter, ProtoMol::XSCReader, ProtoMol::TRANSReader, ProtoMol::iSGPARReader, ProtoMol::XYZWriter, ProtoMol::XYZTrajectoryWriter, ProtoMol::XYZTrajectoryReader, ProtoMol::XYZReader, ProtoMol::XYZBinWriter, ProtoMol::XYZBinReader, ProtoMol::XFigWriter, ProtoMol::PSFWriter, ProtoMol::PSFReader, ProtoMol::PPMWriter, ProtoMol::PPMReader, ProtoMol::PNGWriter, ProtoMol::PGMWriter, ProtoMol::PGMReader, ProtoMol::PDBWriter, ProtoMol::PDBReader, ProtoMol::PARWriter, ProtoMol::PARReader, ProtoMol::File, ProtoMol::DCDTrajectoryWriter, ProtoMol::DCDTrajectoryReader, ProtoMol::ConfigurationReader, ProtoMol::OutputFile, ProtoMol::InputPosVel
operator *() : ProtoMol::Vector3D, ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3
operator *=() : ProtoMol::Vector3D, ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3
operator bool() : ProtoMol::Value
operator Enum() : ProtoMol::ValueEnum::Enum2ValueType< e >, ProtoMol::ConstraintValueEnum::Enum2Type< e >, ProtoMol::AbstractEnumType< T, noCase >
operator int() : ProtoMol::Value
operator Real() : ProtoMol::Value
operator std::string() : ProtoMol::ValueEnum::Enum2ValueType< e >, ProtoMol::Value, ProtoMol::AbstractEnumType< T, noCase >
operator std::vector() : ProtoMol::Vector< T >, ProtoMol::VectorPacker< T, N >, ProtoMol::Value
operator T() : ProtoMol::InputValue< TBase, type, constraint >
operator UIntArrayN() : ProtoMol::ArraySize< N >
operator unsigned int() : ProtoMol::Value
operator Value() : ProtoMol::InputValue< TBase, type, constraint >
operator Vector3D() : ProtoMol::Value
operator void *() : ProtoMol::File, ProtoMol::InputPosVel
operator!() : ProtoMol::File, ProtoMol::InputPosVel
operator!=() : ProtoMol::Vector3D, ProtoMol::Value, ProtoMol::Matrix3by3, ProtoMol::AbstractEnumType< T, noCase >
operator()() : ProtoMol::iSGLennardJonesTableForce, ProtoMol::iSGLennardJonesForce, ProtoMol::iSGIdealGasLennardJonesForce, ProtoMol::iSGIdealGasCoulombForce, ProtoMol::iSGCoulombForce, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::iSGCoulombEwaldRealForce, ProtoMol::UniversalSwitchingFunction, ProtoMol::ShiftSwitchingFunction, ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::LennardJonesParameterTable, ProtoMol::CutoffSwitchingFunction, ProtoMol::ComplementSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction, ProtoMol::BankLennardJonesParameterTable, ProtoMol::ReducedHessLennardJones, ProtoMol::ReducedHessCoulomb, ProtoMol::MagneticDipoleForce, ProtoMol::LennardJonesTableForce, ProtoMol::LennardJonesForce, ProtoMol::GravitationForce, ProtoMol::CoulombMultiGridDirectTableForce< TKernel >, ProtoMol::CoulombMultiGridDirectForce< TKernel >, ProtoMol::CoulombForce, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::CoulombEwaldRealForce, ProtoMol::Vector< T >, ProtoMol::VectorPacker< T, N >, ProtoMol::ltstrNocase, ProtoMol::Report::reportlevel, ProtoMol::Report::debug, ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3, ProtoMol::ArraySizes, ProtoMol::ArraySize< N >, ProtoMol::ArraySizes, ProtoMol::ArraySize< N >
operator+() : ProtoMol::CubicCellLocation, ProtoMol::Vector3D, ProtoMol::TimeRep, ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3
operator+=() : ProtoMol::Vector3D, ProtoMol::Timer, ProtoMol::TimeRep, ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3
operator-() : ProtoMol::CubicCellLocation, ProtoMol::Vector3D, ProtoMol::TimeRep, ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3
operator-=() : ProtoMol::Vector3D, ProtoMol::Timer, ProtoMol::TimeRep, ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3
operator/() : ProtoMol::Vector3D, ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3
operator/=() : ProtoMol::Vector3D, ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3
operator<() : ProtoMol::ExclusionPair, ProtoMol::CubicCellLocation, ProtoMol::Modifier, ProtoMol::BSplineMOLLYIntegrator::BondIndex, ProtoMol::Value, ProtoMol::PairIntSorted
operator<<() : ProtoMol::XSCWriter, ProtoMol::XYZWriter, ProtoMol::XYZTrajectoryWriter, ProtoMol::XYZBinWriter, ProtoMol::XFigWriter, ProtoMol::PSFWriter, ProtoMol::PPMWriter, ProtoMol::PNGWriter, ProtoMol::PGMWriter, ProtoMol::PDBWriter, ProtoMol::PARWriter, ProtoMol::DCDTrajectoryWriter, ProtoMol::InputValue< TBase, type, constraint >, ProtoMol::Vector3D, ProtoMol::Value, ProtoMol::TimerStatistic, ProtoMol::Timer, ProtoMol::TimeRep, ProtoMol::Report::MyStreamer, ProtoMol::ReducedHessAngle, ProtoMol::PDB::PDBAtom, ProtoMol::PAR::Hbond, ProtoMol::PAR::Nbfix, ProtoMol::PAR::Nonbonded, ProtoMol::PAR::Improper, ProtoMol::PAR::Dihedral, ProtoMol::PAR::Angle, ProtoMol::PAR::Bond, ProtoMol::Matrix3by3, ProtoMol::iSGPAR::Nonbonded, ProtoMol::iSGPAR::Improper, ProtoMol::iSGPAR::Dihedral, ProtoMol::iSGPAR::Angle, ProtoMol::iSGPAR::Bond, ProtoMol::AbstractEnumType< T, noCase >
operator=() : ProtoMol::iSGLennardJonesTableForce, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::Parallel, ProtoMol::TopologyFactoryDetails, ProtoMol::OutputFactoryDetails, ProtoMol::IntegratorFactoryDetails, ProtoMol::InputValue< TBase, type, constraint >, ProtoMol::HelpTextFactory, ProtoMol::ForceFactoryDetails, ProtoMol::Factory< Type >, ProtoMol::FactoryBase< Type >, ProtoMol::LennardJonesTableForce, ProtoMol::CoulombMultiGridDirectTableForce< TKernel >, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::Vector3D, ProtoMol::Value, ProtoMol::PPM, ProtoMol::PGM, ProtoMol::Array< T, N >, ProtoMol::AbstractEnumType< T, noCase >
operator==() : ProtoMol::CubicCellLocation, ProtoMol::Vector3D, ProtoMol::Value, ProtoMol::PairIntSorted, ProtoMol::Matrix3by3, ProtoMol::Array< T, N >, ProtoMol::AbstractEnumType< T, noCase >
operator[]() : ProtoMol::ArrayCellListStructure, ProtoMol::Vector3D, ProtoMol::ScalarStructure, ProtoMol::Molecule, ProtoMol::Configuration, ProtoMol::Array< T, N >, ProtoMol::Array< T, N >::RefArray< 1 >, ProtoMol::Array< T, N >::RefArray< N >, ProtoMol::Array< T, N >, ProtoMol::RefArray< T, 1 >, ProtoMol::RefArray< T, N >
operator^() : ProtoMol::Vector3D
order() : ProtoMol::Modifier
origin() : ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
orphanAtoms() : ProtoMol::PDBReader
orphanConfiguration() : ProtoMol::ConfigurationReader
orphanCoords() : ProtoMol::XYZTrajectoryReader, ProtoMol::XYZReader, ProtoMol::XYZBinReader, ProtoMol::PDBReader, ProtoMol::DCDTrajectoryReader
orphanNames() : ProtoMol::XYZTrajectoryReader, ProtoMol::XYZReader
orphanPAR() : ProtoMol::iSGPARReader, ProtoMol::PARReader
orphanPGM() : ProtoMol::PGMReader
orphanPPM() : ProtoMol::PPMReader
orphanPSF() : ProtoMol::PSFReader
orphanTRANS() : ProtoMol::TRANSReader
orphanXSC() : ProtoMol::XSCReader
ostringstream() : std::ostringstream
output() : ProtoMol::ScalarStructure
Output() : ProtoMol::Output
OutputCache() : ProtoMol::OutputCache
OutputCollection() : ProtoMol::OutputCollection
OutputDCDTrajectory() : ProtoMol::OutputDCDTrajectory
OutputDiffusion() : ProtoMol::OutputDiffusion
OutputDihedrals() : ProtoMol::OutputDihedrals
OutputEnergies() : ProtoMol::OutputEnergies
OutputFactoryDetails() : ProtoMol::OutputFactoryDetails, ProtoMol::OutputCollection
OutputFile() : ProtoMol::OutputFile
OutputFinalPDBPos() : ProtoMol::OutputFinalPDBPos
OutputFinalPSF() : ProtoMol::OutputFinalPSF
OutputFinalXSC() : ProtoMol::OutputFinalXSC
OutputFinalXYZBinPos() : ProtoMol::OutputFinalXYZBinPos
OutputFinalXYZBinVel() : ProtoMol::OutputFinalXYZBinVel
OutputFinalXYZPos() : ProtoMol::OutputFinalXYZPos
OutputFinalXYZVel() : ProtoMol::OutputFinalXYZVel
OutputISGProperties() : ProtoMol::OutputISGProperties
OutputMomentum() : ProtoMol::OutputMomentum
OutputPaulTrap() : ProtoMol::OutputPaulTrap
OutputPDBFramePos() : ProtoMol::OutputPDBFramePos
OutputScreen() : ProtoMol::OutputScreen
OutputTemperatures() : ProtoMol::OutputTemperatures
OutputXYZTrajectoryForce() : ProtoMol::OutputXYZTrajectoryForce
OutputXYZTrajectoryPos() : ProtoMol::OutputXYZTrajectoryPos
OutputXYZTrajectoryVel() : ProtoMol::OutputXYZTrajectoryVel
overflow() : std::stringbuf

- p -

PairIntSorted() : ProtoMol::PairIntSorted
par() : ProtoMol::OutputCache
Parallel() : ProtoMol::Parallel
parallelEvaluate() : ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::iSGImproperSystemForce< TBoundaryConditions >, ProtoMol::iSGDihedralSystemForce< TBoundaryConditions >, ProtoMol::iSGBondSystemForce< TBoundaryConditions >, ProtoMol::iSGAngleSystemForce< TBoundaryConditions >, ProtoMol::SystemTimeForce, ProtoMol::SystemForce, ProtoMol::SystemCompareForce, ProtoMol::SphericalSystemForce, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >, ProtoMol::NonbondedSimpleFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::NonbondedFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedCutoffSystemForce< TCellManager, TOneAtomPair >, ProtoMol::NonbondedCutoffMollyForce< TCellManager, TOneAtomPair >, ProtoMol::MollyForce, ProtoMol::ImproperSystemForce< TBoundaryConditions >, ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >, ProtoMol::FrictionExtendedForce, ProtoMol::ExternalMagneticFieldExtendedForce, ProtoMol::ExternalGravitationSystemForce, ProtoMol::ExtendedTimeForce, ProtoMol::ExtendedForce, ProtoMol::ExtendedCompareForce, ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >, ProtoMol::DihedralSystemForce< TBoundaryConditions >, ProtoMol::BondSystemForce< TBoundaryConditions >, ProtoMol::AngleSystemForce< TBoundaryConditions >
Parameter() : ProtoMol::Parameter
PARReader() : ProtoMol::PARReader
PARWriter() : ProtoMol::PARWriter
PaulTrapExtendedForce() : ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
PaulTrapIntegrator() : ProtoMol::PaulTrapIntegrator
pdb() : ProtoMol::OutputCache
PDB() : ProtoMol::PDB, Format, ProtoMol::InputPosVelEnum
PDBAtom() : ProtoMol::PDB::PDBAtom
PDBReader() : ProtoMol::PDBReader
PDBWriter() : ProtoMol::PDBWriter
PeriodicBoundaryConditions() : ProtoMol::PeriodicBoundaryConditions
periodicCell() : ProtoMol::ArrayCellListStructure
perturbSystem() : ProtoMol::ShadowHMCIntegrator, ProtoMol::MCIntegrator, ProtoMol::HMCIntegrator, ProtoMol::DLMCIntegrator
PGM() : ProtoMol::PGM
PGMReader() : ProtoMol::PGMReader
PGMWriter() : ProtoMol::PGMWriter
pickNewMolecule() : ProtoMol::ModifierISG
PLeapfrogIntegrator() : ProtoMol::PLeapfrogIntegrator
PNGWriter() : ProtoMol::PNGWriter
popElement() : ProtoMol::Stack< T >
postDriftOrNextModify() : ProtoMol::Integrator
PostForceBarostat() : ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator
PostForceChemostat() : ProtoMol::iSGIntegrator
postForceModify() : ProtoMol::Integrator
PostForceThermostat() : ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
postprocess() : ProtoMol::TimeForce, ProtoMol::CompareForce
postStepModify() : ProtoMol::Integrator
potentialEnergy() : ProtoMol::OutputCache, ProtoMol::ScalarStructure
PPM() : ProtoMol::PPM
PPMReader() : ProtoMol::PPMReader
PPMWriter() : ProtoMol::PPMWriter
precision() : ProtoMol::Report::MyStreamer
precomputeG() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
preDriftOrNextModify() : ProtoMol::Integrator
PreForceBarostat() : ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator
PreForceChemostat() : ProtoMol::iSGIntegrator
preForceModify() : ProtoMol::Integrator
PreForceThermostat() : ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
preprocess() : ProtoMol::TimeForce, ProtoMol::CompareForce
pressure() : ProtoMol::OutputCache, ProtoMol::ScalarStructure
preStepModify() : ProtoMol::Integrator
previous() : ProtoMol::StandardIntegrator, ProtoMol::Integrator
print() : ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Topology< TBoundaryConditions, TCellManager >, ProtoMol::GenericTopology, ProtoMol::Modifier, ProtoMol::IntegratorDefinition, ProtoMol::Factory< Type >, ProtoMol::Report::MyStreamer, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >, ProtoMol::Configuration
printConst() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
printQ() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
printV() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
Proxy() : ProtoMol::Proxy
psf() : ProtoMol::OutputCache
PSFReader() : ProtoMol::PSFReader
PSFWriter() : ProtoMol::PSFWriter
pushShadowHistory() : ProtoMol::ShadowHMCIntegrator

- r -

RangeSwitchingFunction() : ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >
rdbuf() : std::stringstreambase
read() : ProtoMol::XSCReader, ProtoMol::TRANSReader, ProtoMol::iSGPARReader, ProtoMol::XYZTrajectoryReader, ProtoMol::XYZReader, ProtoMol::XYZBinReader, ProtoMol::Reader, ProtoMol::PSFReader, ProtoMol::PPMReader, ProtoMol::PGMReader, ProtoMol::PDBReader, ProtoMol::PARReader, ProtoMol::File, ProtoMol::DCDTrajectoryReader, ProtoMol::ConfigurationReader, ProtoMol::ValueTraits< ValueType::Force >, ProtoMol::ValueTraits< ValueType::Integrator >, ProtoMol::ValueTraits< std::vector< Real > >, ProtoMol::ValueTraits< Vector3D >, ProtoMol::ValueTraits< bool >, ProtoMol::ValueTraits< Real >, ProtoMol::ValueTraits< unsigned int >, ProtoMol::ValueTraits< int >, ProtoMol::ValueTraits< std::string >, ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder
Reader() : ProtoMol::Reader
readXSCs() : ProtoMol::ModifierISG
realTerm() : ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
reciprocalTerm() : ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
reciprocalTermParallel() : ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >
reclose() : ProtoMol::OutputFile
reduce() : ProtoMol::Parallel, ProtoMol::Proxy
ReducedHessAngle() : ProtoMol::ReducedHessAngle
reduceSlaves() : ProtoMol::Parallel
RefArray() : ProtoMol::Array< T, N >::RefArray< 1 >, ProtoMol::Array< T, N >::RefArray< N >, ProtoMol::RefArray< T, 1 >, ProtoMol::RefArray< T, N >
registerAliases() : ProtoMol::Configuration
registerAllExemplarsConfiguration() : ProtoMol::TopologyFactoryDetails, ProtoMol::OutputFactoryDetails
registerConfiguration() : ProtoMol::InputValue< TBase, type, constraint >
registerExemplar() : ProtoMol::HelpTextFactory, ProtoMol::Factory< Type >
registerExemplars() : ProtoMol::HelpTextFactory
registerHelpText() : ProtoMol::Factory< Type >
registerKeyword() : ProtoMol::Configuration
removeModifier() : ProtoMol::Integrator
reopen() : ProtoMol::XYZTrajectoryWriter, ProtoMol::DCDTrajectoryWriter, ProtoMol::OutputFile
reportlevel() : ProtoMol::Report::reportlevel
rescaleVolume() : ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::GenericTopology
reset() : ProtoMol::Timer, ProtoMol::TimeRep, ProtoMol::Stack< T >, ProtoMol::Report::MyStreamer, ProtoMol::Cycles
ResetDimensions() : ProtoMol::RefArray< T, 1 >, ProtoMol::RefArray< T, N >
resetHistory() : ProtoMol::ShadowHMCIntegrator
resetNext() : ProtoMol::Parallel
resize() : ProtoMol::LennardJonesParameterTable, ProtoMol::ExclusionTable, ProtoMol::XYZ, ProtoMol::PPM, ProtoMol::PGM, ProtoMol::PDB, ProtoMol::Array< T, N >
restoreValues() : ProtoMol::ShadowHMCIntegrator, ProtoMol::MCIntegrator, ProtoMol::HMCIntegrator, ProtoMol::DLMCIntegrator, ProtoMol::DihedralHMCIntegrator
rotate() : ProtoMol::Matrix3by3
roughTest() : ProtoMol::UniversalSwitchingFunction, ProtoMol::ShiftSwitchingFunction, ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::CutoffSwitchingFunction, ProtoMol::ComplementSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction
run() : ProtoMol::iSGIntegrator, ProtoMol::UmbrellaIntegrator, ProtoMol::StandardIntegrator, ProtoMol::ShadowHMCIntegrator, ProtoMol::PLeapfrogIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::MCIntegrator, ProtoMol::LeapfrogIntegrator, ProtoMol::Integrator, ProtoMol::DMDLeapfrogIntegrator, ProtoMol::DihedralHMCIntegrator, ProtoMol::BBKIntegrator, ProtoMol::OutputCollection, ProtoMol::Output
runPostSteps() : ProtoMol::ShadowHMCIntegrator
runPreSteps() : ProtoMol::ShadowHMCIntegrator

- s -

saveValues() : ProtoMol::ShadowHMCIntegrator, ProtoMol::MCIntegrator, ProtoMol::HMCIntegrator, ProtoMol::DLMCIntegrator, ProtoMol::DihedralHMCIntegrator
ScalarStructure() : ProtoMol::ScalarStructure
scalarSum() : ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
scale() : ProtoMol::Matrix3by3
search() : ProtoMol::HelpTextFactory
SemiGenericTopology() : ProtoMol::SemiGenericTopology< TBoundaryConditions >
send_coords() : ProtoMol::IMDElf
set() : ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions, ProtoMol::LennardJonesParameterTable, ProtoMol::BankLennardJonesParameterTable, ProtoMol::Hermite, ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder, ProtoMol::TimeRep, ProtoMol::PPM, ProtoMol::PGM, ProtoMol::Lagrange, ProtoMol::Configuration, ProtoMol::BSpline
setAbort() : ProtoMol::Report::MyStreamer
setAlias() : ProtoMol::Makeable
setAllNodes() : ProtoMol::Report::MyStreamer
setAngle() : ProtoMol::AngleInfo
setAtomID() : ProtoMol::AngleInfo
setAutofit() : ProtoMol::XFigWriter
setAxes() : ProtoMol::XFigWriter
setBarrier() : ProtoMol::Parallel
setCache() : ProtoMol::Output
setCellSize() : ProtoMol::CubicCellManager
setCharmmType() : ProtoMol::iSGPARReader, ProtoMol::PARWriter, ProtoMol::PARReader
setColor() : ProtoMol::XFigWriter
setComment() : ProtoMol::Writer
setCoords() : ProtoMol::XYZTrajectoryWriter
setExclusionAtom() : ProtoMol::AngleInfo
setf() : ProtoMol::Report::MyStreamer
setFilename() : ProtoMol::File, ProtoMol::InputPosVel
setFirststep() : ProtoMol::DCDTrajectoryWriter
setForce() : ProtoMol::HapticSystemForce
setForcesAfterTransformation() : ProtoMol::ModifierISG
setFromZ() : ProtoMol::XFigWriter
setIAmMaster() : ProtoMol::Report::MyStreamer
setInnerAtom() : ProtoMol::AngleInfo
setLegend() : ProtoMol::XFigWriter
setLevel() : ProtoMol::Report::MyStreamer
setLittleEndian() : ProtoMol::XYZBinWriter, ProtoMol::DCDTrajectoryWriter
setMaxPackages() : ProtoMol::Parallel
setMode() : ProtoMol::Parallel
setMyNumIterMOLLYStepsize() : ProtoMol::BSplineMOLLYIntegrator
setNames() : ProtoMol::XYZTrajectoryWriter
setNumComps() : ProtoMol::iSGPARReader
setOrder() : ProtoMol::Hermite, ProtoMol::Lagrange, ProtoMol::BSpline
setPAR() : ProtoMol::PARWriter
setParallel() : ProtoMol::TimerStatistic
setParameter() : ProtoMol::Force
setParameters() : ProtoMol::Force
setParametersBySwapping() : ProtoMol::Force
setPipeSize() : ProtoMol::Parallel
setPointer() : ProtoMol::AngleInfo
setQuit() : ProtoMol::Report::MyStreamer
setRadius() : ProtoMol::XFigWriter
setReportLevel() : ProtoMol::Report::MyStreamer
setSize() : ProtoMol::XYZBinWriter
setStream() : ProtoMol::Report::MyStreamer
setText() : ProtoMol::Configuration
setTimestep() : ProtoMol::DCDTrajectoryWriter
setToZ() : ProtoMol::XFigWriter
setTransformation() : ProtoMol::XFigWriter
SetupDimensions() : ProtoMol::RefArray< T, 1 >, ProtoMol::RefArray< T, N >
setVisited() : ProtoMol::AngleInfo
ShadowHMCIntegrator() : ProtoMol::ShadowHMCIntegrator
ShiftSwitchingFunction() : ProtoMol::ShiftSwitchingFunction
shortRangeTerm() : ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >
size() : ProtoMol::LennardJonesParameterTable, ProtoMol::ArrayCellListStructure, ProtoMol::Integrator, ProtoMol::XYZ, ProtoMol::ValueTraits< ValueType::Force >, ProtoMol::ValueTraits< ValueType::Integrator >, ProtoMol::ValueTraits< std::vector< Real > >, ProtoMol::ValueTraits< Vector3D >, ProtoMol::ValueTraits< bool >, ProtoMol::ValueTraits< Real >, ProtoMol::ValueTraits< unsigned int >, ProtoMol::ValueTraits< int >, ProtoMol::ValueTraits< std::string >, ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder, ProtoMol::PPM, ProtoMol::PGM, ProtoMol::PDB, ProtoMol::Molecule, ProtoMol::Array< T, N >, ProtoMol::Array< T, N >::RefArray< 1 >, ProtoMol::Array< T, N >::RefArray< N >, ProtoMol::Array< T, N >, ProtoMol::RefArray< T, 1 >, ProtoMol::RefArray< T, N >
smooth() : ProtoMol::iSGIdealGasCoulombForce::C4, ProtoMol::iSGIdealGasCoulombForce::C3, ProtoMol::iSGIdealGasCoulombForce::C2, ProtoMol::iSGIdealGasCoulombForce::C1, ProtoMol::iSGCoulombForce::C4, ProtoMol::iSGCoulombForce::C3, ProtoMol::iSGCoulombForce::C2, ProtoMol::iSGCoulombForce::C1, ProtoMol::CoulombForce::C4, ProtoMol::CoulombForce::C3, ProtoMol::CoulombForce::C2, ProtoMol::CoulombForce::C1
smooth0() : ProtoMol::iSGIdealGasCoulombForce::C4, ProtoMol::iSGIdealGasCoulombForce::C3, ProtoMol::iSGIdealGasCoulombForce::C2, ProtoMol::iSGIdealGasCoulombForce::C1, ProtoMol::iSGCoulombForce::C4, ProtoMol::iSGCoulombForce::C3, ProtoMol::iSGCoulombForce::C2, ProtoMol::iSGCoulombForce::C1, ProtoMol::CoulombForce::C4, ProtoMol::CoulombForce::C3, ProtoMol::CoulombForce::C2, ProtoMol::CoulombForce::C1
smoothKernel() : ProtoMol::iSGIdealGasCoulombForce::C4, ProtoMol::iSGIdealGasCoulombForce::C3, ProtoMol::iSGIdealGasCoulombForce::C2, ProtoMol::iSGIdealGasCoulombForce::C1, ProtoMol::iSGCoulombForce::C4, ProtoMol::iSGCoulombForce::C3, ProtoMol::iSGCoulombForce::C2, ProtoMol::iSGCoulombForce::C1, ProtoMol::CoulombForce::C4, ProtoMol::CoulombForce::C3, ProtoMol::CoulombForce::C2, ProtoMol::CoulombForce::C1
sortForceString() : ProtoMol::ForceFactoryDetails
SphericalSystemForce() : ProtoMol::SphericalSystemForce
splitForceString() : ProtoMol::ForceFactoryDetails
splitForceStringSorted() : ProtoMol::ForceFactoryDetails
Stack() : ProtoMol::Stack< T >
StandardIntegrator() : ProtoMol::StandardIntegrator
start() : ProtoMol::Timer, ProtoMol::Cycles
stop() : ProtoMol::Timer, ProtoMol::Cycles
str() : std::stringstreambase, std::stringbuf, ProtoMol::ExclusionEnum, ProtoMol::ParallelEnum, ProtoMol::ThermostatEnum, ProtoMol::InputPosVelEnum, ProtoMol::ValueEnum, ProtoMol::ValueEnum::Enum2ValueType< e >, ProtoMol::ConstraintValueEnum, ProtoMol::BSplineEnum
stringbuf() : std::stringbuf
stringstream() : std::stringstream
stringstreambase() : std::stringstreambase
STSIntegrator() : ProtoMol::STSIntegrator
subtract() : ProtoMol::Vector3D
sum() : ProtoMol::Vector3DBlock
sumQ() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
sumV() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
surfaceDipoleTerm() : ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
swap() : ProtoMol::InputValue< TBase, type, constraint >, ProtoMol::Value, ProtoMol::Array< T, N >
sync() : ProtoMol::Parallel, std::stringbuf
syncSlave() : ProtoMol::Parallel
SystemCompareForce() : ProtoMol::SystemCompareForce
SystemForce() : ProtoMol::SystemForce
SystemTimeForce() : ProtoMol::SystemTimeForce

- t -

temperature() : ProtoMol::OutputCache
temperatureForNonWater() : ProtoMol::OutputCache
temperatureForWater() : ProtoMol::OutputCache
Text() : ProtoMol::Text
time() : ProtoMol::OutputCache, ProtoMol::GenericTopology
TimeForce() : ProtoMol::TimeForce
Timer() : ProtoMol::Timer, ProtoMol::TimeRep
TimeRep() : ProtoMol::TimeRep
top() : ProtoMol::Integrator
Topology() : ProtoMol::Topology< TBoundaryConditions, TCellManager >
TopologyFactoryDetails() : ProtoMol::TopologyFactoryDetails
Torsion() : ProtoMol::Torsion
totalEnergy() : ProtoMol::OutputCache
TransformMap() : ProtoMol::ModifierISG::TransformMap
transpose() : ProtoMol::Matrix3by3
transposed() : ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3
TRANSReader() : ProtoMol::TRANSReader
TripleInt() : ProtoMol::TripleInt
tryFormat() : ProtoMol::XSCReader, ProtoMol::TRANSReader, ProtoMol::iSGPARReader, ProtoMol::XYZTrajectoryReader, ProtoMol::XYZReader, ProtoMol::XYZBinReader, ProtoMol::Reader, ProtoMol::PSFReader, ProtoMol::PPMReader, ProtoMol::PGMReader, ProtoMol::PDBReader, ProtoMol::PARReader, ProtoMol::DCDTrajectoryReader, ProtoMol::ConfigurationReader, ProtoMol::InputPosVel
type() : ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder, ProtoMol::IMD::IMDheader, ProtoMol::TypeSelection::Float< size >, ProtoMol::TypeSelection::Int< size >, ProtoMol::TypeSelection::SelectTypeCheck< A, size >, ProtoMol::TypeSelection::SelectTypeCheckHelper< true, A >, ProtoMol::TypeSelection::SelectType< size, A, B >, ProtoMol::TypeSelection::SelectTypeHelper< true, A, B >, ProtoMol::TypeSelection::SelectTypeHelper< cmp, A, B >, ProtoMol::Molecule, ProtoMol::Atom

- u -

UmbrellaIntegrator() : ProtoMol::UmbrellaIntegrator
uncache() : ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::ArrayCellListStructure, ProtoMol::Integrator, ProtoMol::HapticSystemForce, ProtoMol::OutputCache, ProtoMol::TimeForce, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >, ProtoMol::NonbondedSimpleFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::NonbondedFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::ForceGroup, ProtoMol::Force, ProtoMol::CompareForce
uncacheCellList() : ProtoMol::Topology< TBoundaryConditions, TCellManager >, ProtoMol::GenericTopology
underflow() : std::stringbuf
uniqueForceString() : ProtoMol::ForceFactoryDetails
unregisterAllExemplars() : ProtoMol::HelpTextFactory, ProtoMol::Factory< Type >
unregisterExemplar() : ProtoMol::HelpTextFactory, ProtoMol::Factory< Type >
unregisterKeyword() : ProtoMol::Configuration
updateB_Bx() : ProtoMol::BSplineMOLLYIntegrator
updateB_Bx_Px_for1Kick() : ProtoMol::BSplineMOLLYIntegrator
updateB_Bx_Px_for1stHalfKick() : ProtoMol::BSplineMOLLYIntegrator
updateBeta() : ProtoMol::ShadowHMCIntegrator
updateCache() : ProtoMol::CubicCellManager, ProtoMol::ArrayCellListStructure, ProtoMol::ForceFactoryDetails
updateCellLists() : ProtoMol::Topology< TBoundaryConditions, TCellManager >
updateSize() : ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
updateXx() : ProtoMol::BSplineMOLLYIntegrator

- v -

valid() : ProtoMol::InputValue< TBase, type, constraint >, ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder, ProtoMol::Configuration, ProtoMol::AbstractEnumType< T, noCase >, ProtoMol::ArrayCellListStructure
validConfiguration() : ProtoMol::Configuration
Value() : ProtoMol::Value
Vect() : ProtoMol::ArraySize< N >
Vector() : ProtoMol::Vector< T >, ProtoMol::ArraySizes, ProtoMol::ArraySize< N >
Vector3D() : ProtoMol::Vector3D
Vector3DBlock() : ProtoMol::Vector3DBlock
VectorPacker() : ProtoMol::VectorPacker< T, N >
virial() : ProtoMol::ScalarStructure
volume() : ProtoMol::OutputCache

- w -

walk() : ProtoMol::MCIntegrator
width() : ProtoMol::Report::MyStreamer, ProtoMol::PPM, ProtoMol::PGM
WrapperMetaForce() : ProtoMol::WrapperMetaForce
write() : ProtoMol::XSCWriter, ProtoMol::XYZWriter, ProtoMol::XYZTrajectoryWriter, ProtoMol::XYZBinWriter, ProtoMol::XFigWriter, ProtoMol::PSFWriter, ProtoMol::PPMWriter, ProtoMol::PNGWriter, ProtoMol::PGMWriter, ProtoMol::PDBWriter, ProtoMol::PARWriter, ProtoMol::DCDTrajectoryWriter
Writer() : ProtoMol::Writer

- x -

XFigWriter() : ProtoMol::XFigWriter
XSCReader() : ProtoMol::XSCReader
XSCWriter() : ProtoMol::XSCWriter
XYZ() : ProtoMol::XYZ, Format, ProtoMol::InputPosVelEnum
XYZBinReader() : ProtoMol::XYZBinReader
XYZBinWriter() : ProtoMol::XYZBinWriter
XYZReader() : ProtoMol::XYZReader
XYZTrajectoryReader() : ProtoMol::XYZTrajectoryReader
XYZTrajectoryWriter() : ProtoMol::XYZTrajectoryWriter
XYZWriter() : ProtoMol::XYZWriter

- z -

zero() : ProtoMol::Vector3DBlock, ProtoMol::Matrix3by3
zeroMatrix() : ProtoMol::Matrix3by3

- ~ -

~AngleInfo() : ProtoMol::AngleInfo
~AngleSystemForceBase() : ProtoMol::AngleSystemForceBase
~Array() : ProtoMol::Array< T, N >
~BondSystemForceBase() : ProtoMol::BondSystemForceBase
~BSpline() : ProtoMol::BSpline
~BSplineEnum() : ProtoMol::BSplineEnum
~BSplineMOLLYIntegrator() : ProtoMol::BSplineMOLLYIntegrator
~CompareForce() : ProtoMol::CompareForce
~ConfigurationReader() : ProtoMol::ConfigurationReader
~ConstraintValueEnum() : ProtoMol::ConstraintValueEnum
~CoulombEwaldRealTableForce() : ProtoMol::CoulombEwaldRealTableForce
~CoulombMultiGridDirectTableForce() : ProtoMol::CoulombMultiGridDirectTableForce< TKernel >
~DCDTrajectoryReader() : ProtoMol::DCDTrajectoryReader
~DihedralHMCIntegrator() : ProtoMol::DihedralHMCIntegrator
~DihedralSystemForceBase() : ProtoMol::DihedralSystemForceBase
~DMDLeapfrogIntegrator() : ProtoMol::DMDLeapfrogIntegrator
~ElectricFieldSystemForceBase() : ProtoMol::ElectricFieldSystemForceBase
~EquilibriumMOLLYIntegrator() : ProtoMol::EquilibriumMOLLYIntegrator
~ExclusionEnum() : ProtoMol::ExclusionEnum
~ExtendedForce() : ProtoMol::ExtendedForce
~Factory() : ProtoMol::Factory< Type >
~FactoryBase() : ProtoMol::FactoryBase< Type >
~FFTComplex() : ProtoMol::FFTComplex
~FFTInternal() : ProtoMol::FFTInternal
~File() : ProtoMol::File
~Force() : ProtoMol::Force
~ForceFactoryDetails() : ProtoMol::ForceFactoryDetails
~ForceGroup() : ProtoMol::ForceGroup
~GenericTopology() : ProtoMol::GenericTopology
~Grid() : ProtoMol::Grid< TInterpolation >
~HapticSystemForce() : ProtoMol::HapticSystemForce
~HarmDihedralSystemForceBase() : ProtoMol::HarmDihedralSystemForceBase
~HelpTextFactory() : ProtoMol::HelpTextFactory
~Hermite() : ProtoMol::Hermite
~IMDElf() : ProtoMol::IMDElf
~ImproperSystemForceBase() : ProtoMol::ImproperSystemForceBase
~InputBoundaryConditionsIdentifier() : ProtoMol::InputBoundaryConditionsIdentifier
~InputCellManagerIdentifier() : ProtoMol::InputCellManagerIdentifier
~InputConfigIdentifier() : ProtoMol::InputConfigIdentifier
~InputDebugIdentifier() : ProtoMol::InputDebugIdentifier
~InputDihedralMultPSFIdentifier() : ProtoMol::InputDihedralMultPSFIdentifier
~InputFirststepIdentifier() : ProtoMol::InputFirststepIdentifier
~InputIntegratorIdentifier() : ProtoMol::InputIntegratorIdentifier
~InputMaxPackagesIdentifier() : ProtoMol::InputMaxPackagesIdentifier
~InputMolVirialCalcIdentifier() : ProtoMol::InputMolVirialCalcIdentifier
~InputNumstepsIdentifier() : ProtoMol::InputNumstepsIdentifier
~InputOutputfreqIdentifier() : ProtoMol::InputOutputfreqIdentifier
~InputOutputIdentifier() : ProtoMol::InputOutputIdentifier
~InputParallelModeIdentifier() : ProtoMol::InputParallelModeIdentifier
~InputParallelPipeIdentifier() : ProtoMol::InputParallelPipeIdentifier
~InputPARIdentifier() : ProtoMol::InputPARIdentifier
~InputPDBScalingIdentifier() : ProtoMol::InputPDBScalingIdentifier
~InputPositionsIdentifier() : ProtoMol::InputPositionsIdentifier
~InputPosVelEnum() : ProtoMol::InputPosVelEnum
~InputPSFIdentifier() : ProtoMol::InputPSFIdentifier
~InputRattleEpsilonIdentifier() : ProtoMol::InputRattleEpsilonIdentifier
~InputRattleIdentifier() : ProtoMol::InputRattleIdentifier
~InputRattleMaxIterIdentifier() : ProtoMol::InputRattleMaxIterIdentifier
~InputReducedImageIdentifier() : ProtoMol::InputReducedImageIdentifier
~InputRemoveAngularMomentumIdentifier() : ProtoMol::InputRemoveAngularMomentumIdentifier
~InputRemoveLinearMomentumIdentifier() : ProtoMol::InputRemoveLinearMomentumIdentifier
~InputSeedIdentifier() : ProtoMol::InputSeedIdentifier
~InputShakeEpsilonIdentifier() : ProtoMol::InputShakeEpsilonIdentifier
~InputShakeIdentifier() : ProtoMol::InputShakeIdentifier
~InputShakeMaxIterIdentifier() : ProtoMol::InputShakeMaxIterIdentifier
~InputTemperatureIdentifier() : ProtoMol::InputTemperatureIdentifier
~InputUseBarrierIdentifier() : ProtoMol::InputUseBarrierIdentifier
~InputValue() : ProtoMol::InputValue< TBase, type, constraint >
~InputVelocitiesIdentifier() : ProtoMol::InputVelocitiesIdentifier
~InputVirialCalcIdentifier() : ProtoMol::InputVirialCalcIdentifier
~Integrator() : ProtoMol::Integrator
~IntegratorFactoryDetails() : ProtoMol::IntegratorFactoryDetails
~iSGAngleSystemForceBase() : ProtoMol::iSGAngleSystemForceBase
~iSGBondSystemForceBase() : ProtoMol::iSGBondSystemForceBase
~iSGCoulombEwaldRealTableForce() : ProtoMol::iSGCoulombEwaldRealTableForce
~iSGDihedralSystemForceBase() : ProtoMol::iSGDihedralSystemForceBase
~iSGGrid() : ProtoMol::iSGGrid< TInterpolation >
~iSGImproperSystemForceBase() : ProtoMol::iSGImproperSystemForceBase
~iSGLennardJonesTableForce() : ProtoMol::iSGLennardJonesTableForce
~iSGNonbondedFullEwaldSystemForce() : ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
~iSGNonbondedPMEwaldSystemForce() : ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >
~iSGPARReader() : ProtoMol::iSGPARReader
~Lagrange() : ProtoMol::Lagrange
~LeapfrogIntegrator() : ProtoMol::LeapfrogIntegrator
~LennardJonesParameterTable() : ProtoMol::LennardJonesParameterTable
~LennardJonesTableForce() : ProtoMol::LennardJonesTableForce
~Makeable() : ProtoMol::Makeable
~MCIntegrator() : ProtoMol::MCIntegrator
~MetaForce() : ProtoMol::MetaForce
~Modifier() : ProtoMol::Modifier
~MollyForce() : ProtoMol::MollyForce
~MOLLYIntegrator() : ProtoMol::MOLLYIntegrator
~MTSIntegrator() : ProtoMol::MTSIntegrator
~NonbondedCutoffForceBase() : ProtoMol::NonbondedCutoffForceBase
~NonbondedFullEwaldSystemForce() : ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
~NonbondedFullSystemForce() : ProtoMol::NonbondedFullSystemForce< TOneAtomPair >
~NonbondedMultiGridSystemForce() : ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >
~NonbondedPMEwaldSystemForce() : ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >
~NonbondedSimpleFullSystemForce() : ProtoMol::NonbondedSimpleFullSystemForce< TOneAtomPair >
~NonbondedSimpleFullSystemForceBase() : ProtoMol::NonbondedSimpleFullSystemForceBase
~OutputCache() : ProtoMol::OutputCache
~OutputCollection() : ProtoMol::OutputCollection
~OutputDCDTrajectory() : ProtoMol::OutputDCDTrajectory
~OutputDihedrals() : ProtoMol::OutputDihedrals
~OutputFactoryDetails() : ProtoMol::OutputFactoryDetails
~OutputFile() : ProtoMol::OutputFile
~OutputTemperatures() : ProtoMol::OutputTemperatures
~OutputXYZTrajectoryForce() : ProtoMol::OutputXYZTrajectoryForce
~OutputXYZTrajectoryPos() : ProtoMol::OutputXYZTrajectoryPos
~OutputXYZTrajectoryVel() : ProtoMol::OutputXYZTrajectoryVel
~Parallel() : ProtoMol::Parallel
~ParallelEnum() : ProtoMol::ParallelEnum
~PARReader() : ProtoMol::PARReader
~PaulTrapExtendedForceBase() : ProtoMol::PaulTrapExtendedForceBase
~PDBReader() : ProtoMol::PDBReader
~PGM() : ProtoMol::PGM
~PGMReader() : ProtoMol::PGMReader
~PlaceHolder() : ProtoMol::Value::PlaceHolder
~PLeapfrogIntegrator() : ProtoMol::PLeapfrogIntegrator
~PPM() : ProtoMol::PPM
~PPMReader() : ProtoMol::PPMReader
~Proxy() : ProtoMol::Proxy
~PSFReader() : ProtoMol::PSFReader
~PSFWriter() : ProtoMol::PSFWriter
~Reader() : ProtoMol::Reader
~ReducedHessAngle() : ProtoMol::ReducedHessAngle
~SemiGenericTopology() : ProtoMol::SemiGenericTopology< TBoundaryConditions >
~ShadowHMCIntegrator() : ProtoMol::ShadowHMCIntegrator
~Stack() : ProtoMol::Stack< T >
~SystemForce() : ProtoMol::SystemForce
~SystemTimeForce() : ProtoMol::SystemTimeForce
~TimeForce() : ProtoMol::TimeForce
~Topology() : ProtoMol::Topology< TBoundaryConditions, TCellManager >
~TopologyFactoryDetails() : ProtoMol::TopologyFactoryDetails
~TRANSReader() : ProtoMol::TRANSReader
~UmbrellaIntegrator() : ProtoMol::UmbrellaIntegrator
~UniversalSwitchingFunctionBase() : ProtoMol::UniversalSwitchingFunctionBase
~Value() : ProtoMol::Value
~ValueEnum() : ProtoMol::ValueEnum
~WrapperMetaForce() : ProtoMol::WrapperMetaForce
~Writer() : ProtoMol::Writer
~XSCReader() : ProtoMol::XSCReader
~XYZBinReader() : ProtoMol::XYZBinReader
~XYZReader() : ProtoMol::XYZReader
~XYZTrajectoryReader() : ProtoMol::XYZTrajectoryReader
~XYZTrajectoryWriter() : ProtoMol::XYZTrajectoryWriter

Last update: . GNU GENERAL PUBLIC LICENSE, copyrighted by the University of Notre Dame and the University of Bergen, Norway.