
ProtoMol - an
object-oriented component based framework for Molecular Dynamics
simulations.
Here is a list of all class members with links to the classes they belong to:
- a
: ProtoMol::PAR::Nbfix
- A
: ProtoMol::LennardJonesParameters
- a1
: ProtoMol::ExclusionPair, ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond
- a14
: ProtoMol::PAR::Nbfix
- A14
: ProtoMol::LennardJonesParameters
- a2
: ProtoMol::ExclusionPair, ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond
- aborting
: ProtoMol::Report::MyStreamer
- absF2
: ProtoMol::CompareForce::CompareError
- AbstractEnumType()
: ProtoMol::AbstractEnumType< T, noCase >
- Acceptor()
: ProtoMol::PSF::Acceptor
- acceptors
: ProtoMol::PSF
- 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
- aliases
: ProtoMol::InputReducedImageIdentifier, ProtoMol::InputRattleMaxIterIdentifier, ProtoMol::InputRattleEpsilonIdentifier, ProtoMol::InputRattleIdentifier, ProtoMol::InputShakeMaxIterIdentifier, ProtoMol::InputShakeEpsilonIdentifier, ProtoMol::InputShakeIdentifier, ProtoMol::InputMolVirialCalcIdentifier, ProtoMol::InputVirialCalcIdentifier, ProtoMol::InputDihedralMultPSFIdentifier, ProtoMol::InputCellManagerIdentifier, ProtoMol::InputBoundaryConditionsIdentifier, ProtoMol::InputPDBScalingIdentifier, ProtoMol::InputMaxPackagesIdentifier, ProtoMol::InputParallelModeIdentifier, ProtoMol::InputParallelPipeIdentifier, ProtoMol::InputUseBarrierIdentifier, ProtoMol::InputRemoveAngularMomentumIdentifier, ProtoMol::InputRemoveLinearMomentumIdentifier, ProtoMol::InputPARIdentifier, ProtoMol::InputPSFIdentifier, ProtoMol::InputVelocitiesIdentifier, ProtoMol::InputPositionsIdentifier, ProtoMol::InputIntegratorIdentifier, ProtoMol::InputOutputfreqIdentifier, ProtoMol::InputNumstepsIdentifier, ProtoMol::InputFirststepIdentifier, ProtoMol::InputConfigIdentifier, ProtoMol::InputSeedIdentifier, ProtoMol::InputTemperatureIdentifier, ProtoMol::InputDebugIdentifier, ProtoMol::InputOutputIdentifier
- AliasMapType
: ProtoMol::Configuration
- allnodes
: ProtoMol::Report::MyStreamer
- allnodesserial
: ProtoMol::Report::MyStreamer
- allslavesserial
: ProtoMol::Report::MyStreamer
- alpha
: ProtoMol::iSGLennardJonesTableForce
- alphaLJ
: ProtoMol::ModifierISG::TransformMap, ProtoMol::TRANS::AtomType, ProtoMol::Atom
- altLoc
: ProtoMol::PDB::PDBAtom
- ANGLE
: ProtoMol::iSGPARReader, ProtoMol::PARReader, ProtoMol::ScalarStructure
- Angle()
: ProtoMol::Angle, ProtoMol::PSF::Angle, ProtoMol::PAR::Angle, ProtoMol::iSGPAR::Angle
- angle
: ProtoMol::BSplineMOLLYIntegrator::AngleIndex
- ANGLE_DELTAMU
: ProtoMol::ScalarStructure
- ANGLE_NOTSET
: ProtoMol::AngleInfo
- ANGLE_POINTER
: ProtoMol::AngleInfo
- ANGLE_VALUE
: ProtoMol::AngleInfo
- AngleIndex()
: ProtoMol::BSplineMOLLYIntegrator::AngleIndex
- AngleInfo()
: ProtoMol::AngleInfo
- angleList
: ProtoMol::Molecule
- angles
: ProtoMol::ModifierISG, ProtoMol::GenericTopology, ProtoMol::PSF, ProtoMol::PAR, ProtoMol::iSGPAR
- angleval
: ProtoMol::PAR::Angle, ProtoMol::iSGPAR::Angle
- angularMomentum()
: ProtoMol::OutputCache
- anterpolateCharge()
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- anyExclsForThisDelta
: ProtoMol::ExclusionTable
- 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 >
- Array< T, 1 >
: ProtoMol::Array< T, N >::RefArray< 1 >, ProtoMol::RefArray< T, 1 >
- Array< T, 2 >
: ProtoMol::Array< T, N >::RefArray< 1 >, ProtoMol::RefArray< T, 1 >
- Array< T, N >
: ProtoMol::Array< T, N >::RefArray< N >, ProtoMol::RefArray< T, N >
- Array< T, N+1 >
: ProtoMol::Array< T, N >::RefArray< N >, ProtoMol::RefArray< T, N >
- array_dims
: ProtoMol::Array< T, N >::RefArray< 1 >, ProtoMol::Array< T, N >::RefArray< N >, ProtoMol::Array< T, N >, ProtoMol::RefArray< T, 1 >, ProtoMol::RefArray< T, N >
- ArrayCellListStructure()
: ProtoMol::ArrayCellListStructure
- ArraySize()
: ProtoMol::ArraySize< N >
- ArraySize< N-1 >
: ProtoMol::ArraySize< N >
- ArraySizes
: ProtoMol::ArraySizes, ProtoMol::ArraySize< N >
- Atom()
: ProtoMol::PSF::Atom, ProtoMol::Atom
- atom
: ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
- atom1
: ProtoMol::Torsion, ProtoMol::Bond, ProtoMol::Bond::Constraint, ProtoMol::Angle, ProtoMol::PSF::Ngrp, ProtoMol::PSF::Nonbonded, ProtoMol::PSF::Acceptor, ProtoMol::PSF::Donor, ProtoMol::PSF::Improper, ProtoMol::PSF::Dihedral, ProtoMol::PSF::Angle, ProtoMol::PSF::Bond, ProtoMol::PAR::Hbond, ProtoMol::PAR::Nbfix, ProtoMol::PAR::Improper, ProtoMol::PAR::Dihedral, ProtoMol::PAR::Angle, ProtoMol::PAR::Bond, ProtoMol::iSGPAR::Improper, ProtoMol::iSGPAR::Dihedral, ProtoMol::iSGPAR::Angle, ProtoMol::iSGPAR::Bond
- atom2
: ProtoMol::Torsion, ProtoMol::Bond, ProtoMol::Bond::Constraint, ProtoMol::Angle, ProtoMol::PSF::Ngrp, ProtoMol::PSF::Acceptor, ProtoMol::PSF::Donor, ProtoMol::PSF::Improper, ProtoMol::PSF::Dihedral, ProtoMol::PSF::Angle, ProtoMol::PSF::Bond, ProtoMol::PAR::Hbond, ProtoMol::PAR::Nbfix, ProtoMol::PAR::Improper, ProtoMol::PAR::Dihedral, ProtoMol::PAR::Angle, ProtoMol::PAR::Bond, ProtoMol::iSGPAR::Improper, ProtoMol::iSGPAR::Dihedral, ProtoMol::iSGPAR::Angle, ProtoMol::iSGPAR::Bond
- atom3
: ProtoMol::Torsion, ProtoMol::Angle, ProtoMol::PSF::Ngrp, ProtoMol::PSF::Improper, ProtoMol::PSF::Dihedral, ProtoMol::PSF::Angle, ProtoMol::PAR::Improper, ProtoMol::PAR::Dihedral, ProtoMol::PAR::Angle, ProtoMol::iSGPAR::Improper, ProtoMol::iSGPAR::Dihedral, ProtoMol::iSGPAR::Angle
- atom4
: ProtoMol::Torsion, ProtoMol::PSF::Improper, ProtoMol::PSF::Dihedral, ProtoMol::PAR::Improper, ProtoMol::PAR::Dihedral, ProtoMol::iSGPAR::Improper, ProtoMol::iSGPAR::Dihedral
- atom_name
: ProtoMol::PSF::Atom
- atom_type
: ProtoMol::PSF::Atom
- ATOMCHARGE
: ProtoMol::TRANSReader
- atomNum
: ProtoMol::Atom
- atoms
: ProtoMol::GenericTopology, ProtoMol::PSF, ProtoMol::PDB, ProtoMol::Molecule
- ATOMTYPE
: ProtoMol::TRANSReader
- AtomType()
: ProtoMol::TRANS::AtomType, ProtoMol::iSGPAR::AtomType, ProtoMol::AtomType
- atomTypes
: ProtoMol::ModifierISG, ProtoMol::TRANS, ProtoMol::GenericTopology
- AveCQ
: ProtoMol::iSGIntegrator
- AveCQSq
: ProtoMol::iSGIntegrator
- AveDeltaMu
: ProtoMol::iSGIntegrator
- averagingPositions()
: ProtoMol::MOLLYIntegrator
- b
: ProtoMol::PAR::Nbfix
- B
: ProtoMol::LennardJonesParameters
- b1
: ProtoMol::BSplineMOLLYIntegrator::BondIndex
- b14
: ProtoMol::PAR::Nbfix
- B14
: ProtoMol::LennardJonesParameters
- b2
: ProtoMol::BSplineMOLLYIntegrator::BondIndex
- 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 >
- BERENDSEN
: ProtoMol::ThermostatEnum
- BERENDSEN_GLOBAL
: ProtoMol::ThermostatEnum
- BERENDSEN_IND
: ProtoMol::ThermostatEnum
- BERENDSEN_SHELL
: ProtoMol::ThermostatEnum
- BERENDSEN_ZERO
: ProtoMol::ThermostatEnum
- blocksCorrection()
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- Bond()
: ProtoMol::Bond, ProtoMol::PSF::Bond, ProtoMol::PAR::Bond, ProtoMol::iSGPAR::Bond
- BOND
: ProtoMol::iSGPARReader, ProtoMol::PARReader, ProtoMol::ScalarStructure
- bond1
: ProtoMol::BSplineMOLLYIntegrator::AngleIndex
- bond2
: ProtoMol::BSplineMOLLYIntegrator::AngleIndex
- BOND_DELTAMU
: ProtoMol::ScalarStructure
- BondIndex()
: ProtoMol::BSplineMOLLYIntegrator::BondIndex
- bondList
: ProtoMol::Molecule
- bondRattleShakeConstraints
: ProtoMol::GenericTopology
- bonds
: ProtoMol::ModifierISG, ProtoMol::GenericTopology, ProtoMol::PSF, ProtoMol::PAR, ProtoMol::iSGPAR
- BOOL
: ProtoMol::ValueEnum
- bottom()
: ProtoMol::Integrator
- BoundaryConditions
: 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::SemiGenericTopology< 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::NonbondedCutoffSystemForce< TCellManager, TOneAtomPair >, ProtoMol::NonbondedCutoffMollyForce< TCellManager, TOneAtomPair >, ProtoMol::NonbondedCutoffForce< TCellManager, TOneAtomPair, TForce, TImplForce >
- boundaryConditions
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- boundingbox()
: ProtoMol::Vector3DBlock
- brent()
: ProtoMol::OutputCache
- brentMaxima()
: ProtoMol::OutputCache
- BSpline()
: ProtoMol::BSpline
- BSplineMOLLYIntegrator()
: ProtoMol::BSplineMOLLYIntegrator
- buf
: std::stringbuf
- bufsize
: std::stringbuf
- buildLatticeVectors()
: ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
- 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
- Cell
: ProtoMol::CubicCellManager
- CellListEnumerator()
: ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
- cellListNext
: ProtoMol::Atom
- cellLists
: ProtoMol::Topology< TBoundaryConditions, TCellManager >
- CellListStructure
: ProtoMol::CubicCellManager
- CellManager
: ProtoMol::Topology< TBoundaryConditions, TCellManager >
- cellManager
: ProtoMol::Topology< TBoundaryConditions, TCellManager >
- CellPairType
: 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 >, ProtoMol::NonbondedCutoffSystemForce< TCellManager, TOneAtomPair >, ProtoMol::NonbondedCutoffMollyForce< TCellManager, TOneAtomPair >, ProtoMol::NonbondedCutoffForce< TCellManager, TOneAtomPair, TForce, TImplForce >
- centerOfMass()
: ProtoMol::OutputCache
- chainID
: ProtoMol::PDB::PDBAtom
- char_type
: std::stringbuf
- charge
: ProtoMol::TRANS::AtomType, ProtoMol::PSF::Atom, ProtoMol::PDB::PDBAtom, ProtoMol::iSGPAR::AtomType, ProtoMol::AtomType
- CHARMM19
: ProtoMol::PAR, ProtoMol::iSGPAR
- CHARMM28
: ProtoMol::PAR, ProtoMol::iSGPAR
- CharmmTypeEnum
: ProtoMol::PAR, ProtoMol::iSGPAR
- 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
- clientsock
: 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 >
- COMMUNICATION
: ProtoMol::TimerStatistic
- CompareError()
: ProtoMol::CompareForce::CompareError
- CompareForce()
: ProtoMol::CompareForce
- ComplementSwitchingFunction()
: ProtoMol::ComplementSwitchingFunction< TOriginalSwitchingFunction >
- computeOthers
: ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >
- ConfigurationReader()
: ProtoMol::ConfigurationReader
- confstrings
: ProtoMol::OutputDihedrals
- confstringsCounter
: ProtoMol::OutputDihedrals
- connect()
: ProtoMol::IMDElf
- const_iterator
: ProtoMol::ArrayCellListStructure, ProtoMol::OutputCollection, ProtoMol::HelpTextFactory, ProtoMol::Factory< Type >, 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 >
- const_pointer
: ProtoMol::ArrayCellListStructure, 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 >
- const_reference
: ProtoMol::ArrayCellListStructure, 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 >
- Constraint
: ProtoMol::Bond::Constraint, ProtoMol::InputValue< TBase, type, constraint >
- Container
: ProtoMol::OutputCollection
- 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 >
- coords
: ProtoMol::XYZ, ProtoMol::PDB
- 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 >
- COULOMB
: ProtoMol::ScalarStructure
- COULOMB_DELTAMU
: ProtoMol::ScalarStructure
- CoulombEwaldRealForce()
: ProtoMol::CoulombEwaldRealForce
- CoulombEwaldRealTableForce()
: ProtoMol::CoulombEwaldRealTableForce
- CoulombMultiGridDirectForce()
: ProtoMol::CoulombMultiGridDirectForce< TKernel >
- CoulombMultiGridDirectTableForce()
: ProtoMol::CoulombMultiGridDirectTableForce< TKernel >
- coulombScalingFactor
: ProtoMol::GenericTopology
- CQFLUCTUATION
: ProtoMol::ScalarStructure
- 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
- curAngle
: ProtoMol::UmbrellaIntegrator
- cutoffSquared()
: ProtoMol::UniversalSwitchingFunction, ProtoMol::ShiftSwitchingFunction, ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::CutoffSwitchingFunction, ProtoMol::ComplementSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction
- CutoffSwitchingFunction()
: ProtoMol::CutoffSwitchingFunction
- Cycles()
: ProtoMol::Cycles
- DCD
: Format
- DCDTrajectoryReader()
: ProtoMol::DCDTrajectoryReader
- DCDTrajectoryWriter()
: ProtoMol::DCDTrajectoryWriter
- debug()
: ProtoMol::Value, ProtoMol::Report::debug
- DEFAULT__SIZE
: ProtoMol::CoulombMultiGridDirectTableForce< TKernel >
- DEFAULT_TABLE_SIZE
: ProtoMol::iSGLennardJonesTableForce, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::LennardJonesTableForce, ProtoMol::CoulombEwaldRealTableForce
- defaultBlockSize
: ProtoMol::NonbondedSimpleFullSystemForceBase, ProtoMol::NonbondedFullSystemForceBase
- defaultCharmmType
: ProtoMol::PARWriter
- defaultValue
: ProtoMol::HelpText, ProtoMol::Parameter
- defbuf
: std::stringbuf
- defined()
: ProtoMol::Value, ProtoMol::Configuration
- degreesOfFreedom
: ProtoMol::GenericTopology
- deleteExternalModifiers()
: ProtoMol::Integrator
- deleteInternalModifiers()
: ProtoMol::Integrator
- deleteModifier()
: ProtoMol::Integrator
- Delta_ubK
: ProtoMol::Angle
- Delta_ubR0
: ProtoMol::Angle
- DeltaK
: ProtoMol::Torsion, ProtoMol::Bond, ProtoMol::Angle
- deltaM
: ProtoMol::Atom
- deltaMu()
: ProtoMol::ScalarStructure
- DeltaMuIG
: ProtoMol::TRANS
- DeltaPhase
: ProtoMol::Torsion
- deltaQ
: ProtoMol::Atom
- DeltaR0
: ProtoMol::Bond
- DeltaTheta0
: ProtoMol::Angle
- DELTATIME
: ProtoMol::ScalarStructure
- density()
: ProtoMol::OutputCache
- det()
: ProtoMol::Matrix3by3
- Details
: ProtoMol::FactoryTraits< GenericTopology >, ProtoMol::FactoryTraits< Output >, ProtoMol::FactoryTraits< Integrator >, ProtoMol::FactoryTraits< Force >
- dftmod()
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- difference_type
: ProtoMol::ArrayCellListStructure, 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 >
- diffusion()
: ProtoMol::OutputCache
- Dihedral()
: ProtoMol::PSF::Dihedral, ProtoMol::PAR::Dihedral, ProtoMol::iSGPAR::Dihedral
- DIHEDRAL
: ProtoMol::iSGPARReader, ProtoMol::PARReader, ProtoMol::ScalarStructure
- DIHEDRAL_DELTAMU
: ProtoMol::ScalarStructure
- DihedralHMCIntegrator()
: ProtoMol::DihedralHMCIntegrator
- dihedralList
: ProtoMol::Molecule
- dihedralPhi()
: ProtoMol::OutputCache
- dihedralPhis()
: ProtoMol::OutputCache
- dihedrals
: ProtoMol::ModifierISG, ProtoMol::GenericTopology, ProtoMol::PSF, ProtoMol::PAR, ProtoMol::iSGPAR
- dimensions()
: 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 >
- direct()
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- disable()
: ProtoMol::Modifier
- disableBetaUpdate()
: ProtoMol::ShadowHMCIntegrator
- distance
: ProtoMol::PAR::Bond, ProtoMol::iSGPAR::Bond
- distCount()
: ProtoMol::Proxy
- distribute()
: ProtoMol::Parallel, ProtoMol::Proxy
- distributed()
: ProtoMol::Proxy
- divide()
: ProtoMol::Vector3D
- dKernel()
: 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
- dKernelR()
: 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
- DLMCIntegrator()
: ProtoMol::DLMCIntegrator
- DMDLeapfrogIntegrator()
: ProtoMol::DMDLeapfrogIntegrator
- do2ndHalfKick()
: ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
- doAveragingPositions()
: ProtoMol::MOLLYIntegrator, ProtoMol::EquilibriumMOLLYIntegrator, ProtoMol::BSplineMOLLYIntegrator
- doDrift()
: ProtoMol::iSGIntegrator, ProtoMol::STSIntegrator, ProtoMol::PaulTrapIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::LangevinImpulseIntegrator
- doDriftOrNextIntegrator()
: ProtoMol::STSIntegrator, ProtoMol::StandardIntegrator, ProtoMol::MTSIntegrator
- doEvaluate()
: ProtoMol::SphericalSystemForce, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >, ProtoMol::NonbondedSimpleFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedCutoffForce< TCellManager, TOneAtomPair, TForce, TImplForce >, ProtoMol::FrictionExtendedForce, ProtoMol::ExternalMagneticFieldExtendedForce, ProtoMol::ExternalGravitationSystemForce, ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >
- doExecute()
: ProtoMol::ModifierISG, ProtoMol::iSGModifierPreForceChemostat, ProtoMol::iSGModifierPostForceChemostat, ProtoMol::ModifierUmbrella, ProtoMol::ModifierUpdateBetaAndPush, ProtoMol::ModifierUpdateBeta, ProtoMol::ModifierShake, ProtoMol::ModifierRemoveLinearMomentum, ProtoMol::ModifierRemoveAngularMomentum, ProtoMol::ModifierRattle, ProtoMol::ModifierPreForceThermostat< TIntegrator >, ProtoMol::ModifierPreForceBarostat< TIntegrator >, ProtoMol::ModifierPostForceThermostat< TIntegrator >, ProtoMol::ModifierPostForceBarostat< TIntegrator >, ProtoMol::ModifierNVTShakeDetails, ProtoMol::ModifierNVTRattleDetails, ProtoMol::ModifierNPTShakeDetails, ProtoMol::ModifierNPTRattleDetails, ProtoMol::ModifierMollification, ProtoMol::ModifierIncrementTimestep, ProtoMol::ModifierFriction, ProtoMol::ModifierAveraging, ProtoMol::Modifier
- doFinalize()
: ProtoMol::OutputFinalXSC, ProtoMol::OutputFinalPSF, ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputScreen, ProtoMol::OutputPDBFramePos, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputFile, ProtoMol::OutputDihedrals, ProtoMol::OutputDCDTrajectory, ProtoMol::Output
- doFirstHalfKick()
: ProtoMol::BBKIntegrator
- doFlushCache()
: ProtoMol::OutputPaulTrap, ProtoMol::OutputFile
- doHalfDrift()
: ProtoMol::PLeapfrogIntegrator
- doHalfKick()
: ProtoMol::iSGIntegrator, ProtoMol::StandardIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::DMDLeapfrogIntegrator
- doHalfKickdoDrift()
: ProtoMol::LeapfrogIntegrator
- doHalfKickIterate()
: ProtoMol::DMDLeapfrogIntegrator
- doHalfKickVhat()
: ProtoMol::DMDLeapfrogIntegrator
- dohint
: ProtoMol::Report::MyStreamer
- doInitialize()
: ProtoMol::ModifierISG, ProtoMol::OutputISGProperties, ProtoMol::OutputFinalXSC, ProtoMol::OutputFinalPSF, ProtoMol::ModifierRemoveLinearMomentum, ProtoMol::ModifierRemoveAngularMomentum, ProtoMol::ModifierMetaRattleShake, ProtoMol::Modifier, ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputTemperatures, ProtoMol::OutputScreen, ProtoMol::OutputPDBFramePos, ProtoMol::OutputPaulTrap, ProtoMol::OutputMomentum, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputEnergies, ProtoMol::OutputDihedrals, ProtoMol::OutputDiffusion, ProtoMol::OutputDCDTrajectory, ProtoMol::Output
- doKeywords()
: ProtoMol::HelpTextFactory
- doKick()
: ProtoMol::StandardIntegrator
- doKickdoDrift()
: ProtoMol::PLeapfrogIntegrator, ProtoMol::LeapfrogIntegrator
- doKickdoHalfDrift()
: ProtoMol::PLeapfrogIntegrator
- doMake()
: ProtoMol::iSGIntegrator, ProtoMol::OutputISGProperties, ProtoMol::OutputFinalXSC, ProtoMol::OutputFinalPSF, 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::Topology< TBoundaryConditions, TCellManager >, ProtoMol::GenericTopology, ProtoMol::UmbrellaIntegrator, ProtoMol::STSIntegrator, ProtoMol::ShadowHMCIntegrator, ProtoMol::PLeapfrogIntegrator, ProtoMol::PaulTrapIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::NoseNVTLeapfrogIntegrator, ProtoMol::MTSIntegrator, ProtoMol::LeapfrogIntegrator, ProtoMol::LangevinImpulseIntegrator, ProtoMol::ImpulseIntegrator, ProtoMol::HMCIntegrator, ProtoMol::EquilibriumMOLLYIntegrator, ProtoMol::DMDLeapfrogIntegrator, ProtoMol::DLMCIntegrator, ProtoMol::DihedralHMCIntegrator, ProtoMol::BSplineMOLLYIntegrator, ProtoMol::BBKIntegrator, ProtoMol::HapticSystemForce, ProtoMol::TopologyFactoryDetails, ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputTemperatures, ProtoMol::OutputScreen, ProtoMol::OutputPDBFramePos, ProtoMol::OutputPaulTrap, ProtoMol::OutputMomentum, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputFactoryDetails, ProtoMol::OutputEnergies, ProtoMol::OutputDihedrals, ProtoMol::OutputDiffusion, ProtoMol::OutputDCDTrajectory, ProtoMol::Output, ProtoMol::IntegratorFactoryDetails, ProtoMol::ForceFactoryDetails, ProtoMol::WrapperMetaForce, 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::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, 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 >
- doMakeCollection()
: ProtoMol::OutputFactoryDetails
- doMollification()
: ProtoMol::MOLLYIntegrator, ProtoMol::EquilibriumMOLLYIntegrator, ProtoMol::BSplineMOLLYIntegrator
- DONE
: ProtoMol::Parallel
- done()
: ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
- Donor()
: ProtoMol::PSF::Donor
- donors
: ProtoMol::PSF
- donthint
: ProtoMol::Report::MyStreamer
- doOneAtomPair()
: 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::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 >
- doPrint()
: ProtoMol::ModifierISG, ProtoMol::iSGModifierPreForceChemostat, ProtoMol::iSGModifierPostForceChemostat, ProtoMol::ModifierUmbrella, ProtoMol::ModifierUpdateBetaAndPush, ProtoMol::ModifierUpdateBeta, ProtoMol::ModifierShake, ProtoMol::ModifierRemoveLinearMomentum, ProtoMol::ModifierRemoveAngularMomentum, ProtoMol::ModifierRattle, ProtoMol::ModifierPreForceThermostat< TIntegrator >, ProtoMol::ModifierPreForceBarostat< TIntegrator >, ProtoMol::ModifierPostForceThermostat< TIntegrator >, ProtoMol::ModifierPostForceBarostat< TIntegrator >, ProtoMol::ModifierNVTShakeDetails, ProtoMol::ModifierNVTRattleDetails, ProtoMol::ModifierNPTShakeDetails, ProtoMol::ModifierNPTRattleDetails, ProtoMol::ModifierMollification, ProtoMol::ModifierIncrementTimestep, ProtoMol::ModifierFriction, ProtoMol::ModifierAveraging, ProtoMol::Modifier, ProtoMol::TopologyFactoryDetails, ProtoMol::OutputFactoryDetails, ProtoMol::IntegratorFactoryDetails, ProtoMol::ForceFactoryDetails, ProtoMol::FactoryBase< Type >
- doRegisterAllExemplarsConfiguration()
: ProtoMol::TopologyFactoryDetails, ProtoMol::OutputFactoryDetails
- doRegisterExemplar()
: ProtoMol::HelpTextFactory, ProtoMol::Factory< Type >
- doRegisterExemplars()
: ProtoMol::HelpTextFactory
- doRegisterHelpText()
: ProtoMol::TopologyFactoryDetails, ProtoMol::OutputFactoryDetails, ProtoMol::IntegratorFactoryDetails, ProtoMol::ForceFactoryDetails, ProtoMol::FactoryBase< Type >
- doResize()
: ProtoMol::Array< T, N >
- doRun()
: ProtoMol::OutputFinalXSC, ProtoMol::OutputFinalPSF, ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputScreen, ProtoMol::OutputPDBFramePos, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputFile, ProtoMol::OutputDCDTrajectory, ProtoMol::Output
- doRunCached()
: ProtoMol::OutputISGProperties, ProtoMol::OutputTemperatures, ProtoMol::OutputPaulTrap, ProtoMol::OutputMomentum, ProtoMol::OutputFile, ProtoMol::OutputEnergies, ProtoMol::OutputDihedrals, ProtoMol::OutputDiffusion
- doSearch()
: ProtoMol::HelpTextFactory
- doSecondHalfKick()
: ProtoMol::BBKIntegrator
- doSetParameters()
: ProtoMol::TimeForce, ProtoMol::ImproperSystemForce< TBoundaryConditions >, ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >, ProtoMol::Force, ProtoMol::DihedralSystemForce< TBoundaryConditions >, ProtoMol::CompareForce, ProtoMol::BondSystemForce< TBoundaryConditions >, ProtoMol::AngleSystemForce< TBoundaryConditions >
- dot()
: ProtoMol::Vector3D
- doUncache()
: ProtoMol::PaulTrapIntegrator, ProtoMol::Integrator, ProtoMol::BSplineMOLLYIntegrator
- doUnregisterExemplar()
: ProtoMol::HelpTextFactory, ProtoMol::Factory< Type >
- doWrite()
: ProtoMol::OutputPaulTrap
- dSmooth()
: 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
- dSmoothKernel()
: 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
- dTheta
: ProtoMol::Hermite, ProtoMol::Lagrange, ProtoMol::BSpline
- DYNAMIC
: ProtoMol::ParallelEnum
- 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
- Eangle
: ProtoMol::IMD::IMDEnergies
- Ebond
: ProtoMol::IMD::IMDEnergies
- Edihe
: ProtoMol::IMD::IMDEnergies
- Eelec
: ProtoMol::IMD::IMDEnergies
- Eimpr
: ProtoMol::IMD::IMDEnergies
- ElectricFieldSystemForce()
: ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >
- elementName
: ProtoMol::PDB::PDBAtom
- elementNum
: ProtoMol::PDB::PDBAtom
- elementType
: ProtoMol::PDB::PDBAtom
- emin
: ProtoMol::PAR::Hbond
- Empty
: ProtoMol::ConstraintValueEnum
- 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 >
- EMPTY
: ProtoMol::ConstraintValueEnum
- 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 >
- endr
: ProtoMol::Report::MyStreamer
- energies
: 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::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 >
- energy()
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- Enum
: ProtoMol::ExclusionEnum, ProtoMol::ParallelEnum, ProtoMol::ThermostatEnum, ProtoMol::InputPosVelEnum, ProtoMol::ValueEnum, ProtoMol::TimerStatistic, ProtoMol::ConstraintValueEnum, ProtoMol::BSplineEnum, ProtoMol::AbstractEnumType< T, noCase >
- Enum2ValueType()
: ProtoMol::ValueEnum::Enum2ValueType< e >
- enumerator
: 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 >, ProtoMol::NonbondedCutoffForce< TCellManager, TOneAtomPair, TForce, TImplForce >
- Enumerator
: ProtoMol::Topology< TBoundaryConditions, TCellManager >
- EnumeratorType
: 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 >, ProtoMol::NonbondedCutoffSystemForce< TCellManager, TOneAtomPair >, ProtoMol::NonbondedCutoffMollyForce< TCellManager, TOneAtomPair >, ProtoMol::NonbondedCutoffForce< TCellManager, TOneAtomPair, TForce, TImplForce >
- Epot
: ProtoMol::IMD::IMDEnergies
- epsilon
: ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
- epsilon14
: ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
- Epsilon_vel
: ProtoMol::XSC
- epsilonEnergy()
: ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
- equal()
: ProtoMol::Value
- equalConstraint()
: ProtoMol::Value
- equalType()
: ProtoMol::Value
- equalTypeAndConstraint()
: ProtoMol::Value
- EquilibriumMOLLYIntegrator()
: ProtoMol::EquilibriumMOLLYIntegrator
- error
: ProtoMol::Report::MyStreamer
- Eta
: ProtoMol::XSC
- Eta_vel
: ProtoMol::XSC
- EtaVol
: ProtoMol::XSC
- EtaVol_vel
: ProtoMol::XSC
- Etot
: ProtoMol::IMD::IMDEnergies
- 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
- Evdw
: ProtoMol::IMD::IMDEnergies
- excl
: ProtoMol::ExclusionPair
- exclude
: ProtoMol::GenericTopology
- ExclusionPair()
: ProtoMol::ExclusionPair
- exclusions
: ProtoMol::GenericTopology
- ExclusionTable()
: ProtoMol::ExclusionTable
- execute()
: ProtoMol::Modifier
- expfactor
: ProtoMol::MagneticDipoleForce
- ExtendedCompareForce()
: ProtoMol::ExtendedCompareForce
- ExtendedForce()
: ProtoMol::ExtendedForce
- ExtendedTimeForce()
: ProtoMol::ExtendedTimeForce
- ExternalGravitationSystemForce()
: ProtoMol::ExternalGravitationSystemForce
- ExternalMagneticFieldExtendedForce()
: ProtoMol::ExternalMagneticFieldExtendedForce
- 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
- FinalType
: ProtoMol::iSGIntegrator
- 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
- FIRST
: ProtoMol::ExclusionEnum, ProtoMol::ParallelEnum, ProtoMol::ThermostatEnum, ProtoMol::InputPosVelEnum, ProtoMol::ValueEnum, ProtoMol::TimerStatistic, ProtoMol::ScalarStructure, ProtoMol::ConstraintValueEnum, ProtoMol::BSplineEnum
- fitplane()
: ProtoMol::Vector3DBlock
- float4
: ProtoMol::DCDTrajectoryWriter, ProtoMol::DCDTrajectoryReader
- fluctuationLI()
: ProtoMol::LangevinImpulseIntegrator
- flushCache()
: ProtoMol::OutputFile
- footnote
: ProtoMol::PDB::PDBAtom
- Force
: ProtoMol::Force, ProtoMol::ValueEnum
- FORCE
: ProtoMol::ValueEnum
- forceConstant
: ProtoMol::Torsion, ProtoMol::Angle, ProtoMol::PAR::Improper, ProtoMol::PAR::Dihedral, ProtoMol::PAR::Angle, ProtoMol::PAR::Bond, ProtoMol::iSGPAR::Improper, ProtoMol::iSGPAR::Dihedral, ProtoMol::iSGPAR::Angle, ProtoMol::iSGPAR::Bond
- ForceFactoryDetails()
: ProtoMol::ForceFactoryDetails
- ForceGroup()
: ProtoMol::ForceGroup
- FORCES
: ProtoMol::TimerStatistic
- forces
: 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::IntegratorDefinition, ProtoMol::IntegratorFactoryDetails::IntegratorInput, 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 >
- forward()
: ProtoMol::Integrator, ProtoMol::FFTComplex, ProtoMol::FFTInternal
- friction()
: ProtoMol::NoseNVTLeapfrogIntegrator
- FrictionExtendedForce()
: ProtoMol::FrictionExtendedForce
- GenericTopology()
: ProtoMol::GenericTopology
- get()
: ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >, ProtoMol::InputValue< TBase, type, constraint >, ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder, ProtoMol::PPM, ProtoMol::PGM, ProtoMol::Configuration
- get_haptics()
: ProtoMol::IMDElf
- getActualTime()
: ProtoMol::Timer
- getAlias()
: ProtoMol::Makeable
- getAliases()
: ProtoMol::Configuration
- getAngle()
: ProtoMol::AngleInfo
- getAngleType()
: ProtoMol::AngleInfo
- getAtomID()
: ProtoMol::AngleInfo
- getAutofit()
: ProtoMol::XFigWriter
- getAvailableId()
: ProtoMol::Parallel
- getAvailableNum()
: ProtoMol::Parallel
- getAveDeltaMu()
: ProtoMol::iSGIntegrator
- getAxes()
: ProtoMol::XFigWriter
- getbackbonedihedrals()
: ProtoMol::OutputDihedrals
- getBlue()
: ProtoMol::PPM, ProtoMol::PGM
- getBond()
: ProtoMol::AngleInfo
- getBottomTimestep()
: ProtoMol::Integrator
- getBoundaryConditionsBox()
: ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::GenericTopology
- getBoundingbox()
: ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::GenericTopology
- getCellSize()
: ProtoMol::CubicCellManager
- getCellVolume()
: ProtoMol::CubicCellManager
- getCharmmType()
: ProtoMol::PARWriter
- getCharmmTypeDetected()
: ProtoMol::iSGPARReader, ProtoMol::PARReader
- getColor()
: ProtoMol::XFigWriter
- getComment()
: ProtoMol::Reader
- getConstraintType()
: ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder
- getConstraintTypeString()
: ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder
- getCounter()
: ProtoMol::Cycles
- getCurrentTime()
: ProtoMol::Timer
- getCycles()
: ProtoMol::Cycles
- getDeepForces()
: ProtoMol::WrapperMetaForce, ProtoMol::MetaForce
- getDeepMetaForces()
: ProtoMol::ForceGroup
- getDefaults()
: ProtoMol::VacuumBoundaryConditions, ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::PeriodicBoundaryConditions, ProtoMol::GenericTopology
- getDefinition()
: ProtoMol::ForceGroup, ProtoMol::Makeable
- getDefinitionTypeString()
: ProtoMol::Value
- getdihedralsfromatomset()
: ProtoMol::OutputDihedrals
- getDimX()
: ProtoMol::ArrayCellListStructure
- getDimY()
: ProtoMol::ArrayCellListStructure
- getDimZ()
: ProtoMol::ArrayCellListStructure
- getElement()
: ProtoMol::Stack< T >
- getEnergies()
: ProtoMol::CompareForce
- getEnergy()
: 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
- getEnum()
: ProtoMol::AbstractEnumType< T, noCase >
- getEpsilonVel()
: ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::ModifierNPTShake< TIntegrator >, ProtoMol::ModifierNPTShakeDetails, ProtoMol::ModifierNPTRattle< TIntegrator >, ProtoMol::ModifierNPTRattleDetails
- getEtaVel()
: ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::ModifierNVTShake< TIntegrator >, ProtoMol::ModifierNVTShakeDetails, ProtoMol::ModifierNVTRattle< TIntegrator >, ProtoMol::ModifierNVTRattleDetails, ProtoMol::ModifierNPTShake< TIntegrator >, ProtoMol::ModifierNPTShakeDetails, ProtoMol::ModifierNPTRattle< TIntegrator >, ProtoMol::ModifierNPTRattleDetails
- getFilename()
: ProtoMol::File
- getFirstStep()
: ProtoMol::Output
- getForceGroup()
: ProtoMol::Integrator
- getForceKeyword()
: 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
- getForceObject()
: ProtoMol::CompareForce
- getForces()
: ProtoMol::Integrator, ProtoMol::ForceGroup, ProtoMol::CompareForce
- getFromZ()
: ProtoMol::XFigWriter
- getGreen()
: ProtoMol::PPM, ProtoMol::PGM
- getId()
: 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::UniversalSwitchingFunction, ProtoMol::ShiftSwitchingFunction, ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::CutoffSwitchingFunction, ProtoMol::ComplementSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction, ProtoMol::Parallel, 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::CoulombMultiGridDirectTableForce< TKernel >, ProtoMol::CoulombMultiGridDirectForce< TKernel >, ProtoMol::CoulombForce, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::CoulombEwaldRealForce, ProtoMol::Makeable
- getIdentity()
: ProtoMol::Matrix3by3
- getIdNoAlias()
: ProtoMol::iSGIntegrator, ProtoMol::OutputISGProperties, ProtoMol::OutputFinalXSC, ProtoMol::OutputFinalPSF, 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::Topology< TBoundaryConditions, TCellManager >, ProtoMol::UmbrellaIntegrator, ProtoMol::ShadowHMCIntegrator, ProtoMol::PLeapfrogIntegrator, ProtoMol::PaulTrapIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::NoseNVTLeapfrogIntegrator, ProtoMol::LeapfrogIntegrator, ProtoMol::LangevinImpulseIntegrator, ProtoMol::ImpulseIntegrator, ProtoMol::HMCIntegrator, ProtoMol::EquilibriumMOLLYIntegrator, ProtoMol::DMDLeapfrogIntegrator, ProtoMol::DLMCIntegrator, ProtoMol::DihedralHMCIntegrator, ProtoMol::BSplineMOLLYIntegrator, ProtoMol::BBKIntegrator, ProtoMol::HapticSystemForce, ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputTemperatures, ProtoMol::OutputScreen, ProtoMol::OutputPDBFramePos, ProtoMol::OutputPaulTrap, ProtoMol::OutputMomentum, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputEnergies, ProtoMol::OutputDihedrals, ProtoMol::OutputDiffusion, ProtoMol::OutputDCDTrajectory, ProtoMol::WrapperMetaForce, 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::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, ProtoMol::ImproperSystemForce< TBoundaryConditions >, ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >, ProtoMol::FrictionExtendedForce, ProtoMol::ExternalMagneticFieldExtendedForce, ProtoMol::ExternalGravitationSystemForce, ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >, ProtoMol::DihedralSystemForce< TBoundaryConditions >, ProtoMol::CompareForce, ProtoMol::BondSystemForce< TBoundaryConditions >, ProtoMol::AngleSystemForce< TBoundaryConditions >, ProtoMol::Makeable
- getIdNumber()
: ProtoMol::TimeForce, ProtoMol::CompareForce
- getInitialTemperature()
: ProtoMol::MCIntegrator
- getIntegratorDefinition()
: ProtoMol::Integrator
- getIntegratorDefinitionAll()
: ProtoMol::Integrator
- getKeyword()
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::iSGImproperSystemForce< TBoundaryConditions >, ProtoMol::iSGIdealGasCoulombForce::C4, ProtoMol::iSGIdealGasCoulombForce::C3, ProtoMol::iSGIdealGasCoulombForce::C2, ProtoMol::iSGIdealGasCoulombForce::C1, ProtoMol::iSGDihedralSystemForce< TBoundaryConditions >, ProtoMol::iSGCoulombForce::C4, ProtoMol::iSGCoulombForce::C3, ProtoMol::iSGCoulombForce::C2, ProtoMol::iSGCoulombForce::C1, ProtoMol::iSGBondSystemForce< TBoundaryConditions >, ProtoMol::iSGAngleSystemForce< TBoundaryConditions >, ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions, ProtoMol::GenericTopology, ProtoMol::CubicCellManager, ProtoMol::HapticSystemForce, ProtoMol::WrapperMetaForce, 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::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, ProtoMol::ImproperSystemForce< TBoundaryConditions >, ProtoMol::Hermite, ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >, ProtoMol::FrictionExtendedForce, ProtoMol::Force, ProtoMol::ExternalMagneticFieldExtendedForce, ProtoMol::ExternalGravitationSystemForce, ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >, ProtoMol::DihedralSystemForce< TBoundaryConditions >, ProtoMol::CoulombForce::C4, ProtoMol::CoulombForce::C3, ProtoMol::CoulombForce::C2, ProtoMol::CoulombForce::C1, ProtoMol::CompareForce, ProtoMol::BondSystemForce< TBoundaryConditions >, ProtoMol::AngleSystemForce< TBoundaryConditions >, ProtoMol::Lagrange, ProtoMol::BSpline
- getLapTime()
: ProtoMol::Timer
- getLastStep()
: ProtoMol::Output
- getLegend()
: ProtoMol::XFigWriter
- getline()
: ProtoMol::File
- getMasterId()
: ProtoMol::Parallel
- getMax()
: ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
- getMaxPackages()
: ProtoMol::Parallel
- getMin()
: ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
- getMode()
: ProtoMol::Parallel
- getNext()
: ProtoMol::OutputCollection, ProtoMol::Output
- getNum()
: ProtoMol::Parallel
- getNumAtoms()
: ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
- getNumberOfPackages()
: ProtoMol::Parallel
- getNumElements()
: ProtoMol::Stack< T >
- getOrder()
: ProtoMol::Hermite, ProtoMol::Lagrange, ProtoMol::BSpline
- getOutputFreq()
: ProtoMol::Output
- getParameters()
: ProtoMol::iSGIntegrator, ProtoMol::OutputISGProperties, ProtoMol::OutputFinalXSC, ProtoMol::OutputFinalPSF, 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::iSGLennardJonesTableForce, ProtoMol::iSGLennardJonesForce, ProtoMol::iSGImproperSystemForce< TBoundaryConditions >, ProtoMol::iSGIdealGasLennardJonesForce, ProtoMol::iSGIdealGasCoulombForce, ProtoMol::iSGDihedralSystemForce< TBoundaryConditions >, ProtoMol::iSGCoulombForce, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::iSGCoulombEwaldRealForce, ProtoMol::iSGBondSystemForce< TBoundaryConditions >, ProtoMol::iSGAngleSystemForce< TBoundaryConditions >, ProtoMol::VacuumBoundaryConditions, ProtoMol::UniversalSwitchingFunction, ProtoMol::Topology< TBoundaryConditions, TCellManager >, ProtoMol::ShiftSwitchingFunction, ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::PeriodicBoundaryConditions, ProtoMol::CutoffSwitchingFunction, ProtoMol::CubicCellManager, ProtoMol::ComplementSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction, ProtoMol::UmbrellaIntegrator, ProtoMol::STSIntegrator, ProtoMol::ShadowHMCIntegrator, ProtoMol::PaulTrapIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::NoseNVTLeapfrogIntegrator, ProtoMol::MTSIntegrator, ProtoMol::MCIntegrator, ProtoMol::LangevinImpulseIntegrator, ProtoMol::DMDLeapfrogIntegrator, ProtoMol::DihedralHMCIntegrator, ProtoMol::BSplineMOLLYIntegrator, ProtoMol::BBKIntegrator, ProtoMol::HapticSystemForce, ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputTemperatures, ProtoMol::OutputScreen, ProtoMol::OutputPDBFramePos, ProtoMol::OutputPaulTrap, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputFile, ProtoMol::OutputEnergies, ProtoMol::OutputDihedrals, ProtoMol::OutputDCDTrajectory, ProtoMol::WrapperMetaForce, ProtoMol::TimeForce, ProtoMol::SphericalSystemForce, 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::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::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, ProtoMol::MagneticDipoleForce, ProtoMol::LennardJonesTableForce, ProtoMol::LennardJonesForce, ProtoMol::ImproperSystemForce< TBoundaryConditions >, ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >, ProtoMol::GravitationForce, ProtoMol::FrictionExtendedForce, ProtoMol::ExternalMagneticFieldExtendedForce, ProtoMol::ExternalGravitationSystemForce, ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >, ProtoMol::DihedralSystemForce< TBoundaryConditions >, ProtoMol::CoulombMultiGridDirectTableForce< TKernel >, ProtoMol::CoulombMultiGridDirectForce< TKernel >, ProtoMol::CoulombForce, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::CoulombEwaldRealForce, ProtoMol::CompareForce, ProtoMol::BondSystemForce< TBoundaryConditions >, ProtoMol::AngleSystemForce< TBoundaryConditions >, ProtoMol::Makeable
- getParameterSize()
: ProtoMol::iSGIntegrator, ProtoMol::OutputISGProperties, ProtoMol::OutputFinalXSC, ProtoMol::OutputFinalPSF, 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::iSGLennardJonesTableForce, ProtoMol::iSGLennardJonesForce, ProtoMol::iSGImproperSystemForce< TBoundaryConditions >, ProtoMol::iSGIdealGasLennardJonesForce, ProtoMol::iSGIdealGasCoulombForce, ProtoMol::iSGDihedralSystemForce< TBoundaryConditions >, ProtoMol::iSGCoulombForce, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::iSGCoulombEwaldRealForce, ProtoMol::iSGBondSystemForce< TBoundaryConditions >, ProtoMol::iSGAngleSystemForce< TBoundaryConditions >, ProtoMol::VacuumBoundaryConditions, ProtoMol::UniversalSwitchingFunction, ProtoMol::Topology< TBoundaryConditions, TCellManager >, ProtoMol::ShiftSwitchingFunction, ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::PeriodicBoundaryConditions, ProtoMol::CutoffSwitchingFunction, ProtoMol::CubicCellManager, ProtoMol::ComplementSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction, ProtoMol::UmbrellaIntegrator, ProtoMol::ShadowHMCIntegrator, ProtoMol::PLeapfrogIntegrator, ProtoMol::PaulTrapIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::NoseNVTLeapfrogIntegrator, ProtoMol::MTSIntegrator, ProtoMol::LeapfrogIntegrator, ProtoMol::LangevinImpulseIntegrator, ProtoMol::HMCIntegrator, ProtoMol::DMDLeapfrogIntegrator, ProtoMol::DLMCIntegrator, ProtoMol::DihedralHMCIntegrator, ProtoMol::BSplineMOLLYIntegrator, ProtoMol::BBKIntegrator, ProtoMol::HapticSystemForce, ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputTemperatures, ProtoMol::OutputScreen, ProtoMol::OutputPDBFramePos, ProtoMol::OutputPaulTrap, ProtoMol::OutputMomentum, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputEnergies, ProtoMol::OutputDihedrals, ProtoMol::OutputDiffusion, ProtoMol::OutputDCDTrajectory, ProtoMol::WrapperMetaForce, ProtoMol::TimeForce, ProtoMol::SphericalSystemForce, 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::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::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, ProtoMol::MagneticDipoleForce, ProtoMol::LennardJonesTableForce, ProtoMol::LennardJonesForce, ProtoMol::ImproperSystemForce< TBoundaryConditions >, ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >, ProtoMol::GravitationForce, ProtoMol::FrictionExtendedForce, ProtoMol::ExternalMagneticFieldExtendedForce, ProtoMol::ExternalGravitationSystemForce, ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >, ProtoMol::DihedralSystemForce< TBoundaryConditions >, ProtoMol::CoulombMultiGridDirectTableForce< TKernel >, ProtoMol::CoulombMultiGridDirectForce< TKernel >, ProtoMol::CoulombForce, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::CoulombEwaldRealForce, ProtoMol::CompareForce, ProtoMol::BondSystemForce< TBoundaryConditions >, ProtoMol::AngleSystemForce< TBoundaryConditions >, ProtoMol::Makeable
- getPDB()
: ProtoMol::PDBReader
- getPipeSize()
: ProtoMol::Parallel
- getPointer()
: ProtoMol::AngleInfo
- getPossibleValues()
: ProtoMol::AbstractEnumType< T, noCase >
- getPostfixId()
: ProtoMol::DebugPostConstraint, ProtoMol::DebugPreConstraint, ProtoMol::NotSameMoleculeConstraint, ProtoMol::SameMoleculeConstraint, ProtoMol::HBondConstraint, ProtoMol::NoConstraint
- getPrefixId()
: ProtoMol::DebugPostConstraint, ProtoMol::DebugPreConstraint, ProtoMol::NotSameMoleculeConstraint, ProtoMol::SameMoleculeConstraint, ProtoMol::HBondConstraint, ProtoMol::NoConstraint
- getProcessTime()
: ProtoMol::TimeRep
- getPrototype()
: ProtoMol::FactoryBase< Type >
- getQ()
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- getRadius()
: ProtoMol::XFigWriter
- getRealCellSize()
: ProtoMol::CubicCellManager
- getRealTime()
: ProtoMol::TimeRep
- getRed()
: ProtoMol::PPM, ProtoMol::PGM
- GetRefArray()
: ProtoMol::Array< T, N >
- getScope()
: ProtoMol::GenericTopology, ProtoMol::Integrator, ProtoMol::Output, ProtoMol::Force, ProtoMol::Makeable
- getString()
: ProtoMol::Value, ProtoMol::AbstractEnumType< T, noCase >
- getSystemTime()
: ProtoMol::TimeRep
- getTable()
: ProtoMol::ExclusionTable
- getText()
: ProtoMol::Makeable, ProtoMol::Configuration
- getTime()
: ProtoMol::Timer
- getTimestep()
: ProtoMol::STSIntegrator, ProtoMol::MTSIntegrator, ProtoMol::ModifierShake, ProtoMol::ModifierRattle, ProtoMol::ModifierNVTShake< TIntegrator >, ProtoMol::ModifierNVTRattle< TIntegrator >, ProtoMol::ModifierNPTShake< TIntegrator >, ProtoMol::ModifierNPTRattle< TIntegrator >, ProtoMol::ModifierMetaRattleShake, ProtoMol::Integrator
- getToZ()
: ProtoMol::XFigWriter
- getTransformation()
: ProtoMol::XFigWriter
- getType()
: ProtoMol::InputPosVel, ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder
- getTypeString()
: ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder
- getUserTime()
: ProtoMol::TimeRep
- getV()
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- getVolume()
: ProtoMol::VacuumBoundaryConditions, ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::PeriodicBoundaryConditions, ProtoMol::GenericTopology
- getWorkState()
: ProtoMol::Parallel
- getXSC()
: ProtoMol::iSGIntegrator
- getXYZ()
: ProtoMol::XYZTrajectoryReader, ProtoMol::XYZReader, ProtoMol::XYZBinReader, ProtoMol::DCDTrajectoryReader
- got_alphaLJ
: ProtoMol::TRANSReader
- gotoEndPair()
: ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
- GravitationForce()
: ProtoMol::GravitationForce
- greater()
: ProtoMol::Value
- greaterEqual()
: ProtoMol::Value
- Grid()
: ProtoMol::Grid< TInterpolation >
- h
: ProtoMol::TripleInt, ProtoMol::PPM, ProtoMol::PGM
- H
: ProtoMol::ReducedHessAngle
- HapticSystemForce()
: ProtoMol::HapticSystemForce
- harmCalcTorsion()
: ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >
- HarmDihedralSystemForce()
: ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >
- Hbond
: ProtoMol::PAR::Hbond, ProtoMol::iSGPAR
- HBOND
: ProtoMol::iSGPARReader, ProtoMol::PARReader
- hbonds
: ProtoMol::PAR, ProtoMol::iSGPAR
- hdf
: ProtoMol::UmbrellaIntegrator, ProtoMol::DLMCIntegrator
- height()
: ProtoMol::PPM, ProtoMol::PGM
- HelpTextFactory()
: ProtoMol::HelpTextFactory
- HelpTextMapType
: ProtoMol::HelpTextFactory
- Hermite()
: ProtoMol::Hermite
- hessian()
: ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction
- Hessian
: ProtoMol::ReducedHessTraits< CoulombForce >, ProtoMol::ReducedHessTraits< LennardJonesForce >
- high
: ProtoMol::IMD::netint
- highDeltas
: ProtoMol::ExclusionTable
- highest
: ProtoMol::IMD::netint
- hint
: ProtoMol::Report::MyStreamer
- HMCIntegrator()
: ProtoMol::HMCIntegrator
- Holder()
: ProtoMol::Value::Holder< ValueTrait, Constraint >
- holder
: ProtoMol::Value::Holder< ValueTrait, Constraint >
- hookup()
: ProtoMol::IMDElf
- hvyAtom
: ProtoMol::Atom
- hvyAtomGrpsize
: ProtoMol::PDB::PDBAtom
- i
: ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
- i1
: ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond
- i2
: ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond
- iAmMaster()
: ProtoMol::Parallel
- iAmSlave()
: ProtoMol::Parallel
- id
: ProtoMol::HelpText, ProtoMol::ObjectDefinition, ProtoMol::MakeableDefinition
- IDEAL_GAS_DELTAMU
: ProtoMol::TRANSReader
- IDENTITIES
: ProtoMol::TRANSReader
- identity
: ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3, ProtoMol::PSF::Atom
- IDLE
: ProtoMol::TimerStatistic
- im
: zomplex
- IMDElf()
: ProtoMol::IMDElf
- Improper()
: ProtoMol::PSF::Improper, ProtoMol::PAR::Improper, ProtoMol::iSGPAR::Improper
- IMPROPER
: ProtoMol::iSGPARReader, ProtoMol::PARReader, ProtoMol::ScalarStructure
- IMPROPER_DELTAMU
: ProtoMol::ScalarStructure
- improperList
: ProtoMol::Molecule
- impropers
: ProtoMol::ModifierISG, ProtoMol::GenericTopology, ProtoMol::PSF, ProtoMol::PAR, ProtoMol::iSGPAR
- ImpulseIntegrator()
: ProtoMol::ImpulseIntegrator
- INCR_SIZE
: ProtoMol::Stack< T >
- incrCoord()
: ProtoMol::UmbrellaIntegrator
- Index
: ProtoMol::ScalarStructure
- 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 >
- insertionCode
: ProtoMol::PDB::PDBAtom
- instance()
: ProtoMol::Parallel, ProtoMol::HelpTextFactory, ProtoMol::Factory< Type >
- INT
: ProtoMol::ValueEnum
- int32
: ProtoMol::DCDTrajectoryWriter, ProtoMol::DCDTrajectoryReader
- int_type
: std::stringbuf
- INTEGRATOR
: ProtoMol::ValueEnum, ProtoMol::TimerStatistic, ProtoMol::ScalarStructure
- integrator
: ProtoMol::IntegratorDefinition
- 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
- ISG
: ProtoMol::XSCReader
- iSGCoulombEwaldRealForce()
: ProtoMol::iSGCoulombEwaldRealForce
- iSGCoulombEwaldRealTableForce()
: ProtoMol::iSGCoulombEwaldRealTableForce
- iSGGrid()
: ProtoMol::iSGGrid< TInterpolation >
- iSGIdealGasLennardJonesForce()
: ProtoMol::iSGIdealGasLennardJonesForce
- iSGIntegrator()
: ProtoMol::iSGIntegrator
- iSGLennardJonesForce()
: ProtoMol::iSGLennardJonesForce
- iSGLennardJonesTableForce()
: ProtoMol::iSGLennardJonesTableForce
- isgLJParms
: ProtoMol::GenericTopology
- iSGmodifierIndex
: ProtoMol::Torsion, ProtoMol::Bond, ProtoMol::Angle
- 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 >
- iSGNumMols
: ProtoMol::GenericTopology
- 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
- isMPI
: ProtoMol::Parallel
- 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
- iterator
: ProtoMol::ArrayCellListStructure, ProtoMol::OutputCollection, ProtoMol::HelpTextFactory, 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 >
- k
: ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >, ProtoMol::TripleInt
- k_ub
: ProtoMol::PAR::Angle, ProtoMol::iSGPAR::Angle
- kappa
: ProtoMol::MagneticDipoleForce
- kbT
: ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
- kernel()
: 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
- kernelR()
: 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
- keyword
: ProtoMol::iSGIntegrator, ProtoMol::OutputISGProperties, ProtoMol::OutputFinalXSC, ProtoMol::OutputFinalPSF, ProtoMol::iSGNonbondedPMEwaldSystemForceBase, ProtoMol::iSGNonbondedFullEwaldSystemForceBase, ProtoMol::iSGLennardJonesTableForce, ProtoMol::iSGLennardJonesForce, ProtoMol::iSGImproperSystemForceBase, ProtoMol::iSGIdealGasLennardJonesForce, ProtoMol::iSGIdealGasCoulombForce, ProtoMol::iSGIdealGasCoulombForce::C4, ProtoMol::iSGIdealGasCoulombForce::C3, ProtoMol::iSGIdealGasCoulombForce::C2, ProtoMol::iSGIdealGasCoulombForce::C1, ProtoMol::iSGDihedralSystemForceBase, ProtoMol::iSGCoulombForce, ProtoMol::iSGCoulombForce::C4, ProtoMol::iSGCoulombForce::C3, ProtoMol::iSGCoulombForce::C2, ProtoMol::iSGCoulombForce::C1, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::iSGCoulombEwaldRealForce, ProtoMol::iSGBondSystemForceBase, ProtoMol::iSGAngleSystemForceBase, ProtoMol::VacuumBoundaryConditions, ProtoMol::UniversalSwitchingFunctionBase, ProtoMol::ShiftSwitchingFunctionBase, ProtoMol::RangeSwitchingFunctionBase, ProtoMol::PeriodicBoundaryConditions, ProtoMol::GenericTopology, ProtoMol::CutoffSwitchingFunctionBase, ProtoMol::CubicCellManager, ProtoMol::ComplementSwitchingFunctionBase, ProtoMol::C2SwitchingFunctionBase, ProtoMol::C1SwitchingFunctionBase, ProtoMol::UmbrellaIntegrator, ProtoMol::ShadowHMCIntegrator, ProtoMol::PLeapfrogIntegrator, ProtoMol::PaulTrapIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::NoseNVTLeapfrogIntegrator, ProtoMol::LeapfrogIntegrator, ProtoMol::LangevinImpulseIntegrator, ProtoMol::ImpulseIntegrator, ProtoMol::HMCIntegrator, ProtoMol::EquilibriumMOLLYIntegrator, ProtoMol::DMDLeapfrogIntegrator, ProtoMol::DLMCIntegrator, ProtoMol::DihedralHMCIntegrator, ProtoMol::BSplineMOLLYIntegrator, ProtoMol::BBKIntegrator, HapticSystemForceBase, ProtoMol::HapticSystemForce, ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputTemperatures, ProtoMol::OutputScreen, ProtoMol::OutputPDBFramePos, ProtoMol::OutputPaulTrap, ProtoMol::OutputMomentum, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputEnergies, ProtoMol::OutputDihedrals, ProtoMol::OutputDiffusion, ProtoMol::OutputDCDTrajectory, ProtoMol::InputReducedImageIdentifier, ProtoMol::InputRattleMaxIterIdentifier, ProtoMol::InputRattleEpsilonIdentifier, ProtoMol::InputRattleIdentifier, ProtoMol::InputShakeMaxIterIdentifier, ProtoMol::InputShakeEpsilonIdentifier, ProtoMol::InputShakeIdentifier, ProtoMol::InputMolVirialCalcIdentifier, ProtoMol::InputVirialCalcIdentifier, ProtoMol::InputDihedralMultPSFIdentifier, ProtoMol::InputCellManagerIdentifier, ProtoMol::InputBoundaryConditionsIdentifier, ProtoMol::InputPDBScalingIdentifier, ProtoMol::InputMaxPackagesIdentifier, ProtoMol::InputParallelModeIdentifier, ProtoMol::InputParallelPipeIdentifier, ProtoMol::InputUseBarrierIdentifier, ProtoMol::InputRemoveAngularMomentumIdentifier, ProtoMol::InputRemoveLinearMomentumIdentifier, ProtoMol::InputPARIdentifier, ProtoMol::InputPSFIdentifier, ProtoMol::InputVelocitiesIdentifier, ProtoMol::InputPositionsIdentifier, ProtoMol::InputIntegratorIdentifier, ProtoMol::InputOutputfreqIdentifier, ProtoMol::InputNumstepsIdentifier, ProtoMol::InputFirststepIdentifier, ProtoMol::InputConfigIdentifier, ProtoMol::InputSeedIdentifier, ProtoMol::InputTemperatureIdentifier, ProtoMol::InputDebugIdentifier, ProtoMol::InputOutputIdentifier, ProtoMol::WrapperMetaForce, ProtoMol::TimeForce, ProtoMol::SphericalSystemForce, ProtoMol::PaulTrapExtendedForceBase, ProtoMol::NonbondedSimpleFullSystemForceBase, ProtoMol::NonbondedPMEwaldSystemForceBase, ProtoMol::NonbondedMultiGridSystemForceBase, ProtoMol::NonbondedFullSystemForceBase, ProtoMol::NonbondedFullEwaldSystemForceBase, ProtoMol::NonbondedCutoffForceBase, ProtoMol::MagneticDipoleMirrorSystemForceBase, ProtoMol::MagneticDipoleForce, ProtoMol::LennardJonesTableForce, ProtoMol::LennardJonesForce, ProtoMol::ImproperSystemForceBase, ProtoMol::Hermite, ProtoMol::HarmDihedralSystemForceBase, ProtoMol::GravitationForce, ProtoMol::FrictionExtendedForce, ProtoMol::ExternalMagneticFieldExtendedForce, ProtoMol::ExternalGravitationSystemForce, ProtoMol::ElectricFieldSystemForceBase, ProtoMol::DihedralSystemForceBase, ProtoMol::CoulombMultiGridDirectTableForceBase, ProtoMol::CoulombMultiGridDirectForceBase, ProtoMol::CoulombForce, ProtoMol::CoulombForce::C4, ProtoMol::CoulombForce::C3, ProtoMol::CoulombForce::C2, ProtoMol::CoulombForce::C1, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::CoulombEwaldRealForce, ProtoMol::CompareForce, ProtoMol::BondSystemForceBase, ProtoMol::AngleSystemForceBase, ProtoMol::Parameter, ProtoMol::Lagrange, ProtoMol::BSpline
- keywords()
: ProtoMol::HelpTextFactory
- kill()
: ProtoMol::Parallel, ProtoMol::HelpTextFactory, ProtoMol::Factory< Type >
- kineticEnergy()
: ProtoMol::OutputCache
- l
: ProtoMol::TripleInt
- l12
: ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond
- L_ALT_LOC
: ProtoMol::PDB::PDBAtom
- L_ATOM_NAME
: ProtoMol::PDB::PDBAtom
- L_CHAIN_ID
: ProtoMol::PDB::PDBAtom
- L_CHARGE
: ProtoMol::PDB::PDBAtom
- L_ELEMENT_SYMBOL
: ProtoMol::PDB::PDBAtom
- L_FOOT_NOTE
: ProtoMol::PDB::PDBAtom
- L_I_CODE
: ProtoMol::PDB::PDBAtom
- L_OCCUP
: ProtoMol::PDB::PDBAtom
- L_RECORD_NAME
: ProtoMol::PDB::PDBAtom
- L_RES_NAME
: ProtoMol::PDB::PDBAtom
- L_RES_SEQ
: ProtoMol::PDB::PDBAtom
- L_SEG_ID
: ProtoMol::PDB::PDBAtom
- L_SERIAL
: ProtoMol::PDB::PDBAtom
- L_TEMP
: ProtoMol::PDB::PDBAtom
- L_X
: ProtoMol::PDB::PDBAtom
- L_Y
: ProtoMol::PDB::PDBAtom
- L_Z
: ProtoMol::PDB::PDBAtom
- Lagrange()
: ProtoMol::Lagrange
- lambda
: ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond, ProtoMol::Molecule
- Lambda
: ProtoMol::XSC
- Lambda_vel
: ProtoMol::XSC
- LangevinImpulseIntegrator()
: ProtoMol::LangevinImpulseIntegrator
- lap()
: ProtoMol::Timer
- LAST
: ProtoMol::ExclusionEnum, ProtoMol::ParallelEnum, ProtoMol::ThermostatEnum, ProtoMol::InputPosVelEnum, ProtoMol::ValueEnum, ProtoMol::TimerStatistic, ProtoMol::ScalarStructure, ProtoMol::ConstraintValueEnum, ProtoMol::BSplineEnum
- LASTREDUCE
: ProtoMol::ScalarStructure
- lattice
: ProtoMol::iSGOneAtomPairTwoFull< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::iSGOneAtomPairFull< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::OneAtomPairTwoFull< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::OneAtomPairFull< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >
- LeapfrogIntegrator()
: ProtoMol::LeapfrogIntegrator
- Length
: ProtoMol::PDB::PDBAtom
- length
: ProtoMol::IMD::IMDheader
- LENNARDJONES
: ProtoMol::ScalarStructure
- LENNARDJONES_DELTAMU
: ProtoMol::ScalarStructure
- lennardJonesBank
: ProtoMol::BankLennardJonesParameterTable
- lennardJonesParameters
: ProtoMol::GenericTopology
- LennardJonesParameters()
: ProtoMol::LennardJonesParameters
- LennardJonesParameterTable()
: ProtoMol::LennardJonesParameterTable
- LennardJonesTableForce()
: ProtoMol::LennardJonesTableForce
- less()
: ProtoMol::Value
- lessEqual()
: ProtoMol::Value
- level()
: ProtoMol::Integrator
- lift
: ProtoMol::DLMCIntegrator
- LIMIT
: ProtoMol::Vector3DBlock
- linearMomentum()
: ProtoMol::OutputCache
- listen()
: ProtoMol::IMDElf
- LONG
: ProtoMol::BSplineEnum
- longRangeTerm()
: ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >
- low
: ProtoMol::IMD::netint
- lowDeltas
: ProtoMol::ExclusionTable
- lowest
: ProtoMol::IMD::netint
- luBksb()
: ProtoMol::EquilibriumMOLLYIntegrator
- luDcmp()
: ProtoMol::EquilibriumMOLLYIntegrator
- m00
: ProtoMol::Matrix3by3
- m01
: ProtoMol::Matrix3by3
- m02
: ProtoMol::Matrix3by3
- m10
: ProtoMol::Matrix3by3
- m11
: ProtoMol::Matrix3by3
- m12
: ProtoMol::Matrix3by3
- m20
: ProtoMol::Matrix3by3
- m21
: ProtoMol::Matrix3by3
- m22
: ProtoMol::Matrix3by3
- m_angle
: ProtoMol::AngleInfo
- m_angleType
: ProtoMol::AngleInfo
- m_atomID
: ProtoMol::AngleInfo
- m_bondedAtoms
: ProtoMol::AngleInfo
- m_Dimensions
: ProtoMol::ArraySizes, ProtoMol::ArraySize< N >
- m_elem
: ProtoMol::Stack< T >
- m_isExclusionAtom
: ProtoMol::AngleInfo
- m_isInnerAtom
: ProtoMol::AngleInfo
- m_nArrayElements
: ProtoMol::Array< T, N >
- m_NDimensions
: ProtoMol::Array< T, N >, ProtoMol::RefArray< T, 1 >, ProtoMol::RefArray< T, N >
- m_numElements
: ProtoMol::Stack< T >
- m_pArrayElements
: ProtoMol::Array< T, N >
- m_pElements
: ProtoMol::Array< T, N >::RefArray< 1 >, ProtoMol::Array< T, N >::RefArray< N >, ProtoMol::RefArray< T, 1 >, ProtoMol::RefArray< T, N >
- m_pNDimensions
: ProtoMol::Array< T, N >::RefArray< 1 >, ProtoMol::Array< T, N >::RefArray< N >
- m_pointer
: ProtoMol::AngleInfo
- m_pSubArrayLen
: ProtoMol::Array< T, N >::RefArray< N >
- m_size
: ProtoMol::Stack< T >
- m_SubArrayLen
: ProtoMol::Array< T, N >, ProtoMol::RefArray< T, N >
- m_TheSubArray
: ProtoMol::Array< T, N >
- m_visited
: ProtoMol::AngleInfo
- 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
- MASTER
: ProtoMol::Parallel
- MASTERSLAVE
: ProtoMol::ParallelEnum
- Matrix3by3()
: ProtoMol::Matrix3by3
- max
: ProtoMol::GenericTopology
- maxGDim
: ProtoMol::EquilibriumMOLLYIntegrator
- MCIntegrator()
: ProtoMol::MCIntegrator
- mediForceModify()
: ProtoMol::Integrator
- MetaForce()
: ProtoMol::MetaForce
- metropolisTest()
: ProtoMol::MCIntegrator, ProtoMol::DihedralHMCIntegrator
- min
: ProtoMol::GenericTopology
- minimalDifference()
: ProtoMol::VacuumBoundaryConditions, ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::PeriodicBoundaryConditions, ProtoMol::GenericTopology
- minimalImage()
: ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::GenericTopology
- minimalMolecularDistances
: ProtoMol::GenericTopology
- minimalPosition()
: ProtoMol::VacuumBoundaryConditions, ProtoMol::SemiGenericTopology< TBoundaryConditions >, ProtoMol::PeriodicBoundaryConditions, ProtoMol::GenericTopology
- minimalTranslationDifference()
: ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
- minimalTranslationPosition()
: ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
- mode
: std::stringbuf
- 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
- molecule
: ProtoMol::Atom
- molecules
: ProtoMol::GenericTopology
- mollification()
: ProtoMol::MOLLYIntegrator
- MollyForce()
: ProtoMol::MollyForce
- MOLLYIntegrator()
: ProtoMol::MOLLYIntegrator
- MOLVIRIALXX
: ProtoMol::ScalarStructure
- MOLVIRIALXY
: ProtoMol::ScalarStructure
- MOLVIRIALXZ
: ProtoMol::ScalarStructure
- MOLVIRIALYX
: ProtoMol::ScalarStructure
- MOLVIRIALYY
: ProtoMol::ScalarStructure
- MOLVIRIALYZ
: ProtoMol::ScalarStructure
- MOLVIRIALZX
: ProtoMol::ScalarStructure
- MOLVIRIALZY
: ProtoMol::ScalarStructure
- MOLVIRIALZZ
: ProtoMol::ScalarStructure
- momentum
: ProtoMol::Molecule
- MTSIntegrator
: ProtoMol::MTSIntegrator, ProtoMol::StandardIntegrator
- MultiGrid()
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- multiplicity
: ProtoMol::Torsion, ProtoMol::PAR::Dihedral, ProtoMol::iSGPAR::Dihedral
- multiply()
: ProtoMol::Vector3D
- my05Cutoff_3
: ProtoMol::C1SwitchingFunction
- my15Cutoff_1
: ProtoMol::C1SwitchingFunction
- my15Cutoff_3
: ProtoMol::C1SwitchingFunction
- my2AlphaPI
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::iSGCoulombEwaldRealForce, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::CoulombEwaldRealForce
- my4Cutoff_2
: ProtoMol::ShiftSwitchingFunction
- myA
: ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >, ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >
- myAbort
: ProtoMol::Report::MyStreamer
- myAccuracy
: 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 >
- myActualForce
: ProtoMol::TimeForce, ProtoMol::CompareForce
- myAlias
: ProtoMol::Makeable
- myAliases
: ProtoMol::Configuration
- myAliasExemplars
: ProtoMol::FactoryBase< Type >
- myAllNodes
: ProtoMol::Report::MyStreamer
- myAllNodesSerial
: ProtoMol::Report::MyStreamer
- myAllSlavesSerial
: ProtoMol::Report::MyStreamer
- myAlpha
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::iSGCoulombEwaldRealForce, ProtoMol::iSGGrid< TInterpolation >, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::CoulombEwaldRealForce, ProtoMol::Grid< TInterpolation >
- myAlphaDefault
: 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 >
- myAlphaR04
: ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
- myAlphaSquared
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::iSGCoulombEwaldRealForce, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::CoulombEwaldRealForce
- myAlphaSquaredr
: 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 >
- myAngle
: ProtoMol::BSplineMOLLYIntegrator
- myAngleFilter
: ProtoMol::BSplineMOLLYIntegrator, ProtoMol::OneMollyPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond >, ProtoMol::OneMollyPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce >
- myAngleIndexes
: ProtoMol::BSplineMOLLYIntegrator
- myAngles
: ProtoMol::DihedralHMCIntegrator
- myAnglesSet
: ProtoMol::DihedralHMCIntegrator
- myAngularMomentum
: ProtoMol::OutputCache
- myArray
: ProtoMol::ArrayCellListStructure, ProtoMol::FFTInternal
- myAtomCount
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myAtoms
: ProtoMol::XYZTrajectoryWriter, ProtoMol::PDBReader
- myAtomTypes
: ProtoMol::XYZTrajectoryWriter
- myAutofit
: ProtoMol::XFigWriter
- myAvailableId
: ProtoMol::Parallel
- myAvailableNum
: ProtoMol::Parallel
- myAveragedPositions
: ProtoMol::EquilibriumMOLLYIntegrator
- myAxes
: ProtoMol::XFigWriter
- myB
: ProtoMol::BSplineMOLLYIntegrator, ProtoMol::ExternalMagneticFieldExtendedForce
- myBathPosition
: ProtoMol::PaulTrapIntegrator, ProtoMol::NoseNVTLeapfrogIntegrator
- myBathVelocity
: ProtoMol::PaulTrapIntegrator
- myBegin
: ProtoMol::ArrayCellListStructure
- myBeginConst
: ProtoMol::ArrayCellListStructure
- myBeta
: ProtoMol::ShadowHMCIntegrator
- myBlockList
: ProtoMol::Parallel
- myBlocksCorrection
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myBlockSize
: ProtoMol::NonbondedSimpleFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedFullSystemForce< TOneAtomPair >
- myBond
: ProtoMol::BSplineMOLLYIntegrator
- mybonds
: ProtoMol::Atom
- myBrentMaxima
: ProtoMol::OutputCache
- myBuffer
: ProtoMol::Parallel, ProtoMol::OutputFile
- myBxAngle
: ProtoMol::BSplineMOLLYIntegrator
- myC
: ProtoMol::ShadowHMCIntegrator, ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >
- myCache
: ProtoMol::OutputCollection, ProtoMol::Output, ProtoMol::FactoryBase< Type >
- myCached
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::PaulTrapIntegrator, ProtoMol::BSplineMOLLYIntegrator, ProtoMol::HapticSystemForce, 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 >
- myCachedAngularMomentum
: ProtoMol::OutputCache
- myCachedBrentMaxima
: ProtoMol::OutputCache
- myCachedCenterOfMass
: ProtoMol::OutputCache
- myCachedDensity
: ProtoMol::OutputCache
- myCachedDiffusion
: ProtoMol::OutputCache
- myCachedDihedralPhi
: ProtoMol::OutputCache
- myCachedDihedralPhis
: ProtoMol::OutputCache
- myCachedKE
: ProtoMol::OutputCache
- myCachedLinearMomentum
: ProtoMol::OutputCache
- myCachedMass
: ProtoMol::OutputCache
- myCachedMolKE
: ProtoMol::OutputCache
- myCachedMolP
: ProtoMol::OutputCache
- myCachedMolT
: ProtoMol::OutputCache
- myCachedNonWaterT
: ProtoMol::OutputCache
- myCachedP
: ProtoMol::OutputCache
- myCachedPE
: ProtoMol::OutputCache
- myCachedV
: ProtoMol::OutputCache
- myCachedWaterT
: ProtoMol::OutputCache
- myCacheFreq
: ProtoMol::OutputFile
- myCacheSize
: ProtoMol::OutputFile
- myCellListStruct
: ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
- myCellSize
: ProtoMol::CubicCellManager, ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >, ProtoMol::ArrayCellListStructure
- myCenter
: ProtoMol::HapticSystemForce, ProtoMol::SphericalSystemForce
- myCenterOfMass
: ProtoMol::OutputCache
- myChargedSystemDeltaMu
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myChargedSystemEnergy
: 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 >
- myCharmmType
: ProtoMol::iSGPARReader, ProtoMol::PARWriter, ProtoMol::PARReader
- myCharmmTypeDetected
: ProtoMol::iSGPARReader, ProtoMol::PARReader
- myChi
: ProtoMol::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, ProtoMol::MagneticDipoleForce
- myCloseTime
: ProtoMol::OutputFile
- myCMax
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myCMin
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myColor
: ProtoMol::XFigWriter
- myComment
: ProtoMol::File
- myCompareForce
: ProtoMol::CompareForce
- myCompareForcename
: ProtoMol::CompareForce
- myConfig
: ProtoMol::ConfigurationReader, ProtoMol::OutputCollection, ProtoMol::OutputCache, ProtoMol::Output
- myConfstrings
: ProtoMol::OutputDihedrals
- myCoords
: ProtoMol::XYZTrajectoryWriter, ProtoMol::XYZTrajectoryReader, ProtoMol::XYZReader, ProtoMol::XYZBinReader, ProtoMol::PDBReader, ProtoMol::DCDTrajectoryReader
- myCoulomb
: ProtoMol::BSplineMOLLYIntegrator
- myCount
: ProtoMol::PaulTrapIntegrator, ProtoMol::OutputFile, ProtoMol::Proxy
- myCounter
: ProtoMol::TimeForce, ProtoMol::CompareForce
- myCurrentSize
: ProtoMol::LennardJonesParameterTable
- myCutoff
: ProtoMol::ShiftSwitchingFunction, ProtoMol::CutoffSwitchingFunction, ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction, ProtoMol::NonbondedFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedCutoffForce< TCellManager, TOneAtomPair, TForce, TImplForce >
- myCutoff2
: ProtoMol::ShiftSwitchingFunction, ProtoMol::CutoffSwitchingFunction, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction
- myCutoff_2
: ProtoMol::ShiftSwitchingFunction
- myCutoff_3
: ProtoMol::C1SwitchingFunction
- myCycleLength
: ProtoMol::MTSIntegrator
- myD
: ProtoMol::PeriodicBoundaryConditions, ProtoMol::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, ProtoMol::MagneticDipoleForce
- myData
: ProtoMol::LennardJonesParameterTable
- myDCD
: ProtoMol::OutputDihedrals, ProtoMol::OutputDCDTrajectory
- myDeltaList
: ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
- myDeltaMuIG
: ProtoMol::iSGIntegrator
- myDensity
: ProtoMol::OutputCache
- myDhmcAnSetFile
: ProtoMol::DihedralHMCIntegrator
- myDhmcDiSetFile
: ProtoMol::DihedralHMCIntegrator
- myDiffusion
: ProtoMol::OutputCache
- myDihedral
: ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >
- myDihedralIndex
: ProtoMol::DihedralHMCIntegrator, ProtoMol::OutputDihedrals
- myDihedralPhi
: ProtoMol::OutputCache
- myDihedralPhis
: ProtoMol::OutputCache
- myDihedralReference
: ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >
- myDihedrals
: ProtoMol::DihedralHMCIntegrator, ProtoMol::OutputDihedrals
- myDihedralsSet
: ProtoMol::DihedralHMCIntegrator, ProtoMol::OutputDihedrals
- myDihedralsSetfile
: ProtoMol::OutputDihedrals
- myDim
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myDissipativeCutoff
: ProtoMol::DMDLeapfrogIntegrator
- myDissipativeForces
: ProtoMol::DMDLeapfrogIntegrator
- myDMU_FFT
: ProtoMol::iSGGrid< TInterpolation >
- myDMU_LastSinCos
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myDMU_Q
: ProtoMol::iSGGrid< TInterpolation >
- myDMU_QTmp
: ProtoMol::iSGGrid< TInterpolation >
- myDMU_SinCos
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myDMU_SinCosA
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myDMuIG
: ProtoMol::iSGIntegrator
- myDoHint
: ProtoMol::Report::MyStreamer
- myDoMolecularTemperature
: ProtoMol::OutputISGProperties, ProtoMol::OutputEnergies
- myDoMolecularVirial
: ProtoMol::ScalarStructure
- myDone
: ProtoMol::Parallel
- myDoOutput
: ProtoMol::ScalarStructure
- myDoPaulLow
: ProtoMol::OutputPaulTrap
- myDoShadow
: ProtoMol::OutputEnergies
- myDoVirial
: ProtoMol::ScalarStructure
- myDX
: ProtoMol::PeriodicBoundaryConditions
- myDY
: ProtoMol::PeriodicBoundaryConditions
- myDZ
: ProtoMol::PeriodicBoundaryConditions
- myE
: ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >
- myE1
: ProtoMol::PeriodicBoundaryConditions
- myE1r
: ProtoMol::PeriodicBoundaryConditions
- myE2
: ProtoMol::PeriodicBoundaryConditions
- myE2r
: ProtoMol::PeriodicBoundaryConditions
- myE3
: ProtoMol::PeriodicBoundaryConditions
- myE3r
: ProtoMol::PeriodicBoundaryConditions
- myEnable
: ProtoMol::Modifier
- myEnd
: ProtoMol::ArrayCellListStructure
- myEndConst
: ProtoMol::ArrayCellListStructure
- myEndTime
: ProtoMol::Cycles
- myEnergies
: ProtoMol::Modifier, ProtoMol::Integrator, ProtoMol::OutputCollection, ProtoMol::OutputCache, ProtoMol::Output, ProtoMol::CompareForce
- myEpsilon
: ProtoMol::ModifierMetaRattleShake
- myEpsilonVel
: ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator
- myERFTable
: ProtoMol::iSGCoulombEwaldRealTableForce
- myErrors
: ProtoMol::CompareForce
- myEta
: ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
- myEtaV
: ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator
- myEtaVel
: ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
- myEtaVolVel
: ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator
- myExemplars
: ProtoMol::HelpTextFactory, ProtoMol::FactoryBase< Type >
- myExpansionFactor
: 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 >
- myExpX
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myExpY
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myExpZ
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myExtendedForcesList
: ProtoMol::ForceGroup
- myF
: ProtoMol::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, ProtoMol::FrictionExtendedForce
- myFac
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::iSGLennardJonesTableForce, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::iSGGrid< TInterpolation >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::LennardJonesTableForce, ProtoMol::CoulombMultiGridDirectTableForce< TKernel >, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::Grid< TInterpolation >
- myFactor
: ProtoMol::OutputScreen, ProtoMol::OutputPaulTrap
- myFFT
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myFFTCoeff
: ProtoMol::FFTInternal
- myFFTInternal
: ProtoMol::FFTComplex
- myFile
: ProtoMol::File, ProtoMol::OutputFile
- myFilename
: ProtoMol::OutputFinalXSC, ProtoMol::OutputFinalPSF, ProtoMol::File, ProtoMol::OutputPDBFramePos, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputFile, ProtoMol::InputPosVel
- myFilenameLow
: ProtoMol::OutputPaulTrap
- myFinalized
: ProtoMol::Parallel
- myFirst
: ProtoMol::XYZTrajectoryWriter, ProtoMol::XYZTrajectoryReader, ProtoMol::DCDTrajectoryWriter, ProtoMol::DCDTrajectoryReader, ProtoMol::Output
- myFirstStep
: ProtoMol::DCDTrajectoryWriter, ProtoMol::Output
- myForcename
: ProtoMol::TimeForce, ProtoMol::CompareForce
- myForces
: ProtoMol::Modifier, ProtoMol::Integrator, ProtoMol::WrapperMetaForce, ProtoMol::CompareForce
- myForcesToEvaluate
: ProtoMol::Integrator
- myForceTypes
: ProtoMol::ForceFactoryDetails
- myForceTypesSorted
: ProtoMol::ForceFactoryDetails
- myForward
: ProtoMol::Integrator
- myFreq
: ProtoMol::ModifierRemoveLinearMomentum, ProtoMol::ModifierRemoveAngularMomentum
- myFromRange
: ProtoMol::NonbondedSimpleFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedFullSystemForce< TOneAtomPair >
- myFromZ
: ProtoMol::XFigWriter
- myFugacityFrac
: ProtoMol::iSGIntegrator
- myG
: ProtoMol::GravitationForce, ProtoMol::ExternalGravitationSystemForce
- myGamma
: ProtoMol::LangevinImpulseIntegrator, ProtoMol::DMDLeapfrogIntegrator, ProtoMol::BBKIntegrator
- myGCorrDimX
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myGCorrDimY
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myGCorrDimZ
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myGCorrection
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myGDirect
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myGrid
: ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >
- myGridInterpolation
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myH
: ProtoMol::PeriodicBoundaryConditions, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myH2
: ProtoMol::PeriodicBoundaryConditions
- myHapticForces
: ProtoMol::HapticSystemForce
- myHBondForces
: ProtoMol::BSplineMOLLYIntegrator
- myHeight
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myHeightr
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myHKLmax
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myHmax
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myHx
: ProtoMol::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, ProtoMol::MagneticDipoleForce
- myHX
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- myHXr
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- myHy
: ProtoMol::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, ProtoMol::MagneticDipoleForce
- myHY
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- myHydrogenAtomGroups
: ProtoMol::EquilibriumMOLLYIntegrator
- myHydrogenConstraintGroups
: ProtoMol::EquilibriumMOLLYIntegrator
- myHYr
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- myHZ
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- myHz
: ProtoMol::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, ProtoMol::MagneticDipoleForce
- myHZr
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- myI
: ProtoMol::Parallel
- myIAmMaster
: ProtoMol::Parallel, ProtoMol::Report::MyStreamer
- myIAmSlave
: ProtoMol::Parallel
- myId
: ProtoMol::Parallel
- myIdNumber
: ProtoMol::TimeForce, ProtoMol::CompareForce
- myIMDElf
: ProtoMol::HapticSystemForce
- myInerpolationModX
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myInerpolationModY
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myInerpolationModZ
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myInitialized
: ProtoMol::Parallel
- myInitialPositions
: ProtoMol::OutputCache
- myInitialTemperature
: ProtoMol::MCIntegrator, ProtoMol::DihedralHMCIntegrator
- myIntegrator
: ProtoMol::OutputCollection, ProtoMol::OutputCache, ProtoMol::Output
- myInterOrder
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGGrid< TInterpolation >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::Hermite, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Lagrange, ProtoMol::Grid< TInterpolation >, ProtoMol::BSpline
- myInterpolations
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- myISGGrid
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >
- myiSGPAR
: ProtoMol::OutputCache
- myIsLittleEndian
: ProtoMol::XYZBinWriter, ProtoMol::DCDTrajectoryWriter
- myIsParallel
: ProtoMol::Parallel, ProtoMol::TimerStatistic
- myJ
: ProtoMol::SphericalSystemForce
- myK
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::SphericalSystemForce, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myKc
: 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 >
- myKE
: ProtoMol::OutputCache
- myKeep
: ProtoMol::PaulTrapIntegrator
- myKInt
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myKmax
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myKSquared
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myLambda
: ProtoMol::iSGIntegrator
- myLambdaVel
: ProtoMol::iSGIntegrator
- myLangevinTemperature
: ProtoMol::LangevinImpulseIntegrator, ProtoMol::BBKIntegrator
- myLapTime
: ProtoMol::Timer
- myLastCompareForce
: ProtoMol::ForceFactoryDetails
- myLastLapTime
: ProtoMol::Timer
- myLastPositions
: ProtoMol::ModifierMetaRattleShake
- myLastSinCos
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myLastStep
: ProtoMol::Output
- myLattice
: 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::NonbondedFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myLayer
: ProtoMol::PaulTrapIntegrator
- myLegend
: ProtoMol::XFigWriter
- myLength
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myLengthr
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myLennardJones
: ProtoMol::BSplineMOLLYIntegrator
- myLevel
: ProtoMol::Report::MyStreamer, ProtoMol::Report::debug
- myLevels
: ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myLinearMomentum
: ProtoMol::OutputCache
- myListModifiers
: ProtoMol::Integrator
- myListOfConstraints
: ProtoMol::ModifierMetaRattleShake
- myLmax
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- mylnMassRatio
: ProtoMol::iSGIntegrator
- myLowComment
: ProtoMol::OutputPaulTrap
- myLowOut
: ProtoMol::OutputPaulTrap
- myLowXYZ
: ProtoMol::OutputPaulTrap
- myLX
: 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 >
- myLXr
: 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 >
- myLY
: 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 >
- myLYr
: 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 >
- myLZ
: 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 >
- myLZr
: 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 >
- myMass
: ProtoMol::OutputCache
- myMasterId
: ProtoMol::Parallel
- myMat
: ProtoMol::XFigWriter
- myMax
: ProtoMol::PeriodicBoundaryConditions, ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myMaxDelta
: ProtoMol::ExclusionTable
- myMaximas
: ProtoMol::OutputDihedrals
- myMaxIter
: ProtoMol::ModifierMetaRattleShake
- myMaxNX
: ProtoMol::ArrayCellListStructure
- myMaxNX1
: ProtoMol::ArrayCellListStructure
- myMaxNY
: ProtoMol::ArrayCellListStructure
- myMaxNY1
: ProtoMol::ArrayCellListStructure
- myMaxNZ
: ProtoMol::ArrayCellListStructure
- myMaxNZ1
: ProtoMol::ArrayCellListStructure
- myMaxPackages
: ProtoMol::Parallel
- myMediForceModifiers
: ProtoMol::Integrator
- myMetaForcesList
: ProtoMol::ForceGroup
- myMin
: ProtoMol::PeriodicBoundaryConditions, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myMinimal
: ProtoMol::WrapperMetaForce
- myMinimas
: ProtoMol::OutputDihedrals
- myMode
: ProtoMol::Parallel, ProtoMol::File
- myModifier1
: ProtoMol::ShadowHMCIntegrator
- myModifier2
: ProtoMol::ShadowHMCIntegrator
- myMolecule
: ProtoMol::XSC
- myMolKE
: ProtoMol::OutputCache
- myMOLLYEnergies
: ProtoMol::BSplineMOLLYIntegrator
- myMOLLYForces
: ProtoMol::BSplineMOLLYIntegrator
- myMOLLYForcesBonded
: ProtoMol::BSplineMOLLYIntegrator
- myMOLLYForcesHBonded
: ProtoMol::BSplineMOLLYIntegrator
- myMollyForcesList
: ProtoMol::ForceGroup
- myMOLLYPositions
: ProtoMol::BSplineMOLLYIntegrator
- myMOLLYStepsize
: ProtoMol::EquilibriumMOLLYIntegrator, ProtoMol::BSplineMOLLYIntegrator
- myMOLLYStepsizeP
: ProtoMol::BSplineMOLLYIntegrator
- myMOLLYStepsizeSquare
: ProtoMol::BSplineMOLLYIntegrator
- myMOLLYVelocities
: ProtoMol::BSplineMOLLYIntegrator
- myMolP
: ProtoMol::OutputCache
- myMolT
: ProtoMol::OutputCache
- myN
: ProtoMol::iSGLennardJonesTableForce, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::LennardJonesTableForce, ProtoMol::CoulombMultiGridDirectTableForce< TKernel >, ProtoMol::CoulombEwaldRealTableForce
- myNames
: ProtoMol::XYZTrajectoryWriter, ProtoMol::XYZTrajectoryReader, ProtoMol::XYZReader
- myNext
: ProtoMol::Parallel
- myNextIntegrator
: ProtoMol::MTSIntegrator
- myNextRange
: ProtoMol::Parallel
- myNextStep
: ProtoMol::Output
- myNonWaterAtomTypes
: ProtoMol::OutputTemperatures
- myNonWaterT
: ProtoMol::OutputCache
- myNum
: ProtoMol::Parallel
- myNumComp
: ProtoMol::iSGIntegrator
- myNumFree
: ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
- myNumIter
: ProtoMol::DMDLeapfrogIntegrator, ProtoMol::BSplineMOLLYIntegrator
- myNumParameters
: ProtoMol::UmbrellaIntegrator, ProtoMol::HMCIntegrator, ProtoMol::DLMCIntegrator
- myNumStages
: ProtoMol::iSGIntegrator
- myNX
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGGrid< TInterpolation >, ProtoMol::ArrayCellListStructure, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >, ProtoMol::FFTInternal
- myNX1
: ProtoMol::ArrayCellListStructure
- myNXOffset
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- myNY
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGGrid< TInterpolation >, ProtoMol::ArrayCellListStructure, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >, ProtoMol::FFTInternal
- myNY1
: ProtoMol::ArrayCellListStructure
- myNYOffset
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- myNZ
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGGrid< TInterpolation >, ProtoMol::ArrayCellListStructure, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >, ProtoMol::FFTInternal
- myNZ1
: ProtoMol::ArrayCellListStructure
- myNZOffset
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- myOk
: ProtoMol::InputPosVel
- myOldAtomCount
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myOldEnergies
: ProtoMol::MCIntegrator, ProtoMol::DihedralHMCIntegrator
- myOldForces
: ProtoMol::ShadowHMCIntegrator
- myOldHKLmax
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myOldKineticEnergy
: ProtoMol::MCIntegrator
- myOldPositions
: ProtoMol::MCIntegrator, ProtoMol::DihedralHMCIntegrator
- myOldVelocities
: ProtoMol::MCIntegrator, ProtoMol::DihedralHMCIntegrator
- myOmega
: ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >, ProtoMol::MagneticDipoleForce
- myOmegaR
: ProtoMol::OutputPaulTrap, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
- myOmegaR1
: ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
- myOmegaTo
: ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
- myOmegaTv
: ProtoMol::NPTVerletIntegrator
- myOmegaZ
: ProtoMol::OutputPaulTrap, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
- myOmegaZ1
: ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
- myOneAtomPair
: ProtoMol::NonbondedSimpleFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedCutoffForce< TCellManager, TOneAtomPair, TForce, TImplForce >
- myOrder
: ProtoMol::ShadowHMCIntegrator, ProtoMol::Modifier
- myOrigFunc
: ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::ComplementSwitchingFunction< TOriginalSwitchingFunction >
- myOrigin
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::PeriodicBoundaryConditions, 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::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myOrthogonal
: ProtoMol::PeriodicBoundaryConditions
- myOutputFreq
: ProtoMol::Output
- myOutputList
: ProtoMol::OutputCollection
- myP
: ProtoMol::Parallel, ProtoMol::OutputCache
- myPAR
: ProtoMol::iSGPARReader, ProtoMol::PARReader, ProtoMol::OutputCache
- myParameters
: ProtoMol::WrapperMetaForce
- myParameterSize
: ProtoMol::WrapperMetaForce
- myPart
: ProtoMol::PaulTrapIntegrator
- myPartReal
: ProtoMol::PaulTrapIntegrator
- myPaulA
: ProtoMol::OutputPaulTrap
- myPaulF
: ProtoMol::OutputPaulTrap, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
- myPaulF2
: ProtoMol::OutputPaulTrap
- myPaulK
: ProtoMol::OutputPaulTrap
- myPaulLow
: ProtoMol::OutputPaulTrap
- myPaulM
: ProtoMol::OutputPaulTrap
- myPaulOmega
: ProtoMol::OutputPaulTrap
- myPaulQ
: ProtoMol::OutputPaulTrap
- myPaulR
: ProtoMol::OutputPaulTrap
- myPaulUHom
: ProtoMol::OutputPaulTrap, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
- myPDBAtoms
: ProtoMol::OutputCache
- myPE
: ProtoMol::OutputCache
- myPGM
: ProtoMol::PGMReader
- myPhi
: ProtoMol::MagneticDipoleForce
- myPipeSize
: ProtoMol::Parallel
- myPointers
: ProtoMol::FactoryBase< Type >
- myPointSelfDeltaMu
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- myPointSelfEnergy
: 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 >
- myPort
: ProtoMol::HapticSystemForce
- myPositions
: ProtoMol::Modifier, ProtoMol::Integrator, ProtoMol::OutputCollection, ProtoMol::OutputCache, ProtoMol::Output
- myPostDriftOrNextModifiers
: ProtoMol::Integrator
- myPostForceModifiers
: ProtoMol::Integrator
- myPostStepModifiers
: ProtoMol::Integrator
- myPPM
: ProtoMol::PPMReader
- myPreDriftOrNextModifiers
: ProtoMol::Integrator
- myPreForceModifiers
: ProtoMol::Integrator
- myPreStepModifiers
: ProtoMol::Integrator
- myPrevBeta
: ProtoMol::ShadowHMCIntegrator
- myPreviousIntegrator
: ProtoMol::StandardIntegrator
- myPrevPositions
: ProtoMol::ShadowHMCIntegrator
- myPrevVelocities
: ProtoMol::ShadowHMCIntegrator
- myPSF
: ProtoMol::PSFReader, ProtoMol::OutputCache
- myPxAngle
: ProtoMol::BSplineMOLLYIntegrator
- myQ
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- myQTmp
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myQuit
: ProtoMol::Report::MyStreamer
- myR
: ProtoMol::MagneticDipoleMirrorSystemForce< TBoundaryConditions >, ProtoMol::MagneticDipoleForce
- myR0
: ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
- myR0Squared
: ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >
- myR1
: ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >
- myR1Squared
: ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >
- myRadius
: ProtoMol::XFigWriter, ProtoMol::SphericalSystemForce
- myRadius2
: ProtoMol::SphericalSystemForce
- myRandomCycLen
: ProtoMol::MCIntegrator, ProtoMol::DihedralHMCIntegrator
- myRandomForces
: ProtoMol::DMDLeapfrogIntegrator
- myRatio
: ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myRc
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::iSGLennardJonesTableForce, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::LennardJonesTableForce, ProtoMol::CoulombEwaldRealTableForce
- myRcSquared
: 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 >
- myRealCellSize
: ProtoMol::CubicCellManager
- myRealRCellSize
: ProtoMol::CubicCellManager
- myRealTime
: ProtoMol::TimeRep
- myRecv
: ProtoMol::Parallel
- myRemoveAngularMotion
: ProtoMol::PaulTrapIntegrator
- myRemoveCommonMotion
: ProtoMol::PaulTrapIntegrator
- myReportlevel
: ProtoMol::Report::reportlevel
- myReportLevel
: ProtoMol::Report::MyStreamer
- myResetFlags
: ProtoMol::Report::MyStreamer
- myRnd
: ProtoMol::FrictionExtendedForce
- myRS
: ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::CoulombMultiGridDirectTableForce< TKernel >, ProtoMol::CoulombMultiGridDirectForce< TKernel >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myRunningFlag
: ProtoMol::Timer, ProtoMol::Cycles
- myS
: ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >, ProtoMol::CoulombMultiGridDirectTableForce< TKernel >, ProtoMol::CoulombMultiGridDirectForce< TKernel >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myS2
: ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >
- myScale
: ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- myScaledParticleIntPositions
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >, ProtoMol::Grid< TInterpolation >
- myScreen
: ProtoMol::OutputPaulTrap
- mySeed
: ProtoMol::LangevinImpulseIntegrator, ProtoMol::DMDLeapfrogIntegrator, ProtoMol::BBKIntegrator
- mySeparateWater
: ProtoMol::OutputTemperatures
- mySet
: ProtoMol::ExclusionTable
- myShadowK
: ProtoMol::ShadowHMCIntegrator
- myShadowKover2
: ProtoMol::ShadowHMCIntegrator
- mySigma
: ProtoMol::DMDLeapfrogIntegrator, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >
- mySilentHint
: ProtoMol::Report::MyStreamer
- mySinCos
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- mySinCosA
: ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- mySize
: ProtoMol::ArrayCellListStructure, ProtoMol::XYZBinWriter
- mySquaredCutoff
: ProtoMol::iSGOneAtomPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::iSGOneAtomPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::OneAtomPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::OneAtomPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >
- myStartTime
: ProtoMol::Timer, ProtoMol::Cycles
- myStep
: ProtoMol::ModifierRemoveLinearMomentum, ProtoMol::ModifierRemoveAngularMomentum
- myStepCounter
: ProtoMol::HapticSystemForce
- myStepInc
: ProtoMol::HapticSystemForce
- myStream
: ProtoMol::Report::MyStreamer
- MyStreamer()
: ProtoMol::Report::MyStreamer
- mySumMass
: ProtoMol::NoseNVTLeapfrogIntegrator
- mySwapEndian
: ProtoMol::DCDTrajectoryReader
- mySwapPositions
: ProtoMol::MOLLYIntegrator
- mySwitch1
: ProtoMol::C2SwitchingFunction
- mySwitch2
: ProtoMol::C2SwitchingFunction
- mySwitch3
: ProtoMol::C2SwitchingFunction
- mySwitchon
: ProtoMol::C2SwitchingFunction
- mySwitchon2
: ProtoMol::C2SwitchingFunction
- mySystemForcesList
: ProtoMol::ForceGroup
- mySystemTime
: ProtoMol::TimeRep
- myT
: ProtoMol::PaulTrapIntegrator, ProtoMol::OutputCache
- myTable
: ProtoMol::iSGLennardJonesTableForce, ProtoMol::iSGCoulombEwaldRealTableForce, ProtoMol::ExclusionTable, ProtoMol::LennardJonesTableForce, ProtoMol::CoulombMultiGridDirectTableForce< TKernel >, ProtoMol::CoulombEwaldRealTableForce, ProtoMol::ScalarStructure
- myTargetDeltaMu
: ProtoMol::iSGIntegrator
- myTargetKE
: ProtoMol::NoseNVTLeapfrogIntegrator
- myTargetMu
: ProtoMol::iSGIntegrator
- myTargetPres
: ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator
- myTargetTemp
: ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
- myTauD
: ProtoMol::iSGIntegrator
- myTauP
: ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator
- myTauT
: ProtoMol::iSGIntegrator
- myTauV
: ProtoMol::iSGIntegrator
- myTemperature
: ProtoMol::PaulTrapIntegrator, ProtoMol::NoseNVTLeapfrogIntegrator, ProtoMol::DMDLeapfrogIntegrator
- myTempForces
: ProtoMol::PLeapfrogIntegrator
- myTexts
: ProtoMol::Configuration
- myTheIntegrator
: ProtoMol::ModifierISG, ProtoMol::iSGModifierPreForceChemostat, ProtoMol::iSGModifierPostForceChemostat, ProtoMol::ModifierUpdateBetaAndPush, ProtoMol::ModifierUpdateBeta, ProtoMol::ModifierShake, ProtoMol::ModifierRattle, ProtoMol::ModifierPreForceThermostat< TIntegrator >, ProtoMol::ModifierPreForceBarostat< TIntegrator >, ProtoMol::ModifierPostForceThermostat< TIntegrator >, ProtoMol::ModifierPostForceBarostat< TIntegrator >, ProtoMol::ModifierNVTShake< TIntegrator >, ProtoMol::ModifierNVTRattle< TIntegrator >, ProtoMol::ModifierNPTShake< TIntegrator >, ProtoMol::ModifierNPTRattle< TIntegrator >, ProtoMol::ModifierMollification, ProtoMol::ModifierIncrementTimestep, ProtoMol::ModifierFriction, ProtoMol::ModifierAveraging
- myThermalInertia
: ProtoMol::PaulTrapIntegrator, ProtoMol::NoseNVTLeapfrogIntegrator
- myThermostatType
: ProtoMol::PaulTrapIntegrator
- myTime
: ProtoMol::PaulTrapIntegrator, ProtoMol::MCIntegrator
- myTimeList
: ProtoMol::TimeForce
- myTimer
: ProtoMol::OutputFile, ProtoMol::TimeForce
- myTimestep
: ProtoMol::STSIntegrator
- myTimeStep
: ProtoMol::DCDTrajectoryWriter
- myTopo
: ProtoMol::Integrator
- myTopology
: ProtoMol::Modifier, ProtoMol::OutputCollection, ProtoMol::OutputCache, ProtoMol::Output
- myToRange
: ProtoMol::NonbondedSimpleFullSystemForce< TOneAtomPair >, ProtoMol::NonbondedFullSystemForce< TOneAtomPair >
- myTotalTime
: ProtoMol::Timer
- myToZ
: ProtoMol::XFigWriter
- myTRANS
: ProtoMol::TRANSReader
- myTRate
: 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 >
- myType
: ProtoMol::InputPosVel, ProtoMol::AbstractEnumType< T, noCase >
- myTypeOfBSpline
: ProtoMol::BSplineMOLLYIntegrator
- myTypes
: ProtoMol::TRANSReader
- myU0
: ProtoMol::PaulTrapExtendedForce< TBoundaryConditions >
- myUnit
: ProtoMol::OutputScreen, ProtoMol::OutputPaulTrap
- myUseBarrier
: ProtoMol::Parallel
- myUserTime
: ProtoMol::TimeRep
- myV
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::iSGGrid< TInterpolation >, ProtoMol::PeriodicBoundaryConditions, ProtoMol::OutputCache, 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 >
- myValue
: ProtoMol::InputValue< TBase, type, constraint >, ProtoMol::Value
- myValues
: ProtoMol::Configuration
- myVector
: ProtoMol::Vector< T >, ProtoMol::VectorPacker< T, N >
- myVelocities
: ProtoMol::Modifier, ProtoMol::Integrator, ProtoMol::OutputCollection, ProtoMol::OutputCache, ProtoMol::Output
- myVhat
: ProtoMol::DMDLeapfrogIntegrator
- myVolume
: ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator
- myVr
: 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 >
- myWaterAtomTypes
: ProtoMol::OutputTemperatures
- myWaterT
: ProtoMol::OutputCache
- myWidth
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myWidthr
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- myWorkState
: ProtoMol::Parallel
- myX
: ProtoMol::DCDTrajectoryWriter, ProtoMol::DCDTrajectoryReader
- myXSCinfo
: ProtoMol::XSCReader
- myXxAngle
: ProtoMol::BSplineMOLLYIntegrator
- myXYZ
: ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryForce
- myY
: ProtoMol::DCDTrajectoryWriter, ProtoMol::DCDTrajectoryReader
- myZ
: ProtoMol::DCDTrajectoryWriter, ProtoMol::DCDTrajectoryReader
- N
: ProtoMol::iSGIntegrator
- name
: ProtoMol::iSGPAR::AtomType, ProtoMol::AtomType
- names
: ProtoMol::XYZ
- Nbfix
: ProtoMol::PAR::Nbfix, ProtoMol::iSGPAR
- NBFIX
: ProtoMol::iSGPARReader, ProtoMol::PARReader
- nbfixs
: ProtoMol::PAR, ProtoMol::iSGPAR
- negative
: ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
- Negative
: ProtoMol::ConstraintValueEnum
- NEGATIVE
: ProtoMol::ConstraintValueEnum
- negative2
: ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
- new_charge
: ProtoMol::ModifierISG::TransformMap, ProtoMol::TRANS::AtomType
- new_type
: ProtoMol::XSC
- NewType
: ProtoMol::iSGIntegrator
- newtype
: ProtoMol::Molecule
- 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()
: ProtoMol::PSF::Ngrp
- NoConstraints
: ProtoMol::ConstraintValueEnum
- NOCONSTRAINTS
: ProtoMol::ConstraintValueEnum
- Nonbonded()
: ProtoMol::PSF::Nonbonded, ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
- NONBONDED
: ProtoMol::iSGPARReader, ProtoMol::PARReader
- NonbondedCutoffForce()
: ProtoMol::NonbondedCutoffForce< TCellManager, TOneAtomPair, TForce, TImplForce >
- NonbondedCutoffMollyForce()
: ProtoMol::NonbondedCutoffMollyForce< TCellManager, TOneAtomPair >
- NonbondedCutoffSystemForce()
: ProtoMol::NonbondedCutoffSystemForce< TCellManager, TOneAtomPair >
- nonbondedForceFunction
: ProtoMol::iSGOneAtomPairFull< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::iSGOneAtomPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::OneMollyPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce >, ProtoMol::OneAtomPairFull< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::OneAtomPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >
- nonbondedForceFunctionFirst
: ProtoMol::iSGOneAtomPairTwoFull< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::iSGOneAtomPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::OneMollyPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond >, ProtoMol::OneAtomPairTwoFull< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::OneAtomPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >
- nonbondedForceFunctionSecond
: ProtoMol::iSGOneAtomPairTwoFull< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::iSGOneAtomPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::OneMollyPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond >, ProtoMol::OneAtomPairTwoFull< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >, ProtoMol::OneAtomPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond, TConstraint >
- NonbondedFullEwaldSystemForce()
: ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >
- NonbondedFullSystemForce()
: ProtoMol::NonbondedFullSystemForce< TOneAtomPair >
- nonbondedHessian
: ProtoMol::OneMollyPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce >
- nonbondedHessianFirst
: ProtoMol::OneMollyPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond >
- nonbondedHessianSecond
: ProtoMol::OneMollyPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond >
- NonbondedMultiGridSystemForce()
: ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >
- NonbondedPMEwaldSystemForce()
: ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >
- nonbondeds
: ProtoMol::PSF, ProtoMol::PAR, ProtoMol::iSGPAR
- NonbondedSimpleFullSystemForce()
: ProtoMol::NonbondedSimpleFullSystemForce< TOneAtomPair >
- NONE
: ProtoMol::ExclusionEnum
- NonStandardIntegrator()
: ProtoMol::NonStandardIntegrator
- norm()
: ProtoMol::Vector3D
- normalize()
: ProtoMol::Vector3D
- normalized()
: ProtoMol::Vector3D
- normSquared()
: ProtoMol::Vector3D
- NoseNVTLeapfrogIntegrator()
: ProtoMol::NoseNVTLeapfrogIntegrator
- NOT_VISITED
: ProtoMol::AngleInfo
- NotEmpty
: ProtoMol::ConstraintValueEnum
- NOTEMPTY
: ProtoMol::ConstraintValueEnum
- NotNegative
: ProtoMol::ConstraintValueEnum
- NOTNEGATIVE
: ProtoMol::ConstraintValueEnum
- NotPositive
: ProtoMol::ConstraintValueEnum
- NOTPOSITIVE
: ProtoMol::ConstraintValueEnum
- notSameCell()
: ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
- NotZero
: ProtoMol::ConstraintValueEnum
- NOTZERO
: ProtoMol::ConstraintValueEnum
- NPT
: ProtoMol::XSCReader
- NPTVerletIntegrator()
: ProtoMol::NPTVerletIntegrator
- NumAtoms
: ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
- number
: ProtoMol::PSF::Ngrp, ProtoMol::PSF::Nonbonded, ProtoMol::PSF::Acceptor, ProtoMol::PSF::Donor, ProtoMol::PSF::Improper, ProtoMol::PSF::Dihedral, ProtoMol::PSF::Angle, ProtoMol::PSF::Bond, ProtoMol::PSF::Atom, ProtoMol::PAR::Hbond, ProtoMol::PAR::Nbfix, ProtoMol::PAR::Nonbonded, ProtoMol::PAR::Improper, ProtoMol::PAR::Dihedral, ProtoMol::PAR::Angle, ProtoMol::PAR::Bond, ProtoMol::iSGPAR::Nonbonded, ProtoMol::iSGPAR::Improper, ProtoMol::iSGPAR::Dihedral, ProtoMol::iSGPAR::Angle, ProtoMol::iSGPAR::Bond
- 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 >
- NumberOfStages
: ProtoMol::TRANS
- numBonds()
: ProtoMol::AngleInfo
- numComp
: ProtoMol::iSGPARReader
- numComps
: ProtoMol::BankLennardJonesParameterTable
- numIdentities
: ProtoMol::TRANSReader
- NumMols
: ProtoMol::iSGIntegrator
- numStages
: ProtoMol::TRANSReader
- numTables
: ProtoMol::BankLennardJonesParameterTable
- NumTransSteps
: ProtoMol::iSGIntegrator
- numTypes
: ProtoMol::TRANSReader
- NVT
: ProtoMol::ThermostatEnum
- NVT_GLOBAL
: ProtoMol::ThermostatEnum
- NVT_IND
: ProtoMol::ThermostatEnum
- NVT_SHELL
: ProtoMol::ThermostatEnum
- NVT_ZERO
: ProtoMol::ThermostatEnum
- NVTLEAPFROG
: ProtoMol::XSCReader
- NVTVerletIntegrator()
: ProtoMol::NVTVerletIntegrator
- obj
: ProtoMol::Parallel, ProtoMol::HelpTextFactory, ProtoMol::Factory< Type >
- ObjectDefinition()
: ProtoMol::ObjectDefinition
- occupancy
: ProtoMol::PDB::PDBAtom
- off_type
: std::stringbuf
- ok
: ProtoMol::Parallel, ProtoMol::Value::Holder< ValueTrait, Constraint >
- old_charge
: ProtoMol::ModifierISG::TransformMap, ProtoMol::TRANS::AtomType
- old_type
: ProtoMol::XSC
- OldType
: ProtoMol::iSGIntegrator
- ONE2
: ProtoMol::ExclusionEnum
- ONE3
: ProtoMol::ExclusionEnum
- ONE4
: ProtoMol::ExclusionEnum
- ONE4MODIFIED
: ProtoMol::ExclusionEnum
- 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::Value
- 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::Value
- operator>=
: ProtoMol::Value
- operator>>
: ProtoMol::XSCReader, ProtoMol::TRANSReader, ProtoMol::iSGPARReader, ProtoMol::XYZTrajectoryReader, ProtoMol::XYZReader, ProtoMol::XYZBinReader, ProtoMol::PSFReader, ProtoMol::PPMReader, ProtoMol::PGMReader, ProtoMol::PDBReader, ProtoMol::PARReader, ProtoMol::DCDTrajectoryReader, ProtoMol::ConfigurationReader, ProtoMol::InputPosVel, ProtoMol::Vector3D, ProtoMol::Value
- 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
- OTHER
: ProtoMol::ScalarStructure
- ourIdentity
: ProtoMol::Matrix3by3
- 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
: ProtoMol::PPM, ProtoMol::PGM
- PairIntSorted()
: ProtoMol::PairIntSorted
- pairs
: ProtoMol::Molecule
- 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
- parameters
: ProtoMol::HelpText, ProtoMol::ObjectDefinition, ProtoMol::MakeableDefinition
- PARReader()
: ProtoMol::PARReader
- PARRecordTypeEnum
: ProtoMol::iSGPARReader, 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
- PERIODIC
: ProtoMol::VacuumBoundaryConditions, ProtoMol::PeriodicBoundaryConditions
- PeriodicBoundaryConditions()
: ProtoMol::PeriodicBoundaryConditions
- periodicCell()
: ProtoMol::ArrayCellListStructure
- periodicity
: ProtoMol::Torsion, ProtoMol::PAR::Improper, ProtoMol::PAR::Dihedral, ProtoMol::iSGPAR::Improper, ProtoMol::iSGPAR::Dihedral
- perturbSystem()
: ProtoMol::ShadowHMCIntegrator, ProtoMol::MCIntegrator, ProtoMol::HMCIntegrator, ProtoMol::DLMCIntegrator
- PGM()
: ProtoMol::PGM
- PGMReader()
: ProtoMol::PGMReader
- PGMWriter()
: ProtoMol::PGMWriter
- phaseShift
: ProtoMol::Torsion, ProtoMol::PAR::Improper, ProtoMol::PAR::Dihedral, ProtoMol::iSGPAR::Improper, ProtoMol::iSGPAR::Dihedral
- pickNewMolecule()
: ProtoMol::ModifierISG
- plain
: ProtoMol::Report::MyStreamer
- PLeapfrogIntegrator()
: ProtoMol::PLeapfrogIntegrator
- PNGWriter()
: ProtoMol::PNGWriter
- pointer
: ProtoMol::ArrayCellListStructure, 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 >
- polarizability
: ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
- polarizability2
: ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
- policies
: ProtoMol::ForceFactoryDetails::ForceType
- policiesSorted
: ProtoMol::ForceFactoryDetails::ForceType
- policy
: ProtoMol::ForceFactoryDetails::ForceType
- popElement()
: ProtoMol::Stack< T >
- port
: ProtoMol::IMDElf
- pos_type
: std::stringbuf
- position
: ProtoMol::Molecule
- positions
: 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::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 >
- Positive
: ProtoMol::ConstraintValueEnum
- POSITIVE
: ProtoMol::ConstraintValueEnum
- POST_CHECK
: ProtoMol::DebugPostConstraint, ProtoMol::DebugPreConstraint, ProtoMol::NotSameMoleculeConstraint, ProtoMol::SameMoleculeConstraint, ProtoMol::HBondConstraint, ProtoMol::NoConstraint
- 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
- PRE_CHECK
: ProtoMol::DebugPostConstraint, ProtoMol::DebugPreConstraint, ProtoMol::NotSameMoleculeConstraint, ProtoMol::SameMoleculeConstraint, ProtoMol::HBondConstraint, ProtoMol::NoConstraint
- 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 >
- prototype
: ProtoMol::IntegratorFactoryDetails::IntegratorInput
- Proxy()
: ProtoMol::Proxy
- psf()
: ProtoMol::OutputCache
- PSFReader()
: ProtoMol::PSFReader
- PSFWriter()
: ProtoMol::PSFWriter
- pushShadowHistory()
: ProtoMol::ShadowHMCIntegrator
- r_ub
: ProtoMol::PAR::Angle, ProtoMol::iSGPAR::Angle
- RangeSwitchingFunction()
: ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >
- rc
: ProtoMol::IMDElf
- rdbuf()
: std::stringstreambase
- re
: zomplex
- 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
- REAL
: ProtoMol::ValueEnum
- realChi
: ProtoMol::MagneticDipoleForce
- 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 >
- realTopo
: 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::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 >
- RealTopologyType
: ProtoMol::iSGNonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::iSGNonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, 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::NonbondedCutoffForce< TCellManager, TOneAtomPair, TForce, TImplForce >
- 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
- recoverable
: ProtoMol::Report::MyStreamer
- 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 >
- RefArray< 2 >
: ProtoMol::Array< T, N >::RefArray< 1 >
- RefArray< N+1 >
: ProtoMol::Array< T, N >::RefArray< N >
- RefArray< T, 2 >
: ProtoMol::RefArray< T, 1 >
- RefArray< T, N+1 >
: ProtoMol::RefArray< T, N >
- reference
: ProtoMol::ArrayCellListStructure, 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 >
- 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
- RepType
: 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 >
- 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
- residue_name
: ProtoMol::PSF::Atom
- residue_sequence
: ProtoMol::PSF::Atom
- residueName
: ProtoMol::PDB::PDBAtom
- residueNum
: ProtoMol::PDB::PDBAtom
- resize()
: ProtoMol::LennardJonesParameterTable, ProtoMol::ExclusionTable, ProtoMol::XYZ, ProtoMol::PPM, ProtoMol::PGM, ProtoMol::PDB, ProtoMol::Array< T, N >
- restAngle
: ProtoMol::Angle
- restLength
: ProtoMol::Bond, ProtoMol::Bond::Constraint
- restoreValues()
: ProtoMol::ShadowHMCIntegrator, ProtoMol::MCIntegrator, ProtoMol::HMCIntegrator, ProtoMol::DLMCIntegrator, ProtoMol::DihedralHMCIntegrator
- rFavg
: ProtoMol::CompareForce::CompareError
- rFmax
: ProtoMol::CompareForce::CompareError
- rmin
: ProtoMol::PAR::Hbond
- rotate()
: ProtoMol::Matrix3by3
- roughTest()
: ProtoMol::UniversalSwitchingFunction, ProtoMol::ShiftSwitchingFunction, ProtoMol::RangeSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::CutoffSwitchingFunction, ProtoMol::ComplementSwitchingFunction< TOriginalSwitchingFunction >, ProtoMol::C2SwitchingFunction, ProtoMol::C1SwitchingFunction
- rPE
: ProtoMol::CompareForce::CompareError
- rpos
: std::stringbuf
- 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
- RUN
: ProtoMol::TimerStatistic
- runPostSteps()
: ProtoMol::ShadowHMCIntegrator
- runPreSteps()
: ProtoMol::ShadowHMCIntegrator
- S_ALT_LOC
: ProtoMol::PDB::PDBAtom
- S_ATOM_NAME
: ProtoMol::PDB::PDBAtom
- S_CHAIN_ID
: ProtoMol::PDB::PDBAtom
- S_CHARGE
: ProtoMol::PDB::PDBAtom
- S_ELEMENT_SYMBOL
: ProtoMol::PDB::PDBAtom
- S_FOOT_NOTE
: ProtoMol::PDB::PDBAtom
- S_I_CODE
: ProtoMol::PDB::PDBAtom
- S_OCCUP
: ProtoMol::PDB::PDBAtom
- S_RECORD_NAME
: ProtoMol::PDB::PDBAtom
- S_RES_NAME
: ProtoMol::PDB::PDBAtom
- S_RES_SEQ
: ProtoMol::PDB::PDBAtom
- S_SEG_ID
: ProtoMol::PDB::PDBAtom
- S_SERIAL
: ProtoMol::PDB::PDBAtom
- S_TEMP
: ProtoMol::PDB::PDBAtom
- S_X
: ProtoMol::PDB::PDBAtom
- S_Y
: ProtoMol::PDB::PDBAtom
- S_Z
: ProtoMol::PDB::PDBAtom
- saveValues()
: ProtoMol::ShadowHMCIntegrator, ProtoMol::MCIntegrator, ProtoMol::HMCIntegrator, ProtoMol::DLMCIntegrator, ProtoMol::DihedralHMCIntegrator
- ScalarStructure()
: ProtoMol::ScalarStructure
- scalarSum()
: ProtoMol::iSGGrid< TInterpolation >, ProtoMol::Grid< TInterpolation >
- scale()
: ProtoMol::Matrix3by3
- scaledCharge
: ProtoMol::Atom
- scaledMass
: ProtoMol::Atom
- scope
: ProtoMol::GenericTopology, ProtoMol::Integrator, ProtoMol::Output, ProtoMol::HelpText, ProtoMol::Force
- search()
: ProtoMol::HelpTextFactory
- second
: ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >::CellPair, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >::CellPair, ProtoMol::PairIntSorted
- seg_id
: ProtoMol::PSF::Atom
- segID
: ProtoMol::PDB::PDBAtom
- SemiGenericTopology()
: ProtoMol::SemiGenericTopology< TBoundaryConditions >
- send_coords()
: ProtoMol::IMDElf
- SEQUENTIAL
: ProtoMol::Parallel
- 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
- SHADOW
: ProtoMol::ScalarStructure
- ShadowHMCIntegrator()
: ProtoMol::ShadowHMCIntegrator
- ShiftSwitchingFunction()
: ProtoMol::ShiftSwitchingFunction
- SHORT
: ProtoMol::BSplineEnum
- shortRangeTerm()
: ProtoMol::NonbondedMultiGridSystemForce< TBoundaryConditions, TCellManager, TInterpolation, TKernel, direct, correction, smooth >
- sigma
: ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
- sigma14
: ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
- SIGMA_CHARMM19_TO_CHARMM28
: ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
- SIGMA_CHARMM28_TO_CHARMM19
: ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
- simType
: ProtoMol::XSC
- 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 >
- size_t
: ProtoMol::ArraySize< N >
- size_type
: ProtoMol::ArrayCellListStructure, 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 >
- sized
: ProtoMol::TRANSReader
- SLAVE
: ProtoMol::Parallel
- 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,