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

---

- _ -

• __my_sb : std::stringstreambase

- a -

• 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
• absF2 : ProtoMol::CompareForce::CompareError
• acceptors : ProtoMol::PSF
• 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
• alpha : ProtoMol::iSGLennardJonesTableForce
• alphaLJ : ProtoMol::ModifierISG::TransformMap, ProtoMol::TRANS::AtomType, ProtoMol::Atom
• altLoc : ProtoMol::PDB::PDBAtom
• angle : ProtoMol::BSplineMOLLYIntegrator::AngleIndex
• angleList : ProtoMol::Molecule
• angles : ProtoMol::ModifierISG, ProtoMol::GenericTopology, ProtoMol::PSF, ProtoMol::PAR, ProtoMol::iSGPAR
• angleval : ProtoMol::PAR::Angle, ProtoMol::iSGPAR::Angle
• anyExclsForThisDelta : ProtoMol::ExclusionTable
• 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
• atomNum : ProtoMol::Atom
• atoms : ProtoMol::GenericTopology, ProtoMol::PSF, ProtoMol::PDB, ProtoMol::Molecule
• atomTypes : ProtoMol::ModifierISG, ProtoMol::TRANS, ProtoMol::GenericTopology
• AveCQ : ProtoMol::iSGIntegrator
• AveCQSq : ProtoMol::iSGIntegrator
• AveDeltaMu : ProtoMol::iSGIntegrator

- b -

• b : ProtoMol::PAR::Nbfix
• B : ProtoMol::LennardJonesParameters
• b1 : ProtoMol::BSplineMOLLYIntegrator::BondIndex
• b14 : ProtoMol::PAR::Nbfix
• B14 : ProtoMol::LennardJonesParameters
• b2 : ProtoMol::BSplineMOLLYIntegrator::BondIndex
• bond1 : ProtoMol::BSplineMOLLYIntegrator::AngleIndex
• bond2 : ProtoMol::BSplineMOLLYIntegrator::AngleIndex
• bondList : ProtoMol::Molecule
• bondRattleShakeConstraints : ProtoMol::GenericTopology
• bonds : ProtoMol::ModifierISG, ProtoMol::GenericTopology, ProtoMol::PSF, ProtoMol::PAR, ProtoMol::iSGPAR
• 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 >
• buf : std::stringbuf
• bufsize : std::stringbuf

- c -

• cellListNext : ProtoMol::Atom
• cellLists : ProtoMol::Topology< TBoundaryConditions, TCellManager >
• cellManager : ProtoMol::Topology< TBoundaryConditions, TCellManager >
• chainID : ProtoMol::PDB::PDBAtom
• charge : ProtoMol::TRANS::AtomType, ProtoMol::PSF::Atom, ProtoMol::PDB::PDBAtom, ProtoMol::iSGPAR::AtomType, ProtoMol::AtomType
• clientsock : ProtoMol::IMDElf
• computeOthers : ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >
• confstrings : ProtoMol::OutputDihedrals
• confstringsCounter : ProtoMol::OutputDihedrals
• coords : ProtoMol::XYZ, ProtoMol::PDB
• coulombScalingFactor : ProtoMol::GenericTopology
• curAngle : ProtoMol::UmbrellaIntegrator

- d -

• defaultBlockSize : ProtoMol::NonbondedSimpleFullSystemForceBase, ProtoMol::NonbondedFullSystemForceBase
• defaultCharmmType : ProtoMol::PARWriter
• defaultValue : ProtoMol::HelpText, ProtoMol::Parameter
• defbuf : std::stringbuf
• degreesOfFreedom : ProtoMol::GenericTopology
• Delta_ubK : ProtoMol::Angle
• Delta_ubR0 : ProtoMol::Angle
• DeltaK : ProtoMol::Torsion, ProtoMol::Bond, ProtoMol::Angle
• deltaM : ProtoMol::Atom
• DeltaMuIG : ProtoMol::TRANS
• DeltaPhase : ProtoMol::Torsion
• deltaQ : ProtoMol::Atom
• DeltaR0 : ProtoMol::Bond
• DeltaTheta0 : ProtoMol::Angle
• dihedralList : ProtoMol::Molecule
• dihedrals : ProtoMol::ModifierISG, ProtoMol::GenericTopology, ProtoMol::PSF, ProtoMol::PAR, ProtoMol::iSGPAR
• distance : ProtoMol::PAR::Bond, ProtoMol::iSGPAR::Bond
• donors : ProtoMol::PSF
• dTheta : ProtoMol::Hermite, ProtoMol::Lagrange, ProtoMol::BSpline

- e -

• Eangle : ProtoMol::IMD::IMDEnergies
• Ebond : ProtoMol::IMD::IMDEnergies
• Edihe : ProtoMol::IMD::IMDEnergies
• Eelec : ProtoMol::IMD::IMDEnergies
• Eimpr : ProtoMol::IMD::IMDEnergies
• elementName : ProtoMol::PDB::PDBAtom
• elementNum : ProtoMol::PDB::PDBAtom
• elementType : ProtoMol::PDB::PDBAtom
• emin : ProtoMol::PAR::Hbond
• 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 >
• 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 >
• Epot : ProtoMol::IMD::IMDEnergies
• epsilon : ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
• epsilon14 : ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
• Epsilon_vel : ProtoMol::XSC
• Eta : ProtoMol::XSC
• Eta_vel : ProtoMol::XSC
• EtaVol : ProtoMol::XSC
• EtaVol_vel : ProtoMol::XSC
• Etot : ProtoMol::IMD::IMDEnergies
• Evdw : ProtoMol::IMD::IMDEnergies
• excl : ProtoMol::ExclusionPair
• exclude : ProtoMol::GenericTopology
• exclusions : ProtoMol::GenericTopology
• expfactor : ProtoMol::MagneticDipoleForce

- f -

• FinalType : ProtoMol::iSGIntegrator
• first : ProtoMol::Output, ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >::CellPair, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >::CellPair, ProtoMol::PairIntSorted
• footnote : ProtoMol::PDB::PDBAtom
• 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
• 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 >

- g -

• got_alphaLJ : ProtoMol::TRANSReader

- h -

• h : ProtoMol::TripleInt, ProtoMol::PPM, ProtoMol::PGM
• H : ProtoMol::ReducedHessAngle
• hbonds : ProtoMol::PAR, ProtoMol::iSGPAR
• hdf : ProtoMol::UmbrellaIntegrator, ProtoMol::DLMCIntegrator
• high : ProtoMol::IMD::netint
• highDeltas : ProtoMol::ExclusionTable
• highest : ProtoMol::IMD::netint
• holder : ProtoMol::Value::Holder< ValueTrait, Constraint >
• hvyAtom : ProtoMol::Atom
• hvyAtomGrpsize : ProtoMol::PDB::PDBAtom

- i -

• i : ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
• i1 : ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond
• i2 : ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond
• id : ProtoMol::HelpText, ProtoMol::ObjectDefinition, ProtoMol::MakeableDefinition
• identity : ProtoMol::ReducedHessAngle, ProtoMol::Matrix3by3, ProtoMol::PSF::Atom
• im : zomplex
• improperList : ProtoMol::Molecule
• impropers : ProtoMol::ModifierISG, ProtoMol::GenericTopology, ProtoMol::PSF, ProtoMol::PAR, ProtoMol::iSGPAR
• INCR_SIZE : ProtoMol::Stack< T >
• insertionCode : ProtoMol::PDB::PDBAtom
• integrator : ProtoMol::IntegratorDefinition
• isgLJParms : ProtoMol::GenericTopology
• iSGmodifierIndex : ProtoMol::Torsion, ProtoMol::Bond, ProtoMol::Angle
• iSGNumMols : ProtoMol::GenericTopology
• isMPI : ProtoMol::Parallel

- j -

• j : ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >

- k -

• k : ProtoMol::HarmDihedralSystemForce< TBoundaryConditions >, ProtoMol::TripleInt
• k_ub : ProtoMol::PAR::Angle, ProtoMol::iSGPAR::Angle
• kappa : ProtoMol::MagneticDipoleForce
• kbT : ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
• 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

- l -

• l : ProtoMol::TripleInt
• l12 : ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond
• lambda : ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond, ProtoMol::Molecule
• Lambda : ProtoMol::XSC
• Lambda_vel : ProtoMol::XSC
• 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 >
• length : ProtoMol::IMD::IMDheader
• lennardJonesBank : ProtoMol::BankLennardJonesParameterTable
• lennardJonesParameters : ProtoMol::GenericTopology
• lift : ProtoMol::DLMCIntegrator
• low : ProtoMol::IMD::netint
• lowDeltas : ProtoMol::ExclusionTable
• lowest : ProtoMol::IMD::netint

- m -

• 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
• mass : ProtoMol::OutputCache, ProtoMol::TRANS::AtomType, ProtoMol::PSF::Atom, ProtoMol::Molecule, ProtoMol::iSGPAR::AtomType, ProtoMol::AtomType
• max : ProtoMol::GenericTopology
• min : ProtoMol::GenericTopology
• minimalMolecularDistances : ProtoMol::GenericTopology
• mode : std::stringbuf
• molecule : ProtoMol::Atom
• molecules : ProtoMol::GenericTopology
• momentum : ProtoMol::Molecule
• multiplicity : ProtoMol::Torsion, ProtoMol::PAR::Dihedral, ProtoMol::iSGPAR::Dihedral
• 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
• 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 -

• N : ProtoMol::iSGIntegrator
• name : ProtoMol::iSGPAR::AtomType, ProtoMol::AtomType
• names : ProtoMol::XYZ
• nbfixs : ProtoMol::PAR, ProtoMol::iSGPAR
• negative : ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
• 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
• ngrp : ProtoMol::PSF
• 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 >
• nonbondedHessian : ProtoMol::OneMollyPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce >
• nonbondedHessianFirst : ProtoMol::OneMollyPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond >
• nonbondedHessianSecond : ProtoMol::OneMollyPairTwo< TBoundaryConditions, TSwitchingFunctionFirst, TNonbondedForceFirst, TSwitchingFunctionSecond, TNonbondedForceSecond >
• nonbondeds : ProtoMol::PSF, ProtoMol::PAR, ProtoMol::iSGPAR
• 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
• NumberOfStages : ProtoMol::TRANS
• numComp : ProtoMol::iSGPARReader
• numComps : ProtoMol::BankLennardJonesParameterTable
• numIdentities : ProtoMol::TRANSReader
• NumMols : ProtoMol::iSGIntegrator
• numStages : ProtoMol::TRANSReader
• numTables : ProtoMol::BankLennardJonesParameterTable
• NumTransSteps : ProtoMol::iSGIntegrator
• numTypes : ProtoMol::TRANSReader

- o -

• obj : ProtoMol::Parallel, ProtoMol::HelpTextFactory, ProtoMol::Factory< Type >
• occupancy : ProtoMol::PDB::PDBAtom
• ok : ProtoMol::Parallel, ProtoMol::Value::Holder< ValueTrait, Constraint >
• old_charge : ProtoMol::ModifierISG::TransformMap, ProtoMol::TRANS::AtomType
• old_type : ProtoMol::XSC
• OldType : ProtoMol::iSGIntegrator
• ourIdentity : ProtoMol::Matrix3by3

- p -

• p : ProtoMol::PPM, ProtoMol::PGM
• pairs : ProtoMol::Molecule
• parameters : ProtoMol::HelpText, ProtoMol::ObjectDefinition, ProtoMol::MakeableDefinition
• periodicity : ProtoMol::Torsion, ProtoMol::PAR::Improper, ProtoMol::PAR::Dihedral, ProtoMol::iSGPAR::Improper, ProtoMol::iSGPAR::Dihedral
• phaseShift : ProtoMol::Torsion, ProtoMol::PAR::Improper, ProtoMol::PAR::Dihedral, ProtoMol::iSGPAR::Improper, ProtoMol::iSGPAR::Dihedral
• 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
• port : ProtoMol::IMDElf
• 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 >
• prototype : ProtoMol::IntegratorFactoryDetails::IntegratorInput

- q -

• Qd : ProtoMol::iSGIntegrator
• Qnew : ProtoMol::Atom
• Qo : ProtoMol::iSGIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::NPTVerletIntegrator
• Qold : ProtoMol::Atom
• Qv : ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator

- r -

• r_ub : ProtoMol::PAR::Angle, ProtoMol::iSGPAR::Angle
• rc : ProtoMol::IMDElf
• re : zomplex
• realChi : ProtoMol::MagneticDipoleForce
• 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 >
• residue_name : ProtoMol::PSF::Atom
• residue_sequence : ProtoMol::PSF::Atom
• residueName : ProtoMol::PDB::PDBAtom
• residueNum : ProtoMol::PDB::PDBAtom
• restAngle : ProtoMol::Angle
• restLength : ProtoMol::Bond, ProtoMol::Bond::Constraint
• rFavg : ProtoMol::CompareForce::CompareError
• rFmax : ProtoMol::CompareForce::CompareError
• rmin : ProtoMol::PAR::Hbond
• rPE : ProtoMol::CompareForce::CompareError
• rpos : std::stringbuf

- s -

• scaledCharge : ProtoMol::Atom
• scaledMass : ProtoMol::Atom
• scope : ProtoMol::GenericTopology, ProtoMol::Integrator, ProtoMol::Output, ProtoMol::HelpText, ProtoMol::Force
• second : ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >::CellPair, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >::CellPair, ProtoMol::PairIntSorted
• seg_id : ProtoMol::PSF::Atom
• segID : ProtoMol::PDB::PDBAtom
• 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
• sized : ProtoMol::TRANSReader
• sock : ProtoMol::IMDElf
• springConstant : ProtoMol::Bond
• stage : ProtoMol::TRANS::AtomType
• stageNumber : ProtoMol::iSGPAR::AtomType, ProtoMol::Atom
• str : std::stringstreambase, std::stringbuf, ProtoMol::ExclusionEnum, ProtoMol::ParallelEnum, ProtoMol::ThermostatEnum, ProtoMol::InputPosVelEnum, ProtoMol::ValueEnum, ProtoMol::ValueEnum::Enum2ValueType< e >, ProtoMol::ConstraintValueEnum, ProtoMol::BSplineEnum
• sumTotalEnergy : ProtoMol::ShadowHMCIntegrator
• switchingFunction : 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::OneMollyPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce >, ProtoMol::OneAtomPairFull< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::OneAtomPair< TBoundaryConditions, TSwitchingFunction, TNonbondedForce, TConstraint >, ProtoMol::NonbondedPMEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TInterpolation, TSwitchingFunction >, ProtoMol::NonbondedFullEwaldSystemForce< TBoundaryConditions, TCellManager, real, reciprocal, correction, TSwitchingFunction >, ProtoMol::ElectricFieldSystemForce< TBoundaryConditions, TSwitchingFunction, TConstraint >
• switchingFunctionFirst : 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 >
• switchingFunctionSecond : 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 >
• symbol : ProtoMol::PDB::PDBAtom
• symbolName : ProtoMol::iSGPAR::AtomType, ProtoMol::AtomType

- t -

• T : ProtoMol::iSGIntegrator, ProtoMol::ArrayCellListStructure, ProtoMol::IMD::IMDEnergies
• tempFactor : ProtoMol::PDB::PDBAtom
• text : 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::HelpText, ProtoMol::Text, ProtoMol::Parameter
• the_beginning : ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
• the_counter : ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
• the_end : ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
• the_first : ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
• the_last : ProtoMol::CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >, ProtoMol::CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
• theta : ProtoMol::Hermite, ProtoMol::Lagrange, ProtoMol::BSpline
• thisStage : ProtoMol::iSGIntegrator
• time : ProtoMol::OutputCache, ProtoMol::GenericTopology
• timeout : ProtoMol::IMDElf
• timer : ProtoMol::TimerStatistic
• Transformed : ProtoMol::iSGIntegrator
• transformMaps : ProtoMol::ModifierISG
• trate : ProtoMol::IMDElf
• tstep : ProtoMol::IMD::IMDEnergies
• type : ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder, ProtoMol::IMD::IMDheader, ProtoMol::TypeSelection::Float< size >, ProtoMol::TypeSelection::Int< size >, ProtoMol::TypeSelection::SelectTypeCheck< A, size >, ProtoMol::TypeSelection::SelectTypeCheckHelper< true, A >, ProtoMol::TypeSelection::SelectType< size, A, B >, ProtoMol::TypeSelection::SelectTypeHelper< true, A, B >, ProtoMol::TypeSelection::SelectTypeHelper< cmp, A, B >, ProtoMol::Molecule, ProtoMol::Atom
• type_name : ProtoMol::TRANS::AtomType

- u -

• ub_flag : ProtoMol::PAR::Angle, ProtoMol::iSGPAR::Angle
• undefined : ProtoMol::Value
• ureyBradleyConstant : ProtoMol::Angle
• ureyBradleyRestLength : ProtoMol::Angle

- v -

• valid : ProtoMol::InputValue< TBase, type, constraint >, ProtoMol::Value, ProtoMol::Value::Holder< ValueTrait, Constraint >, ProtoMol::Value::PlaceHolder, ProtoMol::Configuration, ProtoMol::AbstractEnumType< T, noCase >, ProtoMol::ArrayCellListStructure
• value : 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::ValueEnum::Enum2ValueType< e >, ProtoMol::Parameter, ProtoMol::ConstraintValueEnum::Enum2Type< e >
• values : ProtoMol::IntegratorFactoryDetails::IntegratorInput
• vdw : ProtoMol::PAR::Nonbonded, ProtoMol::iSGPAR::Nonbonded
• Vector : ProtoMol::Vector< T >, ProtoMol::ArraySizes, ProtoMol::ArraySize< N >
• vmd_atoms : ProtoMol::IMDElf
• vmd_forces : ProtoMol::IMDElf
• Vol : ProtoMol::XSC
• volum : ProtoMol::MagneticDipoleForce

- w -

• W : ProtoMol::iSGIntegrator, ProtoMol::NPTVerletIntegrator
• w : ProtoMol::PPM, ProtoMol::PGM
• wait_imd : ProtoMol::IMDElf
• water : ProtoMol::Molecule

- x -

• x : ProtoMol::iSGGrid< TInterpolation >::Interpolation3D, ProtoMol::iSGGrid< TInterpolation >::Int3D, ProtoMol::CubicCellLocation, ProtoMol::Vector3D, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >::Interpolation3D, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >::Int3D, ProtoMol::Grid< TInterpolation >::Interpolation3D, ProtoMol::Grid< TInterpolation >::Int3D

- y -

• y : ProtoMol::iSGGrid< TInterpolation >::Interpolation3D, ProtoMol::iSGGrid< TInterpolation >::Int3D, ProtoMol::CubicCellLocation, ProtoMol::Vector3D, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >::Interpolation3D, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >::Int3D, ProtoMol::Grid< TInterpolation >::Interpolation3D, ProtoMol::Grid< TInterpolation >::Int3D

- z -

• z : ProtoMol::iSGGrid< TInterpolation >::Interpolation3D, ProtoMol::iSGGrid< TInterpolation >::Int3D, ProtoMol::CubicCellLocation, ProtoMol::Vector3D, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >::Interpolation3D, ProtoMol::MultiGrid< TInterpolation, TKernel, pbcX, pbcY, pbcZ >::Int3D, ProtoMol::Grid< TInterpolation >::Interpolation3D, ProtoMol::Grid< TInterpolation >::Int3D

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