- a -
- ABMD()
: PLMD::bias::ABMD
- Abort()
: PLMD::Communicator
- abortIfExceptionsAreDisabled()
: PLMD::Exception
- accumulate()
: PLMD::analysis::Analysis
- accumulateDerivative()
: PLMD::vesselbase::ActionWithVessel
- accumulateDerivativesFromVector()
: PLMD::crystallization::VectorMultiColvar
- accumulateWeightedAverageAndDerivatives()
: PLMD::multicolvar::MultiColvarFunction
- Action()
: PLMD::Action
- ActionAtomistic()
: PLMD::ActionAtomistic
- ActionOptions()
: PLMD::ActionOptions
- ActionPilot()
: PLMD::ActionPilot
- actionRegister()
: PLMD::ActionRegister
- ActionSet()
: PLMD::ActionSet
- ActionSetup()
: PLMD::ActionSetup
- ActionVolume()
: PLMD::multicolvar::ActionVolume
- ActionWithArguments()
: PLMD::ActionWithArguments
- ActionWithInputVessel()
: PLMD::vesselbase::ActionWithInputVessel
- ActionWithValue()
: PLMD::ActionWithValue
- ActionWithVessel()
: PLMD::vesselbase::ActionWithVessel
- ActionWithVirtualAtom()
: PLMD::ActionWithVirtualAtom
- activate()
: PLMD::Action
, PLMD::DynamicList< T >
- activateAll()
: PLMD::DynamicList< T >
- activateIndexes()
: PLMD::multicolvar::MultiColvarBase
, PLMD::vesselbase::ActionWithVessel
- activateIndices()
: PLMD::vesselbase::StoreDataVessel
- activateTheseTasks()
: PLMD::vesselbase::ActionWithVessel
- add()
: PLMD::ActionRegister
, PLMD::analysis::LandmarkRegister
, PLMD::Atoms
, PLMD::CLToolRegister
, PLMD::Keywords
, PLMD::MetricRegister
, PLMD::Value
, PLMD::vesselbase::VesselRegister
- addAtomDerivativeToAllImagComponents()
: PLMD::crystallization::VectorMultiColvar
- addAtomDerivativeToAllRealComponents()
: PLMD::crystallization::VectorMultiColvar
- addAtomicDerivatives()
: PLMD::ReferenceAtoms
- addAtomsDerivative()
: PLMD::crystallization::VectorMultiColvar
- addAtomsDerivativeOfWeight()
: PLMD::multicolvar::MultiColvar
- addAtomsDerivatives()
: PLMD::multicolvar::MultiColvar
, PLMD::multicolvar::MultiColvarBase
, PLMD::multicolvar::StoreCentralAtomsVessel
- addBoxDerivatives()
: PLMD::crystallization::VectorMultiColvar
, PLMD::multicolvar::ActionVolume
, PLMD::multicolvar::MultiColvarBase
, PLMD::ReferenceAtoms
- addBoxDerivativesOfWeight()
: PLMD::multicolvar::MultiColvarBase
- addBoxDerivativesToAllImagComponents()
: PLMD::crystallization::VectorMultiColvar
- addBoxDerivativesToAllRealComponents()
: PLMD::crystallization::VectorMultiColvar
- addBridgeForces()
: PLMD::vesselbase::ActionWithInputVessel
- addBridgingVessel()
: PLMD::vesselbase::ActionWithVessel
- addCentralAtomDerivatives()
: PLMD::multicolvar::MultiColvar
, PLMD::multicolvar::MultiColvarBase
- addCentralAtomDerivativeToFunction()
: PLMD::multicolvar::MultiColvarBase
- addCentralAtomsDerivatives()
: PLMD::multicolvar::MultiColvarFunction
- addColvar()
: PLMD::multicolvar::MultiColvar
, PLMD::secondarystructure::SecondaryStructureRMSD
- addComponent()
: PLMD::ActionWithValue
, PLMD::crystallization::VectorMultiColvar
- addComponentWithDerivatives()
: PLMD::ActionWithValue
, PLMD::function::Function
- addConstantField()
: PLMD::OFile
- addDependency()
: PLMD::Action
- addDerivative()
: PLMD::Value
- addDerivativeOfCentralAtomPos()
: PLMD::multicolvar::MultiColvarFunction
- addDerivativesOnMatrixElement()
: PLMD::multicolvar::AdjacencyMatrixAction
- addDerivativeToFinalValue()
: PLMD::vesselbase::FunctionVessel
- addElementDerivative()
: PLMD::vesselbase::ActionWithVessel
- addElementValue()
: PLMD::vesselbase::ActionWithVessel
- addFlag()
: PLMD::Keywords
- addForce()
: PLMD::Value
- addForcesOnArguments()
: PLMD::ActionWithArguments
, PLMD::vesselbase::ActionWithInputVessel
- addForcesOnAtoms()
: PLMD::crystallization::VectorMultiColvar
- addGaussian()
: PLMD::bias::MetaD
- addGrid()
: PLMD::BiasRepresentation
- addImaginaryAtomsDerivative()
: PLMD::crystallization::VectorMultiColvar
- addImaginaryBoxDerivatives()
: PLMD::crystallization::VectorMultiColvar
- addImaginaryComponent()
: PLMD::crystallization::VectorMultiColvar
- addIndexToList()
: PLMD::DynamicList< T >
- addKernel()
: PLMD::Grid
- addOrientationDerivatives()
: PLMD::multicolvar::MultiColvarFunction
- addOrientationDerivativesToBase()
: PLMD::crystallization::VectorMultiColvar
, PLMD::multicolvar::Density
, PLMD::multicolvar::MultiColvarBase
- addOutputComponent()
: PLMD::Keywords
- addReferenceAtomDerivatives()
: PLMD::multicolvar::ActionVolume
- addStoredDerivative()
: PLMD::multicolvar::MultiColvarFunction
- addTaskToList()
: PLMD::multicolvar::MultiColvarBase
, PLMD::vesselbase::ActionWithVessel
- addToBufferElement()
: PLMD::vesselbase::Vessel
- addValue()
: PLMD::ActionWithValue
, PLMD::Grid
, PLMD::SparseGrid
- addValueAndDerivatives()
: PLMD::Grid
, PLMD::SparseGrid
- addValueIgnoringTolerance()
: PLMD::vesselbase::FunctionVessel
- addValueUsingTolerance()
: PLMD::vesselbase::FunctionVessel
- addValueWithDerivatives()
: PLMD::ActionWithValue
, PLMD::function::Function
- addVessel()
: PLMD::vesselbase::ActionWithVessel
, PLMD::vesselbase::ShortcutVessel
- addVirtualAtom()
: PLMD::Atoms
- addWeightedValueDerivatives()
: PLMD::crystallization::VectorMultiColvar
, PLMD::multicolvar::MultiColvarBase
- AdjacencyMatrixAction()
: PLMD::multicolvar::AdjacencyMatrixAction
- AdjacencyMatrixVessel()
: PLMD::multicolvar::AdjacencyMatrixVessel
- advanceField()
: PLMD::IFile
- Allgather()
: PLMD::Communicator
- Allgatherv()
: PLMD::Communicator
- allowedResidue()
: PLMD::MolDataClass
- allowIgnoredFields()
: PLMD::IFile
- AlphaBeta()
: PLMD::multicolvar::AlphaBeta
- AlphaRMSD()
: PLMD::secondarystructure::AlphaRMSD
- Analysis()
: PLMD::analysis::Analysis
- AnalysisWithLandmarks()
: PLMD::analysis::AnalysisWithLandmarks
- analyzeLandmarks()
: PLMD::analysis::AnalysisWithLandmarks
, PLMD::analysis::ClassicalMultiDimensionalScaling
- Angle()
: PLMD::colvar::Angle
- Angles()
: PLMD::multicolvar::Angles
- AntibetaRMSD()
: PLMD::secondarystructure::AntibetaRMSD
- appendSuffix()
: PLMD::FileBase
- apply()
: PLMD::Action
, PLMD::ActionSetup
, PLMD::ActionWithVirtualAtom
, PLMD::analysis::Analysis
, PLMD::analysis::Committor
, PLMD::bias::Bias
, PLMD::Colvar
, PLMD::function::Function
, PLMD::generic::Debug
, PLMD::generic::DumpAtoms
, PLMD::generic::DumpDerivatives
, PLMD::generic::DumpForces
, PLMD::generic::DumpProjections
, PLMD::generic::FitToTemplate
, PLMD::generic::Flush
, PLMD::generic::Group
, PLMD::generic::Include
, PLMD::generic::Print
, PLMD::generic::RandomExchanges
, PLMD::generic::Read
, PLMD::generic::Time
, PLMD::generic::WholeMolecules
, PLMD::IMD
, PLMD::manyrestraints::ManyRestraintsBase
, PLMD::mapping::Mapping
, PLMD::multicolvar::ActionVolume
, PLMD::multicolvar::DumpMultiColvar
, PLMD::multicolvar::MultiColvarBase
, PLMD::multicolvar::Sprint
, PLMD::secondarystructure::SecondaryStructureRMSD
- applyBridgeForces()
: PLMD::manyrestraints::ManyRestraintsBase
, PLMD::multicolvar::ActionVolume
, PLMD::vesselbase::ActionWithInputVessel
, PLMD::vesselbase::ActionWithVessel
- applyChainRuleForDerivatives()
: PLMD::manyrestraints::ManyRestraintsBase
- applyForce()
: PLMD::Value
, PLMD::vesselbase::BridgeVessel
, PLMD::vesselbase::FunctionVessel
, PLMD::vesselbase::Moments
, PLMD::vesselbase::ShortcutVessel
, PLMD::vesselbase::StoreDataVessel
, PLMD::vesselbase::Vessel
- applyForces()
: PLMD::ActionAtomistic
- applyFunctionAllValuesAndDerivatives()
: PLMD::Grid
- applyPeriodicity()
: PLMD::Value
- ArgumentOnlyDistance()
: PLMD::ArgumentOnlyDistance
- assignAlign()
: PLMD::Kearsley
, PLMD::OptimalAlignment
- assignDisplace()
: PLMD::OptimalAlignment
- assignP0()
: PLMD::Kearsley
, PLMD::OptimalAlignment
- assignP1()
: PLMD::Kearsley
, PLMD::OptimalAlignment
- atomHasDerivative()
: PLMD::multicolvar::MultiColvarFunction
- AtomNumber()
: PLMD::AtomNumber
- Atoms()
: PLMD::Atoms