Classes providing input directives

Classes which implement directive that we used in the plumed input file. More...

Classes
class	PLMD::bias::ABMD
	Provides the keyword ABMD More...
class	PLMD::analysis::Accumulate
	Provides the keyword ACCUMULATE More...
class	PLMD::ActionToGetData
	Provides the keyword GET More...
class	PLMD::ActionToPutData
	Provides the keyword PUT More...
class	PLMD::mapping::AdaptivePath
	Provides the keyword ADAPTIVE_PATH More...
class	PLMD::multicolvar::AlphaBeta
	Provides the keyword ALPHABETA More...
class	PLMD::secondarystructure::AlphaRMSD
	Provides the keyword ALPHARMSD More...
class	PLMD::colvar::Angle
	Provides the keyword ANGLE_SCALAR More...
class	AngleMulti
	Provides the keyword ANGLE_VECTOR More...
class	PLMD::multicolvar::Angles
	Provides the keyword ANGLES More...
class	AngleShortcut
	Provides the keyword ANGLE More...
class	PLMD::symfunc::AngularTetra
	Provides the keyword TETRA_ANGULAR More...
class	ANN
	Provides the keyword ANN More...
class	PLMD::secondarystructure::AntibetaRMSD
	Provides the keyword ANTIBETARMSD More...
class	PLMD::vatom::ArgsToVatom
	Provides the keyword ARGS2VATOM More...
class	PLMD::dimred::ArrangePoints
	Provides the keyword ARRANGE_POINTS More...
class	PLMD::symfunc::AtomicSMAC
	Provides the keyword ATOMIC_SMAC More...
class	PLMD::analysis::Average
	Provides the keyword AVERAGE More...
class	BesselShortcut
	Provides the keyword BESSEL More...
class	BetweenShortcut
	Provides the keyword BETWEEN More...
class	PLMD::ves::BF_Chebyshev
	Provides the keyword BF_CHEBYSHEV More...
class	PLMD::ves::BF_Combined
	Provides the keyword BF_COMBINED More...
class	PLMD::ves::BF_Cosine
	Provides the keyword BF_COSINE More...
class	PLMD::ves::BF_CubicBsplines
	Provides the keyword BF_CUBIC_B_SPLINES More...
class	PLMD::ves::BF_Custom
	Provides the keyword BF_CUSTOM More...
class	PLMD::ves::BF_Fourier
	Provides the keyword BF_FOURIER More...
class	PLMD::ves::BF_Gaussians
	Provides the keyword BF_GAUSSIANS More...
class	PLMD::ves::BF_Legendre
	Provides the keyword BF_LEGENDRE More...
class	PLMD::ves::BF_Powers
	Provides the keyword BF_POWERS More...
class	PLMD::ves::BF_Sine
	Provides the keyword BF_SINE More...
class	PLMD::ves::BF_Wavelets
	Provides the keyword BF_WAVELETS More...
class	PLMD::bias::BiasValue
	Provides the keyword BIASVALUE More...
class	PLMD::crystdistrib::BopsShortcut
	Provides the keyword BOPS More...
class	PLMD::adjmat::Bridge
	Provides the keyword BRIDGE More...
class	PLMD::adjmat::BridgeMatrix
	Provides the keyword BRIDGE_MATRIX More...
class	PLMD::isdb::Caliber
	Provides the keyword CALIBER More...
class	PLMD::colvar::Cell
	Provides the keyword CELL More...
class	PLMD::vatom::Center
	Provides the keyword CENTER_FAST More...
class	PLMD::vatom::CenterShortcut
	Provides the keyword CENTER More...
class	PLMD::dimred::ClassicalMultiDimensionalScaling
	Provides the keyword CLASSICAL_MDS More...
class	PLMD::clusters::ClusterDiameter
	Provides the keyword CLUSTER_DIAMETER More...
class	PLMD::clusters::ClusterDistribution
	Provides the keyword CLUSTER_DISTRIBUTION_CALC More...
class	PLMD::clusters::ClusterDistributionShortcut
	Provides the keyword CLUSTER_DISTRIBUTION More...
class	PLMD::clusters::ClusterNatoms
	Provides the keyword CLUSTER_NATOMS More...
class	PLMD::clusters::ClusterProperties
	Provides the keyword CLUSTER_PROPERTIES More...
class	PLMD::clusters::ClusterWeights
	Provides the keyword CLUSTER_WEIGHTS More...
class	PLMD::clusters::ClusterWithSurface
	Provides the keyword CLUSTER_WITHSURFACE More...
class	PLMD::analysis::Collect
	Provides the keyword COLLECT More...
class	PLMD::analysis::CollectFrames
	Provides the keyword COLLECT_FRAMES More...
class	PLMD::colvar::ColvarFake
	Provides the keyword FAKE More...
class	CombineShortcut
	Provides the keyword COMBINE More...
class	PLMD::analysis::Committor
	Provides the keyword COMMITTOR More...
class	PLMD::valtools::Concatenate
	Provides the keyword CONCATENATE More...
class	PLMD::generic::Constant
	Provides the keyword CONSTANT More...
class	PLMD::colvar::ContactMap
	Provides the keyword CONTACTMAP More...
class	PLMD::adjmat::ContactMatrix
	Provides the keyword CONTACT_MATRIX_PROPER More...
class	PLMD::adjmat::ContactMatrixShortcut
	Provides the keyword CONTACT_MATRIX More...
class	PLMD::gridtools::ConvertToFES
	Provides the keyword CONVERT_TO_FES More...
class	PLMD::multicolvar::CoordAngles
	Provides the keyword COORD_ANGLES More...
class	PLMD::colvar::Coordination
	Provides the keyword COORDINATION More...
class	PLMD::symfunc::CoordinationNumbers
	Provides the keyword COORDINATIONNUMBER More...
class	PLMD::symfunc::CoordShellVectorFunction
	Provides the keyword FCCUBIC More...
class	PLMD::adjmat::CovarianceMatrix
	Provides the keyword COVARIANCE_MATRIX More...
class	PLMD::analysis::CreateMask
	Provides the keyword CREATE_MASK More...
class	PLMD::isdb::CS2Backbone
	Provides the keyword CS2BACKBONE More...
class	CustomShortcut
	Provides the keyword CUSTOM More...
class	CyHarmShortcut
	Provides the keyword CYLINDRICAL_HARMONIC More...
class	PLMD::generic::Debug
	Provides the keyword DEBUG More...
class	PLMD::volumes::Density
	Provides the keyword DENSITY More...
class	PLMD::adjmat::Determinant
	Provides the keyword DETERMINANT More...
class	PLMD::clusters::DFSClustering
	Provides the keyword DFSCLUSTERING More...
class	PLMD::colvar::DHEnergy
	Provides the keyword DHENERGY More...
class	PLMD::adjmat::DiagonalizeMatrix
	Provides the keyword DIAGONALIZE More...
class	DifferenceShortcut
	Provides the keyword DIFFERENCE More...
class	PLMD::multicolvar::Dihcor
	Provides the keyword DIHCOR More...
class	PLMD::colvar::DihedralCorrelation
	Provides the keyword DIHEDRAL_CORRELATION_SCALAR More...
class	DihedralCorrelationMulti
	Provides the keyword DIHEDRAL_CORRELATION_VECTOR More...
class	DihedralCorrelationShortcut
	Provides the keyword DIHEDRAL_CORRELATION More...
class	PLMD::colvar::Dimer
	Provides the keyword <a href="../../user-doc/html/_"_d_i_m_e_r.html"> "DIMER More...
class	PLMD::colvar::Dipole
	Provides the keyword DIPOLE_SCALAR More...
class	DipoleMulti
	Provides the keyword DIPOLE_VECTOR More...
class	DipoleShortcut
	Provides the keyword DIPOLE More...
class	PLMD::refdist::Displacement
	Provides the keyword DISPLACEMENT More...
class	PLMD::colvar::Distance
	Provides the keyword DISTANCE_SCALAR More...
class	PLMD::contour::DistanceFromContour
	Provides the keyword DISTANCE_FROM_CONTOUR More...
class	PLMD::contour::DistanceFromSphericalContour
	Provides the keyword DISTANCE_FROM_SPHERICAL_CONTOUR More...
class	PLMD::adjmat::DistanceMatrix
	Provides the keyword DISTANCE_MATRIX More...
class	DistanceMulti
	Provides the keyword DISTANCE_VECTOR More...
class	PLMD::multicolvar::Distances
	Provides the keyword DISTANCES More...
class	DistanceShortcut
	Provides the keyword DISTANCE More...
class	DomainDecomposition
	Provides the keyword DOMAIN_DECOMPOSITION More...
class	PLMD::crystdistrib::DopsShortcut
	Provides the keyword DOPS More...
class	PLMD::colvar::DRMSD
	Provides the keyword DRMSD More...
class	PLMD::generic::DumpAtoms
	Provides the keyword DUMPATOMS More...
class	PLMD::contour::DumpContour
	Provides the keyword DUMPCONTOUR More...
class	PLMD::generic::DumpDerivatives
	Provides the keyword DUMPDERIVATIVES More...
class	PLMD::generic::DumpForces
	Provides the keyword DUMPFORCES More...
class	PLMD::gridtools::DumpGrid
	Provides the keyword DUMPCUBE More...
class	PLMD::generic::DumpMassCharge
	Provides the keyword DUMPMASSCHARGE More...
class	PLMD::multicolvar::DumpMultiColvar
	Provides the keyword DUMPMULTICOLVAR More...
class	PLMD::generic::DumpPDB
	Provides the keyword DUMPPDB More...
class	PLMD::generic::DumpProjections
	Provides the keyword DUMPPROJECTIONS More...
class	PLMD::generic::DumpVector
	Provides the keyword DUMPVECTOR More...
class	DynamicReferenceRestraining
	Provides the keyword <a href="../../user-doc/html/_"_d_r_r.html"> "DRR More...
class	PLMD::opes::ECVcustom
	Provides the keyword ECV_CUSTOM More...
class	PLMD::opes::ECVlinear
	Provides the keyword ECV_LINEAR More...
class	PLMD::opes::ECVmultiThermal
	Provides the keyword ECV_MULTITHERMAL More...
class	PLMD::opes::ECVmultiThermalBaric
	Provides the keyword ECV_MULTITHERMAL_MULTIBARIC More...
class	PLMD::opes::ECVumbrellasFile
	Provides the keyword ECV_UMBRELLAS_FILE More...
class	PLMD::opes::ECVumbrellasLine
	Provides the keyword ECV_UMBRELLAS_LINE More...
class	PLMD::eds::EDS
	Provides the keyword <a href="../../user-doc/html/_"_e_d_s.html"> "EDS More...
class	PLMD::colvar::EEFSolv
	Provides the keyword EEFSOLV More...
class	PLMD::generic::EffectiveEnergyDrift
	Provides the keyword EFFECTIVE_ENERGY_DRIFT More...
class	PLMD::isdb::EMMI
	Provides the keyword EMMI More...
class	EMMIVOX
	Provides the keyword EMMIVOX More...
class	PLMD::generic::EndPlumed
	Provides the keyword ENDPLUMED More...
class	PLMD::colvar::Energy
	Provides the keyword ENERGY More...
class	PLMD::function::Ensemble
	Provides the keyword ENSEMBLE More...
class	PLMD::envsim::EnvironmentSimilarity
	Provides the keyword ENVIRONMENTSIMILARITY More...
class	PLMD::colvar::ERMSD
	Provides the keyword ERMSD More...
class	PLMD::refdist::EuclideanDistance
	Provides the keyword EUCLIDEAN_DISTANCE More...
class	PLMD::gridtools::EvaluateFunctionOnGrid
	Provides the keyword EVALUATE_FUNCTION_FROM_GRID More...
class	PLMD::bias::ExtendedLagrangian
	Provides the keyword EXTENDED_LAGRANGIAN More...
class	PLMD::bias::External
	Provides the keyword EXTERNAL More...
class	PLMD::colvar::ExtraCV
	Provides the keyword EXTRACV More...
class	PLMD::analysis::FarthestPointSampling
	Provides the keyword FARTHEST_POINT_SAMPLING More...
class	FccubicShortcut
	Provides the keyword FCCUBIC_FUNC More...
class	PLMD::contour::FindContour
	Provides the keyword FIND_CONTOUR More...
class	PLMD::contour::FindContourSurface
	Provides the keyword FIND_CONTOUR_SURFACE More...
class	PLMD::gridtools::FindGridOptimum
	Provides the keyword FIND_GRID_MAXIMUM More...
class	PLMD::contour::FindSphericalContour
	Provides the keyword FIND_SPHERICAL_CONTOUR More...
class	PLMD::fisst::FISST
	Provides the keyword FISST More...
class	PLMD::generic::FitToTemplate
	Provides the keyword FIT_TO_TEMPLATE More...
class	PLMD::vatom::FixedAtom
	Provides the keyword FIXEDATOM More...
class	PLMD::valtools::Flatten
	Provides the keyword FLATTEN More...
class	PLMD::generic::Flush
	Provides the keyword FLUSH More...
class	PLMD::fourier::FourierTransform
	Provides the keyword FOURIER_TRANSFORM More...
class	PLMD::isdb::FretEfficiency
	Provides the keyword FRET More...
class	PLMD::function::FuncPathGeneral
	Provides the keyword <a href="../../user-doc/html/_"_f_u_n_c_p_a_t_h_g_e_n_e_r_a_l.html"> "FUNCPATHGENERAL More...
class	PLMD::function::FuncPathMSD
	Provides the keyword FUNCPATHMSD More...
class	PLMD::function::FuncSumHills
	Provides the keyword FUNCSUMHILLS More...
class	PLMD::funnel::Funnel
	Provides the keyword FUNNEL More...
class	PLMD::funnel::FUNNEL_PS
	Provides the keyword FUNNEL_PS More...
class	PLMD::membranefusion::fusionPoreExpansionP
	Provides the keyword <a href="../../user-doc/html/_"_f_u_s_i_o_n_p_o_r_e_e_x_p_a_n_s_i_o_n_p.html"> "FUSIONPOREEXPANSIONP More...
class	PLMD::membranefusion::fusionPoreNucleationP
	Provides the keyword <a href="../../user-doc/html/_"_f_u_s_i_o_n_p_o_r_e_n_u_c_l_e_a_t_i_o_n_p.html"> "FUSIONPORENUCLEATIONP More...
class	PLMD::analysis::GatherReplicas
	Provides the keyword GATHER_REPLICAS More...
class	PLMD::mapping::GeometricPath
	Provides the keyword GEOMETRIC_PATH More...
class	PLMD::mapping::GeometricPathShortcut
	Provides the keyword GPATH More...
class	PLMD::colvar::GHBFIX
	Provides the keyword GHBFIX More...
class	PLMD::vatom::Ghost
	Provides the keyword GHOST More...
class	PLMD::gridtools::Gradient
	Provides the keyword GRADIENT More...
class	GridCustom
	Provides the keyword CUSTOM_GRID More...
class	GridSum
	Provides the keyword SUM_GRID More...
class	PLMD::Group
	Provides the keyword GROUP More...
class	PLMD::colvar::Gyration
	Provides the keyword GYRATION_FAST More...
class	PLMD::colvar::GyrationShortcut
	Provides the keyword GYRATION More...
class	PLMD::adjmat::HbondMatrix
	Provides the keyword HBOND_MATRIX More...
class	PLMD::pamm::HBPammMatrix
	Provides the keyword HBPAMM_MATRIX More...
class	PLMD::pamm::HBPammShortcut
	Provides the keyword HBPAMM_SD More...
class	PLMD::symfunc::HexacticParameter
	Provides the keyword HEXACTIC_PARAMETER More...
class	HighestShortcut
	Provides the keyword HIGHEST More...
class	PLMD::analysis::Histogram
	Provides the keyword HISTOGRAM More...
class	PLMD::generic::Include
	Provides the keyword INCLUDE More...
class	PLMD::multicolvar::InPlaneDistances
	Provides the keyword INPLANEDISTANCES More...
class	PLMD::gridtools::InterpolateGrid
	Provides the keyword INTERPOLATE_GRID More...
class	PLMD::adjmat::InvertMatrix
	Provides the keyword INVERT_MATRIX More...
class	PLMD::isdb::JCoupling
	Provides the keyword <a href="../../user-doc/html/_"_j_c_o_u_p_l_i_n_g.html"> "JCOUPLING More...
class	PLMD::gridtools::KDE
	Provides the keyword KDE More...
class	PLMD::refdist::Kernel
	Provides the keyword KERNEL More...
class	PLMD::gridtools::KLEntropy
	Provides the keyword KL_ENTROPY More...
class	PLMD::analysis::LandmarkSelection
	Provides the keyword LANDMARK_SELECT_STRIDE More...
class	LessThanShortcut
	Provides the keyword LESS_THAN More...
class	PLMD::setup::Load
	Provides the keyword LOAD More...
class	PLMD::symfunc::LocalAverage
	Provides the keyword LOCAL_AVERAGE More...
class	PLMD::symfunc::LocalCrystallinity
	Provides the keyword LOCAL_CRYSTALINITY More...
class	PLMD::function::LocalEnsemble
	Provides the keyword LOCALENSEMBLE More...
class	PLMD::symfunc::LocalSteinhardt
	Provides the keyword LOCAL_Q1 More...
class	PLMD::logmfd::LogMFD
	class for LogMFD parameters, variables and subroutines. More...
class	PLMD::analysis::LogSumExp
	Provides the keyword LOGSUMEXP More...
class	PLMD::maze::Loss
	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__l_o_s_s.html"> "MAZE_LOSS More...
class	PLMD::bias::LWalls
	Provides the keyword LOWER_WALLS_SCALAR More...
class	PLMD::refdist::MahalanobisDistance
	Provides the keyword MAHALANOBIS_DISTANCE More...
class	MatrixBetween
	Provides the keyword BETWEEN_MATRIX More...
class	MatrixCombine
	Provides the keyword COMBINE_MATRIX More...
class	MatrixCustom
	Provides the keyword CUSTOM_MATRIX More...
class	MatrixCyHarm
	Provides the keyword CYLINDRICAL_HARMONIC_MATRIX More...
class	MatrixFccubic
	Provides the keyword FCCUBIC_FUNC_MATRIX More...
class	MatrixLessThan
	Provides the keyword LESS_THAN_MATRIX More...
class	MatrixMoreThan
	Provides the keyword MORE_THAN_MATRIX More...
class	PLMD::refdist::MatrixProductDiagonal
	Provides the keyword MATRIX_PRODUCT_DIAGONAL More...
class	MatrixSpHarm
	Provides the keyword SPHERICAL_HARMONIC_MATRIX More...
class	MatrixSum
	Provides the keyword SUM_MATRIX More...
class	PLMD::adjmat::MatrixTimesMatrix
	Provides the keyword MATRIX_PRODUCT More...
class	PLMD::adjmat::MatrixTimesVector
	Provides the keyword MATRIX_VECTOR_PRODUCT More...
class	PLMD::bias::MaxEnt
	Provides the keyword MAXENT More...
class	PLMD::maze::Memetic
	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__m_e_m_e_t_i_c__s_a_m_p_l_i_n_g.html"> "MAZE_MEMETIC_SAMPLING More...
class	PLMD::membranefusion::memFusionP
	Provides the keyword <a href="../../user-doc/html/_"_m_e_m_f_u_s_i_o_n_p.html"> "MEMFUSIONP More...
class	PLMD::bias::MetaD
	Provides the keyword METAD More...
class	PLMD::isdb::Metainference
	Provides the keyword METAINFERENCE More...
class	PLMD::multicolvar::MFilterLess
	Provides the keyword MFILTER_LESS More...
class	PLMD::multicolvar::MFilterMore
	Provides the keyword MFILTER_MORE More...
class	MolInfo
	Provides the keyword MOLINFO More...
class	MomentsShortcut
	Provides the keyword MOMENTS More...
class	MoreThanShortcut
	Provides the keyword MORE_THAN More...
class	PLMD::bias::MovingRestraint
	Provides the keyword MOVINGRESTRAINT More...
class	MQMulti
	Provides the keyword MASS_VECTOR More...
class	MQShortcut
	Provides the keyword MASS More...
class	PLMD::gridtools::MultiColvarDensity
	Provides the keyword MULTICOLVARDENS More...
class	PLMD::colvar::MultiRMSD
	Provides the keyword MULTI_RMSD More...
class	PLMD::adjmat::Neighbors
	Provides the keyword NEIGHBORS More...
class	PLMD::isdb::NOE
	Provides the keyword NOE More...
class	PLMD::refdist::NormalizedEuclideanDistance
	Provides the keyword NORMALIZED_EUCLIDEAN_DISTANCE More...
class	PLMD::generic::Ones
	Provides the keyword ONES More...
class	PLMD::opes::OPESexpanded
	Provides the keyword OPES_EXPANDED More...
class	OPESmetad_c
	Provides the keyword OPES_METAD More...
class	OPESmetad_e
	Provides the keyword OPES_METAD_EXPLORE More...
class	PLMD::ves::Opt_Adam
	Provides the keyword OPT_ADAM More...
class	PLMD::ves::Opt_BachAveragedSGD
	Provides the keyword OPT_AVERAGED_SGD More...
class	PLMD::ves::Opt_Dummy
	Provides the keyword OPT_DUMMY More...
class	PLMD::ves::Opt_RobbinsMonroSGD
	Provides the keyword OPT_ROBBINS_MONRO_SGD More...
class	PLMD::maze::OptimizerBias
	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__o_p_t_i_m_i_z_e_r__b_i_a_s.html"> "MAZE_OPTIMIZER_BIAS More...
class	PLMD::adjmat::OuterProduct
	Provides the keyword OUTER_PRODUCT More...
class	PLMD::ves::OutputBasisFunctions
	Provides the keyword VES_OUTPUT_BASISFUNCTIONS More...
class	PLMD::clusters::OutputCluster
	Provides the keyword OUTPUT_CLUSTER More...
class	PLMD::ves::OutputFesBias
	Provides the keyword VES_OUTPUT_FES More...
class	PLMD::ves::OutputTargetDistribution
	Provides the keyword VES_OUTPUT_TARGET_DISTRIBUTION More...
class	PLMD::gridtools::PairEntropies
	Provides the keyword PAIRENTROPIES More...
class	PLMD::gridtools::PairEntropy
	Provides the keyword PAIRENTROPY More...
class	PLMD::pamm::PAMM
	Provides the keyword PAMM More...
class	PLMD::secondarystructure::ParabetaRMSD
	Provides the keyword PARABETARMSD More...
class	PLMD::mapping::Path
	Provides the keyword PATH More...
class	PLMD::mapping::PathDisplacements
	Provides the keyword AVERAGE_PATH_DISPLACEMENT More...
class	PLMD::colvar::PathMSD
	Provides the keyword PATHMSD More...
class	PLMD::mapping::PathReparameterization
	Provides the keyword REPARAMETERIZE_PATH More...
class	PLMD::PbcAction
	Provides the keyword PBC More...
class	PLMD::bias::PBMetaD
	Provides the keyword PBMETAD More...
class	PLMD::dimred::PCA
	Provides the keyword PCA More...
class	PLMD::colvar::PCARMSD
	Provides the keyword PCARMSD More...
class	PLMD::mapping::PCAVars
	Provides the keyword PCAVARS More...
class	PLMD::generic::PDB2Constant
	Provides the keyword PDB2CONSTANT More...
class	PiecewiseShortcut
	Provides the keyword PIECEWISE More...
class	PLMD::piv::PIV
	Provides the keyword PIV More...
class	PLMD::colvar::Plane
	Provides the keyword PLANE_SCALAR More...
class	PlaneMulti
	Provides the keyword PLANE_VECTOR More...
class	PLMD::multicolvar::PlaneShortcut
	Provides the keyword PLANES More...
class	PlaneShortcut
	Provides the keyword PLANE More...
class	PLMD::generic::Plumed
	Provides the keyword PLUMED More...
class	PLMD::colvar::Position
	Provides the keyword POSITION_SCALAR More...
class	PositionMulti
	Provides the keyword POSITION_VECTOR More...
class	PositionShortcut
	Provides the keyword POSITION More...
class	PLMD::isdb::PRE
	Provides the keyword PRE More...
class	PLMD::generic::Print
	Provides the keyword PRINT More...
class	PLMD::generic::PrintNDX
	Provides the keyword PRINT_NDX More...
class	PLMD::function::Product
	Provides the keyword PRODUCT More...
class	PLMD::colvar::ProjectionOnAxis
	Provides the keyword PROJECTION_ON_AXIS More...
class	PLMD::dimred::ProjectPoints
	Provides the keyword PROJECT_POINTS More...
class	PLMD::colvar::PropertyMap
	Provides the keyword PROPERTYMAP More...
class	PLMD::colvar::Puckering
	Provides the keyword PUCKERING More...
class	PytorchModel
	Provides the keyword PYTORCH_MODEL More...
class	PLMD::crystdistrib::Quaternion
	Provides the keyword QUATERNION_SCALAR More...
class	PLMD::crystdistrib::QuaternionBondProductMatrix
	Provides the keyword QUATERNION_BOND_PRODUCT_MATRIX More...
class	QuaternionMulti
	Provides the keyword QUATERNION_VECTOR More...
class	PLMD::crystdistrib::QuaternionProductMatrix
	Provides the keyword QUATERNION_PRODUCT_MATRIX More...
class	QuaternionShortcut
	Provides the keyword QUATERNION More...
class	PLMD::symfunc::RadialTetra
	Provides the keyword TETRA_RADIAL More...
class	PLMD::maze::Random_Acceleration_MD
	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__r_a_n_d_o_m__a_c_c_e_l_e_r_a_t_i_o_n__m_d.html"> "MAZE_RANDOM_ACCELERATION_MD More...
class	PLMD::maze::Random_Walk
	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__r_a_n_d_o_m__w_a_l_k.html"> "MAZE_RANDOM_WALK More...
class	PLMD::generic::RandomExchanges
	Provides the keyword RANDOM_EXCHANGES More...
class	PLMD::isdb::RDC
	Provides the keyword RDC More...
class	PLMD::gridtools::RDF
	Provides the keyword RDF More...
class	PLMD::generic::Read
	Provides the keyword READ More...
class	PLMD::gridtools::ReadGridInSetup
	Provides the keyword REFERENCE_GRID More...
class	PLMD::isdb::Rescale
	Provides the keyword RESCALE More...
class	PLMD::generic::ResetCell
	Provides the keyword RESET_CELL More...
class	PLMD::setup::Restart
	Provides the keyword RESTART More...
class	PLMD::bias::Restraint
	Provides the keyword RESTRAINT_SCALAR More...
class	PLMD::bias::RestraintShortcut
	Provides the keyword RESTRAINT More...
class	PLMD::bias::ReweightBias
	Provides the keyword REWEIGHT_BIAS More...
class	PLMD::bias::ReweightMetad
	Provides the keyword REWEIGHT_METAD More...
class	PLMD::bias::ReweightTemperaturePressure
	Provides the keyword REWEIGHT_TEMP_PRESS More...
class	PLMD::colvar::RMSD
	Provides the keyword RMSD_SCALAR More...
class	PLMD::colvar::RMSDShortcut
	Provides the keyword RMSD More...
class	PLMD::colvar::RMSDVector
	Provides the keyword RMSD_VECTOR More...
class	PLMD::crystdistrib::RopsShortcut
	Provides the keyword ROPS More...
class	PLMD::s2cm::S2ContactModel
	Provides the keyword S2CM More...
class	PLMD::sasa::SASA_HASEL
	Provides the keyword SASA_HASEL More...
class	PLMD::sasa::SASA_LCPO
	Provides the keyword SASA_LCPO More...
class	PLMD::isdb::SAXS
	Provides the keyword SAXS More...
class	ScalarBessel
	Provides the keyword BESSEL_SCALAR More...
class	ScalarCombine
	Provides the keyword COMBINE_SCALAR More...
class	ScalarCustom
	Provides the keyword CUSTOM_SCALAR More...
class	ScalarDifference
	Provides the keyword DIFFERENCE_SCALAR More...
class	ScalarEvalGrid
	Provides the keyword EVALUATE_FUNCTION_FROM_GRID_SCALAR More...
class	ScalarHighest
	Provides the keyword HIGHEST_SCALAR More...
class	ScalarMoments
	Provides the keyword MOMENTS_SCALAR More...
class	ScalarPiecewise
	Provides the keyword PIECEWISE_SCALAR More...
class	ScalarSort
	Provides the keyword SORT_SCALAR More...
class	ScalarSum
	Provides the keyword SUM_SCALAR More...
class	PLMD::secondarystructure::SecondaryStructureRMSD
	Base action for calculating things like AlphRMSD, AntibetaRMSD, etc. More...
class	PLMD::isdb::Select
	Provides the keyword SELECT More...
class	PLMD::valtools::SelectComponents
	Provides the keyword SELECT_COMPONENTS More...
class	PLMD::colvar::SelectMassCharge
	Provides the keyword MASS_SCALAR More...
class	PLMD::isdb::Selector
	Provides the keyword SELECTOR More...
class	PLMD::valtools::SelectWithMask
	Provides the keyword SELECT_WITH_MASK More...
class	PLMD::isdb::Shadow
	Provides the keyword SHADOW More...
class	PLMD::maze::Simulated_Annealing
	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__s_i_m_u_l_a_t_e_d__a_n_n_e_a_l_i_n_g.html"> "MAZE_SIMULATED_ANNEALING More...
class	PLMD::dimred::SketchMap
	Provides the keyword SKETCHMAP More...
class	PLMD::dimred::SketchMapProjection
	Provides the keyword SKETCHMAP_PROJECTION More...
class	PLMD::symfunc::SMAC
	Provides the keyword SMAC More...
class	SortShortcut
	Provides the keyword SORT More...
class	SpHarmShortcut
	Provides the keyword SPHERICAL_HARMONIC More...
class	PLMD::adjmat::Sprint
	Provides the keyword SPRINT More...
class	PLMD::function::Stats
	Provides the keyword STATS More...
class	PLMD::maze::Steered_MD
	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__s_t_e_e_r_e_d__m_d.html"> "MAZE_STEERED_MD More...
class	PLMD::symfunc::Steinhardt
	Provides the keyword Q1 More...
class	SumShortcut
	Provides the keyword SUM More...
class	PLMD::ves::TD_Chi
	Provides the keyword TD_CHI More...
class	PLMD::ves::TD_ChiSquared
	Provides the keyword TD_CHISQUARED More...
class	PLMD::ves::TD_Custom
	Provides the keyword TD_CUSTOM More...
class	PLMD::ves::TD_Exponential
	Provides the keyword TD_EXPONENTIAL More...
class	PLMD::ves::TD_ExponentiallyModifiedGaussian
	Provides the keyword TD_EXPONENTIALLY_MODIFIED_GAUSSIAN More...
class	PLMD::ves::TD_Gaussian
	Provides the keyword TD_GAUSSIAN More...
class	PLMD::ves::TD_GeneralizedExtremeValue
	Provides the keyword TD_GENERALIZED_EXTREME_VALUE More...
class	PLMD::ves::TD_GeneralizedNormal
	Provides the keyword TD_GENERALIZED_NORMAL More...
class	PLMD::ves::TD_Grid
	Provides the keyword TD_GRID More...
class	PLMD::ves::TD_LinearCombination
	Provides the keyword TD_LINEAR_COMBINATION More...
class	PLMD::ves::TD_Multicanonical
	Provides the keyword TD_MULTICANONICAL More...
class	PLMD::ves::TD_MultithermalMultibaric
	Provides the keyword TD_MULTITHERMAL_MULTIBARIC More...
class	PLMD::ves::TD_ProductCombination
	Provides the keyword TD_PRODUCT_COMBINATION More...
class	PLMD::ves::TD_ProductDistribution
	Provides the keyword TD_PRODUCT_DISTRIBUTION More...
class	PLMD::ves::TD_Uniform
	Provides the keyword TD_UNIFORM More...
class	PLMD::ves::TD_VonMises
	Provides the keyword TD_VONMISES More...
class	PLMD::ves::TD_WellTempered
	Provides the keyword TD_WELLTEMPERED More...
class	PLMD::colvar::Template
	Provides the keyword TEMPLATE More...
class	PLMD::symfunc::ThreeBodyGFunctions
	Provides the keyword GSYMFUNC_THREEBODY More...
class	PLMD::generic::Time
	Provides the keyword TIME More...
class	PLMD::adjmat::TopologyMatrix
	Provides the keyword TOPOLOGY_MATRIX More...
class	PLMD::colvar::Torsion
	Provides the keyword TORSION_SCALAR More...
class	TorsionMulti
	Provides the keyword TORSION_VECTOR More...
class	PLMD::multicolvar::Torsions
	Provides the keyword TORSIONS More...
class	TorsionShortcut
	Provides the keyword TORSION More...
class	PLMD::adjmat::TorsionsMatrix
	Provides the keyword TORSIONS_MATRIX More...
class	PLMD::adjmat::TransposeMatrix
	Provides the keyword TRANSPOSE More...
class	PLMD::setup::Units
	Provides the keyword UNITS More...
class	PLMD::generic::UpdateIf
	Provides the keyword UPDATE_IF More...
class	PLMD::multicolvar::UWalls
	Provides the keyword UWALLS More...
class	PLMD::bias::UWalls
	Provides the keyword UPPER_WALLS_SCALAR More...
class	VectorBessel
	Provides the keyword BESSEL_VECTOR More...
class	VectorBetween
	Provides the keyword BETWEEN_VECTOR More...
class	VectorCombine
	Provides the keyword COMBINE_VECTOR More...
class	VectorCustom
	Provides the keyword CUSTOM_VECTOR More...
class	VectorDifference
	Provides the keyword DIFFERENCE_VECTOR More...
class	VectorEvalGrid
	Provides the keyword EVALUATE_FUNCTION_FROM_GRID_VECTOR More...
class	VectorHighest
	Provides the keyword HIGHEST_VECTOR More...
class	VectorLessThan
	Provides the keyword LESS_THAN_VECTOR More...
class	VectorMoments
	Provides the keyword MOMENTS_VECTOR More...
class	VectorMoreThan
	Provides the keyword MORE_THAN_VECTOR More...
class	VectorSort
	Provides the keyword SORT_VECTOR More...
class	VectorSum
	Provides the keyword SUM_VECTOR More...
class	PLMD::ves::VesDeltaF
	Provides the keyword VES_DELTA_F More...
class	PLMD::ves::VesLinearExpansion
	Provides the keyword VES_LINEAR_EXPANSION More...
class	PLMD::colvar::Volume
	Provides the keyword VOLUME More...
class	PLMD::volumes::VolumeAround
	Provides the keyword AROUND_CALC More...
class	VolumeAroundShortcut
	Provides the keyword AROUND More...
class	PLMD::volumes::VolumeCavity
	Provides the keyword CAVITY_CALC More...
class	VolumeCavityShortcut
	Provides the keyword CAVITY More...
class	PLMD::volumes::VolumeInCylinder
	Provides the keyword INCYLINDER_CALC More...
class	VolumeInCylinderShortcut
	Provides the keyword INCYLINDER More...
class	PLMD::volumes::VolumeInEnvelope
	Provides the keyword INENVELOPE_CALC More...
class	VolumeInEnvelopeShortcut
	Provides the keyword INENVELOPE More...
class	PLMD::volumes::VolumeInSphere
	Provides the keyword INSPHERE_CALC More...
class	VolumeInSphereShortcut
	Provides the keyword INSPHERE More...
class	PLMD::volumes::VolumeTetrapore
	Provides the keyword TETRAHEDRALPORE_CALC More...
class	VolumeTetraporeShortcut
	Provides the keyword TETRAHEDRALPORE More...
class	PLMD::adjmat::Voronoi
	Provides the keyword VORONOI More...
class	PLMD::adjmat::VStack
	Provides the keyword VSTACK More...
class	PLMD::bias::Walls
	Provides the keyword UPPER_WALLS More...
class	PLMD::analysis::Wham
	Provides the keyword WHAM More...
class	PLMD::analysis::WhamHistogram
	Provides the keyword WHAM_HISTOGRAM More...
class	PLMD::analysis::WhamWeights
	Provides the keyword WHAM_WEIGHTS More...
class	PLMD::generic::WholeMolecules
	Provides the keyword WHOLEMOLECULES More...
class	PLMD::generic::WrapAround
	Provides the keyword WRAPAROUND More...
class	PLMD::multicolvar::XAngle
	Provides the keyword XANGLES More...
class	PLMD::multicolvar::XYTorsions
	Provides the keyword XYTORSIONS More...

Detailed Description

Classes which implement directive that we used in the plumed input file.

Most of these classes are only used to provide a new feature which will be available from the plumed input file. As such, they are typically not reused in other places of the code. For this reason, almost all of them are directly provided into an implementation file (.cpp), and have no accociated header file (.h). A notable exceptions is PLMD::SetupMolInfo, which needs to be accessed directly from other classes.

Each of these classes provides one directive for the plumed input file. This list is built automatically based on the PLUMED_REGISTER_ACTION macro.