Classes providing input directives

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

Classes
class	PLMD::adjmat::ClusterDiameter
	Provides the keyword CLUSTER_DIAMETER More...
class	PLMD::adjmat::ClusterDistribution
	Provides the keyword CLUSTER_DISTRIBUTION More...
class	PLMD::adjmat::ClusterProperties
	Provides the keyword CLUSTER_PROPERTIES More...
class	PLMD::adjmat::ClusterSize
	Provides the keyword CLUSTER_NATOMS More...
class	PLMD::adjmat::ClusterWithSurface
	Provides the keyword CLUSTER_WITHSURFACE More...
class	PLMD::adjmat::ContactAlignedMatrix
	Provides the keyword ALIGNED_MATRIX More...
class	PLMD::adjmat::ContactMatrix
	Provides the keyword CONTACT_MATRIX More...
class	PLMD::adjmat::DFSClustering
	Provides the keyword DFSCLUSTERING More...
class	PLMD::adjmat::HBondMatrix
	Provides the keyword HBOND_MATRIX More...
class	PLMD::adjmat::MatrixColumnSums
	Provides the keyword COLUMNSUMS More...
class	PLMD::adjmat::MatrixRowSums
	Provides the keyword ROWSUMS More...
class	PLMD::adjmat::OutputCluster
	Provides the keyword OUTPUT_CLUSTER More...
class	PLMD::adjmat::SMACMatrix
	Provides the keyword SMAC_MATRIX More...
class	PLMD::adjmat::Sprint
	Provides the keyword SPRINT More...
class	PLMD::analysis::Average
	Provides the keyword AVERAGE More...
class	PLMD::analysis::ClassicalMultiDimensionalScaling
	Provides the keyword CLASSICAL_MDS More...
class	PLMD::analysis::Committor
	Provides the keyword COMMITTOR More...
class	PLMD::analysis::Histogram
	Provides the keyword HISTOGRAM More...
class	PLMD::analysis::PCA
	Provides the keyword PCA More...
class	PLMD::bias::ABMD
	Provides the keyword ABMD More...
class	PLMD::bias::BiasValue
	Provides the keyword BIASVALUE More...
class	PLMD::bias::ExtendedLagrangian
	Provides the keyword EXTENDED_LAGRANGIAN More...
class	PLMD::bias::External
	Provides the keyword EXTERNAL More...
class	PLMD::bias::LWalls
	Provides the keyword LOWER_WALLS More...
class	PLMD::bias::MetaD
	Provides the keyword METAD More...
class	PLMD::bias::Metainference
	Provides the keyword METAINFERENCE More...
class	PLMD::bias::MovingRestraint
	Provides the keyword MOVINGRESTRAINT More...
class	PLMD::bias::PBMetaD
	Provides the keyword PBMETAD More...
class	PLMD::bias::Restraint
	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::ReweightTemperature
	Provides the keyword REWEIGHT_TEMP More...
class	PLMD::bias::UWalls
	Provides the keyword UPPER_WALLS More...
class	PLMD::colvar::Angle
	Provides the keyword ANGLE More...
class	PLMD::colvar::Cell
	Provides the keyword CELL More...
class	PLMD::colvar::Constant
	Provides the keyword CONSTANT More...
class	PLMD::colvar::ContactMap
	Provides the keyword CONTACTMAP More...
class	PLMD::colvar::Coordination
	Provides the keyword COORDINATION More...
class	PLMD::colvar::CS2Backbone
	Provides the keyword CS2BACKBONE More...
class	PLMD::colvar::DHEnergy
	Provides the keyword DHENERGY More...
class	PLMD::colvar::Dipole
	Provides the keyword DIPOLE More...
class	PLMD::colvar::Distance
	Provides the keyword DISTANCE More...
class	PLMD::colvar::DRMSD
	Provides the keyword DRMSD More...
class	PLMD::colvar::Energy
	Provides the keyword ENERGY More...
class	PLMD::colvar::ERMSD
	Provides the keyword ERMSD More...
class	PLMD::colvar::ColvarFake
	Provides the keyword FAKE More...
class	PLMD::colvar::FretEfficiency
	Provides the keyword FRET More...
class	PLMD::colvar::Gyration
	Provides the keyword GYRATION More...
class	PLMD::colvar::JCoupling
	Provides the keyword <a href="../../user-doc/html/_"_j_c_o_u_p_l_i_n_g.html"> "JCOUPLING More...
class	PLMD::colvar::MultiRMSD
	Provides the keyword MULTI-RMSD More...
class	PLMD::colvar::NOE
	Provides the keyword NOE More...
class	PLMD::colvar::PathMSD
	Provides the keyword PATHMSD More...
class	PLMD::colvar::PCARMSD
	Provides the keyword PCARMSD More...
class	PLMD::colvar::Position
	Provides the keyword POSITION More...
class	PLMD::colvar::PRE
	Provides the keyword PRE More...
class	PLMD::colvar::PropertyMap
	Provides the keyword PROPERTYMAP More...
class	PLMD::colvar::Puckering
	Provides the keyword PUCKERING More...
class	PLMD::colvar::RDC
	Provides the keyword RDC More...
class	PLMD::colvar::RMSD
	Provides the keyword RMSD More...
class	PLMD::colvar::Template
	Provides the keyword TEMPLATE More...
class	PLMD::colvar::Torsion
	Provides the keyword TORSION More...
class	PLMD::colvar::Volume
	Provides the keyword VOLUME More...
class	PLMD::crystallization::Fccubic
	Provides the keyword FCCUBIC More...
class	PLMD::crystallization::Gradient
	Provides the keyword GRADIENT More...
class	PLMD::crystallization::InterMolecularTorsions
	Provides the keyword INTERMOLECULARTORSIONS More...
class	PLMD::crystallization::MoleculeOrientation
	Provides the keyword MOLECULES More...
class	PLMD::crystallization::MoleculePlane
	Provides the keyword PLANES More...
class	PLMD::crystallization::Q3
	Provides the keyword Q3 More...
class	PLMD::crystallization::LOCAL_Q3
	Provides the keyword LOCAL_Q3 More...
class	PLMD::crystallization::Q4
	Provides the keyword Q4 More...
class	PLMD::crystallization::LOCAL_Q4
	Provides the keyword LOCAL_Q4 More...
class	PLMD::crystallization::Q6
	Provides the keyword Q6 More...
class	PLMD::crystallization::LOCAL_Q6
	Provides the keyword LOCAL_Q6 More...
class	PLMD::crystallization::SimpleCubic
	Provides the keyword SIMPLECUBIC More...
class	PLMD::crystallization::SMAC
	Provides the keyword SMAC More...
class	PLMD::crystallization::Tetrahedral
	Provides the keyword TETRAHEDRAL More...
class	PLMD::function::Combine
	Provides the keyword COMBINE More...
class	PLMD::function::Ensemble
	Provides the keyword ENSEMBLE More...
class	PLMD::function::FuncPathMSD
	Provides the keyword FUNCPATHMSD More...
class	PLMD::function::FuncSumHills
	Provides the keyword FUNCSUMHILLS More...
class	PLMD::function::LocalEnsemble
	Provides the keyword LOCALENSEMBLE More...
class	PLMD::function::Matheval
	Provides the keyword MATHEVAL More...
class	PLMD::function::Piecewise
	Provides the keyword PIECEWISE More...
class	PLMD::function::Sort
	Provides the keyword SORT More...
class	PLMD::function::Stats
	Provides the keyword STATS More...
class	PLMD::function::Target
	Provides the keyword TARGET More...
class	PLMD::generic::Debug
	Provides the keyword DEBUG More...
class	PLMD::generic::DumpAtoms
	Provides the keyword DUMPATOMS More...
class	PLMD::generic::DumpDerivatives
	Provides the keyword DUMPDERIVATIVES More...
class	PLMD::generic::DumpForces
	Provides the keyword DUMPFORCES More...
class	PLMD::generic::DumpMassCharge
	Provides the keyword DUMPMASSCHARGE More...
class	PLMD::generic::DumpProjections
	Provides the keyword DUMPPROJECTIONS More...
class	PLMD::generic::EffectiveEnergyDrift
	Provides the keyword EFFECTIVE_ENERGY_DRIFT More...
class	PLMD::generic::FitToTemplate
	Provides the keyword FIT_TO_TEMPLATE More...
class	PLMD::generic::Flush
	Provides the keyword FLUSH More...
class	PLMD::generic::Group
	Provides the keyword GROUP More...
class	PLMD::generic::Include
	Provides the keyword INCLUDE More...
class	PLMD::generic::Print
	Provides the keyword PRINT More...
class	PLMD::generic::RandomExchanges
	Provides the keyword RANDOM_EXCHANGES More...
class	PLMD::generic::Read
	Provides the keyword READ More...
class	PLMD::generic::ResetCell
	Provides the keyword RESET_CELL More...
class	PLMD::generic::Time
	Provides the keyword TIME More...
class	PLMD::generic::UpdateIf
	Provides the keyword UPDATE_IF More...
class	PLMD::generic::WholeMolecules
	Provides the keyword WHOLEMOLECULES More...
class	PLMD::generic::WrapAround
	Provides the keyword WRAPAROUND More...
class	PLMD::gridtools::ConvertToFES
	Provides the keyword CONVERT_TO_FES More...
class	PLMD::gridtools::DumpCube
	Provides the keyword DUMPCUBE More...
class	PLMD::gridtools::DumpGrid
	Provides the keyword DUMPGRID More...
class	PLMD::gridtools::FindContour
	Provides the keyword FIND_CONTOUR More...
class	PLMD::gridtools::FindContourSurface
	Provides the keyword FIND_CONTOUR_SURFACE More...
class	PLMD::gridtools::FindSphericalContour
	Provides the keyword FIND_SPHERICAL_CONTOUR More...
class	PLMD::gridtools::FourierTransform
	Provides the keyword FOURIER_TRANSFORM More...
class	PLMD::gridtools::InterpolateGrid
	Provides the keyword INTERPOLATE_GRID More...
class	PLMD::manyrestraints::UWalls
	Provides the keyword UWALLS More...
class	PLMD::mapping::Path
	Provides the keyword PATH More...
class	PLMD::mapping::PCAVars
	Provides the keyword PCAVARS More...
class	PLMD::mapping::PropertyMap
	Provides the keyword GPROPERTYMAP More...
class	PLMD::multicolvar::AlphaBeta
	Provides the keyword ALPHABETA More...
class	PLMD::multicolvar::Angles
	Provides the keyword ANGLES More...
class	PLMD::multicolvar::Bridge
	Provides the keyword BRIDGE More...
class	PLMD::multicolvar::CenterOfMultiColvar
	Provides the keyword CENTER_OF_MULTICOLVAR More...
class	PLMD::multicolvar::CoordinationNumbers
	Provides the keyword COORDINATIONNUMBER More...
class	PLMD::multicolvar::Density
	Provides the keyword DENSITY More...
class	PLMD::multicolvar::DihedralCorrelation
	Provides the keyword DIHCOR More...
class	PLMD::multicolvar::DistanceFromContour
	Provides the keyword DISTANCE_FROM_CONTOUR More...
class	PLMD::multicolvar::Distances
	Provides the keyword DISTANCES More...
class	PLMD::multicolvar::DumpMultiColvar
	Provides the keyword DUMPMULTICOLVAR More...
class	PLMD::multicolvar::FilterBetween
	Provides the keyword MFILTER_BETWEEN More...
class	PLMD::multicolvar::FilterLess
	Provides the keyword MFILTER_LESS More...
class	PLMD::multicolvar::FilterMore
	Provides the keyword MFILTER_MORE More...
class	PLMD::multicolvar::InPlaneDistances
	Provides the keyword INPLANEDISTANCES More...
class	PLMD::multicolvar::LocalAverage
	Provides the keyword LOCAL_AVERAGE More...
class	PLMD::multicolvar::MultiColvarDensity
	Provides the keyword MULTICOLVARDENS More...
class	PLMD::multicolvar::NumberOfLinks
	Provides the keyword NLINKS More...
class	PLMD::multicolvar::Torsions
	Provides the keyword TORSIONS More...
class	PLMD::multicolvar::VolumeAround
	Provides the keyword AROUND More...
class	PLMD::multicolvar::VolumeCavity
	Provides the keyword CAVITY More...
class	PLMD::multicolvar::VolumeInCylinder
	Provides the keyword INCYLINDER More...
class	PLMD::multicolvar::VolumeInSphere
	Provides the keyword INSPHERE More...
class	PLMD::multicolvar::VolumeTetrapore
	Provides the keyword TETRAHEDRALPORE More...
class	PLMD::multicolvar::XDistances
	Provides the keyword XDISTANCES More...
class	PLMD::multicolvar::XYDistances
	Provides the keyword XYDISTANCES More...
class	PLMD::secondarystructure::AlphaRMSD
	Provides the keyword ALPHARMSD More...
class	PLMD::secondarystructure::AntibetaRMSD
	Provides the keyword ANTIBETARMSD More...
class	PLMD::secondarystructure::ParabetaRMSD
	Provides the keyword PARABETARMSD More...
class	PLMD::setup::Load
	Provides the keyword LOAD More...
class	PLMD::setup::MolInfo
	Provides the keyword MOLINFO More...
class	PLMD::setup::Restart
	Provides the keyword RESTART More...
class	PLMD::setup::Units
	Provides the keyword UNITS More...
class	PLMD::vatom::Center
	Provides the keyword CENTER More...
class	PLMD::vatom::COM
	Provides the keyword COM More...
class	PLMD::vatom::FixedAtom
	Provides the keyword FIXEDATOM More...
class	PLMD::vatom::Ghost
	Provides the keyword GHOST 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.