| CPLMD::Tools::_Unique_if< T > | Mimic C++14 std::make_unique |
| CPLMD::Tools::_Unique_if< T[]> | |
| CPLMD::Tools::_Unique_if< T[N]> | |
| CPLMD::Action | Base class for all the input Actions |
| CPLMD::ActionAnyorder | Action used to create a PLMD::Action that can go both before and after ActionSetup actions |
| CPLMD::GenericMolInfo | |
| CPLMD::generic::Include | Provides the keyword INCLUDE |
| CPLMD::ActionAtomistic | Action used to create objects that access the positions of the atoms from the MD code |
| CPLMD::ActionWithVirtualAtom | Inherit from here if you are calculating the position of a virtual atom (eg a center of mass) |
| CPLMD::multicolvar::CenterOfMultiColvar | Provides the keyword CENTER_OF_MULTICOLVAR |
| CPLMD::vatom::Center | Provides the keyword CENTER |
| CPLMD::vatom::FixedAtom | Provides the keyword FIXEDATOM |
| CPLMD::vatom::Ghost | Provides the keyword GHOST |
| CPLMD::Colvar | This is the abstract base class to use for implementing new collective variables, within it there is information as to how to go about implementing a new CV |
| CPLMD::colvar::Angle | Provides the keyword ANGLE |
| CPLMD::colvar::Cell | Provides the keyword CELL |
| CPLMD::colvar::ColvarFake | Provides the keyword FAKE |
| CPLMD::colvar::Constant | Provides the keyword CONSTANT |
| CPLMD::colvar::ContactMap | Provides the keyword CONTACTMAP |
| CPLMD::colvar::CoordinationBase | |
| CPLMD::colvar::Coordination | Provides the keyword COORDINATION |
| CPLMD::colvar::DHEnergy | Provides the keyword DHENERGY |
| CPLMD::colvar::GHBFIX | Provides the keyword GHBFIX |
| CPLMD::colvar::DRMSD | Provides the keyword DRMSD |
| CPLMD::colvar::Dimer | Provides the keyword <a href="../../user-doc/html/_"_d_i_m_e_r.html"> "DIMER |
| CPLMD::colvar::Dipole | Provides the keyword DIPOLE |
| CPLMD::colvar::Distance | Provides the keyword DISTANCE |
| CPLMD::colvar::EEFSolv | Provides the keyword EEFSOLV |
| CPLMD::colvar::ERMSD | Provides the keyword ERMSD |
| CPLMD::colvar::Energy | Provides the keyword ENERGY |
| CPLMD::colvar::ExtraCV | Provides the keyword EXTRACV |
| CPLMD::colvar::Gyration | Provides the keyword GYRATION |
| CPLMD::colvar::MultiRMSD | Provides the keyword MULTI_RMSD |
| CPLMD::colvar::PCARMSD | Provides the keyword PCARMSD |
| CPLMD::colvar::PathMSDBase | |
| CPLMD::colvar::PathMSD | Provides the keyword PATHMSD |
| CPLMD::colvar::PropertyMap | Provides the keyword PROPERTYMAP |
| CPLMD::colvar::Position | Provides the keyword POSITION |
| CPLMD::colvar::ProjectionOnAxis | Provides the keyword PROJECTION_ON_AXIS |
| CPLMD::colvar::Puckering | Provides the keyword PUCKERING |
| CPLMD::colvar::RMSD | Provides the keyword RMSD |
| CPLMD::colvar::Template | Provides the keyword TEMPLATE |
| CPLMD::colvar::Torsion | Provides the keyword TORSION |
| CPLMD::colvar::Volume | Provides the keyword VOLUME |
| CPLMD::funnel::FUNNEL_PS | Provides the keyword FUNNEL_PS |
| CPLMD::isdb::FretEfficiency | Provides the keyword FRET |
| CPLMD::maze::Loss | Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__l_o_s_s.html"> "MAZE_LOSS |
| CPLMD::maze::Optimizer | Base class for implementing optimizers for ligand unbinding |
| CPLMD::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 |
| CPLMD::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 |
| CPLMD::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 |
| CPLMD::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 |
| CPLMD::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 |
| CPLMD::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 |
| CPLMD::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 |
| CPLMD::membranefusion::memFusionP | Provides the keyword <a href="../../user-doc/html/_"_m_e_m_f_u_s_i_o_n_p.html"> "MEMFUSIONP |
| CPLMD::piv::PIV | Provides the keyword PIV |
| CPLMD::s2cm::S2ContactModel | Provides the keyword S2CM |
| CPLMD::sasa::SASA_HASEL | Provides the keyword SASA_HASEL |
| CPLMD::sasa::SASA_LCPO | Provides the keyword SASA_LCPO |
| CPLMD::GenericMolInfo | |
| CPLMD::analysis::AnalysisBase | This is the abstract base class to use for implementing new methods for analyzing the trajectory |
| CPLMD::analysis::EuclideanDissimilarityMatrix | Provides the keyword EUCLIDEAN_DISSIMILARITIES |
| CPLMD::analysis::LandmarkSelectionBase | |
| CPLMD::analysis::FarthestPointSampling | Provides the keyword LANDMARK_SELECT_FPS |
| CPLMD::analysis::LandmarkStaged | Provides the keyword LANDMARK_SELECT_STAGED |
| CPLMD::analysis::ReselectLandmarks | Provides the keyword RESELECT_LANDMARKS |
| CPLMD::analysis::SelectRandomFrames | Provides the keyword LANDMARK_SELECT_RANDOM |
| CPLMD::analysis::SelectWithStride | Provides the keyword LANDMARK_SELECT_STRIDE |
| CPLMD::analysis::OutputColvarFile | Provides the keyword OUTPUT_ANALYSIS_DATA_TO_COLVAR |
| CPLMD::analysis::OutputPDBFile | Provides the keyword OUTPUT_ANALYSIS_DATA_TO_PDB |
| CPLMD::analysis::PrintDissimilarityMatrix | Provides the keyword PRINT_DISSIMILARITY_MATRIX |
| CPLMD::analysis::ReadAnalysisFrames | Provides the keyword COLLECT_FRAMES |
| CPLMD::analysis::ReadDissimilarityMatrix | Provides the keyword READ_DISSIMILARITY_MATRIX |
| CPLMD::dimred::DimensionalityReductionBase | |
| CPLMD::dimred::ClassicalMultiDimensionalScaling | Provides the keyword CLASSICAL_MDS |
| CPLMD::dimred::PCA | Provides the keyword PCA |
| CPLMD::dimred::SketchMapBase | |
| CPLMD::dimred::SketchMapConjGrad | Provides the keyword SKETCHMAP_CONJGRAD |
| CPLMD::dimred::SketchMapPointwise | Provides the keyword SKETCHMAP_POINTWISE |
| CPLMD::dimred::SketchMapRead | Provides the keyword SKETCHMAP_READ |
| CPLMD::dimred::SketchMapSmacof | Provides the keyword SKETCHMAP_SMACOF |
| CPLMD::dimred::SmacofMDS | Provides the keyword SMACOF_MDS |
| CPLMD::dimred::OutputPCAProjection | Provides the keyword OUTPUT_PCA_PROJECTION |
| CPLMD::dimred::ProjectNonLandmarkPoints | Provides the keyword PROJECT_ALL_ANALYSIS_DATA |
| CPLMD::generic::DumpAtoms | Provides the keyword DUMPATOMS |
| CPLMD::generic::DumpMassCharge | Provides the keyword DUMPMASSCHARGE |
| CPLMD::generic::FitToTemplate | Provides the keyword FIT_TO_TEMPLATE |
| CPLMD::generic::Group | Provides the keyword GROUP |
| CPLMD::generic::Plumed | Provides the keyword PLUMED |
| CPLMD::generic::ResetCell | Provides the keyword RESET_CELL |
| CPLMD::generic::WholeMolecules | Provides the keyword WHOLEMOLECULES |
| CPLMD::generic::WrapAround | Provides the keyword WRAPAROUND |
| CPLMD::isdb::EMMI | Provides the keyword EMMI |
| CPLMD::isdb::MetainferenceBase | This is the abstract base class to use for implementing new ISDB Metainference actions, within it there is information as to how to go about implementing a new Metainference action |
| CPLMD::isdb::CS2Backbone | Provides the keyword CS2BACKBONE |
| CPLMD::isdb::JCoupling | Provides the keyword <a href="../../user-doc/html/_"_j_c_o_u_p_l_i_n_g.html"> "JCOUPLING |
| CPLMD::isdb::NOE | Provides the keyword NOE |
| CPLMD::isdb::PRE | Provides the keyword PRE |
| CPLMD::isdb::RDC | Provides the keyword RDC |
| CPLMD::isdb::SAXS | Provides the keyword SAXS |
| CPLMD::mapping::Mapping | |
| CPLMD::mapping::AdaptivePath | Provides the keyword ADAPTIVE_PATH |
| CPLMD::mapping::PathBase | |
| CPLMD::mapping::Path | Provides the keyword PATH |
| CPLMD::mapping::PropertyMap | Provides the keyword GPROPERTYMAP |
| CPLMD::mapping::PCAVars | Provides the keyword PCAVARS |
| CPLMD::multicolvar::DumpMultiColvar | Provides the keyword DUMPMULTICOLVAR |
| CPLMD::multicolvar::MultiColvarBase | |
| CPLMD::adjmat::ActionWithInputMatrix | |
| CPLMD::adjmat::ClusteringBase | |
| CPLMD::adjmat::ClusterWithSurface | Provides the keyword CLUSTER_WITHSURFACE |
| CPLMD::adjmat::DFSClustering | Provides the keyword DFSCLUSTERING |
| CPLMD::adjmat::MatrixColumnSums | Provides the keyword COLUMNSUMS |
| CPLMD::adjmat::MatrixRowSums | Provides the keyword ROWSUMS |
| CPLMD::adjmat::Sprint | Provides the keyword SPRINT |
| CPLMD::adjmat::AdjacencyMatrixBase | |
| CPLMD::adjmat::AlignedMatrixBase | |
| CPLMD::adjmat::ContactAlignedMatrix | Provides the keyword ALIGNED_MATRIX |
| CPLMD::adjmat::SMACMatrix | Provides the keyword SMAC_MATRIX |
| CPLMD::adjmat::ContactMatrix | Provides the keyword CONTACT_MATRIX |
| CPLMD::adjmat::HBondMatrix | Provides the keyword HBOND_MATRIX |
| CPLMD::adjmat::TopologyMatrix | Provides the keyword TOPOLOGY_MATRIX |
| CPLMD::pamm::HBPammMatrix | Provides the keyword HBPAMM_MATRIX |
| CPLMD::adjmat::ClusterAnalysisBase | |
| CPLMD::adjmat::ClusterDiameter | Provides the keyword CLUSTER_DIAMETER |
| CPLMD::adjmat::ClusterDistribution | Provides the keyword CLUSTER_DISTRIBUTION |
| CPLMD::adjmat::ClusterProperties | Provides the keyword CLUSTER_PROPERTIES |
| CPLMD::adjmat::ClusterSize | Provides the keyword CLUSTER_NATOMS |
| CPLMD::crystallization::CubicHarmonicBase | |
| CPLMD::crystallization::Fccubic | Provides the keyword FCCUBIC |
| CPLMD::crystallization::SimpleCubic | Provides the keyword SIMPLECUBIC |
| CPLMD::crystallization::Tetrahedral | Provides the keyword TETRAHEDRAL |
| CPLMD::crystallization::EnvironmentSimilarity | Provides the keyword ENVIRONMENTSIMILARITY |
| CPLMD::crystallization::InterMolecularTorsions | Provides the keyword INTERMOLECULARTORSIONS |
| CPLMD::crystallization::OrientationSphere | |
| CPLMD::crystallization::LocalSteinhardt< Q3 > | |
| CPLMD::crystallization::LocalSteinhardt< Q4 > | |
| CPLMD::crystallization::LocalSteinhardt< Q6 > | |
| CPLMD::crystallization::LocalSteinhardt< T > | |
| CPLMD::crystallization::PolymerAngles | Provides the keyword POLYMER_ANGLES |
| CPLMD::crystallization::SMAC | Provides the keyword SMAC |
| CPLMD::crystallization::VectorMultiColvar | |
| CPLMD::crystallization::BondOrientation | Provides the keyword BOND_DIRECTIONS |
| CPLMD::crystallization::MoleculeOrientation | Provides the keyword MOLECULES |
| CPLMD::crystallization::MoleculePlane | Provides the keyword PLANES |
| CPLMD::crystallization::Steinhardt | |
| CPLMD::crystallization::Q3 | Provides the keyword Q3 |
| CPLMD::crystallization::Q4 | Provides the keyword Q4 |
| CPLMD::crystallization::Q6 | Provides the keyword Q6 |
| CPLMD::multicolvar::AlphaBeta | Provides the keyword ALPHABETA |
| CPLMD::multicolvar::Angles | Provides the keyword ANGLES |
| CPLMD::multicolvar::Bridge | Provides the keyword BRIDGE |
| CPLMD::multicolvar::BridgedMultiColvarFunction | |
| CPLMD::multicolvar::MultiColvarFilter | This is the abstract base class to use for implementing a new way of filtering collective variable values to see whether or not they are within a certain range |
| CPLMD::multicolvar::FilterBetween | Provides the keyword MFILTER_BETWEEN |
| CPLMD::multicolvar::FilterLess | Provides the keyword MFILTER_LESS |
| CPLMD::multicolvar::FilterMore | Provides the keyword MFILTER_MORE |
| CPLMD::multicolvar::VolumeGradientBase | |
| CPLMD::crystallization::Gradient | Provides the keyword GRADIENT |
| CPLMD::multicolvar::ActionVolume | This is the abstract base class to use for implementing a new way of defining a particular region of the simulation box |
| CPLMD::multicolvar::VolumeAround | Provides the keyword AROUND |
| CPLMD::multicolvar::VolumeCavity | Provides the keyword CAVITY |
| CPLMD::multicolvar::VolumeInCylinder | Provides the keyword INCYLINDER |
| CPLMD::multicolvar::VolumeInEnvelope | Provides the keyword INENVELOPE |
| CPLMD::multicolvar::VolumeInSphere | Provides the keyword INSPHERE |
| CPLMD::multicolvar::VolumeTetrapore | Provides the keyword TETRAHEDRALPORE |
| CPLMD::multicolvar::CoordinationNumbers | Provides the keyword COORDINATIONNUMBER |
| CPLMD::multicolvar::Density | Provides the keyword DENSITY |
| CPLMD::multicolvar::DihedralCorrelation | Provides the keyword DIHCOR |
| CPLMD::multicolvar::DistanceFromContour | Provides the keyword DISTANCE_FROM_CONTOUR |
| CPLMD::multicolvar::Distances | Provides the keyword DISTANCES |
| CPLMD::multicolvar::InPlaneDistances | Provides the keyword INPLANEDISTANCES |
| CPLMD::multicolvar::LocalAverage | Provides the keyword LOCAL_AVERAGE |
| CPLMD::multicolvar::MultiColvarCombine | Provides the keyword MCOLV_COMBINE |
| CPLMD::multicolvar::MultiColvarProduct | Provides the keyword MCOLV_PRODUCT |
| CPLMD::multicolvar::NumberOfLinks | Provides the keyword NLINKS |
| CPLMD::multicolvar::Torsions | Provides the keyword TORSIONS |
| CPLMD::multicolvar::XAngles | Provides the keyword XANGLES |
| CPLMD::multicolvar::XDistances | Provides the keyword XDISTANCES |
| CPLMD::multicolvar::XYDistances | Provides the keyword XYDISTANCES |
| CPLMD::multicolvar::XYTorsion | Provides the keyword XYTORSIONS |
| CPLMD::pamm::HBPammHydrogens | Provides the keyword HBPAMM_SH |
| CPLMD::pamm::PAMM | Provides the keyword PAMM |
| CPLMD::secondarystructure::SecondaryStructureRMSD | Base action for calculating things like AlphRMSD, AntibetaRMSD, etc |
| CPLMD::secondarystructure::AlphaRMSD | Provides the keyword ALPHARMSD |
| CPLMD::secondarystructure::AntibetaRMSD | Provides the keyword ANTIBETARMSD |
| CPLMD::secondarystructure::ParabetaRMSD | Provides the keyword PARABETARMSD |
| CPLMD::vesselbase::ActionWithAveraging | This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames |
| CPLMD::analysis::Average | Provides the keyword AVERAGE |
| CPLMD::gridtools::ActionWithGrid | |
| CPLMD::analysis::Histogram | Provides the keyword HISTOGRAM |
| CPLMD::gridtools::ActionWithInputGrid | |
| CPLMD::gridtools::ActionWithIntegral | |
| CPLMD::gridtools::IntegrateGrid | Provides the keyword INTEGRATE_GRID |
| CPLMD::gridtools::ContourFindingBase | |
| CPLMD::gridtools::FindContour | Provides the keyword FIND_CONTOUR |
| CPLMD::gridtools::FindContourSurface | Provides the keyword FIND_CONTOUR_SURFACE |
| CPLMD::gridtools::FindSphericalContour | Provides the keyword FIND_SPHERICAL_CONTOUR |
| CPLMD::gridtools::ConvertToFES | Provides the keyword CONVERT_TO_FES |
| CPLMD::gridtools::FourierTransform | Provides the keyword FOURIER_TRANSFORM |
| CPLMD::gridtools::InterpolateGrid | Provides the keyword INTERPOLATE_GRID |
| CPLMD::multicolvar::MultiColvarDensity | Provides the keyword MULTICOLVARDENS |
| CPLMD::ActionPilot | This is used to create PLMD::Action objects that are run with some set frequency |
| CPLMD::GenericMolInfo | |
| CPLMD::adjmat::DumpGraph | Provides the keyword DUMPGRAPH |
| CPLMD::adjmat::OutputCluster | Provides the keyword OUTPUT_CLUSTER |
| CPLMD::analysis::AnalysisBase | This is the abstract base class to use for implementing new methods for analyzing the trajectory |
| CPLMD::analysis::Committor | Provides the keyword COMMITTOR |
| CPLMD::bias::Bias | This is the abstract base class to use for implementing new simulation biases, within it there is information as to how to go about implementing a new bias |
| CPLMD::opes::OPESmetad< convergence > | |
| CPLMD::opes::OPESmetad< exploration > | |
| CPLMD::bias::ABMD | Provides the keyword ABMD |
| CPLMD::bias::BiasValue | Provides the keyword BIASVALUE |
| CPLMD::bias::ExtendedLagrangian | Provides the keyword EXTENDED_LAGRANGIAN |
| CPLMD::bias::External | Provides the keyword EXTERNAL |
| CPLMD::bias::LWalls | Provides the keyword LOWER_WALLS |
| CPLMD::bias::MaxEnt | Provides the keyword MAXENT |
| CPLMD::bias::MetaD | Provides the keyword METAD |
| CPLMD::bias::MovingRestraint | Provides the keyword MOVINGRESTRAINT |
| CPLMD::bias::PBMetaD | Provides the keyword PBMETAD |
| CPLMD::bias::Restraint | Provides the keyword RESTRAINT |
| CPLMD::bias::UWalls | Provides the keyword UPPER_WALLS |
| CPLMD::eds::EDS | Provides the keyword <a href="../../user-doc/html/_"_e_d_s.html"> "EDS |
| CPLMD::fisst::FISST | Provides the keyword FISST |
| CPLMD::funnel::Funnel | Provides the keyword FUNNEL |
| CPLMD::isdb::Caliber | Provides the keyword CALIBER |
| CPLMD::isdb::Metainference | Provides the keyword METAINFERENCE |
| CPLMD::isdb::Rescale | Provides the keyword RESCALE |
| CPLMD::logmfd::LogMFD | Class for LogMFD parameters, variables and subroutines |
| CPLMD::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 |
| CPLMD::opes::OPESexpanded | Provides the keyword OPES_EXPANDED |
| CPLMD::opes::OPESmetad< mode > | |
| CPLMD::ves::VesBias | Abstract base class for implementing biases the extents the normal Bias.h class to include functions related to the variational approach |
| CPLMD::ves::VesLinearExpansion | Provides the keyword VES_LINEAR_EXPANSION |
| CPLMD::ves::VesDeltaF | Provides the keyword VES_DELTA_F |
| CPLMD::generic::Debug | Provides the keyword DEBUG |
| CPLMD::generic::DumpAtoms | Provides the keyword DUMPATOMS |
| CPLMD::generic::DumpDerivatives | Provides the keyword DUMPDERIVATIVES |
| CPLMD::generic::DumpForces | Provides the keyword DUMPFORCES |
| CPLMD::generic::DumpMassCharge | Provides the keyword DUMPMASSCHARGE |
| CPLMD::generic::DumpProjections | Provides the keyword DUMPPROJECTIONS |
| CPLMD::generic::EffectiveEnergyDrift | Provides the keyword EFFECTIVE_ENERGY_DRIFT |
| CPLMD::generic::FitToTemplate | Provides the keyword FIT_TO_TEMPLATE |
| CPLMD::generic::Flush | Provides the keyword FLUSH |
| CPLMD::generic::Plumed | Provides the keyword PLUMED |
| CPLMD::generic::Print | Provides the keyword PRINT |
| CPLMD::generic::Read | Provides the keyword READ |
| CPLMD::generic::ResetCell | Provides the keyword RESET_CELL |
| CPLMD::generic::UpdateIf | Provides the keyword UPDATE_IF |
| CPLMD::generic::WholeMolecules | Provides the keyword WHOLEMOLECULES |
| CPLMD::generic::WrapAround | Provides the keyword WRAPAROUND |
| CPLMD::gridtools::GridPrintingBase | |
| CPLMD::gridtools::DumpCube | Provides the keyword DUMPCUBE |
| CPLMD::gridtools::DumpGrid | Provides the keyword DUMPGRID |
| CPLMD::gridtools::GridToXYZ | Provides the keyword GRID_TO_XYZ |
| CPLMD::manyrestraints::ManyRestraintsBase | |
| CPLMD::manyrestraints::LWalls | Provides the keyword LWALLS |
| CPLMD::manyrestraints::UWalls | Provides the keyword UWALLS |
| CPLMD::multicolvar::DumpMultiColvar | Provides the keyword DUMPMULTICOLVAR |
| CPLMD::ves::Optimizer | |
| CPLMD::ves::Opt_Adam | Provides the keyword OPT_ADAM |
| CPLMD::ves::Opt_BachAveragedSGD | Provides the keyword OPT_AVERAGED_SGD |
| CPLMD::ves::Opt_Dummy | Provides the keyword OPT_DUMMY |
| CPLMD::ves::Opt_RobbinsMonroSGD | Provides the keyword OPT_ROBBINS_MONRO_SGD |
| CPLMD::vesselbase::ActionWithAveraging | This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames |
| CPLMD::ActionSetup | Action used to create a PLMD::Action that do something during setup only e.g |
| CPLMD::setup::Load | Provides the keyword LOAD |
| CPLMD::setup::Restart | Provides the keyword RESTART |
| CPLMD::setup::Units | Provides the keyword UNITS |
| CPLMD::ActionShortcut | Action used to create a command that expands to multiple PLMD::Action commands when read in during input |
| CPLMD::analysis::WhamHistogram | Provides the keyword WHAM_HISTOGRAM |
| CPLMD::analysis::WhamWeights | Provides the keyword WHAM_WEIGHTS |
| CPLMD::dimred::SketchMap | Provides the keyword SKETCH_MAP |
| CPLMD::ActionWithArguments | This is used to create PLMD::Action objects that take the output from some other Action as input |
| CPLMD::analysis::AnalysisBase | This is the abstract base class to use for implementing new methods for analyzing the trajectory |
| CPLMD::analysis::Committor | Provides the keyword COMMITTOR |
| CPLMD::bias::Bias | This is the abstract base class to use for implementing new simulation biases, within it there is information as to how to go about implementing a new bias |
| CPLMD::bias::ReweightBase | |
| CPLMD::bias::ReweightBias | Provides the keyword REWEIGHT_BIAS |
| CPLMD::bias::ReweightMetad | Provides the keyword REWEIGHT_METAD |
| CPLMD::bias::ReweightTemperaturePressure | Provides the keyword REWEIGHT_TEMP_PRESS |
| CPLMD::bias::ReweightWham | Provides the keyword REWEIGHT_WHAM |
| CPLMD::function::Function | This is the abstract base class to use for implementing new CV function, within it there is information as to how to go about implementing a new function |
| CPLMD::function::Combine | Provides the keyword COMBINE |
| CPLMD::function::Custom | Provides the keyword CUSTOM |
| CPLMD::function::Matheval | |
| CPLMD::function::Ensemble | Provides the keyword ENSEMBLE |
| CPLMD::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 |
| CPLMD::function::FuncPathMSD | Provides the keyword FUNCPATHMSD |
| CPLMD::function::FuncSumHills | Provides the keyword FUNCSUMHILLS |
| CPLMD::function::LocalEnsemble | Provides the keyword LOCALENSEMBLE |
| CPLMD::function::Piecewise | Provides the keyword PIECEWISE |
| CPLMD::function::Sort | Provides the keyword SORT |
| CPLMD::function::Stats | Provides the keyword STATS |
| CPLMD::function::Target | Provides the keyword TARGET |
| CPLMD::function::annfunc::ANN | |
| CPLMD::isdb::Select | Provides the keyword SELECT |
| CPLMD::generic::DumpDerivatives | Provides the keyword DUMPDERIVATIVES |
| CPLMD::generic::DumpForces | Provides the keyword DUMPFORCES |
| CPLMD::generic::DumpProjections | Provides the keyword DUMPPROJECTIONS |
| CPLMD::generic::Print | Provides the keyword PRINT |
| CPLMD::generic::UpdateIf | Provides the keyword UPDATE_IF |
| CPLMD::isdb::EMMI | Provides the keyword EMMI |
| CPLMD::isdb::MetainferenceBase | This is the abstract base class to use for implementing new ISDB Metainference actions, within it there is information as to how to go about implementing a new Metainference action |
| CPLMD::mapping::Mapping | |
| CPLMD::mapping::PCAVars | Provides the keyword PCAVARS |
| CPLMD::opes::ExpansionCVs | |
| CPLMD::opes::ECVcustom | Provides the keyword ECV_CUSTOM |
| CPLMD::opes::ECVlinear | Provides the keyword ECV_LINEAR |
| CPLMD::opes::ECVmultiThermal | Provides the keyword ECV_MULTITHERMAL |
| CPLMD::opes::ECVmultiThermalBaric | Provides the keyword ECV_MULTITHERMAL_MULTIBARIC |
| CPLMD::opes::ECVumbrellasFile | Provides the keyword ECV_UMBRELLAS_FILE |
| CPLMD::opes::ECVumbrellasLine | Provides the keyword ECV_UMBRELLAS_LINE |
| CPLMD::vesselbase::ActionWithAveraging | This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames |
| CPLMD::ActionWithValue | Used to create a PLMD::Action that has some scalar or vectorial output that may or may not have some derivatives |
| CPLMD::Colvar | This is the abstract base class to use for implementing new collective variables, within it there is information as to how to go about implementing a new CV |
| CPLMD::analysis::AnalysisBase | This is the abstract base class to use for implementing new methods for analyzing the trajectory |
| CPLMD::bias::Bias | This is the abstract base class to use for implementing new simulation biases, within it there is information as to how to go about implementing a new bias |
| CPLMD::bias::ReweightBase | |
| CPLMD::function::Function | This is the abstract base class to use for implementing new CV function, within it there is information as to how to go about implementing a new function |
| CPLMD::generic::FitToTemplate | Provides the keyword FIT_TO_TEMPLATE |
| CPLMD::generic::Plumed | Provides the keyword PLUMED |
| CPLMD::generic::Read | Provides the keyword READ |
| CPLMD::generic::Time | Provides the keyword TIME |
| CPLMD::isdb::EMMI | Provides the keyword EMMI |
| CPLMD::isdb::MetainferenceBase | This is the abstract base class to use for implementing new ISDB Metainference actions, within it there is information as to how to go about implementing a new Metainference action |
| CPLMD::manyrestraints::ManyRestraintsBase | |
| CPLMD::mapping::Mapping | |
| CPLMD::mapping::PCAVars | Provides the keyword PCAVARS |
| CPLMD::multicolvar::MultiColvarBase | |
| CPLMD::opes::ExpansionCVs | |
| CPLMD::secondarystructure::SecondaryStructureRMSD | Base action for calculating things like AlphRMSD, AntibetaRMSD, etc |
| CPLMD::ves::Optimizer | |
| CPLMD::vesselbase::ActionWithAveraging | This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames |
| CPLMD::generic::EndPlumed | Provides the keyword ENDPLUMED |
| CPLMD::generic::RandomExchanges | Provides the keyword RANDOM_EXCHANGES |
| CPLMD::isdb::Selector | Provides the keyword SELECTOR |
| CPLMD::ves::BasisFunctions | |
| CPLMD::ves::BF_Chebyshev | Provides the keyword BF_CHEBYSHEV |
| CPLMD::ves::BF_Combined | Provides the keyword BF_COMBINED |
| CPLMD::ves::BF_Cosine | Provides the keyword BF_COSINE |
| CPLMD::ves::BF_CubicBsplines | Provides the keyword BF_CUBIC_B_SPLINES |
| CPLMD::ves::BF_Custom | Provides the keyword BF_CUSTOM |
| CPLMD::ves::BF_Fourier | Provides the keyword BF_FOURIER |
| CPLMD::ves::BF_Gaussians | Provides the keyword BF_GAUSSIANS |
| CPLMD::ves::BF_Legendre | Provides the keyword BF_LEGENDRE |
| CPLMD::ves::BF_Powers | Provides the keyword BF_POWERS |
| CPLMD::ves::BF_Sine | Provides the keyword BF_SINE |
| CPLMD::ves::BF_Wavelets | Provides the keyword BF_WAVELETS |
| CPLMD::ves::OutputBasisFunctions | Provides the keyword VES_OUTPUT_BASISFUNCTIONS |
| CPLMD::ves::OutputFesBias | Provides the keyword VES_OUTPUT_FES |
| CPLMD::ves::OutputTargetDistribution | Provides the keyword VES_OUTPUT_TARGET_DISTRIBUTION |
| CPLMD::ves::TargetDistribution | |
| CPLMD::ves::TD_Chi | Provides the keyword TD_CHI |
| CPLMD::ves::TD_ChiSquared | Provides the keyword TD_CHISQUARED |
| CPLMD::ves::TD_Custom | Provides the keyword TD_CUSTOM |
| CPLMD::ves::TD_Exponential | Provides the keyword TD_EXPONENTIAL |
| CPLMD::ves::TD_ExponentiallyModifiedGaussian | Provides the keyword TD_EXPONENTIALLY_MODIFIED_GAUSSIAN |
| CPLMD::ves::TD_Gaussian | Provides the keyword TD_GAUSSIAN |
| CPLMD::ves::TD_GeneralizedExtremeValue | Provides the keyword TD_GENERALIZED_EXTREME_VALUE |
| CPLMD::ves::TD_GeneralizedNormal | Provides the keyword TD_GENERALIZED_NORMAL |
| CPLMD::ves::TD_Grid | Provides the keyword TD_GRID |
| CPLMD::ves::TD_LinearCombination | Provides the keyword TD_LINEAR_COMBINATION |
| CPLMD::ves::TD_Multicanonical | Provides the keyword TD_MULTICANONICAL |
| CPLMD::ves::TD_MultithermalMultibaric | Provides the keyword TD_MULTITHERMAL_MULTIBARIC |
| CPLMD::ves::TD_ProductCombination | Provides the keyword TD_PRODUCT_COMBINATION |
| CPLMD::ves::TD_ProductDistribution | Provides the keyword TD_PRODUCT_DISTRIBUTION |
| CPLMD::ves::TD_Uniform | Provides the keyword TD_UNIFORM |
| CPLMD::ves::TD_VonMises | Provides the keyword TD_VONMISES |
| CPLMD::ves::TD_WellTempered | Provides the keyword TD_WELLTEMPERED |
| CPLMD::vesselbase::ActionWithInputVessel | |
| CPLMD::manyrestraints::ManyRestraintsBase | |
| CPLMD::multicolvar::DumpMultiColvar | Provides the keyword DUMPMULTICOLVAR |
| CPLMD::vesselbase::ActionWithVessel | This is used to create PLMD::Action objects that are computed by calculating the same function multiple times |
| CPLMD::analysis::AnalysisBase | This is the abstract base class to use for implementing new methods for analyzing the trajectory |
| CPLMD::manyrestraints::ManyRestraintsBase | |
| CPLMD::mapping::Mapping | |
| CPLMD::multicolvar::MultiColvarBase | |
| CPLMD::secondarystructure::SecondaryStructureRMSD | Base action for calculating things like AlphRMSD, AntibetaRMSD, etc |
| CPLMD::vesselbase::ActionWithAveraging | This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames |
| CPLMD::ActionOptions | This class is used to bring the relevant information to the Action constructor |
| CPLMD::ActionRegister | Register holding all the allowed keywords |
| CPLMD::Angle | Class to compute angles |
| CANN | Provides the keyword ANN |
| CPLMD::lepton::AsmJitRuntimePtr | |
| CPLMD::Exception::Assertion | Auxiliary containing the failed assertion |
| CPLMD::AtomNumber | Simple class to store the index of an atom |
| CPLMD::Atoms | Class containing atom related quantities from the MD code |
| CPLMD::multicolvar::AtomValuePack | |
| CPLMD::BiasRepresentation | This class implements a general purpose class that aims to provide a Grid/list transparently add gaussians to a bias |
| CPLMD::Brent1DRootSearch< FCLASS > | A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method |
| CPLMD::multicolvar::CatomPack | |
| CPLMD::isdb::CS2Backbone::ChemicalShift | |
| CPLMD::Citations | Class taking care of bibliography |
| CPLMD::CLTool | This is the abstract base class to use for implementing new command line tool, within it there is information as to how to go about implemneting a new tool |
| CPLMD::cltools::Driver< double > | |
| CPLMD::cltools::Driver< float > | |
| CPLMD::cltools::CLToolSumHills | |
| CPLMD::cltools::Completion | |
| CPLMD::cltools::Driver< real > | |
| CPLMD::cltools::GenExample | |
| CPLMD::cltools::GenJson | |
| CPLMD::cltools::GenTemplate | |
| CPLMD::cltools::Info | |
| CPLMD::cltools::Manual | |
| CPLMD::cltools::PdbRenumber | |
| CPLMD::cltools::PesMD | |
| CPLMD::cltools::SimpleMD | |
| CPLMD::cltools::kt | |
| CPLMD::mapping::PathTools | |
| CPLMD::ves::MD_LinearExpansionPES | |
| CPLMD::cltools::CLTool | This is the abstract base class to use for implementing new command line tool, within it there is information as to how to go about implemneting a new tool |
| CPLMD::cltools::Driver< double > | |
| CPLMD::cltools::Driver< float > | |
| CPLMD::cltools::CLToolSumHills | |
| CPLMD::cltools::Completion | |
| CPLMD::cltools::Driver< real > | |
| CPLMD::cltools::GenExample | |
| CPLMD::cltools::GenJson | |
| CPLMD::cltools::GenTemplate | |
| CPLMD::cltools::Info | |
| CPLMD::cltools::Manual | |
| CPLMD::cltools::PdbRenumber | |
| CPLMD::cltools::PesMD | |
| CPLMD::cltools::SimpleMD | |
| CPLMD::cltools::kt | |
| CPLMD::mapping::PathTools | |
| CPLMD::ves::MD_LinearExpansionPES | |
| CPLMD::CLToolOptions | |
| CPLMD::CLToolRegister | Same as ActionRegister, but for CLTools |
| CPLMD::ves::CoeffsBase | |
| CPLMD::ves::CoeffsMatrix | |
| CPLMD::ves::CoeffsVector | |
| CPLMD::Communicator | Class containing wrappers to MPI |
| CPLMD::Atoms::DomainDecomposition | |
| CPLMD::lepton::CompiledExpression | A CompiledExpression is a highly optimized representation of an expression for cases when you want to evaluate it many times as quickly as possible |
| CPLMD::MatrixSquareBracketsAccess< T, C, I, J >::Const_row | Small utility class which just contains a pointer to the T and the row number |
| CPLMD::Communicator::ConstData | Const version of Communicator::Data See Communicator::Data documentation |
| CPLMD::opes::convergence | |
| CPLMD::isdb::CS2BackboneDB | |
| CPLMD::lepton::CustomFunction | This class is the interface for defining your own function that may be included in expressions |
| CPLMD::lepton::PlaceholderFunction | This class is an implementation of CustomFunction that does no computation |
| CPLMD::Communicator::Data | Structure defining a buffer for MPI |
| CPLMD::analysis::DataCollectionObject | |
| CPLMD::DataFetchingObject | |
| CPLMD::DataFetchingObjectTyped< T > | |
| CPLMD::maze::tls::delete_ptr | |
| CPLMD::Tools::DirectoryChanger | Tiny class that changes directory and comes back when going out of scope |
| CPLMD::DLLoader | Class taking care of dynamic loading |
| CPLMD::DynamicList< T > | A class for storing a list that changes which members are active as a function of time |
| CDynamicReferenceRestraining | Provides the keyword <a href="../../user-doc/html/_"_d_r_r.html"> "DRR |
| CPLMD::ERMSD | A class that implements ERMSD calculations |
| Cstd::exception | STL class |
| CPLMD::Exception | Class to deal with Plumed runtime errors |
| CPLMD::lepton::Exception | This class is used for all exceptions thrown by lepton |
| CPLMD::ExceptionDebug | Class representing a debug error (can only be thrown when using debug options) |
| CPLMD::ExceptionError | Class representing a generic error |
| CPLMD::ExceptionTypeError | Class representing a type error in the PLMD::Plumed interface |
| CPLMD::ExchangePatterns | |
| CPLMD::opes::exploration | |
| CPLMD::lepton::ExpressionProgram | An ExpressionProgram is a linear sequence of Operations for evaluating an expression |
| CPLMD::lepton::ExpressionTreeNode | This class represents a node in the abstract syntax tree representation of an expression |
| CPLMD::F1dim< FCLASS > | |
| CPLMD::ves::FermiSwitchingFunction | Small class to compute fermi switching function |
| CPLMD::FileBase::FieldBase | Internal tool |
| CPLMD::IFile::Field | |
| CPLMD::OFile::Field | Class identifying a single field for fielded output |
| CPLMD::FileBase | Base class for dealing with files |
| CPLMD::IFile | Class for input files |
| CPLMD::OFile | Class for output files |
| CPLMD::Log | Class containing the log stream |
| CPLMD::function::FilesHandler | |
| CPLMD::molfile::fio_iovec | |
| CPLMD::FlexibleBin | |
| CPLMD::bias::MetaD::Gaussian | |
| CPLMD::bias::PBMetaD::Gaussian | |
| CPLMD::GridBase | |
| CPLMD::Grid | |
| CPLMD::SparseGrid | |
| CPLMD::ves::GridIntegrationWeights | |
| CPLMD::ves::GridLinearInterpolation | |
| CPLMD::gridtools::GridSearch< FCLASS > | |
| CPLMD::Stopwatch::Handler | Auxiliary class for handling exception-safe start/pause and start/stop |
| CPLMD::Subprocess::Handler | Class used to cont/stop a Subprocess in an exception safe manner |
| CPLMD::pamm::HBPammObject | |
| CPLMD::HistogramBead | A class for calculating whether or not values are within a given range using : \( \sum_i \int_a^b G( s_i, \sigma*(b-a) ) \) |
| CPLMD::colvar::PathMSDBase::ImagePath | This class is a general container for path stuff |
| CPLMD::colvar::PathMSDBase::imgOrderByDist | |
| CPLMD::colvar::PathMSDBase::imgOrderBySimilarity | |
| CPLMD::opes::OPESmetad< mode >::kernel | |
| CPLMD::KernelFunctions | |
| CPLMD::Keywords::KeyType | This class lets me pass keyword types easily |
| CPLMD::Keywords | This class holds the keywords and their documentation |
| CPLMD::LatticeReduction | Class implementing algorithms for lattice reduction |
| CPLMD::ves::LinearBasisSetExpansion | |
| CPLMD::LinkCells | A class for doing link cells |
| CLOCAL_Q3 | Provides the keyword LOCAL_Q3 |
| CLOCAL_Q4 | Provides the keyword LOCAL_Q4 |
| CLOCAL_Q6 | Provides the keyword LOCAL_Q6 |
| CPLMD::Exception::Location | Auxiliary containing the location of the exception in the file |
| CPLMD::LoopUnroller< n > | Utiliy class for loop unrolling |
| CPLMD::MatrixSquareBracketsAccess< T, C, I, J > | Utility class to add [][] access |
| CPLMD::MatrixSquareBracketsAccess< Matrix< double >, double > | |
| CPLMD::Matrix< double > | |
| CPLMD::MatrixSquareBracketsAccess< Matrix< PLMD::pamm::HBPammObject >, PLMD::pamm::HBPammObject > | |
| CPLMD::Matrix< PLMD::pamm::HBPammObject > | |
| CPLMD::MatrixSquareBracketsAccess< Matrix< PLMD::SwitchingFunction >, PLMD::SwitchingFunction > | |
| CPLMD::Matrix< PLMD::SwitchingFunction > | |
| CPLMD::MatrixSquareBracketsAccess< Matrix< std::pair< unsigned, unsigned > >, std::pair< unsigned, unsigned > > | |
| CPLMD::Matrix< std::pair< unsigned, unsigned > > | |
| CPLMD::MatrixSquareBracketsAccess< Matrix< std::vector< PLMD::KernelFunctions > >, std::vector< PLMD::KernelFunctions > > | |
| CPLMD::Matrix< std::vector< PLMD::KernelFunctions > > | |
| CPLMD::MatrixSquareBracketsAccess< Matrix< std::vector< PLMD::VectorGeneric< 3 > > >, std::vector< PLMD::VectorGeneric< 3 > > > | |
| CPLMD::Matrix< std::vector< PLMD::VectorGeneric< 3 > > > | |
| CPLMD::MatrixSquareBracketsAccess< Matrix< T >, T > | |
| CPLMD::Matrix< T > | This class stores a full matrix and allows one to do some simple matrix operations |
| CPLMD::MatrixSquareBracketsAccess< Matrix< unsigned >, unsigned > | |
| CPLMD::Matrix< unsigned > | |
| CPLMD::MatrixSquareBracketsAccess< TensorGeneric< n, m >, double > | |
| CPLMD::TensorGeneric< 1, 1 > | |
| CPLMD::TensorGeneric< 2, 2 > | |
| CPLMD::TensorGeneric< 3, 3 > | |
| CPLMD::TensorGeneric< 4, 4 > | |
| CPLMD::TensorGeneric< 5, 5 > | |
| CPLMD::TensorGeneric< n, m > | Class implementing fixed size matrices of doubles |
| CPLMD::molfile::md_atom | |
| CPLMD::molfile::md_box | |
| CPLMD::molfile::md_file | |
| CPLMD::molfile::md_header | |
| CPLMD::molfile::md_ts | |
| CPLMD::MDAtomsBase | Class containing interface to MDAtomsTyped |
| CPLMD::MDAtomsTyped< T > | Class containing the pointers to the MD data It is templated so that single and double precision versions coexist IT IS STILL UNDOCUMENTED |
| CPLMD::maze::Member | Defines the encoding for a ligand conformation |
| CPLMD::MetricRegister | |
| CPLMD::Minimise1DBrent< FCLASS > | A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method |
| CPLMD::MinimiseBase< FCLASS > | |
| CPLMD::ConjugateGradient< FCLASS > | |
| CPLMD::MolDataClass | This class provides information on various kinds of molecules for instance the kinds of residues that are in a protein the atoms involved in the backbone of a particular residue etc |
| CPLMD::molfile::molfile_atom_t | Per-atom attributes and information |
| CPLMD::molfile::molfile_graphics_t | Individual graphics object/element data |
| CPLMD::molfile::molfile_metadata_t | File level comments, origin information, and annotations |
| CPLMD::molfile::molfile_plugin_t | Main file reader API |
| CPLMD::molfile::molfile_qm_basis_t | Data for QM basis set |
| CPLMD::molfile::molfile_qm_hessian_t | Data from QM Hessian/normal mode runs |
| CPLMD::molfile::molfile_qm_metadata_t | Sizes of various QM-related, timestep independent data arrays which must be allocated by the caller (VMD) so that the plugin can fill in the arrays with data |
| CPLMD::molfile::molfile_qm_sysinfo_t | QM run info |
| CPLMD::molfile::molfile_qm_t | QM related information that is timestep independent |
| CPLMD::molfile::molfile_qm_timestep_metadata | Sizes of various QM-related, per-timestep data arrays which must be allocated by the caller (VMD) so that the plugin can fill in the arrays with data |
| CPLMD::molfile::molfile_qm_timestep_t | QM per trajectory timestep info Note that each timestep can contain multiple wavefunctions |
| CPLMD::molfile::molfile_qm_wavefunction_t | QM wavefunction |
| CPLMD::molfile::molfile_timestep_metadata | |
| CPLMD::molfile::molfile_timestep_t | Per-timestep atom coordinates, velocities, time, energies and periodic cell info |
| CPLMD::molfile::molfile_volumetric_t | Metadata for volumetric datasets, read initially and used for subsequent memory allocations and file loading |
| CMolInfo | Provides the keyword MOLINFO |
| CPLMD::MPI_Comm | Surrogate of MPI_Comm when MPI library is not available |
| CPLMD::MPI_Datatype | Surrogate of MPI_Datatype when MPI library is not available |
| CPLMD::MPI_Request | Surrogate of MPI_Request when MPI library is not available |
| CPLMD::MPI_Status | Surrogate of MPI_Status when MPI library is not available |
| CPLMD::MultiValue | |
| CPLMD::drr::UIestimator::n_matrix | |
| CPLMD::drr::UIestimator::n_vector< T > | |
| CPLMD::NeighborList | A class that implements neighbor lists from two lists or a single list of atoms |
| CPLMD::OpenMP | |
| CPLMD::OpenMPVars | |
| CPLMD::lepton::Operation | An Operation represents a single step in the evaluation of an expression, such as a function, an operator, or a constant value |
| CPLMD::lepton::Operation::Abs | |
| CPLMD::lepton::Operation::Acos | |
| CPLMD::lepton::Operation::Add | |
| CPLMD::lepton::Operation::AddConstant | |
| CPLMD::lepton::Operation::Asin | |
| CPLMD::lepton::Operation::Atan | |
| CPLMD::lepton::Operation::Atan2 | |
| CPLMD::lepton::Operation::Ceil | |
| CPLMD::lepton::Operation::Constant | |
| CPLMD::lepton::Operation::Cos | |
| CPLMD::lepton::Operation::Cosh | |
| CPLMD::lepton::Operation::Cot | |
| CPLMD::lepton::Operation::Csc | |
| CPLMD::lepton::Operation::Cube | |
| CPLMD::lepton::Operation::Custom | |
| CPLMD::lepton::Operation::Delta | |
| CPLMD::lepton::Operation::Divide | |
| CPLMD::lepton::Operation::Erf | |
| CPLMD::lepton::Operation::Erfc | |
| CPLMD::lepton::Operation::Exp | |
| CPLMD::lepton::Operation::Floor | |
| CPLMD::lepton::Operation::Log | |
| CPLMD::lepton::Operation::Max | |
| CPLMD::lepton::Operation::Min | |
| CPLMD::lepton::Operation::Multiply | |
| CPLMD::lepton::Operation::MultiplyConstant | |
| CPLMD::lepton::Operation::Nandelta | |
| CPLMD::lepton::Operation::Negate | |
| CPLMD::lepton::Operation::Power | |
| CPLMD::lepton::Operation::PowerConstant | |
| CPLMD::lepton::Operation::Reciprocal | |
| CPLMD::lepton::Operation::Sec | |
| CPLMD::lepton::Operation::Select | |
| CPLMD::lepton::Operation::Sin | |
| CPLMD::lepton::Operation::Sinh | |
| CPLMD::lepton::Operation::Sqrt | |
| CPLMD::lepton::Operation::Square | |
| CPLMD::lepton::Operation::Step | |
| CPLMD::lepton::Operation::Subtract | |
| CPLMD::lepton::Operation::Tan | |
| CPLMD::lepton::Operation::Tanh | |
| CPLMD::lepton::Operation::Variable | |
| COPESmetad_c | Provides the keyword OPES_METAD |
| COPESmetad_e | Provides the keyword OPES_METAD_EXPLORE |
| CPLMD::function::FuncPathMSD::ordering | |
| CPLMD::function::FuncPathGeneral::pairordering | |
| CPLMD::function::FuncPathMSD::pairordering | |
| CPLMD::pamm::PammObject | |
| CPLMD::lepton::ParsedExpression | This class represents the result of parsing an expression |
| CPLMD::lepton::Parser | This class provides the main interface for parsing expressions |
| CPLMD::lepton::ParseToken | |
| CPLMD::mapping::PathReparameterization | This class can be used to make a set of reference configurations equidistant |
| CPLMD::Pbc | |
| CPLMD::PDB | Minimalistic pdb parser |
| Cplumed | Main plumed object |
| Cplumed_error | Small structure that is only defined locally to retrieve errors |
| CPLMD::PlumedMain::plumed_error_handler | Error handler |
| Cplumed_function_holder | |
| Cplumed_nothrow_handler | |
| Cplumed_nothrow_handler_x | |
| Cplumed_plumedmain_function_holder_x | Container for plumedmain function pointers (create, cmd and finalize) |
| Cplumed_safeptr | Structure holding a typesafe pointer |
| Cplumed_safeptr_x | |
| Cplumed_symbol_table_type_x | Container for symbol table |
| CPytorchModel | Provides the keyword PYTORCH_MODEL |
| CPLMD::Random | |
| CPLMD::ReferenceConfiguration | Abstract base class for calculating the distance from a reference configuration |
| CPLMD::FakeFrame | |
| CPLMD::ReferenceArguments | In many applications (e.g |
| CPLMD::ArgumentOnlyDistance | |
| CPLMD::DotProductDistance | |
| CPLMD::EuclideanDistance | |
| CPLMD::MahalanobisDistance | |
| CPLMD::NormalizedEuclideanDistance | |
| CPLMD::Direction | |
| CPLMD::ReferenceAtoms | In many applications (e.g |
| CPLMD::Direction | |
| CPLMD::MultiDomainRMSD | |
| CPLMD::SingleDomainRMSD | |
| CPLMD::DRMSD | |
| CPLMD::IntermolecularDRMSD | |
| CPLMD::IntramolecularDRMSD | |
| CPLMD::RMSDBase | |
| CPLMD::OptimalRMSD | |
| CPLMD::SimpleRMSD | |
| CPLMD::ReferenceConfigurationOptions | |
| CPLMD::ReferenceValuePack | |
| CPLMD::Communicator::Request | Wrapper class for MPI_Request |
| CPLMD::isdb::CS2Backbone::RingInfo | |
| CPLMD::RMSD | A class that implements RMSD calculations This is a class that implements the various infrastructure to calculate the RMSD or MSD respect a given frame |
| CPLMD::RMSDCoreData | This is a class which is needed to share information across the various non-threadsafe routines so that the public function of rmsd are threadsafe while the inner core can safely share information |
| CPLMD::maze::rnd | Mersenne Twister sampler for random variables |
| CPLMD::RootFindingBase< FCLASS > | |
| CPLMD::MatrixSquareBracketsAccess< T, C, I, J >::Row | Small utility class which just contains a pointer to the T and the row number |
| CPLMD::piv::PIV::SharedData | Local structure, used to store data that should be shared across multiple PIV instances |
| CPLMD::dimred::SMACOF | |
| CPLMD::Communicator::Status | Wrapper class for MPI_Status |
| CPLMD::Stopwatch | |
| CPLMD::Subprocess | Class managing a subprocess |
| CPLMD::SubprocessPid | Small utility class, used to avoid inclusion of unistd.h> in a header file |
| CPLMD::SwitchingFunction | Small class to compute switching functions |
| CPLMD::xdrfile::t_trnheader | |
| CPLMD::TargetDist | |
| CPLMD::ves::TargetDistModifer | |
| CPLMD::ves::WellTemperedModifer | |
| CPLMD::bias::MetaD::TemperingSpecs | |
| CPLMD::TensorGenericAux | Small class to contain local utilities |
| CPLMD::Exception::Throw | Auxiliary class used to throw exceptions |
| CPLMD::maze::tls | Helper functions |
| CPLMD::Tools | Empty class which just contains several (static) tools |
| CPLMD::Torsion | Class to compute torsional angles |
| CPLMD::Tree | |
| CPLMD::molfile::trx_hdr | |
| CPLMD::TypesafePtr | Class to deal with propoagation of typesafe pointers |
| CPLMD::drr::UIestimator::UIestimator | |
| Cstd::unique_ptr< T > | STL class |
| CPLMD::ForwardDecl< PLMD::Pbc > | |
| CPLMD::ForwardDecl< PLMD::Communicator > | |
| CPLMD::ForwardDecl< PLMD::Random > | |
| CPLMD::ForwardDecl< PLMD::PDB > | |
| CPLMD::ForwardDecl< PLMD::DLLoader > | |
| CPLMD::ForwardDecl< PLMD::Log > | |
| CPLMD::ForwardDecl< PLMD::Stopwatch > | |
| CPLMD::ForwardDecl< PLMD::Citations > | |
| CPLMD::ForwardDecl< PLMD::Atoms > | |
| CPLMD::ForwardDecl< PLMD::ActionSet > | |
| CPLMD::ForwardDecl< PLMD::ExchangePatterns > | |
| CPLMD::ForwardDecl< PLMD::TypesafePtr > | |
| CPLMD::ForwardDecl< T > | Utility class for forward declaration of references |
| CPLMD::Units | Small utility class that contains information about units |
| CPLMD::Value | A class for holding the value of a function together with its derivatives |
| Cstd::vector< T > | STL class |
| CPLMD::ActionSet | Std::vector containing the sequence of Action to be done |
| CPLMD::VectorGeneric< n > | Class implementing fixed size vectors of doubles |
| CPLMD::vesselbase::Vessel | |
| CPLMD::vesselbase::AveragingVessel | |
| CPLMD::analysis::AverageVessel | |
| CPLMD::gridtools::GridVessel | |
| CPLMD::gridtools::HistogramOnGrid | |
| CPLMD::gridtools::AverageOnGrid | |
| CPLMD::vesselbase::BridgeVessel | This class allows you to calculate the vessel in one ActionWithVessel |
| CPLMD::vesselbase::Moments | |
| CPLMD::vesselbase::ShortcutVessel | |
| CPLMD::vesselbase::Histogram | |
| CPLMD::vesselbase::StoreDataVessel | Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to store values and derivatives for a set of scalars or vectors that are calculated by a PLMD::vesselbase::ActionWithVessel |
| CPLMD::adjmat::AdjacencyMatrixVessel | |
| CPLMD::mapping::TrigonometricPathVessel | |
| CPLMD::vesselbase::ValueVessel | |
| CPLMD::vesselbase::FunctionVessel | Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to calculate functions of the form \(\prod_k H_k[ \sum_j \prod_i g_i(x) ]\) |
| CPLMD::crystallization::GradientVessel | |
| CPLMD::crystallization::VectorMean | |
| CPLMD::crystallization::VectorSum | |
| CPLMD::mapping::SpathVessel | |
| CPLMD::mapping::ZpathVessel | |
| CPLMD::vesselbase::AltMin | |
| CPLMD::vesselbase::Between | |
| CPLMD::vesselbase::LessThan | |
| CPLMD::vesselbase::Max | |
| CPLMD::vesselbase::Mean | |
| CPLMD::vesselbase::Min | |
| CPLMD::vesselbase::MoreThan | |
| CPLMD::vesselbase::Sum | |
| CPLMD::vesselbase::OrderingVessel | |
| CPLMD::vesselbase::Highest | |
| CPLMD::vesselbase::Lowest | |
| CPLMD::vesselbase::VesselOptions | This class is used to pass the input to Vessels |
| CPLMD::vesselbase::VesselRegister | |
| CPLMD::ves::VesTools | |
| CPLMD::molfile::vmdplugin_t | Typedef for generic plugin header, individual plugins can make their own structures as long as the header info remains the same as the generic plugin header, most easily done by using the vmdplugin_HEAD macro |
| CPLMD::Stopwatch::Watch | Class to store a single stopwatch |
| CPLMD::ves::WaveletGrid | |
| CPLMD::WeightBase | |
| CPLMD::BiasWeight | |
| CPLMD::ProbWeight | |
| CPLMD::ves::FesWeight | |
| CPLMD::ves::MarginalWeight | |
| CPLMD::WithCmd | Base for classes with cmd() method |
| CPLMD::CLToolMain | Class providing cmd() access to command line tools |
| CPLMD::GREX | |
| CPLMD::PlumedHandle | Tiny local class to load a PLUMED kernel |
| CPLMD::PlumedMain | Main plumed object |
| CPLMD::xdrfile::XDR | |
| CPLMD::xdrfile::XDR::xdr_ops | |
| CPLMD::xdrfile::XDRFILE | Contents of the abstract XDRFILE data structure |
1.17.0