File List

Here is a list of all files with brief descriptions:

[detail level 123]

▶ adjmat
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ multicolvar
ActionVolume.h
AtomValuePack.h
BridgedMultiColvarFunction.h
CatomPack.h
MultiColvarBase.h
MultiColvarFilter.h
VolumeGradientBase.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
ActionWithInputMatrix.cpp
ActionWithInputMatrix.h
AdjacencyMatrixBase.cpp
AdjacencyMatrixBase.h
AdjacencyMatrixVessel.cpp
AdjacencyMatrixVessel.h
AlignedMatrixBase.cpp
AlignedMatrixBase.h
ClusterAnalysisBase.cpp
ClusterAnalysisBase.h
ClusterDiameter.cpp
ClusterDistribution.cpp
ClusteringBase.cpp
ClusteringBase.h
ClusterProperties.cpp
ClusterSize.cpp
ClusterWithSurface.cpp
ContactAlignedMatrix.cpp
ContactMatrix.cpp
DFSClustering.cpp
DumpGraph.cpp
HbondMatrix.cpp
MatrixColumnSums.cpp
MatrixRowSums.cpp
OutputCluster.cpp
SMACMatrix.cpp
Sprint.cpp
TopologyMatrix.cpp
▶ analysis
▶ bias
ActionRegister.h
Bias.h
ReweightBase.h
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ gridtools
ActionWithGrid.h
ActionWithInputGrid.h
ActionWithIntegral.h
AverageOnGrid.h
ContourFindingBase.h
GridPrintingBase.h
GridSearch.h
GridVessel.h
HistogramOnGrid.h
▶ multicolvar
ActionVolume.h
AtomValuePack.h
BridgedMultiColvarFunction.h
CatomPack.h
MultiColvarBase.h
MultiColvarFilter.h
VolumeGradientBase.h
▶ reference
ArgumentOnlyDistance.h
Direction.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SingleDomainRMSD.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
AnalysisBase.cpp
AnalysisBase.h
Average.cpp
AverageVessel.cpp
AverageVessel.h
Committor.cpp
DataCollectionObject.cpp
DataCollectionObject.h
EuclideanDissimilarityMatrix.cpp
FarthestPointSampling.cpp
Histogram.cpp
LandmarkSelectionBase.cpp
LandmarkSelectionBase.h
LandmarkStaged.cpp
OutputColvarFile.cpp
OutputPDBFile.cpp
PrintDissimilarityMatrix.cpp
ReadAnalysisFrames.cpp
ReadAnalysisFrames.h
ReadDissimilarityMatrix.cpp
ReselectLandmarks.cpp
SelectRandomFrames.cpp
SelectWithStride.cpp
WhamHistogram.cpp
WhamWeights.cpp
▶ bias
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ABMD.cpp
ActionRegister.h
Bias.cpp
Bias.h
BiasValue.cpp
ExtendedLagrangian.cpp
External.cpp
LWalls.cpp
MaxEnt.cpp
MetaD.cpp
MovingRestraint.cpp
PBMetaD.cpp
Restraint.cpp
ReweightBase.cpp
ReweightBase.h
ReweightBias.cpp
ReweightMetad.cpp
ReweightTemperature.cpp
ReweightWham.cpp
UWalls.cpp
▶ blas
blas.cpp
blas.h
def_external.h
def_internal.h
real.h
▶ cltools
▶ config
Config.h
version.h
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ molfile
endianswap.h
fastio.h
Gromacs.h
largefiles.h
libmolfile_plugin.h
molfile_plugin.h
periodic_table.h
readpdb.h
vmdplugin.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
CLTool.cpp
CLTool.h
CLToolRegister.h
Completion.cpp
Driver.cpp
DriverDouble.cpp
DriverFloat.cpp
GenTemplate.cpp
Info.cpp
kT.cpp
Manual.cpp
PdbRenumber.cpp
pesmd.cpp
SimpleMD.cpp
SumHills.cpp
▶ colvar
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ reference
ArgumentOnlyDistance.h
Direction.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SingleDomainRMSD.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionRegister.h
Angle.cpp
Cell.cpp
Colvar.cpp
Colvar.h
Constant.cpp
ContactMap.cpp
Coordination.cpp
CoordinationBase.cpp
CoordinationBase.h
DHEnergy.cpp
Dimer.cpp
Dipole.cpp
Distance.cpp
DRMSD.cpp
EEFSolv.cpp
Energy.cpp
ERMSD.cpp
ExtraCV.cpp
Fake.cpp
Gyration.cpp
MultiRMSD.cpp
PathMSD.cpp
PathMSDBase.cpp
PathMSDBase.h
PCARMSD.cpp
Position.cpp
PropertyMap.cpp
Puckering.cpp
RMSD.cpp
Template.cpp
Torsion.cpp
Volume.cpp
▶ config
Config.cpp
Config.h
ConfigInstall.cpp
version.h
▶ core
▶ config
Config.h
version.h
▶ lepton
CompiledExpression.h
CustomFunction.h
Exception.h
ExpressionProgram.h
ExpressionTreeNode.h
Lepton.h
MSVC_erfc.h
Operation.h
ParsedExpression.h
Parser.h
windowsIncludes.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
Action.cpp
Action.h
ActionAnyorder.cpp
ActionAnyorder.h
ActionAtomistic.cpp
ActionAtomistic.h
ActionPilot.cpp
ActionPilot.h
ActionRegister.cpp
ActionRegister.h
ActionSet.cpp
ActionSet.h
ActionSetup.cpp
ActionSetup.h
ActionShortcut.cpp
ActionShortcut.h
ActionWithArguments.cpp
ActionWithArguments.h
ActionWithValue.cpp
ActionWithValue.h
ActionWithVirtualAtom.cpp
ActionWithVirtualAtom.h
Atoms.cpp
Atoms.h
CLTool.cpp
CLTool.h
CLToolMain.cpp
CLToolMain.h
CLToolRegister.cpp
CLToolRegister.h
Colvar.cpp
Colvar.h
DataFetchingObject.cpp
DataFetchingObject.h
ExchangePatterns.cpp
ExchangePatterns.h
FlexibleBin.cpp
FlexibleBin.h
GREX.cpp
GREX.h
MDAtoms.cpp
MDAtoms.h
PlumedMain.cpp
PlumedMain.h
PlumedMainInitializer.cpp
PlumedMainInitializer.h
SetupMolInfo.cpp
SetupMolInfo.h
TargetDist.cpp
TargetDist.h
Value.cpp
Value.h
WithCmd.cpp
WithCmd.h
▶ crystallization
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ multicolvar
ActionVolume.h
AtomValuePack.h
BridgedMultiColvarFunction.h
CatomPack.h
MultiColvarBase.h
MultiColvarFilter.h
VolumeGradientBase.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
BondOrientation.cpp
CubicHarmonicBase.cpp
CubicHarmonicBase.h
Fccubic.cpp
Gradient.cpp
Gradient.h
GradientVessel.cpp
InterMolecularTorsions.cpp
LocalSteinhardt.cpp
LocalSteinhardt.h
MoleculeOrientation.cpp
MoleculePlane.cpp
OrientationSphere.cpp
OrientationSphere.h
PolymerAngles.cpp
Q3.cpp
Q4.cpp
Q6.cpp
SimpleCubic.cpp
SMAC.cpp
Steinhardt.cpp
Steinhardt.h
Tetrahedral.cpp
VectorMean.cpp
VectorMultiColvar.cpp
VectorMultiColvar.h
VectorSum.cpp
▶ dimred
▶ analysis
AnalysisBase.h
AverageVessel.h
DataCollectionObject.h
LandmarkSelectionBase.h
ReadAnalysisFrames.h
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ gridtools
ActionWithGrid.h
ActionWithInputGrid.h
ActionWithIntegral.h
AverageOnGrid.h
ContourFindingBase.h
GridPrintingBase.h
GridSearch.h
GridVessel.h
HistogramOnGrid.h
▶ reference
ArgumentOnlyDistance.h
Direction.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SingleDomainRMSD.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ClassicalMultiDimensionalScaling.cpp
DimensionalityReductionBase.cpp
DimensionalityReductionBase.h
OutputPCAProjections.cpp
PCA.cpp
PCA.h
ProjectNonLandmarkPoints.cpp
SketchMap.cpp
SketchMapBase.cpp
SketchMapBase.h
SketchMapConjGrad.cpp
SketchMapPointwise.cpp
SketchMapRead.cpp
SketchMapSmacof.cpp
SMACOF.cpp
SMACOF.h
SmacoffMDS.cpp
▶ drr
▶ bias
ActionRegister.h
Bias.h
ReweightBase.h
▶ cltools
CLTool.h
CLToolRegister.h
▶ config
Config.h
version.h
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
colvar_UIestimator.cpp
colvar_UIestimator.h
DRR.cpp
DRR.h
drrtool.cpp
DynamicReferenceRestraining.cpp
▶ eds
▶ bias
ActionRegister.h
Bias.h
ReweightBase.h
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
EDS.cpp
▶ function
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ lepton
CompiledExpression.h
CustomFunction.h
Exception.h
ExpressionProgram.h
ExpressionTreeNode.h
Lepton.h
MSVC_erfc.h
Operation.h
ParsedExpression.h
Parser.h
windowsIncludes.h
▶ reference
ArgumentOnlyDistance.h
Direction.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SingleDomainRMSD.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionRegister.h
Combine.cpp
Custom.cpp
Ensemble.cpp
FuncPathMSD.cpp
FuncSumHills.cpp
Function.cpp
Function.h
LocalEnsemble.cpp
Piecewise.cpp
Sort.cpp
Stats.cpp
Target.cpp
▶ generic
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
Debug.cpp
DumpAtoms.cpp
DumpDerivatives.cpp
DumpForces.cpp
DumpMassCharge.cpp
DumpProjections.cpp
EffectiveEnergyDrift.cpp
EndPlumed.cpp
FitToTemplate.cpp
Flush.cpp
Group.cpp
Include.cpp
Plumed.cpp
Print.cpp
RandomExchanges.cpp
Read.cpp
ResetCell.cpp
Time.cpp
UpdateIf.cpp
WholeMolecules.cpp
WrapAround.cpp
▶ gridtools
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
ActionWithGrid.cpp
ActionWithGrid.h
ActionWithInputGrid.cpp
ActionWithInputGrid.h
ActionWithIntegral.cpp
ActionWithIntegral.h
AverageOnGrid.cpp
AverageOnGrid.h
ContourFindingBase.cpp
ContourFindingBase.h
ConvertToFES.cpp
DumpCube.cpp
DumpGrid.cpp
FindContour.cpp
FindContourSurface.cpp
FindSphericalContour.cpp
FourierTransform.cpp
GridPrintingBase.cpp
GridPrintingBase.h
GridSearch.cpp
GridSearch.h
GridToXYZ.cpp
GridVessel.cpp
GridVessel.h
HistogramOnGrid.cpp
HistogramOnGrid.h
IntegrateGrid.cpp
InterpolateGrid.cpp
▶ isdb
▶ bias
ActionRegister.h
Bias.h
ReweightBase.h
▶ colvar
ActionRegister.h
Colvar.h
CoordinationBase.h
PathMSDBase.h
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ function
ActionRegister.h
Function.h
▶ reference
ArgumentOnlyDistance.h
Direction.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SingleDomainRMSD.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
Caliber.cpp
CS2Backbone.cpp
EMMI.cpp
FretEfficiency.cpp
Jcoupling.cpp
Metainference.cpp
MetainferenceBase.cpp
MetainferenceBase.h
NOE.cpp
PRE.cpp
RDC.cpp
Rescale.cpp
SAXS.cpp
Select.cpp
Selector.cpp
▶ lapack
▶ blas
blas.h
def_external.h
def_internal.h
real.h
def_external.h
def_internal.h
lapack.cpp
lapack.h
lapack_limits.h
real.h
▶ lepton
CompiledExpression.cpp
CompiledExpression.h
CustomFunction.h
Exception.h
ExpressionProgram.cpp
ExpressionProgram.h
ExpressionTreeNode.cpp
ExpressionTreeNode.h
Lepton.h
MSVC_erfc.h
Operation.cpp
Operation.h
ParsedExpression.cpp
ParsedExpression.h
Parser.cpp
Parser.h
windowsIncludes.h
▶ logmfd
▶ bias
ActionRegister.h
Bias.h
ReweightBase.h
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
LogMFD.cpp
▶ main
▶ wrapper
Plumed.h
main.cpp
▶ manyrestraints
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
LWalls.cpp
ManyRestraintsBase.cpp
ManyRestraintsBase.h
UWalls.cpp
▶ mapping
▶ cltools
CLTool.h
CLToolRegister.h
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ reference
ArgumentOnlyDistance.h
Direction.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SingleDomainRMSD.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
AdaptivePath.cpp
Mapping.cpp
Mapping.h
Path.cpp
PathBase.cpp
PathBase.h
PathReparameterization.cpp
PathReparameterization.h
PathTools.cpp
PCAVars.cpp
PropertyMap.cpp
SpathVessel.cpp
TrigonometricPathVessel.cpp
TrigonometricPathVessel.h
ZpathVessel.cpp
▶ molfile
crdplugin.cpp
dcdplugin.cpp
endianswap.h
fastio.h
Gromacs.h
gromacsplugin.cpp
largefiles.h
libmolfile_plugin.h
molfile_plugin.h	API for C extensions to define a way to load structure, coordinate, trajectory, and volumetric data files
pdbplugin.cpp
periodic_table.h
readpdb.h
vmdplugin.h	This header must be included by every VMD plugin library
▶ multicolvar
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ gridtools
ActionWithGrid.h
ActionWithInputGrid.h
ActionWithIntegral.h
AverageOnGrid.h
ContourFindingBase.h
GridPrintingBase.h
GridSearch.h
GridVessel.h
HistogramOnGrid.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
ActionVolume.cpp
ActionVolume.h
AlphaBeta.cpp
Angles.cpp
AtomValuePack.cpp
AtomValuePack.h
Bridge.cpp
BridgedMultiColvarFunction.cpp
BridgedMultiColvarFunction.h
CatomPack.cpp
CatomPack.h
CenterOfMultiColvar.cpp
CoordinationNumbers.cpp
Density.cpp
DihedralCorrelation.cpp
DistanceFromContour.cpp
Distances.cpp
DumpMultiColvar.cpp
FilterBetween.cpp
FilterLessThan.cpp
FilterMoreThan.cpp
InPlaneDistances.cpp
LocalAverage.cpp
MultiColvarBase.cpp
MultiColvarBase.h
MultiColvarCombine.cpp
MultiColvarDensity.cpp
MultiColvarFilter.cpp
MultiColvarFilter.h
MultiColvarProduct.cpp
NumberOfLinks.cpp
Torsions.cpp
VolumeAround.cpp
VolumeBetweenContours.cpp
VolumeCavity.cpp
VolumeGradientBase.cpp
VolumeGradientBase.h
VolumeInCylinder.cpp
VolumeInSphere.cpp
VolumeTetrapore.cpp
XAngle.cpp
XDistances.cpp
XYDistances.cpp
XYTorsion.cpp
▶ pamm
▶ adjmat
ActionWithInputMatrix.h
AdjacencyMatrixBase.h
AdjacencyMatrixVessel.h
AlignedMatrixBase.h
ClusterAnalysisBase.h
ClusteringBase.h
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ multicolvar
ActionVolume.h
AtomValuePack.h
BridgedMultiColvarFunction.h
CatomPack.h
MultiColvarBase.h
MultiColvarFilter.h
VolumeGradientBase.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
HBPammHydrogens.cpp
HBPammMatrix.cpp
HBPammObject.cpp
HBPammObject.h
PAMM.cpp
PammObject.cpp
PammObject.h
▶ piv
▶ bias
ActionRegister.h
Bias.h
ReweightBase.h
▶ colvar
ActionRegister.h
Colvar.h
CoordinationBase.h
PathMSDBase.h
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
PIV.cpp
▶ reference
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ArgumentOnlyDistance.cpp
ArgumentOnlyDistance.h
Direction.cpp
Direction.h
DotProductDistance.cpp
DRMSD.cpp
DRMSD.h
EuclideanDistance.cpp
FakeFrame.cpp
FakeFrame.h
IntermolecularDRMSD.cpp
IntramolecularDRMSD.cpp
MahalanobisDistance.cpp
MetricRegister.cpp
MetricRegister.h
MultiDomainRMSD.cpp
MultiDomainRMSD.h
NormalizedEuclideanDistance.cpp
OptimalRMSD.cpp
ReferenceArguments.cpp
ReferenceArguments.h
ReferenceAtoms.cpp
ReferenceAtoms.h
ReferenceConfiguration.cpp
ReferenceConfiguration.h
ReferenceValuePack.cpp
ReferenceValuePack.h
RMSDBase.cpp
RMSDBase.h
SimpleRMSD.cpp
SingleDomainRMSD.cpp
SingleDomainRMSD.h
▶ secondarystructure
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ reference
ArgumentOnlyDistance.h
Direction.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SingleDomainRMSD.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
▶ vesselbase
ActionWithAveraging.h
ActionWithInputVessel.h
ActionWithVessel.h
AveragingVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
AlphaRMSD.cpp
AntibetaRMSD.cpp
ParabetaRMSD.cpp
SecondaryStructureRMSD.cpp
SecondaryStructureRMSD.h
▶ setup
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionSetup.h
Load.cpp
MolInfo.cpp
Restart.cpp
Units.cpp
▶ tools
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ lapack
def_external.h
def_internal.h
lapack.h
lapack_limits.h
real.h
▶ lepton
CompiledExpression.h
CustomFunction.h
Exception.h
ExpressionProgram.h
ExpressionTreeNode.h
Lepton.h
MSVC_erfc.h
Operation.h
ParsedExpression.h
Parser.h
windowsIncludes.h
Angle.cpp
Angle.h
AtomNumber.cpp
AtomNumber.h
BiasRepresentation.cpp
BiasRepresentation.h
Brent1DRootSearch.cpp
Brent1DRootSearch.h
Citations.cpp
Citations.h
Communicator.cpp
Communicator.h
ConjugateGradient.cpp
ConjugateGradient.h
DLLoader.cpp
DLLoader.h
DynamicList.cpp
DynamicList.h
ERMSD.cpp
ERMSD.h
Exception.cpp
Exception.h
File.h
FileBase.cpp
FileBase.h
ForwardDecl.cpp
ForwardDecl.h
Grid.cpp
Grid.h
h36.cpp
h36.h
HistogramBead.cpp
HistogramBead.h
IFile.cpp
IFile.h
KernelFunctions.cpp
KernelFunctions.h
Keywords.cpp
Keywords.h
LatticeReduction.cpp
LatticeReduction.h
LinkCells.cpp
LinkCells.h
Log.cpp
Log.h
LoopUnroller.cpp
LoopUnroller.h
Matrix.cpp
Matrix.h
MatrixSquareBracketsAccess.cpp
MatrixSquareBracketsAccess.h
Minimise1DBrent.cpp
Minimise1DBrent.h
MinimiseBase.cpp
MinimiseBase.h
MolDataClass.cpp
MolDataClass.h
MultiValue.cpp
MultiValue.h
NeighborList.cpp
NeighborList.h
OFile.cpp
OFile.h
OpenMP.cpp
OpenMP.h
Pbc.cpp
Pbc.h
PDB.cpp
PDB.h
PlumedHandle.cpp
PlumedHandle.h
Random.cpp
Random.h
RMSD.cpp
RMSD.h
RootFindingBase.cpp
RootFindingBase.h
Stopwatch.cpp
Stopwatch.h
SwitchingFunction.cpp
SwitchingFunction.h
Tensor.cpp
Tensor.h
Tools.cpp
Tools.h
Torsion.cpp
Torsion.h
Units.cpp
Units.h
Vector.cpp
Vector.h
▶ vatom
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionRegister.h
ActionWithVirtualAtom.cpp
ActionWithVirtualAtom.h
Center.cpp
FixedAtom.cpp
Ghost.cpp
▶ ves
▶ bias
ActionRegister.h
Bias.h
ReweightBase.h
▶ cltools
CLTool.h
CLToolRegister.h
▶ colvar
ActionRegister.h
Colvar.h
CoordinationBase.h
PathMSDBase.h
▶ config
Config.h
version.h
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ lepton
CompiledExpression.h
CustomFunction.h
Exception.h
ExpressionProgram.h
ExpressionTreeNode.h
Lepton.h
MSVC_erfc.h
Operation.h
ParsedExpression.h
Parser.h
windowsIncludes.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
BasisFunctions.cpp
BasisFunctions.h
BF_Chebyshev.cpp
BF_Combined.cpp
BF_Cosine.cpp
BF_Custom.cpp
BF_Fourier.cpp
BF_Legendre.cpp
BF_Powers.cpp
BF_Sine.cpp
CoeffsBase.cpp
CoeffsBase.h
CoeffsMatrix.cpp
CoeffsMatrix.h
CoeffsVector.cpp
CoeffsVector.h
FermiSwitchingFunction.cpp
FermiSwitchingFunction.h
GridIntegrationWeights.cpp
GridIntegrationWeights.h
GridLinearInterpolation.cpp
GridLinearInterpolation.h
GridProjWeights.cpp
GridProjWeights.h
LinearBasisSetExpansion.cpp
LinearBasisSetExpansion.h
MD_LinearExpansionPES.cpp
Opt_BachAveragedSGD.cpp
Opt_Dummy.cpp
Optimizer.cpp
Optimizer.h
OutputBasisFunctions.cpp
OutputFesBias.cpp
OutputTargetDistribution.cpp
TargetDistModifer.cpp
TargetDistModifer.h
TargetDistribution.cpp
TargetDistribution.h
TD_Chi.cpp
TD_ChiSquared.cpp
TD_Custom.cpp
TD_Exponential.cpp
TD_ExponentiallyModifiedGaussian.cpp
TD_Gaussian.cpp
TD_GeneralizedExtremeValue.cpp
TD_GeneralizedNormal.cpp
TD_Grid.cpp
TD_LinearCombination.cpp
TD_ProductCombination.cpp
TD_ProductDistribution.cpp
TD_Uniform.cpp
TD_VonMises.cpp
TD_WellTempered.cpp
VesBias.cpp
VesBias.h
VesLinearExpansion.cpp
VesTools.cpp
VesTools.h
▶ vesselbase
▶ analysis
AnalysisBase.h
AverageVessel.h
DataCollectionObject.h
LandmarkSelectionBase.h
ReadAnalysisFrames.h
▶ bias
ActionRegister.h
Bias.h
ReweightBase.h
▶ core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataFetchingObject.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
PlumedMainInitializer.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
▶ tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Brent1DRootSearch.h
Citations.h
Communicator.h
ConjugateGradient.h
DLLoader.h
DynamicList.h
ERMSD.h
Exception.h
File.h
FileBase.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionWithAveraging.cpp
ActionWithAveraging.h
ActionWithInputVessel.cpp
ActionWithInputVessel.h
ActionWithVessel.cpp
ActionWithVessel.h
AltMin.cpp
AveragingVessel.cpp
AveragingVessel.h
Between.cpp
Between.h
BridgeVessel.cpp
BridgeVessel.h
FunctionVessel.cpp
FunctionVessel.h
Highest.cpp
Histogram.cpp
LessThan.cpp
LessThan.h
Lowest.cpp
Max.cpp
Mean.cpp
Min.cpp
Moments.cpp
MoreThan.cpp
OrderingVessel.cpp
OrderingVessel.h
ShortcutVessel.cpp
ShortcutVessel.h
StoreDataVessel.cpp
StoreDataVessel.h
Sum.cpp
ValueVessel.cpp
ValueVessel.h
Vessel.cpp
Vessel.h
VesselRegister.cpp
VesselRegister.h
▶ wrapper
Plumed.c
Plumed.h
PlumedStatic.cpp