File List

Here is a list of all files with brief descriptions:

[detail level 123]

► analysis
► core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► reference
ArgumentOnlyDistance.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
MultiReferenceBase.h
PointWiseMapping.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SimpleRMSD.h
SingleDomainRMSD.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
► vesselbase
ActionWithInputVessel.h
ActionWithVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
Analysis.cpp
Analysis.h
AnalysisWithLandmarks.cpp
AnalysisWithLandmarks.h
ClassicalMultiDimensionalScaling.cpp
ClassicalScaling.cpp
ClassicalScaling.h
Commit.cpp
Histogram.cpp
LandmarkRegister.cpp
LandmarkRegister.h
LandmarkSelectionBase.cpp
LandmarkSelectionBase.h
SelectAllFrames.cpp
► bias
► core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.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
MetaD.cpp
MovingRestraint.cpp
PBMetaD.cpp
Restraint.cpp
UWalls.cpp
► blas
blas.cpp
blas.h	Header definitions for the standard BLAS library
def_external.h
def_internal.h
simple.h
► cltools
► config
Config.h
version.h
► core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.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
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
► wrapper
Plumed.h
CLTool.h
CLToolRegister.h
Driver.cpp
DriverDouble.cpp
DriverFloat.cpp
GenTemplate.cpp
Info.cpp
kT.cpp
Manual.cpp
SimpleMD.cpp
SumHills.cpp
► colvar
► core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► reference
ArgumentOnlyDistance.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
MultiReferenceBase.h
PointWiseMapping.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SimpleRMSD.h
SingleDomainRMSD.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionRegister.h
Angle.cpp
Cell.cpp
CH3Shifts.cpp
Colvar.h
Constant.cpp
ContactMap.cpp
Coordination.cpp
CoordinationBase.cpp
CoordinationBase.h
CS2Backbone.cpp
DHEnergy.cpp
Dipole.cpp
Distance.cpp
DRMSD.cpp
Energy.cpp
Fake.cpp
Gyration.cpp
MultiRMSD.cpp
NOE.cpp
PathMSD.cpp
PathMSDBase.cpp
PathMSDBase.h
PCARMSD.cpp
Position.cpp
PropertyMap.cpp
Puckering.cpp
RDC.cpp
RMSD.cpp
Template.cpp
Torsion.cpp
Volume.cpp
► config
Config.cpp
Config.h
ConfigInstall.cpp
version.h
► core
► config
Config.h
version.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
Action.cpp
Action.h
ActionAtomistic.cpp
ActionAtomistic.h
ActionPilot.cpp
ActionPilot.h
ActionRegister.cpp
ActionRegister.h
ActionSet.cpp
ActionSet.h
ActionSetup.cpp
ActionSetup.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
ExchangePatterns.cpp
ExchangePatterns.h
FlexibleBin.cpp
FlexibleBin.h
GREX.cpp
GREX.h
MDAtoms.cpp
MDAtoms.h
PlumedMain.cpp
PlumedMain.h
PlumedMainInitializer.cpp
SetupMolInfo.cpp
SetupMolInfo.h
TargetDist.cpp
TargetDist.h
Value.cpp
Value.h
WithCmd.h
► crystallization
► core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► multicolvar
ActionVolume.h
AdjacencyMatrixAction.h
AdjacencyMatrixVessel.h
AtomValuePack.h
BridgedMultiColvarFunction.h
CatomPack.h
MultiColvar.h
MultiColvarBase.h
MultiColvarFilter.h
MultiColvarFunction.h
VolumeGradientBase.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
► vesselbase
ActionWithInputVessel.h
ActionWithVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
DFSBasic.cpp
DFSClustering.cpp
DFSClustering.h
DFSClusterRadius.cpp
DFSMaxSize.cpp
DFSNumberOfClusters.cpp
Fccubic.cpp
Gradient.cpp
Gradient.h
GradientVessel.cpp
LocalSteinhardt.h
MoleculeOrientation.cpp
MoleculePlane.cpp
OrientationSphere.cpp
OrientationSphere.h
Q3.cpp
Q4.cpp
Q6.cpp
SimpleCubic.cpp
SMAC.cpp
Steinhardt.cpp
Steinhardt.h
Tetrahedral.cpp
VectorMean.cpp
VectorMultiColvar.cpp
VectorMultiColvar.h
VectorSum.cpp
► function
► core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► reference
ArgumentOnlyDistance.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
MultiReferenceBase.h
PointWiseMapping.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SimpleRMSD.h
SingleDomainRMSD.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionRegister.h
Combine.cpp
Ensemble.cpp
FuncPathMSD.cpp
FuncSumHills.cpp
Function.cpp
Function.h
Matheval.cpp
Piecewise.cpp
Sort.cpp
Target.cpp
► generic
► core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.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
FitToTemplate.cpp
Flush.cpp
Group.cpp
Include.cpp
Print.cpp
RandomExchanges.cpp
Read.cpp
Time.cpp
WholeMolecules.cpp
WrapAround.cpp
► imd
ActionIMD.cpp
► lapack
► blas
blas.h
def_external.h
def_internal.h
simple.h
def_external.h
def_internal.h
lapack.cpp
lapack.h	Header definitions for the standard LAPACK library
lapack_limits.h
simple.h
► main
► wrapper
Plumed.h
main.cpp
► manyrestraints
► core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
► vesselbase
ActionWithInputVessel.h
ActionWithVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
ManyRestraintsBase.cpp
ManyRestraintsBase.h
UWalls.cpp
► mapping
► core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► reference
ArgumentOnlyDistance.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
MultiReferenceBase.h
PointWiseMapping.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SimpleRMSD.h
SingleDomainRMSD.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
► vesselbase
ActionWithInputVessel.h
ActionWithVessel.h
Between.h
BridgeVessel.h
FunctionVessel.h
LessThan.h
OrderingVessel.h
ShortcutVessel.h
StoreDataVessel.h
ValueVessel.h
Vessel.h
VesselRegister.h
Mapping.cpp
Mapping.h
Path.cpp
PathBase.cpp
PathBase.h
PCAVars.cpp
PropertyMap.cpp
SpathVessel.cpp
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
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
► vesselbase
ActionWithInputVessel.h
ActionWithVessel.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
AdjacencyMatrixAction.cpp
AdjacencyMatrixAction.h
AdjacencyMatrixVessel.cpp
AdjacencyMatrixVessel.h
AlphaBeta.cpp
Angles.cpp
AtomValuePack.cpp
AtomValuePack.h
Bridge.cpp
BridgedMultiColvarFunction.cpp
BridgedMultiColvarFunction.h
CatomPack.cpp
CatomPack.h
CoordinationNumbers.cpp
Density.cpp
DihedralCorrelation.cpp
Distances.cpp
DumpMultiColvar.cpp
FilterBetween.cpp
FilterLessThan.cpp
FilterMoreThan.cpp
InPlaneDistances.cpp
LocalAverage.cpp
MultiColvar.cpp
MultiColvar.h
MultiColvarBase.cpp
MultiColvarBase.h
MultiColvarDensity.cpp
MultiColvarFilter.cpp
MultiColvarFilter.h
MultiColvarFunction.cpp
MultiColvarFunction.h
NumberOfLinks.cpp
Sprint.cpp
Torsions.cpp
VolumeAround.cpp
VolumeCavity.cpp
VolumeGradientBase.cpp
VolumeGradientBase.h
VolumeInCylinder.cpp
VolumeTetrapore.cpp
XDistances.cpp
XYDistances.cpp
► reference
► core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ArgumentOnlyDistance.cpp
ArgumentOnlyDistance.h
Direction.cpp
DotProductDistance.cpp
DRMSD.cpp
DRMSD.h
EuclideanDistance.cpp
FakeFrame.h
MahalanobisDistance.cpp
MetricRegister.cpp
MetricRegister.h
MultiDomainRMSD.cpp
MultiDomainRMSD.h
MultiReferenceBase.cpp
MultiReferenceBase.h
NormalizedEuclideanDistance.cpp
OptimalRMSD.cpp
PointWiseMapping.cpp
PointWiseMapping.h
ReferenceArguments.cpp
ReferenceArguments.h
ReferenceAtoms.cpp
ReferenceAtoms.h
ReferenceConfiguration.cpp
ReferenceConfiguration.h
ReferenceValuePack.cpp
ReferenceValuePack.h
RMSDBase.cpp
RMSDBase.h
SimpleRMSD.cpp
SimpleRMSD.h
SingleDomainRMSD.cpp
SingleDomainRMSD.h
► secondarystructure
► core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► reference
ArgumentOnlyDistance.h
DRMSD.h
FakeFrame.h
MetricRegister.h
MultiDomainRMSD.h
MultiReferenceBase.h
PointWiseMapping.h
ReferenceArguments.h
ReferenceAtoms.h
ReferenceConfiguration.h
ReferenceValuePack.h
RMSDBase.h
SimpleRMSD.h
SingleDomainRMSD.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
► vesselbase
ActionWithInputVessel.h
ActionWithVessel.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
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.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
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► lapack
def_external.h
def_internal.h
lapack.h
lapack_limits.h
simple.h
Angle.cpp
Angle.h
AtomNumber.h
BiasRepresentation.cpp
BiasRepresentation.h
Citations.cpp
Citations.h
Communicator.cpp
Communicator.h
CubicInterpolation.cpp
CubicInterpolation.h
DLLoader.cpp
DLLoader.h
DynamicList.h
Exception.cpp
Exception.h
File.h
FileBase.cpp
FileBase.h
Grid.cpp
Grid.h
HistogramBead.cpp
HistogramBead.h
IFile.cpp
IFile.h
Kearsley.cpp
Kearsley.h
KernelFunctions.cpp
KernelFunctions.h
Keywords.cpp
Keywords.h
LatticeReduction.cpp
LatticeReduction.h
LinkCells.cpp
LinkCells.h
Log.cpp
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.cpp
MolDataClass.h
MultiValue.cpp
MultiValue.h
NeighborList.cpp
NeighborList.h
OFile.cpp
OFile.h
OpenMP.cpp
OpenMP.h
OptimalAlignment.cpp
OptimalAlignment.h
Pbc.cpp
Pbc.h
PDB.cpp
PDB.h
Random.cpp
Random.h
RMSD.cpp
RMSD.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
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionRegister.h
ActionWithVirtualAtom.h
Center.cpp
COM.cpp
Ghost.cpp
► vesselbase
► core
Action.h
ActionAtomistic.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionWithArguments.h
ActionWithValue.h
ActionWithVirtualAtom.h
Atoms.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
ExchangePatterns.h
FlexibleBin.h
GREX.h
MDAtoms.h
PlumedMain.h
SetupMolInfo.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomNumber.h
BiasRepresentation.h
Citations.h
Communicator.h
CubicInterpolation.h
DLLoader.h
DynamicList.h
Exception.h
File.h
FileBase.h
Grid.h
HistogramBead.h
IFile.h
Kearsley.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MolDataClass.h
MultiValue.h
NeighborList.h
OFile.h
OpenMP.h
OptimalAlignment.h
Pbc.h
PDB.h
Random.h
RMSD.h
Stopwatch.h
SwitchingFunction.h
Tensor.h
Tools.h
Torsion.h
Units.h
Vector.h
ActionWithInputVessel.cpp
ActionWithInputVessel.h
ActionWithVessel.cpp
ActionWithVessel.h
AltMin.cpp
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