File List

Here is a list of all files with brief descriptions:

[detail level 123]

.github
► adjmat
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
AdjacencyMatrixBase.cpp
AdjacencyMatrixBase.h
Bridge.cpp
BridgeMatrix.cpp
ContactMatrix.cpp
ContactMatrix.h
ContactMatrixShortcut.cpp
DistanceMatrix.cpp
HbondMatrix.cpp
Neighbors.cpp
TopologyMatrix.cpp
TorsionsMatrix.cpp
► annfunc
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► function
Custom.h
Function.h
FunctionOfMatrix.h
FunctionOfScalar.h
FunctionOfVector.h
FunctionSetup.h
FunctionShortcut.h
FunctionWithSingleArgument.h
ANN.cpp
► asmjit
arch.cpp
arch.h
arm.h
asmjit.h
asmjit_apibegin.h
asmjit_apiend.h
asmjit_build.h
assembler.cpp
assembler.h
base.h
codebuilder.cpp
codebuilder.h
codecompiler.cpp
codecompiler.h
codeemitter.cpp
codeemitter.h
codeholder.cpp
codeholder.h
constpool.cpp
constpool.h
cpuinfo.cpp
cpuinfo.h
func.cpp
func.h
globals.cpp
globals.h
inst.cpp
inst.h
logging.cpp
logging.h
misc_p.h
moved_string.h
operand.cpp
operand.h
osutils.cpp
osutils.h
regalloc.cpp
regalloc_p.h
runtime.cpp
runtime.h
simdtypes.h
string.cpp
utils.cpp
utils.h
vmem.cpp
vmem.h
x86.h
x86assembler.cpp
x86assembler.h
x86builder.cpp
x86builder.h
x86compiler.cpp
x86compiler.h
x86emitter.h
x86globals.h
x86inst.cpp
x86inst.h
x86instimpl.cpp
x86instimpl_p.h
x86internal.cpp
x86internal_p.h
x86logging.cpp
x86logging_p.h
x86misc.h
x86operand.cpp
x86operand.h
x86operand_regs.cpp
x86regalloc.cpp
x86regalloc_p.h
zone.cpp
zone.h
► bias
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
ABMD.cpp
Bias.cpp
Bias.h
BiasValue.cpp
ExtendedLagrangian.cpp
External.cpp
LWalls.cpp
MaxEnt.cpp
MetaD.cpp
MovingRestraint.cpp
PBMetaD.cpp
Restraint.cpp
RestraintShortcut.cpp
ReweightBase.cpp
ReweightBase.h
ReweightBias.cpp
ReweightMetad.cpp
ReweightTemperaturePressure.cpp
UWalls.cpp
Walls.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
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.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
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
► xdrfile
xdrfile.h
xdrfile_trr.h
xdrfile_xtc.h
Benchmark.cpp
CLTool.cpp
CLTool.h
Completion.cpp
Driver.cpp
DriverDouble.cpp
DriverFloat.cpp
GenExample.cpp
GenJson.cpp
GenTemplate.cpp
Info.cpp
kT.cpp
Manual.cpp
PdbRenumber.cpp
pesmd.cpp
ShowGraph.cpp
SimpleMD.cpp
SumHills.cpp
SwitchingPlotter.cpp
► clusters
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► matrixtools
MatrixOperationBase.h
MatrixTimesMatrix.h
MatrixTimesVectorBase.h
OuterProduct.h
► multicolvar
MultiColvarShortcuts.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
ClusterDiameter.cpp
ClusterDistribution.cpp
ClusteringBase.cpp
ClusteringBase.h
ClusterNatoms.cpp
ClusterProperties.cpp
ClusterWeights.cpp
ClusterWithSurface.cpp
DFSClustering.cpp
OutputCluster.cpp
► colvar
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
Angle.cpp
Cell.cpp
Colvar.cpp
Colvar.h
ColvarInput.cpp
ColvarInput.h
ColvarShortcut.cpp
ColvarShortcut.h
ContactMap.cpp
Coordination.cpp
CoordinationBase.cpp
CoordinationBase.h
DHEnergy.cpp
DihedralCorrelation.cpp
Dimer.cpp
Dipole.cpp
Distance.cpp
DRMSD.cpp
EEFSolv.cpp
Energy.cpp
ERMSD.cpp
ExtraCV.cpp
Fake.cpp
GHBFIX.cpp
Gyration.cpp
GyrationShortcut.cpp
MultiColvarTemplate.cpp
MultiColvarTemplate.h
MultiRMSD.cpp
PathMSD.cpp
PathMSDBase.cpp
PathMSDBase.h
PCARMSD.cpp
Plane.cpp
Position.cpp
ProjectionOnAxis.cpp
PropertyMap.cpp
Puckering.cpp
RMSD.cpp
RMSDShortcut.cpp
RMSDVector.cpp
RMSDVector.h
SelectMassCharge.cpp
Template.cpp
Torsion.cpp
Volume.cpp
► config
Config.cpp
Config.h
ConfigInstall.cpp
version.h
► contour
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► function
Custom.h
Function.h
FunctionOfMatrix.h
FunctionOfScalar.h
FunctionOfVector.h
FunctionSetup.h
FunctionShortcut.h
FunctionWithSingleArgument.h
► gridtools
ActionWithGrid.h
EvaluateGridFunction.h
FunctionOfGrid.h
GridCoordinatesObject.h
GridSearch.h
Interpolator.h
KDE.h
RDF.h
SumOfKernels.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
ContourFindingObject.cpp
ContourFindingObject.h
DistanceFromContour.cpp
DistanceFromContourBase.cpp
DistanceFromContourBase.h
DistanceFromSphericalContour.cpp
DumpContour.cpp
FindContour.cpp
FindContour.h
FindContourSurface.cpp
FindSphericalContour.cpp
► core
► blas
blas.h
def_external.h
def_internal.h
real.h
► 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
► small_vector
small_vector.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
Action.cpp
Action.h
ActionAnyorder.cpp
ActionAnyorder.h
ActionAtomistic.cpp
ActionAtomistic.h
ActionForInterface.cpp
ActionForInterface.h
ActionPilot.cpp
ActionPilot.h
ActionRegister.cpp
ActionRegister.h
ActionSet.cpp
ActionSet.h
ActionSetup.cpp
ActionSetup.h
ActionShortcut.cpp
ActionShortcut.h
ActionToGetData.cpp
ActionToGetData.h
ActionToPutData.cpp
ActionToPutData.h
ActionWithArguments.cpp
ActionWithArguments.h
ActionWithMatrix.cpp
ActionWithMatrix.h
ActionWithValue.cpp
ActionWithValue.h
ActionWithVector.cpp
ActionWithVector.h
ActionWithVirtualAtom.cpp
ActionWithVirtualAtom.h
CLTool.cpp
CLTool.h
CLToolMain.cpp
CLToolMain.h
CLToolRegister.cpp
CLToolRegister.h
Colvar.cpp
Colvar.h
DataPassingObject.cpp
DataPassingObject.h
DataPassingTools.cpp
DataPassingTools.h
DomainDecomposition.cpp
DomainDecomposition.h
ExchangePatterns.cpp
ExchangePatterns.h
FlexibleBin.cpp
FlexibleBin.h
GenericMolInfo.cpp
GenericMolInfo.h
GREX.cpp
GREX.h
Group.cpp
Group.h
ModuleMap.cpp
ModuleMap.h
ParallelTaskManager.cpp
ParallelTaskManager.h
PbcAction.cpp
PbcAction.h
PlumedMain.cpp
PlumedMain.h
PlumedMainInitializer.cpp
PlumedMainInitializer.h
RegisterBase.cpp
RegisterBase.h
TargetDist.cpp
TargetDist.h
Value.cpp
Value.h
WithCmd.cpp
WithCmd.h
► crystdistrib
► colvar
Colvar.h
ColvarInput.h
ColvarShortcut.h
CoordinationBase.h
MultiColvarTemplate.h
PathMSDBase.h
RMSDVector.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► matrixtools
MatrixOperationBase.h
MatrixTimesMatrix.h
MatrixTimesVectorBase.h
OuterProduct.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
BopsShortcut.cpp
DopsShortcut.cpp
Quaternion.cpp
QuaternionBondProductMatrix.cpp
QuaternionProductMatrix.cpp
RopsShortcut.cpp
developer-doc
► dimred
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► gridtools
ActionWithGrid.h
EvaluateGridFunction.h
FunctionOfGrid.h
GridCoordinatesObject.h
GridSearch.h
Interpolator.h
KDE.h
RDF.h
SumOfKernels.h
► mapping
Path.h
PathProjectionCalculator.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
ArrangePoints.cpp
ClassicalMultiDimensionalScaling.cpp
PCA.cpp
ProjectPoints.cpp
SketchMap.cpp
SketchMapProjection.cpp
SMACOF.cpp
SMACOF.h
► drr
► bias
Bias.h
ReweightBase.h
► cltools
CLTool.h
► config
Config.h
version.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
colvar_UIestimator.cpp
colvar_UIestimator.h
DRR.cpp
DRR.h
drrtool.cpp
DynamicReferenceRestraining.cpp
► eds
► bias
Bias.h
ReweightBase.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
EDS.cpp
► envsim
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► multicolvar
MultiColvarShortcuts.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
EnvironmentSimilarity.cpp
► fisst
► bias
Bias.h
ReweightBase.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
FISST.cpp
legendre_rule_fast.cpp
legendre_rule_fast.h
► fourier
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► gridtools
ActionWithGrid.h
EvaluateGridFunction.h
FunctionOfGrid.h
GridCoordinatesObject.h
GridSearch.h
Interpolator.h
KDE.h
RDF.h
SumOfKernels.h
FourierTransform.cpp
► function
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
Bessel.cpp
Between.cpp
Combine.cpp
Custom.cpp
Custom.h
Ensemble.cpp
FuncPathGeneral.cpp
FuncPathMSD.cpp
FuncSumHills.cpp
Function.cpp
Function.h
FunctionOfMatrix.cpp
FunctionOfMatrix.h
FunctionOfScalar.cpp
FunctionOfScalar.h
FunctionOfVector.cpp
FunctionOfVector.h
FunctionSetup.cpp
FunctionSetup.h
FunctionShortcut.cpp
FunctionShortcut.h
FunctionWithSingleArgument.cpp
FunctionWithSingleArgument.h
Highest.cpp
LessThan.cpp
LocalEnsemble.cpp
Moments.cpp
MoreThan.cpp
Piecewise.cpp
Product.cpp
Sort.cpp
SortWithSingleArgument.cpp
Stats.cpp
Sum.cpp
► funnel
► bias
Bias.h
ReweightBase.h
► colvar
Colvar.h
ColvarInput.h
ColvarShortcut.h
CoordinationBase.h
MultiColvarTemplate.h
PathMSDBase.h
RMSDVector.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
FPS.cpp
Funnel.cpp
► generic
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
► xdrfile
xdrfile.h
xdrfile_trr.h
xdrfile_xtc.h
Accumulate.cpp
Average.cpp
Collect.cpp
Committor.cpp
Constant.cpp
CreateMask.cpp
Debug.cpp
DumpAtoms.cpp
DumpDerivatives.cpp
DumpForces.cpp
DumpMassCharge.cpp
DumpPDB.cpp
DumpProjections.cpp
DumpVector.cpp
EffectiveEnergyDrift.cpp
EndPlumed.cpp
FitToTemplate.cpp
Flush.cpp
GatherReplicas.cpp
Include.cpp
MassChargeInput.cpp
MolInfo.cpp
Ones.cpp
PDB2Constant.cpp
Plumed.cpp
Print.cpp
PrintNDX.cpp
RandomExchanges.cpp
Read.cpp
ResetCell.cpp
Time.cpp
UpdateIf.cpp
WholeMolecules.cpp
WrapAround.cpp
► gridtools
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► function
Custom.h
Function.h
FunctionOfMatrix.h
FunctionOfScalar.h
FunctionOfVector.h
FunctionSetup.h
FunctionShortcut.h
FunctionWithSingleArgument.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
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
ActionWithGrid.cpp
ActionWithGrid.h
ConvertToFES.cpp
DumpGrid.cpp
EvaluateFunctionOnGrid.cpp
EvaluateGridFunction.cpp
EvaluateGridFunction.h
FindGridOptimum.cpp
FunctionOfGrid.cpp
FunctionOfGrid.h
GetGridVolumeElement.cpp
Gradient.cpp
GridCoordinatesObject.cpp
GridCoordinatesObject.h
GridSearch.cpp
GridSearch.h
Histogram.cpp
IntegrateGrid.cpp
InterpolateGrid.cpp
Interpolator.cpp
Interpolator.h
KDE.cpp
KDE.h
KLEntropy.cpp
Marginal.cpp
MultiColvarDensity.cpp
PairEntropy.cpp
RDF.cpp
RDF.h
ReadGridInSetup.cpp
SumOfKernels.cpp
SumOfKernels.h
► isdb
► bias
Bias.h
ReweightBase.h
► colvar
Colvar.h
ColvarInput.h
ColvarShortcut.h
CoordinationBase.h
MultiColvarTemplate.h
PathMSDBase.h
RMSDVector.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► function
Custom.h
Function.h
FunctionOfMatrix.h
FunctionOfScalar.h
FunctionOfVector.h
FunctionSetup.h
FunctionShortcut.h
FunctionWithSingleArgument.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
bAIes.cpp
Caliber.cpp
CS2Backbone.cpp
EMMI.cpp
EMMIVox.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
Shadow.cpp
► landmarks
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► matrixtools
MatrixOperationBase.h
MatrixTimesMatrix.h
MatrixTimesVectorBase.h
OuterProduct.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
CollectFrames.cpp
FarthestPointSampling.cpp
LandmarkSelection.cpp
LogSumExp.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
► asmjit
arch.h
arm.h
asmjit.h
asmjit_apibegin.h
asmjit_apiend.h
asmjit_build.h
assembler.h
base.h
codebuilder.h
codecompiler.h
codeemitter.h
codeholder.h
constpool.h
cpuinfo.h
func.h
globals.h
inst.h
logging.h
misc_p.h
moved_string.h
operand.h
osutils.h
regalloc_p.h
runtime.h
simdtypes.h
utils.h
vmem.h
x86.h
x86assembler.h
x86builder.h
x86compiler.h
x86emitter.h
x86globals.h
x86inst.h
x86instimpl_p.h
x86internal_p.h
x86logging_p.h
x86misc.h
x86operand.h
x86regalloc_p.h
zone.h
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
► liquid_crystal
► colvar
Colvar.h
ColvarInput.h
ColvarShortcut.h
CoordinationBase.h
MultiColvarTemplate.h
PathMSDBase.h
RMSDVector.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► multicolvar
MultiColvarShortcuts.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
FerroNematicOrder.cpp
NematicOrder.cpp
► logmfd
► bias
Bias.h
ReweightBase.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
LogMFD.cpp
► main
► wrapper
Plumed.h
main.cpp
► mapping
► colvar
Colvar.h
ColvarInput.h
ColvarShortcut.h
CoordinationBase.h
MultiColvarTemplate.h
PathMSDBase.h
RMSDVector.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
AdaptivePath.cpp
GeometricPath.cpp
GeometricPathShortcut.cpp
Path.cpp
Path.h
PathDisplacements.cpp
PathProjectionCalculator.cpp
PathProjectionCalculator.h
PathReparameterization.cpp
PathTools.cpp
PCAVars.cpp
► matrixtools
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
CovarianceMatrix.cpp
Determinent.cpp
DiagonalizeMatrix.cpp
InvertMatrix.cpp
MatrixOperationBase.cpp
MatrixOperationBase.h
MatrixTimesMatrix.cpp
MatrixTimesMatrix.h
MatrixTimesVector.cpp
MatrixTimesVectorBase.cpp
MatrixTimesVectorBase.h
OuterProduct.cpp
OuterProduct.h
TransposeMatrix.cpp
Voronoi.cpp
► maze
► bias
Bias.h
ReweightBase.h
► colvar
Colvar.h
ColvarInput.h
ColvarShortcut.h
CoordinationBase.h
MultiColvarTemplate.h
PathMSDBase.h
RMSDVector.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
Core.cpp	Dummy cpp file
Core.h	Header with needed includes from std and PLMD
Loss.cpp
Loss.h
Member.cpp	Dummy cpp file
Member.h
Memetic.cpp
Memetic.h
Optimizer.cpp
Optimizer.h
Optimizer_Bias.cpp
Random_Acceleration_MD.cpp
Random_MT.cpp	Dummy cpp file
Random_MT.h
Random_Walk.cpp
Simulated_Annealing.cpp
Steered_MD.cpp
Tools.cpp	Dummy cpp file
Tools.h
► membranefusion
► colvar
Colvar.h
ColvarInput.h
ColvarShortcut.h
CoordinationBase.h
MultiColvarTemplate.h
PathMSDBase.h
RMSDVector.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
FusionPoreExpansionP.cpp
FusionPoreNucleationP.cpp
MemFusionP.cpp
► metatomic
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
metatomic.cpp
vesin.cpp
vesin.h
► 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
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
AlphaBeta.cpp
Angles.cpp
CoordAngles.cpp
Dihcor.cpp
Distances.cpp
DumpMultiColvar.cpp
InPlaneDistances.cpp
MFilterLess.cpp
MFilterMore.cpp
MultiColvarShortcuts.cpp
MultiColvarShortcuts.h
Planes.cpp
Torsions.cpp
UWalls.cpp
XAngle.cpp
XYTorsions.cpp
► opes
► bias
Bias.h
ReweightBase.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
ECVcustom.cpp
ECVlinear.cpp
ECVmultiThermal.cpp
ECVmultiThermalBaric.cpp
ECVumbrellasFile.cpp
ECVumbrellasLine.cpp
ExpansionCVs.cpp
ExpansionCVs.h
OPESexpanded.cpp
OPESmetad.cpp
► pamm
► adjmat
AdjacencyMatrixBase.h
ContactMatrix.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► multicolvar
MultiColvarShortcuts.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
HBPammMatrix.cpp
PAMM.cpp
► piv
► colvar
Colvar.h
ColvarInput.h
ColvarShortcut.h
CoordinationBase.h
MultiColvarTemplate.h
PathMSDBase.h
RMSDVector.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
PIV.cpp
► pytorch
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► function
Custom.h
Function.h
FunctionOfMatrix.h
FunctionOfScalar.h
FunctionOfVector.h
FunctionSetup.h
FunctionShortcut.h
FunctionWithSingleArgument.h
PytorchModel.cpp
► refdist
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► function
Custom.h
Function.h
FunctionOfMatrix.h
FunctionOfScalar.h
FunctionOfVector.h
FunctionSetup.h
FunctionShortcut.h
FunctionWithSingleArgument.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
Difference.cpp
Displacement.cpp
EuclideanDistance.cpp
Kernel.cpp
MahalanobisDistance.cpp
MatrixProductDiagonal.cpp
NormalizedEuclideanDistance.cpp
► s2cm
► colvar
Colvar.h
ColvarInput.h
ColvarShortcut.h
CoordinationBase.h
MultiColvarTemplate.h
PathMSDBase.h
RMSDVector.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
S2ContactModel.cpp
► sasa
► config
Config.h
version.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
Sasa.cpp
Sasa.h
sasa_HASEL.cpp
sasa_LCPO.cpp
► secondarystructure
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
AlphaRMSD.cpp
AntibetaRMSD.cpp
ParabetaRMSD.cpp
SecondaryStructureBase.cpp
SecondaryStructureBase.h
SecondaryStructureDRMSD.cpp
SecondaryStructureRMSD.cpp
► setup
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
ActionSetup.h
Load.cpp
Restart.cpp
Units.cpp
► sizeshape
► colvar
Colvar.h
ColvarInput.h
ColvarShortcut.h
CoordinationBase.h
MultiColvarTemplate.h
PathMSDBase.h
RMSDVector.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
mahadist.cpp
pos_proj.cpp
► small_vector
small_vector.cpp
small_vector.h
► sprint
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
Sprint.cpp
► symfunc
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► function
Custom.h
Function.h
FunctionOfMatrix.h
FunctionOfScalar.h
FunctionOfVector.h
FunctionSetup.h
FunctionShortcut.h
FunctionWithSingleArgument.h
► multicolvar
MultiColvarShortcuts.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
AngularTetra.cpp
AtomicSMAC.cpp
CoordinationNumbers.cpp
CoordinationNumbers.h
CoordShellVectorFunction.cpp
CylindricalHarmonic.cpp
Fccubic.cpp
HexaticParameter.cpp
LocalAverage.cpp
LocalCrystalinity.cpp
LocalSteinhardt.cpp
RadialTetra.cpp
SMAC.cpp
SphericalHarmonic.cpp
Steinhardt.cpp
ThreeBodyGFunctions.cpp
► tools
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.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
► molfile
endianswap.h
fastio.h
Gromacs.h
largefiles.h
libmolfile_plugin.h
molfile_plugin.h
periodic_table.h
readpdb.h
vmdplugin.h
► small_vector
small_vector.h
► xdrfile
xdrfile.h
xdrfile_trr.h
xdrfile_xtc.h
Angle.cpp
Angle.h
AtomDistribution.cpp
AtomDistribution.h
AtomNumber.cpp
AtomNumber.h
BiasRepresentation.cpp
BiasRepresentation.h
BitmaskEnum.cpp
BitmaskEnum.h
Brent1DRootSearch.cpp
Brent1DRootSearch.h
CheckInRange.cpp
CheckInRange.h
Citations.cpp
Citations.h
ColvarOutput.cpp
ColvarOutput.h
Communicator.cpp
Communicator.h
ConjugateGradient.cpp
ConjugateGradient.h
DLLoader.cpp
DLLoader.h
ERMSD.cpp
ERMSD.h
Exception.cpp
Exception.h
File.h
FileBase.cpp
FileBase.h
FileTools.cpp
FileTools.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
LeptonCall.cpp
LeptonCall.h
LinkCells.cpp
LinkCells.h
Log.cpp
Log.h
LoopUnroller.cpp
LoopUnroller.h
Matrix.cpp
Matrix.h
MatrixSquareBracketsAccess.cpp
MatrixSquareBracketsAccess.h
MergeVectorTools.cpp
MergeVectorTools.h
Minimise1DBrent.cpp
Minimise1DBrent.h
MinimiseBase.cpp
MinimiseBase.h
MolDataClass.cpp
MolDataClass.h
NeighborList.cpp
NeighborList.h
OFile.cpp
OFile.h
OpenACC.cpp
OpenACC.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
Subprocess.cpp
Subprocess.h
SwitchingFunction.cpp
SwitchingFunction.h
Tensor.cpp
Tensor.h
TokenizedLine.cpp
TokenizedLine.h
Tools.cpp
Tools.h
Torsion.cpp
Torsion.h
TrajectoryParser.cpp
TrajectoryParser.h
Tree.cpp
Tree.h
TypesafePtr.cpp
TypesafePtr.h
Units.cpp
Units.h
Vector.cpp
Vector.h
View.cpp
View.h
View2D.cpp
View2D.h
► valtools
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
Concatenate.cpp
Flatten.cpp
SelectComponents.cpp
SelectWithMask.cpp
VStack.cpp
► vatom
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
ActionWithVirtualAtom.cpp
ActionWithVirtualAtom.h
ArgsToVatom.cpp
Center.cpp
CenterShortcut.cpp
FixedAtom.cpp
Ghost.cpp
► ves
► bias
Bias.h
ReweightBase.h
► cltools
CLTool.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.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
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
BasisFunctions.cpp
BasisFunctions.h
BF_Chebyshev.cpp
BF_Combined.cpp
BF_Cosine.cpp
BF_CubicBsplines.cpp
BF_Custom.cpp
BF_Fourier.cpp
BF_Gaussians.cpp
BF_Legendre.cpp
BF_Powers.cpp
BF_Sine.cpp
BF_Wavelets.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_Adam.cpp
Opt_BachAveragedSGD.cpp
Opt_Dummy.cpp
Opt_RobbinsMonroSGD.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_Multicanonical.cpp
TD_MultithermalMultibaric.cpp
TD_ProductCombination.cpp
TD_ProductDistribution.cpp
TD_Uniform.cpp
TD_VonMises.cpp
TD_WellTempered.cpp
VesBias.cpp
VesBias.h
VesDeltaF.cpp
VesLinearExpansion.cpp
VesTools.cpp
VesTools.h
WaveletCoeffs.cpp
WaveletGrid.cpp
WaveletGrid.h
► volumes
► colvar
Colvar.h
ColvarInput.h
ColvarShortcut.h
CoordinationBase.h
MultiColvarTemplate.h
PathMSDBase.h
RMSDVector.h
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
ActionVolume.cpp
ActionVolume.h
Density.cpp
VolumeAround.cpp
VolumeBetweenContours.cpp
VolumeCavity.cpp
VolumeInCylinder.cpp
VolumeInSphere.cpp
VolumeShortcut.cpp
VolumeShortcut.h
VolumeTetrapore.cpp
► wham
► core
Action.h
ActionAnyorder.h
ActionAtomistic.h
ActionForInterface.h
ActionPilot.h
ActionRegister.h
ActionSet.h
ActionSetup.h
ActionShortcut.h
ActionToGetData.h
ActionToPutData.h
ActionWithArguments.h
ActionWithMatrix.h
ActionWithValue.h
ActionWithVector.h
ActionWithVirtualAtom.h
CLTool.h
CLToolMain.h
CLToolRegister.h
Colvar.h
DataPassingObject.h
DataPassingTools.h
DomainDecomposition.h
ExchangePatterns.h
FlexibleBin.h
GenericMolInfo.h
GREX.h
Group.h
ModuleMap.h
ParallelTaskManager.h
PbcAction.h
PlumedMain.h
PlumedMainInitializer.h
RegisterBase.h
TargetDist.h
Value.h
WithCmd.h
► tools
Angle.h
AtomDistribution.h
AtomNumber.h
BiasRepresentation.h
BitmaskEnum.h
Brent1DRootSearch.h
CheckInRange.h
Citations.h
ColvarOutput.h
Communicator.h
ConjugateGradient.h
DLLoader.h
ERMSD.h
Exception.h
File.h
FileBase.h
FileTools.h
ForwardDecl.h
Grid.h
h36.h
HistogramBead.h
IFile.h
KernelFunctions.h
Keywords.h
LatticeReduction.h
LeptonCall.h
LinkCells.h
Log.h
LoopUnroller.h
Matrix.h
MatrixSquareBracketsAccess.h
MergeVectorTools.h
Minimise1DBrent.h
MinimiseBase.h
MolDataClass.h
NeighborList.h
OFile.h
OpenACC.h
OpenMP.h
Pbc.h
PDB.h
PlumedHandle.h
Random.h
RMSD.h
RootFindingBase.h
Stopwatch.h
Subprocess.h
SwitchingFunction.h
Tensor.h
TokenizedLine.h
Tools.h
Torsion.h
TrajectoryParser.h
Tree.h
TypesafePtr.h
Units.h
Vector.h
View.h
View2D.h
Wham.cpp
WhamHistogram.cpp
WhamWeights.cpp
► wrapper
Plumed.c
Plumed.h
PlumedStatic.cpp
► xdrfile
xdrfile.cpp
xdrfile.h	Interface to read/write portabile binary files using XDR
xdrfile_trr.cpp
xdrfile_trr.h
xdrfile_xtc.cpp
xdrfile_xtc.h