Index

A

AddDataToWindow() (Phase method)

AddWindow() (System method)

C

CalculateDiffusionConstants() (System method) CalculatePMF() (System method) CalculatePMFConvergence() (System method)

CalculateWindowsHistConvergence() (System method) CollectiveVariable (class in other)

D

DefineQstat() (Environment method)

DefineQsub() (Environment method)

E

Environment (class in environment)

environment (module)

F

FindPhase() (System method) (Window method) FindWindow() (System method)

FindWindows() (System method)

G

GenerateInputFile() (Job method) GenerateJobFile() (Job method) GenerateNewWindows() (System method) GetCurvatures() (PMF method) GetDataCount() (Phase method) GetInitInputReplacementDict() (Job method) GetInitJobReplacementDict() (Job method) GetInputReplacementDict() (Job method)

GetJobReplacementDict() (Job method) GetPathToInitInputFile() (System method) GetPathToInitJobFile() (System method) GetPathToRunInputFile() (System method) GetPathToRunJobFile() (System method) GetRunInputReplacementDict() (Job method) GetRunJobReplacementDict() (Job method) GetValue() (PMF method)

I

Initialize() (Phase method) (System method) (Window method)

J

Job (class in job)

job (module)

L

LoadSystem() (in module system)

O

other (module), [1]

P

Phase (class in phase) phase (module) Plot() (PMF method)

PlotHistogram() (System method) PlotPMF() (System method) PMF (class in other)

R

ReadDataFile() (Window method) ReadPMFFile() (System method)

RebuildWindowsAndPhasesFromDirectoryTree() (in module system) Run() (SiPMF method)

S

Save() (System method) SetNewBaseDir() (System method) ShiftWindowFreeEnergies() (System method) SiPMF (class in siPMF) siPMF (module)

Submit() (Job method) SubmitNewJobs() (System method) SubmitNextPhase() (Window method) System (class in system) system (module)

U

UpdateDataCount() (Phase method) (Window method) UpdateDataCounts() (System method) UpdateDataFile() (Window method) UpdateDataFiles() (System method)

UpdatePMF() (System method) UpdateStatus() (Job method) UpdateUnfinishedJobList() (System method)

W

Window (class in window)

window (module)