lionanalysis documentation

• About lionanalysis
  • Quickstart
  • Features
  • Who should use lionanalysis?
  • Current limitations
  • Compilation
  • Running the program
  • References
• Examples
  • Getting started with lionanalysis
    • Introduction
    • Example trajectory: RuH.xyz
    • Simple lionanalysis run to print number of Ru and H atoms as a function of time
    • Load and plot data with pandas, matplotlib, seaborn
    • Defining groups and finding out atomic environments
    • Visualize atoms in different groups
  • Number density of particles for an axis
  • Radial and angular distribution functions, hydrogen bond definition
    • Radial distribution functions
    • Angular distribution function
    • Hydrogen bond statistics and defining groups based on angle criteria
    • Plot coordination number vs. frame number
  • Lifetime time correlation functions and hydroxide ions
    • Hydroxide ion definition, show hydroxides in different color
    • Lifetime from continuous and intermittent time correlation functions
    • Lifetime from SSP: Stable States Picture
  • Mean squared displacement and proton transfer free energy landscape
    • Sodium diffusion coefficient
    • Hydroxide ion diffusion coefficient
    • Na-O radial distribution function
    • Proton transfer free energy landscape
    • Advanced PTFEL for local environments
  • Block averages (standard deviation, standard error)
• Input
  • AngleRDF
  • AverageSize
  • BasicTimeUnit
  • Break
  • CalculateVelocities
  • ChangeGroupTime
  • CheckOverlap
  • Const
  • CoutFrequency
  • DefineGroup
  • DefineGroup ADDCOORDINATION
  • DefineGroup ATOMICNUMBER
  • DefineGroup BOND
  • DefineGroup COORDINATIONTABLEINTERSECTION
  • DefineGroup DIFF
  • DefineGroup FINDSHORTEST
  • DefineGroup INCLUDECOORDINATION
  • DefineGroup INTERSECTION
  • DefineGroup INVERTCOORDINATION
  • DefineGroup LIST
  • DefineGroup MEMBERHISTORY
  • DefineGroup READ
  • DefineGroup REGION
  • DefineGroup SUBGROUP
  • DefineGroup SUBGROUPCN
  • DefineGroup SUBGROUPRANDOM
  • DefineGroup SUM
  • Density
  • DevNullIfFileExists
  • DihedralRDF
  • DoubleCoordinationShortDelta
  • DumpFile
  • DumpFileFormat
  • FinalPrintProperties
  • FinalShell
  • FindVacuum
  • FrameNumbersMustIncrease
  • GlobalDistanceGroup
  • GlobalDistanceGroups
  • Histogram
  • HydrogenBond
  • IntelligentUnwrap
  • Loop
  • MaxNumAtoms
  • MaxTimestep
  • MinTimestep
  • MaxTotalSize
  • ModifyGroup
  • MoveCenter
  • NoDistances
  • Overwrite
  • Prefix
  • PrintGroup
  • PrintProperties
  • ReadFile
  • ReadFileBaseDir
  • RDF
  • SharedLigands
  • Shell
  • ShortDelta
  • SingleEnvironment
  • SphericalHarmonics
  • StartByte
  • Suffix
  • SuperEvery
  • T
  • Threads
  • TimeDensity
  • TMSD
  • TMSDFollow
  • TResidenceTime
  • TResidenceTimeCoordinationShell
  • TResidenceTimeSSP
  • TResidenceTimeSSPCoordinationShell
  • TVACF
  • WhenGroupChanged
  • WhenGroupChangedDefineGroup
• Frequently asked questions
• Trajectory and structure file formats
  • XYZ files
    • mattixyz
    • asexyz
    • ceriottixyz
    • ceriotticellbohrxyz
  • LAMMPS “custom” output
    • lammpsrdx
    • lammpsrdxnoq
    • lammpsrdxvelnoq
  • RuNNer files
    • runnerdata
• Utilities
  • ardfgnufiles.sh
  • blocklionanalysis.sh
  • vim
• Developer documentation
  • Actions
  • Implementing new features