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 User manual
  • Introduction
  • Programming framework
    • Supported platforms
    • Dependencies and requirements
  • Features
    • Main window
    • Workspace and project tree
    • Files
      • Importing atomic coordinates
      • Reading atomes project file(s)
      • Reading atomes workspace file(s)
    • User preferences
      • Analysis options
      • OpenGL rendering options
      • Model options
      • Representation options
    • Analyzing models using atomes
    • Visual analysis using atomes
    • Visual edition and model creation using atomes
    • Preparing MD calculations in atomes
  • Physico-chemical analysis in atomes
    • Visualisation of the results of the calculations
    • Data and plot edition
      • Data edition
      • Plot edition
    • Mouse interaction with the data plot
      • Right button contextual menu
      • Left button zoom in and out
    • Saving the data
    • Keyboard shortcuts
  • Visual analysis in atomes
    • Window top bar menu
      • The OpenGL menu
      • The Model menu
      • The Chemistry menu
      • The Tools menu
      • The View menu
      • The Animate menu
    • Mouse interaction with the OpenGL window: visualization
      • Object selection
      • Object contextual menu
    • Keyboard shortcuts
  • Visual edition in atomes
    • The Edit submenu
      • The Crystal builder window
      • The Cell edition window
      • The Model edition window
      • The Extract/rebuild buttons
    • Mouse interaction with the OpenGL window: edition
      • Atom selection
      • The edition contextual menu
      • The object edition contextual menu
    • Keyboard shortcuts
  • Preparing molecular dynamics calculations in atomes
    • Classical MD
      • DL-POLY v4.09
      • LAMMPS
    • Ab-initio MD
      • CPMD v4.3.0
      • CP2K v9.1
    • Quantum Mechanics and Molecular Mechanics MD
      • CPMD
  • Appendix
    • Supported atomic coordinates file formats
    • Keyboard shortcuts and command line options
      • Keyboard shortcuts
      • Command line options
    • The Library in atomes
    • Crystal building in atomes
    • The physics in atomes
      • The periodic boundary conditions
      • Radial distribution functions
      • Neutrons and X-rays scattering
        • Total scattering - Debye approach
        • Partial structure factors
      • Local atomic coordination properties
        • Average first coordination numbers
        • Individual atomic neighbor analysis
        • Proportion of tetrahedral links and units in the structure model
        • Distribution of bond lengths for the first coordination spheres
        • Angles distributions
      • Ring statistics
        • Size of the rings
        • Definitions
        • Description of a network using ring statistics - existing tools
        • Rings and connectivity: the R.I.N.G.S. method implemented in atomes
        • Bond defects in ring statistics
        • Number of rings not found and that "potentially exist"
      • Chain statistics
      • Invariants of spherical harmonics as atomic order parameters
      • Mean square displacement of atoms
    • The chemical properties database in atomes
      • Atomic radii
        • Covalent radii
        • Ionic radii
        • VDW radii
        • Shannon radii in crystal
      • Neutron scattering lenghts
  • GitHub repository

© 2022-2025 Sébastien Le Roux
C.C. Attribution 4.0 International License  
Licence Creative Commons

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