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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)
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
Appendix
The chemical properties database in atomes
Atomic radii
Shannon radii in crystal
Shannon radii in crystal
Figure 6.1:
Shannon radii in crystals used in the
atomes
program.
User manual 
