Atomes documentation
Introduction
Programming framework
Supported platforms
Dependencies and requirements
Features
Main window
Workspace and project tree
Files
1. Importing atomic coordinates
2. Reading Atomes project file(s)
3. 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
1. Data edition
2. Plot edition
Mouse interaction with the data plot
1. Right button contextual menu
2. Left button zoom in and out
Saving the data
Keyboard shortcuts
Visual analysis in Atomes
Window top bar menu
1. The OpenGL menu
2. The Model menu
3. The Chemistry menu
4. The Tools menu
5. The View menu
6. The Animate menu
Mouse interaction with the OpenGL window: visualization
1. Object selection
2. Object contextual menu
Keyboard shortcuts
Visual edition in Atomes
The Edit submenu
1. The Crystal builder window
2. The Cell edition window
3. The Model edition window
4. The Extract/rebuild buttons
Mouse interaction with the OpenGL window: edition
1. Atom selection
2. The edition contextual menu
3. The object edition contextual menu
Keyboard shortcuts
Preparing molecular dynamics calculations in Atomes
Classical MD
1. DL-POLY v4.09
2. LAMMPS
Ab-initio MD
1. CPMD v4.3.0
2. CP2K v9.1
Quantum Mechanics and Molecular Mechanics MD
1. 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 fundamentals
Neutrons and X-rays scattering
1. Total scattering - Debye approach
2. Partial structure factors
Local atomic coordination properties
1. Average first coordination numbers
2. Individual atomic neighbor analysis
3. Proportion of tetrahedral links and units in the structure model
4. Distribution of bond lengths for the first coordination spheres
5. Angles distributions
Ring statistics
1. Size of the rings
2. Definitions
3. Description of a network using ring
4. Rings and connectivity: the R.I.N.G.S. method implemented in Atomes
5. Bond defects in ring statistics
6. 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
1. Covalent radii
2. Ionic radii
3. VDW radii
4. Shannon radii in crystal
Neutron scattering lenghts
Atomes documentation
appendix
app-6
section-1
sub-section-3.md
VDW radii
Figure 6.3:
Van Der Waals radii used in the
Atomes
program.
Figure
6.3
presents the Van Der Waals radii used in
Atomes
see
[1]
for details.
A. Bondi,
J. Phys. Chem.
, vol. 68, no. 3, p. 441, 1964.
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2022-2024,
Sébastien Le Roux
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