# Atomsk

Atom/Molecule/Material Software Kit - https://atomsk.univ-lille.fr/

© Pierre Hirel 2010 - Version master

## Contents:

1. License - Read first!
2. Overview - Quick start
3. Examples
4. Compilation and installation
5. Supported file formats
6. Options
   - add-atom - Insert one or more new atoms
   - add-shells - Create shells for some or all atoms
   - alignx - Align the first cell vector with the X axis
   - bind-shells - Re-associate shells with their core
   - cell - Modify cell vectors
   - center - Shift the system at the center of the box
   - crack - Insert a crack in the system
   - cut - Wipe out part of the system
   - deform - Apply uniaxial strain or simple shear
   - dislocation - Insert a dislocation in the system
   - disturb - Randomly move atoms out of their positions
   - duplicate - Duplicate the system, construct supercells
   - freeze - Freeze the coordinates of some atoms
   - fractional - Convert to reduced coordinates
   - mirror - Apply a mirror transformation
   - options - Apply options read from a file
   - orient - Change the crystallographic orientation of the system
   - orthogonal-cell - Find a suitable equivalent orthogonal cell
   - properties - Set properties of the system
   - rebox - Try to guess supercell parameters
   - reduce-cell - Try to reduce the system into a smaller cell
   - remove-atom - Remove one or several atoms
   - remove-doubles - Remove duplicate atoms
   - remove-property - Remove one or all auxiliary properties
   - remove-shells - Remove shells on some or all atoms
   - roll - Bend or roll the system around an axis
   - rotate - Rotate the system around an axis
   - round-off - Round off coordinates or properties
   - select - Select atoms according to a criterion
   - separate - Pull apart atoms that are too close
   - shift - Shift part of the system
   - sort - Change the order in which atoms are written
   - spacegroup - Apply symmetry operations of a space group
   - stress - Apply stress to the system
   - substitute - Replace atoms by other atoms
   - swap - Swap two atoms, or Cartesian axes, or auxiliary properties
   - torsion - Apply torsion along an axis
   - unit - Change the unit of coordinates
   - unskew - Reduce the skew of the box
   - velocity - Create a Maxwell-Boltzmann distribution of velocities
   - wrap - Wrap atoms back into the box
7. Modes (click for more)
   - Average - Average atom positions over several configurations
   - Copy-Properties - Copy properties from a system to another
   - Create - Create a system from scratch
   - ddplot - Create a file for visualization with the ddplot program
   - Gather - Gather several files into one file containing all snapshots
   - List - Convert all files in a list
   - Help - Displays help
   - Interactive - Manipulate systems interactively or with scripts
   - Interpolate - Interpolates atom positions between two configurations
   - Match-ID - Find equivalent atoms between two systems
   - Merge - Merge two or more systems into one
   - Normal - Convert a file to one or many formats
   - Polycrystal - Create a polycrystal using Voronoi method
   - Unfold - Unfold a file containing several snapshots into several files
   - Unwrap - Unwrap atom coordinates
8. Program behaviour
   - ignore - Always ignore existing files
   - language - Set language of messages
   - logfile - Set up log file name
   - nthreads - Set number of OpenMP parallel threads
   - overwrite - Always overwrite existing files
   - verbosity - Set verbosity level
9. Companion tools
10. Acknowledgements
11. FAQ - Frequently Asked Questions
12. Information for developers
13. Contact
14. Other useful codes