Atomsk

Atom/Molecule/Material Software Kit

© Pierre Hirel 2010 - Version Beta 0.13.1

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 shear strain
   • dislocation - Insert a dislocation in the system
   • disturb - Randomly move atoms out of their positions
   • duplicate - Duplicate the system, construct supercells
   • fix - Fix 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