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Modes

Modes specify what Atomsk will do with the files, e.g. convert a file to other format(s), merge several files, compute some properties... Only one mode can be used at a time.

If the program is invoked without any command-line argument (i.e. just type "atomsk") then the program will enter the interactive mode.

If command-line arguments are given but no mode is specified then the program will run in normal mode.

Other modes must be called explicitely with their name, always prefixed with two dashes, in the form --<mode>. Please refer to the documentation for each mode below.

• 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

The modes below perform some particular calculation on one or several systems.

• Density - Compute the density of a property
• Difference - Compute the difference in atomic positions between two files
• Electric dipole moments - Compute individual electric dipole moments
• Electronic polarization - Compute polarization of ions in core-shell model
• Local symmetry - Compute a local symmetry parameter for each atom
• Nye tensor - Compute Nye tensor
• RDF - Compute the radial distribution function

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