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## Options

Options are operations that allow to transform the system, e.g. rotate it, add, remove or displace atoms, etc.

Several options can be called in a single command-line. They are applied to the atomic system sequentially, i.e. one after the other in the same order as they are called. Options can appear anywhere in the command-line (i.e. before or after the input file or the formats to output), however when an option is invoked it must be followed by its parameters in the correct order.

Options apply to all files converted in one run. For instance, if the mode 'list' is used, options apply to all files in the list. Please refer to the page describing each mode for more details about how they deal with options.

A special case is the option `-select`, which can be used to restrict the following options to only some atoms. Please read the corresponding page to know more.

In options using crystallographic directions, Miller indices must be given either as a contiguous string, or as values separated with underscores; square brackets are optional. For instance, the direction `[110]` can be specified as "`[1-10]`", or "`[1_-1_0]`", or "`1-10`" (without quotation marks). Note that the indices must never be separated by blank spaces. Similarly, for hexagonal systems it is possible to use the four-indices notation [hkil], where h+k+i=0.

In some options that require a position, it is possible to provide a cartesian position in angströms, or a relative position thanks to the keyword BOX. See this page to know more.

Below the available options are listed in alphabetical order.

#### List of 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
- 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

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