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 system consecutively, in the order in which 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 can be given 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", "[1-10]", "1_-1_0" or "[1_-1_0]" (without quotation marks). Note that the indices must never be separated by blank spaces.

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
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 unidirectional stress or strain to the system
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
properties - Set properties of the system
rebox - Try to guess supercell parameters
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
select - Select atoms according to a criterion
separate - Pull apart atoms that are too close
shear - Shear the system
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 atoms atoms or Cartesian axes
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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