\(\renewcommand{\AA}{\text{Å}}\)

fix graphics/periodic command

Syntax

fix ID group-ID graphics/periodic Nevery keyword args ...

  • ID, group-ID are documented in fix command

  • graphics/periodic = style name of this fix command

  • Nevery = update graphics information every this many time steps

  • zero or more keywords or keyword/value pairs may be appended

  • keyword = xlo or xhi or ylo or yhi or zlo or zhi or radius or atoms or bonds

    xlo, xhi, ylo, yhi, zlo, zhi = enable periodic images of atoms and bonds to either side of the simulation box in the given direction
radius value = sets the atom radius
   value = either "auto" or a number (distance units)
atoms yes/no = enables or disables displaying periodic images of atoms
bonds yes/no = enables or disables displaying periodic images of bonds

Examples

fix vec all graphics/periodic 10 ylo zhi zlo yhi xlo
fix vec all graphics/periodic 1000 ylo zhi zlo yhi bonds no radius 0.5

Description

Added in version TBD.

This fix allows to add graphics of periodic images of atoms and bonds to dump image images using the fix keyword. This can be useful to visualize periodic systems.

The group-ID sets the group ID of the atoms selected to be displayed as periodic images. For bonds to be displayed, both atoms of the bond have to be inside the group.

The Nevery keyword determines how often the arrows graphics data is updated. This should be the same value as the corresponding N parameter of the dump image command. LAMMPS will stop with an error message if the settings for this fix and the dump command are not compatible.

The xlo, xhi, ylo, yhi, zlo, zhi keywords, if set, enable display of a periodic image of the system to the corresponding side in the corresponding direction of the principal simulations cell. If all keywords are used, there will be 26 additional copies of the system rendered.

The radius keyword determines the radius of the atoms. If a value of “auto” is used, the radius is inherited from the atom type.

Dump image info

Added in version TBD.

Fix graphics/periodic is designed to be used with the fix keyword of dump image. The fix adds graphics objects of periodic images of atoms and bonds in the fix group to dump image so that they are included in the rendered image.

The color of the atoms and bonds is by default the same as that of the atoms and bonds in the principal simulation cell when using color styles “type” or “element” with the fix command. With fix color style “const” the default value of “white” can be changed using dump_modify fcolor. The transparency is by default fully opaque and can be changed with dump_modify ftrans.

The fflag1 setting of dump of dump image fix determines if the bonds are capped with spheres: a value of 0 means no caps, a value of 1 a cap at the lower end, a value of 2 a cap at the upper end, and a value of 3 caps at both ends. When also replicating atoms, a value other than 0 would be redundant, otherwise a value of 3 is probably the desired choice.

The fflag2 settings of dump image fix allows to modify the bond diameter relative to the automatically chosen one. In most use cases a value of 0.0 is probably the desired choice.

Restart, fix_modify, output, run start/stop, minimize info

No information about this fix is written to binary restart files.

None of the fix_modify options apply to this fix.

Restrictions

This fix is part of the GRAPHICS package. It is only enabled if LAMMPS was built with that package. See the Build package page for more info.

Currently only periodic images of atoms and bonds in each direction can be displayed.

Body particles or ellipsoids and similar are not fully supported; they are shown as spheres with this fix.

Default

radius = auto, atoms = yes, bonds = yes, if supported by atom style otherwise no, no periodic graphics