compute voronoi/atom command

Syntax

compute ID group-ID voronoi/atom general_keyword general_values keyword arg ...
  • ID, group-ID are documented in compute command
  • voronoi/atom = style name of this compute command
  • general_keywords general_values are documented in compute
  • zero or more keyword/value pairs may be appended
  • keyword = only_group or surface or radius or edge_histo or edge_threshold or face_threshold
only_group = no arg
surface arg = sgroup-ID
  sgroup-ID = compute the dividing surface between group-ID and sgroup-ID
    this keyword adds a third column to the compute output
radius arg = v_r
  v_r = radius atom style variable for a poly-disperse voronoi tessellation
edge_histo arg = maxedge
  maxedge = maximum number of voronoi cell edges to be accounted in the histogram
edge_threshold arg = minlength
  minlength = minimum length for an edge to be counted
face_threshold arg = minarea
  minarea = minimum area for a face to be counted

Examples

compute 1 all voronoi/atom
compute 2 precipitate voronoi/atom surface matrix
compute 3b precipitate voronoi/atom radius v_r
compute 4 solute voronoi/atom only_group

Description

Define a computation that calculates the Voronoi tessellation of the atoms in the simulation box. The tessellation is calculated using all atoms in the simulation, but non-zero values are only stored for atoms in the group.

By default two quantities per atom are calculated by this compute. The first is the volume of the Voronoi cell around each atom. Any point in an atom’s Voronoi cell is closer to that atom than any other. The second is the number of faces of the Voronoi cell, which is also the number of nearest neighbors of the atom in the middle of the cell.

If the only_group keyword is specified the tessellation is performed only with respect to the atoms contained in the compute group. This is equivalent to deleting all atoms not contained in the group prior to evaluating the tessellation.

If the surface keyword is specified a third quantity per atom is computed: the voronoi cell surface of the given atom. surface takes a group ID as an argument. If a group other than all is specified, only the voronoi cell facets facing a neighbor atom from the specified group are counted towards the surface area.

In the example above, a precipitate embedded in a matrix, only atoms at the surface of the precipitate will have non-zero surface area, and only the outward facing facets of the voronoi cells are counted (the hull of the precipitate). The total surface area of the precipitate can be obtained by running a “reduce sum” compute on c_2[3]

If the radius keyword is specified with an atom style variable as the argument, a poly-disperse voronoi tessellation is performed. Examples for radius variables are

variable r1 atom (type==1)*0.1+(type==2)*0.4
compute radius all property/atom radius
variable r2 atom c_radius

Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms and 0.4 units for type 2 atoms, and v_r2 accesses the radius property present in atom_style sphere for granular models.

The edge_histo keyword activates the compilation of a histogram of number of edges on the faces of the voronoi cells in the compute group. The argument maxedge of the this keyword is the largest number of edges on a single voronoi cell face expected to occur in the sample. This keyword adds the generation of a global vector with maxedge+1 entries. The last entry in the vector contains the number of faces with with more than maxedge edges. Since the polygon with the smallest amount of edges is a triangle, entries 1 and 2 of the vector will always be zero.

The edge_threshold and face_threshold keywords allow the suppression of edges below a given minimum length and faces below a given minimum area. Ultra short edges and ultra small faces can occur as artifacts of the voronoi tessellation. These keywords will affect the neighbor count and edge histogram outputs.

The Voronoi calculation is performed by the freely available Voro++ package, written by Chris Rycroft at UC Berkeley and LBL, which must be installed on your system when building LIGGGHTS(R)-PUBLIC for use with this compute. See instructions on obtaining and installing the Voro++ software in the src/VORONOI/README file.

Warning

The calculation of Voronoi volumes is performed by each processor for the atoms it owns, and includes the effect of ghost atoms stored by the processor. This assumes that the Voronoi cells of owned atoms are not affected by atoms beyond the ghost atom cut-off distance. This is usually a good assumption for liquid and solid systems, but may lead to underestimation of Voronoi volumes in low density systems. By default, the set of ghost atoms stored by each processor is determined by the cutoff used for pair_style interactions. The cutoff can be set explicitly via the communicate cutoff command.

Warning

The Voro++ package performs its calculation in 3d. This should still work for a 2d LIGGGHTS(R)-PUBLIC simulation, to effectively compute Voronoi “areas”, so long as the z-dimension of the box is roughly the same (or smaller) compared to the separation of the atoms. Typical values for the z box dimensions in a 2d LIGGGHTS(R)-PUBLIC model are -0.5 to 0.5, which satisfies the criterion for most units systems. Note that you define the z extent of the simulation box for 2d simulations when using the create_box or read_data commands.

Output info

This compute calculates a per-atom array with 2 columns. The first column is the Voronoi volume, the second is the neighbor count, as described above. These values can be accessed by any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LIGGGHTS(R)-PUBLIC output options.

The Voronoi cell volume will be in distance units cubed.

Restrictions

This compute is part of the VORONOI package. It is only enabled if LIGGGHTS(R)-PUBLIC was built with that package. See the Making LIGGGHTS(R)-PUBLIC section for more info.