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### compute voronoi/atom command

Syntax:

    compute ID group-ID voronoi/atom keyword arg ...

- ID, group-ID are documented in compute command
- voronoi/atom = style name of this compute command
- 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
        occupation = 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

    compute 5 defects voronoi/atom occupation

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.

If the occupation keyword is specified the tessellation is only performed for the first invocation of the compute and then stored. For all following invocations of the compute the number of atoms in each Voronoi cell in the stored tessellation is counted. In this mode the compute returns a per-atom array with 2 columns. The first column is the number of atoms currently in the Voronoi volume defined by this atom at the time of the first invocation of the compute (note that the atom may have moved significantly). The second column contains the total number of atoms sharing the Voronoi cell of the stored tessellation at the location of the current atom. Numbers in column one can be any positive integer including zero, while column two values will always be greater than zero. Column one data can be used to locate vacancies (the coordinates are given by the atom coordinates at the time step when the compute was first invoked), while column two data can be used to identify interstitial atoms.

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 LAMMPS for use with this compute. See instructions on obtaining and installing the Voro++ software in the src/VORONOI/README file.

IMPORTANT NOTE: 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 comm_modify cutoff command.

IMPORTANT NOTE: The Voro++ package performs its calculation in 3d. This should still work for a 2d LAMMPS 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 LAMMPS 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. In regular dynamic tessellation mode the first column is the Voronoi volume, the second is the neighbor count, as described above (read above for the output data in case the occupation keyword is specified). 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 LAMMPS 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 LAMMPS was built with that package. See the Making LAMMPS section for more info.

Related commands:

dump custom

Default: none