compute voronoi/atom command — LAMMPS documentation

\(\renewcommand{\AA}{\text{Å}}\)

# 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 occupation or surface or radius or edge_histo or edge_threshold or face_threshold or neighbors or peratom

      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
      neighbors value = yes or no = store list of all neighbors or no
      peratom value = yes or no = per-atom quantities accessible or no

## 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
    compute 6 all voronoi/atom neighbors yes

## 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 per-atom quantities 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. This is equal to the number of nearest neighbors of the central atom, plus any exterior faces (see note below). If the peratom keyword is set to “no”, the per-atom quantities are still calculated, but they are not accessible.

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 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.

If the neighbors value is set to yes, then this compute creates a local array with 3 columns. There is one row for each face of each Voronoi cell. The 3 columns are the atom ID of the atom that owns the cell, the atom ID of the atom in the neighboring cell (or zero if the face is external), and the area of the face. The array can be accessed by any command that uses local values from a compute as input. See the Howto output page for an overview of LAMMPS output options. More specifically, the array can be accessed by a dump local command to write a file containing all the Voronoi neighbors in a system:

    compute 6 all voronoi/atom neighbors yes
    dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]

If the face_threshold keyword is used, then only faces with areas greater than the threshold are stored.

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.

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. The Voronoi cells for atoms adjacent to empty regions will extend into those regions up to the communication cutoff in \(x\), \(y\), or \(z\). In that situation, an exterior face is created at the cutoff distance normal to the \(x\), \(y\), or \(z\) direction. For triclinic systems, the exterior face is parallel to the corresponding reciprocal lattice vector.

Note

The Voro++ package performs its calculation in 3d. This will still work for a 2d LAMMPS simulation, provided all the atoms have the same \(z\)-coordinate. The Voronoi cell of each atom will be a columnar polyhedron with constant cross-sectional area along the \(z\)-direction and two exterior faces at the top and bottom of the simulation box. If the atoms do not all have the same \(z\)-coordinate, then the columnar cells will be accordingly distorted. The cross-sectional area of each Voronoi cell can be obtained by dividing its volume by the \(z\) extent of the simulation box. 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

By default, this compute calculates a per-atom array with two 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 the Howto output page for an overview of LAMMPS output options. If the peratom keyword is set to “no”, the per-atom array is still created, but it is not accessible.

If the edge_histo keyword is used, then this compute generates a global vector of length maxedge+1, containing a histogram of the number of edges per face.

If the neighbors value is set to yes, then this compute calculates a local array with three columns. There is one row for each face of each Voronoi cell.

Note

Some LAMMPS commands such as the compute reduce command can accept either a per-atom or local quantity. If this compute produces both quantities, the command may access the per-atom quantity, even if you want to access the local quantity. This effect can be eliminated by using the peratom keyword to turn off the production of the per-atom quantities. For the default value yes both quantities are produced. For the value no, only the local array is produced.

The Voronoi cell volume will be in distance units cubed. The Voronoi face area will be in distance units squared.

## Restrictions

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

It also requires you have a copy of the Voro++ library built and installed on your system. See instructions on obtaining and installing the Voro++ software in the src/VORONOI/README file.

## Related commands

dump custom, dump local

## Default

neighbors no, peratom yes