diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt index d084fcee6..a280b2b15 100644 --- a/doc/src/compute_voronoi_atom.txt +++ b/doc/src/compute_voronoi_atom.txt @@ -1,228 +1,228 @@ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line compute voronoi/atom command :h3 [Syntax:] compute ID group-ID voronoi/atom keyword arg ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l voronoi/atom = style name of this compute command :l zero or more keyword/value pairs may be appended :l keyword = {only_group} or {surface} or {radius} or {edge_histo} or {edge_threshold} or {face_threshold} or {neighbors} or {peratom} :l {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 :pre :ule [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 :pre [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. :line 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 :pre 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. 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 "this section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. More specifically, the array can be accessed by a "dump local"_dump.html 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\[3\] :pre If the {face_threshold} keyword is used, then only faces with areas greater than the threshold are stored. :line The Voronoi calculation is performed by the freely available "Voro++ package"_voronoi, 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. :link(voronoi,http://math.lbl.gov/voro++/) 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"_pair_style.html interactions. The cutoff can be set explicitly via the "comm_modify cutoff"_comm_modify.html 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"_create_box.html or "read_data"_read_data.html commands. [Output info:] By default, 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 6.15"_Section_howto.html#howto_15 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 3 columns. There is one row for each face of each Voronoi cell. NOTE: Some LAMMPS commands such as the "compute reduce"_compute_reduce.html 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"_units.html cubed. The Voronoi face area will be in distance "units"_units.html squared. [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_start.html#start_3 section for more info. -It also requiers you have a copy of the Voro++ library built and +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.html, "dump local"_dump.html [Default:] {neighbors} no, {peratom} yes