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
+ 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
+ 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
@@ -45,6 +46,8 @@ 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 @@ -66,19 +69,19 @@ 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 +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 +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 +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 +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 @@ -90,9 +93,9 @@ 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 +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 +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 @@ -102,9 +105,25 @@ 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 +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++ @@ -138,9 +157,11 @@ systems. Note that you define the z extent of the simulation box for
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 +
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. diff --git a/doc/compute_voronoi_atom.txt b/doc/compute_voronoi_atom.txt index d907aad9c0..c4e651418b 100644 --- a/doc/compute_voronoi_atom.txt +++ b/doc/compute_voronoi_atom.txt @@ -17,13 +17,14 @@ 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} :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 + 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 + 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 @@ -36,6 +37,7 @@ 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 :pre +compute 5 defects voronoi/atom occupation :pre [Description:] @@ -58,19 +60,19 @@ 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 +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 +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 +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 +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 @@ -82,9 +84,9 @@ 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 +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 +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 @@ -94,9 +96,25 @@ 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 +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. + :line The Voronoi calculation is performed by the freely available "Voro++ @@ -130,9 +148,11 @@ systems. Note that you define the z extent of the simulation box for [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 +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"_Section_howto.html#howto_15 for an overview of LAMMPS output options.