forked from lijiext/lammps
Added description of peratom keyword
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14469 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -15,7 +15,8 @@ compute ID group-ID voronoi/atom keyword arg ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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voronoi/atom = style name of this compute command :l
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zero or more keyword/value pairs may be appended :l
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keyword = {only_group} or {surface} or {radius} or {edge_histo} or {edge_threshold} or {face_threshold} :l
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keyword = {only_group} or {surface} or {radius} or {edge_histo} or {edge_threshold}
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or {face_threshold} or {neighbors} or {peratom} :l
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{only_group} = no arg
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{occupation} = no arg
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{surface} arg = sgroup-ID
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@ -29,7 +30,8 @@ keyword = {only_group} or {surface} or {radius} or {edge_histo} or {edge_thresho
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minlength = minimum length for an edge to be counted
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{face_threshold} arg = minarea
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minarea = minimum area for a face to be counted
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{neighbors} value = {yes} or {no} = store list of all neighbors or no :pre
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{neighbors} value = {yes} or {no} = store list of all neighbors or no
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{peratom} value = {yes} or {no} = per-atom quantities accessible or no :pre
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:ule
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[Examples:]
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@ -46,14 +48,16 @@ compute 6 all voronoi/atom neighbors yes
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Define a computation that calculates the Voronoi tessellation of the
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atoms in the simulation box. The tessellation is calculated using all
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atoms in the simulation, but non-zero values are only stored for atoms
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in the group.
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in the group.
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By default two quantities per atom are calculated by this compute.
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By default two per-atom quantities are calculated by this compute.
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The first is the volume of the Voronoi cell around each atom. Any
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point in an atom's Voronoi cell is closer to that atom than any other.
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The second is the number of faces of the Voronoi cell. This is
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equal to the number of nearest neighbors of the central atom,
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plus any exterior faces (see note below).
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plus any exterior faces (see note below). If the {peratom} keyword
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is set to "no", the per-atom quantities are still calculated,
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but they are not accessible.
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:line
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@ -180,15 +184,16 @@ when using the "create_box"_create_box.html or
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[Output info:]
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This compute calculates a per-atom array with 2 columns. In regular
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By default, this compute calculates a per-atom array with 2 columns. In regular
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dynamic tessellation mode the first column is the Voronoi volume, the
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second is the neighbor count, as described above (read above for the
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output data in case the {occupation} keyword is specified).
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These values can be accessed by any command that
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uses per-atom values from a compute as input. See "Section_howto
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15"_Section_howto.html#howto_15 for an overview of LAMMPS output
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options.
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options. If the {peratom} keyword is set to "no", the
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per-atom array is still created, but it is not accessible.
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If the {edge_histo} keyword is used, then this compute
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generates a global vector of length {maxedge}+1, containing
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a histogram of the number of edges per face.
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@ -197,6 +202,12 @@ If the {neighbors} value is set to yes, then
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this compute calculates a local array with 3 columns. There
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is one row for each face of each Voronoi cell.
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In LAMMPS contexts such as "compute reduce"_compute_reduce.html that can
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accept either a per-atom vector quantity or a local vector
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quantity, the behavior depends on the value gives for the {peratom}
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keyword: for the default value "yes" the per-atom array is accessed,
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for the value {no} the local array is accessed.
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The Voronoi cell volume will be in distance "units"_units.html cubed.
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The Voronoi face area will be in distance "units"_units.html squared.
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@ -210,4 +221,4 @@ LAMMPS"_Section_start.html#start_3 section for more info.
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"dump custom"_dump.html, "dump local"_dump.html
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[Default:] none
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[Default:] {neighbors} no, {peratom} yes
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