2013-01-26 00:33:10 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>compute voronoi/atom command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID voronoi/atom
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>voronoi/atom = style name of this compute command
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute 1 all voronoi/atom
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Define a computation that calculates the Voronoi tesselation of the
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atoms in the simulation box. The tesselation is calculated using
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all atoms in the simulatoin, but non-zero values are only stored
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for atoms in the group.
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</P>
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<P>Two quantites per atom are calculated by this compute. The first is
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the volume of the Voronoi cell around each atom, which is the volume
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of points in space closest to that atom. The second is the number of
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faces of the Voronoi cell, which is also the number of nearest
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neighbor atoms.
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</P>
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<P>The Voronoi calculation is performed by the freely available <A HREF = "http://math.lbl.gov/voro++">Voro++
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package</A>, written by Chris Rycroft at UC Berkeley and LBL,
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which must be installed on your system when building LAMMPS for use
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with this compute. See instructions on obtaining and installing
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the Voro++ software in the src/VORONOI/README file.
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</P>
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<P>IMPORTANT NOTE: The calculation of Voronoi volumes is performed by
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each processor for the atoms it owns, and includes the effect of ghost
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atoms stored by the processor. This assumes that the Voronoi cells of
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owned atoms are not affected by atoms beyond the ghost atom cut-off
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distance. This is usually a good assumption for liquid and solid
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systems, but may lead to underestimation of Voronoi volumes in low
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density systems. By default, the set of ghost atoms stored by each
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processor is determined by the cutoff used for
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<A HREF = "pair_style.html">pair_style</A> interactions. The cutoff can be set
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2013-01-26 00:37:12 +08:00
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explicitly via the <A HREF = "communicate.html">communicate cutoff</A> command.
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2013-01-26 00:33:10 +08:00
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</P>
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2013-02-15 07:59:38 +08:00
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<P>IMPORTANT NOTE: The Voro++ package performs its calculation in 3d.
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This should still work for a 2d LAMMPS simulation, to effectively
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compute Vornoi "areas", so long as the z-dimension of the box is
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roughly the same (or smaller) compared to the separation of the atoms.
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Typical values for the z box dimensions in a 2d LAMMPS model are -0.5
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to 0.5, which satisfies the criterion for most <A HREF = "doc/units.html">units</A>
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systems. Note that you define the z extent of the simulation box for
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2d simulations when using the <A HREF = "create_box.html">create_box</A> or
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<A HREF = "read_data.html">read_data</A> commands.
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</P>
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2013-01-26 00:33:10 +08:00
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<P><B>Output info:</B>
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</P>
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<P>This compute calculates a per-atom array with 2 columns. The first
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column is the Voronoi volume, the second is the neighbor count, as
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described above. These values can be accessed by any command that
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uses per-atom values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
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15</A> for an overview of LAMMPS output
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options.
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</P>
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<P>The Voronoi cell volume will be in distance <A HREF = "units.html">units</A> cubed.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This compute is part of the VORONOI package. It is only enabled if
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LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "dump.html">dump custom</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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