forked from lijiext/lammps
86 lines
3.2 KiB
Plaintext
86 lines
3.2 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute voronoi/atom command :h3
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[Syntax:]
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compute ID group-ID voronoi/atom :pre
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ID, group-ID are documented in "compute"_compute.html command
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voronoi/atom = style name of this compute command :ul
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[Examples:]
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compute 1 all voronoi/atom :pre
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[Description:]
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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 simulation, but non-zero values are only stored
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for atoms in the group.
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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. Any point in an
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atom's Voronoi cell is closer to that atom than any other. The second
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is the number of faces of the Voronoi cell, which is also the number
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of nearest neighbors of the atom in the middle of the cell.
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The Voronoi calculation is performed by the freely available "Voro++
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package"_voronoi, 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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:link(voronoi,http://math.lbl.gov/voro++)
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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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"pair_style"_pair_style.html interactions. The cutoff can be set
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explicitly via the "communicate cutoff"_communicate.html command.
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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 "units"_units.html
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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 "create_box"_create_box.html or
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"read_data"_read_data.html commands.
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[Output info:]
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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 "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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The Voronoi cell volume will be in distance "units"_units.html cubed.
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[Restrictions:]
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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 "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"dump custom"_dump.html
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[Default:] none
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