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Updated description of 2d and free surface cases

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14457 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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athomps
2016-01-19 22:18:55 +00:00
parent f16130ab67
commit 0d1c7af98b
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29
doc/compute_voronoi_atom.txt
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@ -44,13 +44,14 @@ compute 5 defects voronoi/atom occupation :pre
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.
in the group.
By default two quantities per atom 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, which is also
the number of nearest neighbors of the atom in the middle of the cell.
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).
:line
@ -135,13 +136,23 @@ 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 should
still work for a 2d LAMMPS simulation, to effectively compute Voronoi
"areas", so long as the z-dimension of the box is roughly the same (or
smaller) compared to the separation of the atoms. Typical values for
the z box dimensions in a 2d LAMMPS model are -0.5 to 0.5, which
satisfies the criterion for most "units"_units.html systems. Note
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.