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45
doc/compute_voronoi_atom.html
View File

@ -24,13 +24,14 @@
<LI>keyword = <I>only_group</I> or <I>surface</I> or <I>radius</I> or <I>edge_histo</I> or <I>edge_threshold</I> or <I>face_threshold</I>
<PRE> <I>only_group</I> = no arg
<I>occupation</I> = no arg
<I>surface</I> 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
<I>radius</I> 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
<I>edge_histo</I> 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
<I>edge_threshold</I> arg = minlength
minlength = minimum length for an edge to be counted
<I>face_threshold</I> 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
</PRE>
<PRE>compute 5 defects voronoi/atom occupation
</PRE>
<P><B>Description:</B>
</P>
<P>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.
</P>
<P>If the <I>surface</I> keyword is specified a third quantity per atom is
computed: the voronoi cell surface of the given atom. <I>surface</I> takes
computed: the Voronoi cell surface of the given atom. <I>surface</I> takes
a group ID as an argument. If a group other than <I>all</I> 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.
</P>
<P>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]
</P>
<P>If the <I>radius</I> 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
</P>
<PRE>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.
</P>
<P>The <I>edge_histo</I> 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.
<P>The <I>edge_threshold</I> and <I>face_threshold</I> 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.
</P>
<P>If the <I>occupation</I> 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.
</P>
<HR>
<P>The Voronoi calculation is performed by the freely available <A HREF = "http://math.lbl.gov/voro++">Voro++
@ -138,9 +157,11 @@ systems. Note that you define the z extent of the simulation box for
</P>
<P><B>Output info:</B>
</P>
<P>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
<P>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 <I>occupation</I> keyword is specified).
These values can be accessed by any command that
uses per-atom values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
15</A> for an overview of LAMMPS output
options.

44
doc/compute_voronoi_atom.txt
View File

@ -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.