git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9320 f3b2605a-c512-4ea7-a41b-209d697bcdaa

512ceda1 · sjplimp · 4ce0dc4a · 512ceda1 · 512ceda1 · 512ceda1
Commit 512ceda1 authored 12 years ago by sjplimp
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -389,7 +389,7 @@ each style or click on the style itself for a full description:
 <TR ALIGN="center"><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A> 
+<TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_coord_atom.html">voronoi/atom</A> 
 </TD></TR></TABLE></DIV>
 <P>These are compute styles contributed by users, which can be used if

--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -594,7 +594,8 @@ each style or click on the style itself for a full description:
 "temp/ramp"_compute_temp_ramp.html,
 "temp/region"_compute_temp_region.html,
 "temp/sphere"_compute_temp_sphere.html,
-"ti"_compute_ti.html :tb(c=6,ea=c)
+"ti"_compute_ti.html,
+"voronoi/atom"_compute_coord_atom.html :tb(c=6,ea=c)
 These are compute styles contributed by users, which can be used if
 "LAMMPS is built with the appropriate

--- a/doc/compute.html
+++ b/doc/compute.html
@@ -216,7 +216,8 @@ available in LAMMPS:
 <LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature excluding ramped velocity component
 <LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
 <LI><A HREF = "compute_temp_sphere.html">temp/sphere</A> - temperature of spherical particles
-<LI><A HREF = "compute_ti.html">ti</A> - thermodyanmic integration free energy values 
+<LI><A HREF = "compute_ti.html">ti</A> - thermodyanmic integration free energy values
+<LI><A HREF = "compute_voronoi_atom.html">voronoi/atom</A> - Voronoi volume and neighbors for each atom 
 </UL>
 <P>There are also additional compute styles submitted by users which are
 included in the LAMMPS distribution.  The list of these with links to

--- a/doc/compute.txt
+++ b/doc/compute.txt
@@ -211,7 +211,8 @@ available in LAMMPS:
 "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
 "temp/region"_compute_temp_region.html - temperature of a region of atoms
 "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
-"ti"_compute_ti.html - thermodyanmic integration free energy values :ul
+"ti"_compute_ti.html - thermodyanmic integration free energy values
+"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul
 There are also additional compute styles submitted by users which are
 included in the LAMMPS distribution.  The list of these with links to

--- a/doc/compute_voronoi_atom.html
+++ b/doc/compute_voronoi_atom.html
+<HTML>
+<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> 
+</CENTER>
+<HR>
+<H3>compute voronoi/atom command 
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID voronoi/atom 
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>voronoi/atom = style name of this compute command 
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all voronoi/atom 
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the Voronoi tesselation of the
+atoms in the simulation box.  The tesselation is calculated using
+all atoms in the simulatoin, but non-zero values are only stored
+for atoms in the group.
+</P>
+<P>Two quantites per atom are calculated by this compute.  The first is
+the volume of the Voronoi cell around each atom, which is the volume
+of points in space closest to that atom.  The second is the number of
+faces of the Voronoi cell, which is also the number of nearest
+neighbor atoms.
+</P>
+<P>The Voronoi calculation is performed by the freely available <A HREF = "http://math.lbl.gov/voro++">Voro++
+package</A>, written by Chris Rycroft at UC Berkeley and LBL,
+which must be installed on your system when building LAMMPS for use
+with this compute.  See instructions on obtaining and installing
+the Voro++ software in the src/VORONOI/README file.
+</P>
+<P>IMPORTANT NOTE: The calculation of Voronoi volumes is performed by
+each processor for the atoms it owns, and includes the effect of ghost
+atoms stored by the processor.  This assumes that the Voronoi cells of
+owned atoms are not affected by atoms beyond the ghost atom cut-off
+distance.  This is usually a good assumption for liquid and solid
+systems, but may lead to underestimation of Voronoi volumes in low
+density systems.  By default, the set of ghost atoms stored by each
+processor is determined by the cutoff used for
+<A HREF = "pair_style.html">pair_style</A> interactions.  The cutoff can be set
+explicitly via the <A HREF = "communcicate.html">communicate cutoff</A> command.
+</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
+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.
+</P>
+<P>The Voronoi cell volume will be in distance <A HREF = "units.html">units</A> cubed.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the VORONOI package.  It is only enabled if
+LAMMPS was built with that package.  See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P>This command currently only works for 3d systems.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump custom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
--- a/doc/compute_voronoi_atom.txt
+++ b/doc/compute_voronoi_atom.txt
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+:line
+compute voronoi/atom command :h3
+[Syntax:]
+compute ID group-ID voronoi/atom :pre
+ID, group-ID are documented in "compute"_compute.html command
+voronoi/atom = style name of this compute command :ul
+[Examples:]
+compute 1 all voronoi/atom :pre
+[Description:]
+Define a computation that calculates the Voronoi tesselation of the
+atoms in the simulation box.  The tesselation is calculated using
+all atoms in the simulatoin, but non-zero values are only stored
+for atoms in the group.
+Two quantites per atom are calculated by this compute.  The first is
+the volume of the Voronoi cell around each atom, which is the volume
+of points in space closest to that atom.  The second is the number of
+faces of the Voronoi cell, which is also the number of nearest
+neighbor atoms.
+The Voronoi calculation is performed by the freely available "Voro++
+package"_voronoi, written by Chris Rycroft at UC Berkeley and LBL,
+which must be installed on your system when building LAMMPS for use
+with this compute.  See instructions on obtaining and installing
+the Voro++ software in the src/VORONOI/README file.
+:link(voronoi,http://math.lbl.gov/voro++)
+IMPORTANT NOTE: The calculation of Voronoi volumes is performed by
+each processor for the atoms it owns, and includes the effect of ghost
+atoms stored by the processor.  This assumes that the Voronoi cells of
+owned atoms are not affected by atoms beyond the ghost atom cut-off
+distance.  This is usually a good assumption for liquid and solid
+systems, but may lead to underestimation of Voronoi volumes in low
+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 "communicate cutoff"_communcicate.html command.
+[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
+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.
+The Voronoi cell volume will be in distance "units"_units.html cubed.
+[Restrictions:]
+This compute is part of the VORONOI package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+This command currently only works for 3d systems.
+[Related commands:]
+"dump custom"_dump.html
+[Default:] none