diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 4a8ea4e5252d0cf52a2c20e4f5d1077a06dd2e54..94ad8026e55d6808d9c9d88eefd757dfcb144ba1 100644 --- 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 diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index ceb459d4cc9d52919f80f1a713d64c1ba30c7fbf..85d9101a0e47f97928582b664fbc6fbf3e1b7654 100644 --- 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 diff --git a/doc/compute.html b/doc/compute.html index 24a18f717d77ceef00a83f5c884325f0063d13b7..c25364fa3c9374b8dbccb9f8d614bb3d458a9c1b 100644 --- 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 diff --git a/doc/compute.txt b/doc/compute.txt index ce9243e87a73d701912dd80e1ba00eab64f1ff04..3621654682cb838e128c88aa5c06e6884a67b5d5 100644 --- 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 diff --git a/doc/compute_voronoi_atom.html b/doc/compute_voronoi_atom.html new file mode 100644 index 0000000000000000000000000000000000000000..ba99a6b257c50372a37aea160e77ef232c7ee9b6 --- /dev/null +++ b/doc/compute_voronoi_atom.html @@ -0,0 +1,82 @@ +<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> diff --git a/doc/compute_voronoi_atom.txt b/doc/compute_voronoi_atom.txt new file mode 100644 index 0000000000000000000000000000000000000000..a0c17118afd3c8c15d65459ccc95438cca29f181 --- /dev/null +++ b/doc/compute_voronoi_atom.txt @@ -0,0 +1,77 @@ +"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