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 092b685cd7..fde08b6cc6 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -503,6 +503,7 @@ each style or click on the style itself for a full description: "atom/molecule"_compute_atom_molecule.html, "bond/local"_compute_bond_local.html, "centro/atom"_compute_centro_atom.html, +"cluster/atom"_compute_cluster_atom.html, "cna/atom"_compute_cna_atom.html, "com"_compute_com.html, "com/molecule"_compute_com_molecule.html, diff --git a/doc/compute.html b/doc/compute.html index 0e8f7a687c..4961976758 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -171,6 +171,7 @@ available in LAMMPS:
Syntax: +
+compute ID group-ID cluster/atom cutoff ++
Examples: +
+compute 1 all cluster/atom 1.0 ++
Description: +
+Define a computation that assigns each atom a cluster ID. +
+A cluster is defined as a set of atoms, each of which is within the +cutoff distance from one or more other atoms in the cluster. If an +atom has no neighbors within the cutoff distance, then it is a 1-atom +cluster. The ID of every atom in the cluster will be the smallest +atom ID of any atom in the cluster. +
+Only atoms in the compute group are clustered and assigned cluster +IDs. Atoms not in the compute group are assigned a cluster ID = 0. +
+The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently or to have multiple compute/dump commands, each of a +clsuter/atom style. +
+Output info: +
+This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +this section for an overview of LAMMPS +output options. +
+The per-atom vector values will be an ID > 0, as explained above. +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_cluster_atom.txt b/doc/compute_cluster_atom.txt new file mode 100644 index 0000000000..497417b4cd --- /dev/null +++ b/doc/compute_cluster_atom.txt @@ -0,0 +1,57 @@ +"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 cluster/atom command :h3 + +[Syntax:] + +compute ID group-ID cluster/atom cutoff :pre + +ID, group-ID are documented in "compute"_compute.html command +cluster/atom = style name of this compute command +cutoff = distance within which to label atoms as part of same cluster (distance units) :ul + +[Examples:] + +compute 1 all cluster/atom 1.0 :pre + +[Description:] + +Define a computation that assigns each atom a cluster ID. + +A cluster is defined as a set of atoms, each of which is within the +cutoff distance from one or more other atoms in the cluster. If an +atom has no neighbors within the cutoff distance, then it is a 1-atom +cluster. The ID of every atom in the cluster will be the smallest +atom ID of any atom in the cluster. + +Only atoms in the compute group are clustered and assigned cluster +IDs. Atoms not in the compute group are assigned a cluster ID = 0. + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently or to have multiple compute/dump commands, each of a +{clsuter/atom} style. + +[Output info:] + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. + +The per-atom vector values will be an ID > 0, as explained above. + +[Restrictions:] none + +[Related commands:] + +"compute coord/atom"_compute_coord_atom.html + +[Default:] none diff --git a/doc/compute_coord_atom.html b/doc/compute_coord_atom.html index b9828fbd2a..6ab22c03b3 100644 --- a/doc/compute_coord_atom.html +++ b/doc/compute_coord_atom.html @@ -54,7 +54,9 @@ above.Restrictions: none
-Related commands: none +
Related commands: +
+Default: none
diff --git a/doc/compute_coord_atom.txt b/doc/compute_coord_atom.txt index b418fc4bc7..bd9c471a78 100644 --- a/doc/compute_coord_atom.txt +++ b/doc/compute_coord_atom.txt @@ -51,6 +51,8 @@ above. [Restrictions:] none -[Related commands:] none +[Related commands:] + +"compute cluster/atom"_compute_cluster_atom.html [Default:] none