rattler documentation

doc/src/compute_contact_atom.rst

@@ -69,6 +69,3 @@ Default
 """""""
 
 *group2-ID* = all
-
-
-none

doc/src/compute_rattlers.rst

@@ -1,6 +1,6 @@
-.. index:: compute contact/atom
+.. index:: compute rattlers
 
-compute contact/atom command
+compute rattlers command
 ============================
 
 Syntax
@@ -8,67 +8,68 @@ Syntax
 
 .. parsed-literal::
 
-   compute ID group-ID contact/atom group2-ID
+   compute ID group-ID rattlers cutoff zmin ntries
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
-* contact/atom = style name of this compute command
-* group2-ID = optional argument select group-ID to restrict which atoms to consider for contacts (see below)
+* rattlers = style name of this compute command
+* cutoff = *type* or *radius*
+
+  .. parsed-literal::
+
+       *type* = cutoffs determined based on atom types
+       *radius* = cutoffs determined based on atom diameters (atom style sphere)
+
+* zmin = minimum coordination for a non-rattler particle
+* ntries = maximum number of interations to remove rattlers
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   compute 1 all contact/atom
-   compute 1 all contact/atom mygroup
+   compute 1 all rattlers type 4 10
 
 Description
 """""""""""
 
-Define a computation that calculates the number of contacts
-for each atom in a group.
-
-The contact number is defined for finite-size spherical particles as
-the number of neighbor atoms which overlap the central particle,
-meaning that their distance of separation is less than or equal to the
-sum of the radii of the two particles.
-
-The value of the contact number will be 0.0 for atoms not in the
-specified compute group.
-
-The optional *group2-ID* argument allows to specify from which group atoms
-contribute to the coordination number. Default setting is group 'all'.
+Define a compute that identifies rattlers in a system. Rattlers are
+identified using an interative approach. The coordination number of
+all atoms is first calculated.  The *type* and *radius* settings are
+used to select whether interactions cutoffs are determined by atom
+types or by the sum of atomic radii (atom style sphere), respectively.
+Rattlers are then identified as particles with a coordination number
+less than *zmin* and are removed from consideration. A coordination
+number is then recalaculated, excluding previously identified rattlers,
+to identify new rattlers. This process is looped, up to a maximum
+of *ntries*, until no new rattlers are identified and the remaining
+atoms form a stable network of contacts.
 
 Output info
 """""""""""
 
-This compute calculates a per-atom vector, whose values can be
-accessed by any command that uses per-atom values from a compute as
-input.  See the :doc:`Howto output <Howto_output>` page for an
+This compute calculates a per-atom vector and a global scalar. The vector
+designates which atoms are rattlers, indicated by a value 1. Non-rattlers
+have a value of 0. The global scalar returns the total number of rattlers
+in the system. See the :doc:`Howto output <Howto_output>` page for an
 overview of LAMMPS output options.
 
-The per-atom vector values will be a number >= 0.0, as explained
-above.
-
 Restrictions
 """"""""""""
 
-This compute is part of the GRANULAR package.  It is only enabled if
+This compute is part of the EXTRA-COMPUTE package.  It is only enabled if
 LAMMPS was built with that package.  See the
 :doc:`Build package <Build_package>` page for more info.
 
-This compute requires that atoms store a radius as defined by the
-:doc:`atom_style sphere <atom_style>` command.
+The *radius* cutoff option requires that atoms store a radius as defined by the
+:doc:`atom_style sphere <atom_style>` or similar commands.
 
 Related commands
 """"""""""""""""
 
 :doc:`compute coord/atom <compute_coord_atom>`
+:doc:`compute contact/atom <compute_contact_atom>`
 
 Default
 """""""
 
-*group2-ID* = all
-
-
 none

doc/src/fix_nonaffine_displacement.rst

@@ -1,18 +1,14 @@
-.. index:: fix gravity
-.. index:: fix gravity/omp
-.. index:: fix gravity/kk
+.. index:: fix nonaffine/displacement
 
-fix gravity command
+fix nonaffine/displacement command
 ===================
 
-Accelerator Variants: *gravity/omp*, *gravity/kk*
-
 Syntax
 """"""
 
 .. parsed-literal::
 
-   fix ID group gravity magnitude style args
+   fix ID group nonaffine/displacement style args reference/style args
 
 * ID, group are documented in :doc:`fix <fix>` command
 * gravity = style name of this fix command