update to doc pages
This commit is contained in:
jtclemm
@ -115,7 +115,7 @@ KOKKOS, o = OPENMP, t = OPT.
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* :doc:`property/grid <compute_property_grid>`
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* :doc:`property/local <compute_property_local>`
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* :doc:`ptm/atom <compute_ptm_atom>`
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* :doc:`rattlers <compute_rattlers>`
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* :doc:`rattlers/atom <compute_rattlers_atom>`
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* :doc:`rdf <compute_rdf>`
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* :doc:`reduce <compute_reduce>`
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* :doc:`reduce/chunk <compute_reduce_chunk>`
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@ -269,7 +269,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
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* :doc:`property/grid <compute_property_grid>` - convert per-grid attributes to per-grid vectors/arrays
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* :doc:`property/local <compute_property_local>` - convert local attributes to local vectors/arrays
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* :doc:`ptm/atom <compute_ptm_atom>` - determines the local lattice structure based on the Polyhedral Template Matching method
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* :doc:`rattlers <compute_rattlers>` - identify under-coordinated rattler atoms
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* :doc:`rattlers/atom <compute_rattlers_atom>` - identify under-coordinated rattler atoms
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* :doc:`rdf <compute_rdf>` - radial distribution function :math:`g(r)` histogram of group of atoms
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* :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
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* :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
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@ -1,77 +0,0 @@
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.. index:: compute rattlers
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compute rattlers command
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========================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID rattlers cutoff zmin ntries
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* rattlers = style name of this compute command
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* cutoff = *type* or *radius*
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.. parsed-literal::
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*type* = cutoffs determined based on atom types
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*radius* = cutoffs determined based on atom diameters (atom style sphere)
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* zmin = minimum coordination for a non-rattler particle
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* ntries = maximum number of iterations to remove rattlers
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute 1 all rattlers type 4 10
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Description
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"""""""""""
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.. versionadded:: TBD
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Define a compute that identifies rattlers in a system. Rattlers are
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identified using an interactive approach. The coordination number of
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all atoms is first calculated. The *type* and *radius* settings are
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used to select whether interaction cutoffs are determined by atom
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types or by the sum of atomic radii (atom style sphere), respectively.
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Rattlers are then identified as particles with a coordination number
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less than *zmin* and are removed from consideration. Atomic coordination
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numbers are then recalculated, excluding previously identified rattlers,
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to identify a new set of rattlers. This process is iterated, up to a maximum
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of *ntries*, until no new rattlers are identified and the remaining
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atoms form a stable network of contacts.
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Output info
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"""""""""""
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This compute calculates a per-atom vector and a global scalar. The vector
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designates which atoms are rattlers, indicated by a value 1. Non-rattlers
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have a value of 0. The global scalar returns the total number of rattlers
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in the system. See the :doc:`Howto output <Howto_output>` page for an
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overview of LAMMPS output options.
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Restrictions
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""""""""""""
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This compute is part of the EXTRA-COMPUTE package. It is only enabled if
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LAMMPS was built with that package. See the
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:doc:`Build package <Build_package>` page for more info.
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The *radius* cutoff option requires that atoms store a radius as defined by the
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:doc:`atom_style sphere <atom_style>` or similar commands.
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Related commands
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""""""""""""""""
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:doc:`compute coord/atom <compute_coord_atom>`
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:doc:`compute contact/atom <compute_contact_atom>`
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Default
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"""""""
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none
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92
doc/src/compute_rattlers_atom.rst
Normal file
92
doc/src/compute_rattlers_atom.rst
Normal file
@ -0,0 +1,92 @@
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.. index:: compute rattlers/atom
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compute rattlers/atom command
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========================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID rattlers/atom cutoff zmin ntries
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* rattlers/atom = style name of this compute command
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* cutoff = *type* or *radius*
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.. parsed-literal::
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*type* = cutoffs determined based on atom types
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*radius* = cutoffs determined based on atom diameters (atom style sphere)
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* zmin = minimum coordination for a non-rattler atom
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* ntries = maximum number of iterations to remove rattlers
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute 1 all rattlers/atom type 4 10
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Description
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"""""""""""
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.. versionadded:: TBD
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Define a compute that identifies rattlers in a system. Rattlers are often
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identified in granular or glassy packings as undercoordinated atoms that
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do not have the required number of contacts to constrain their translational
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degrees of freedom. Such atoms are not considered rigid and can often freely
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rattle around in the system. This compute identifies rattlers which can be
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helpful for excluding them from analysis or providing extra damping forces
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to accelerate relaxation processes.
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Rattlers are identified using an interactive approach. The coordination
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number of all atoms is first calculated. The *type* and *radius* settings
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are used to select whether interaction cutoffs are determined by atom
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types or by the sum of atomic radii (atom style sphere), respectively.
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Rattlers are then identified as atoms with a coordination number less
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than *zmin* and are removed from consideration. Atomic coordination
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numbers are then recalculated, excluding previously identified rattlers,
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to identify a new set of rattlers. This process is iterated up to a maximum
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of *ntries* or until no new rattlers are identified and the remaining
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atoms form a stable network of contacts.
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In dense homogeneous systems where the average atom coordination number
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is expected to be larger than *zmin*, this process usually only takes a few
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iterations and a value of *ntries* around ten may be sufficient. In systems
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with significant heterogeneity or average coordination numbers less than
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*zmin*, an appropriate value of *ntries* depends heavily on the specific
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system. For instance, a linear chain of N rattler atoms with a *zmin* of 2
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would take N/2 iterations to identify that all the atoms are rattlers.
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Output info
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"""""""""""
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This compute calculates a per-atom vector and a global scalar. The vector
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designates which atoms are rattlers, indicated by a value 1. Non-rattlers
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have a value of 0. The global scalar returns the total number of rattlers
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in the system. See the :doc:`Howto output <Howto_output>` page for an
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overview of LAMMPS output options.
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Restrictions
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""""""""""""
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This compute is part of the EXTRA-COMPUTE package. It is only enabled if
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LAMMPS was built with that package. See the
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:doc:`Build package <Build_package>` page for more info.
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The *radius* cutoff option requires that atoms store a radius as defined by the
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:doc:`atom_style sphere <atom_style>` or similar commands.
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Related commands
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""""""""""""""""
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:doc:`compute coord/atom <compute_coord_atom>`
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:doc:`compute contact/atom <compute_contact_atom>`
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Default
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"""""""
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none
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