ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

rattler documentation

Browse Source
This commit is contained in:
jtclemm
2023-06-15 23:06:50 -06:00
parent 7012e6ddd4
commit a1513a7d3b
3 changed files with 36 additions and 42 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
doc/src/compute_contact_atom.rst
View File

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

65
doc/src/compute_rattlers.rst
View File

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

10
doc/src/fix_nonaffine_displacement.rst
View File

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