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Merge branch 'master' of https://github.com/lammps/lammps into orientorder-components-parity

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Stan Moore
2020-06-19 14:32:00 -06:00
parent c7874fca86 7e2f29bb65
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doc/src/compute_orientorder_atom.rst
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@ -3,6 +3,9 @@
compute orientorder/atom command
================================
compute orientorder/atom/kk command
===================================
Syntax
""""""
@ -16,13 +19,14 @@ Syntax
.. parsed-literal::
keyword = *cutoff* or *nnn* or *degrees* or *components*
keyword = *cutoff* or *nnn* or *degrees* or *components* or *chunksize*
*cutoff* value = distance cutoff
*nnn* value = number of nearest neighbors
*degrees* values = nlvalues, l1, l2,...
*wl* value = yes or no
*wl/hat* value = yes or no
*components* value = ldegree
*chunksize* value = number of atoms in each pass
Examples
""""""""
@ -107,6 +111,14 @@ in conjunction with :doc:`compute coord_atom <compute_coord_atom>` to
calculate the ten Wolde's criterion to identify crystal-like
particles, as discussed in :ref:`ten Wolde <tenWolde2>`.
The optional keyword *chunksize* is only applicable when using the
the KOKKOS package and is ignored otherwise. This keyword controls
the number of atoms in each pass used to compute the bond-orientational
order parameters and is used to avoid running out of memory. For example
if there are 4000 atoms in the simulation and the *chunksize*
is set to 2000, the parameter calculation will be broken up
into two passes.
The value of :math:`Q_l` is set to zero for atoms not in the
specified compute group, as well as for atoms that have less than
*nnn* neighbors within the distance cutoff, unless *nnn* is NULL.
@ -131,6 +143,30 @@ too frequently.
:doc:`special_bonds <special_bonds>` command that includes all pairs in
the neighbor list.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
----------
**Output info:**
This compute calculates a per-atom array with *nlvalues* columns,
@ -172,7 +208,7 @@ Default
The option defaults are *cutoff* = pair style cutoff, *nnn* = 12,
*degrees* = 5 4 6 8 10 12 i.e. :math:`Q_4`, :math:`Q_6`, :math:`Q_8`, :math:`Q_{10}`, and :math:`Q_{12}`,
*wl* = no, *wl/hat* = no, and *components* off
*wl* = no, *wl/hat* = no, *components* off, and *chunksize* = 2000
----------