compute_orientorder_atom.txt
caf9483a0a7clammps-icms

compute_orientorder_atom.txt
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			.. index:: compute orientorder/atom

			compute orientorder/atom command
			================================

			Syntax
			""""""

			.. parsed-literal::

			compute ID group-ID orientorder/atom keyword values ...

			* ID, group-ID are documented in :doc:`compute <compute>` command
			* orientorder/atom = style name of this compute command
			* one or more keyword/value pairs may be appended
			.. parsed-literal::

			keyword = cutoff or nnn or ql
			cutoff value = distance cutoff
			nnn value = number of nearest neighbors
			degrees values = nlvalues, l1, l2,...



			Examples
			""""""""

			.. parsed-literal::

			compute 1 all orientorder/atom
			compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5

			Description
			"""""""""""

			Define a computation that calculates a set of bond-orientational
			order parameters Ql for each atom in a group. These order parameters
			were introduced by :ref:`Steinhardt et al. <Steinhardt>` as a way to
			characterize the local orientational order in atomic structures.
			For each atom, Ql is a real number defined as follows:

			.. image:: Eqs/orientorder.jpg
			:align: center

			The first equation defines the spherical harmonic order parameters.
			These are complex number components of the 3D analog of the 2D order
			parameter qn\ , which is implemented as LAMMPS compute
			:doc:`hexorder/atom <compute_hexorder_atom>`.
			The summation is over the nnn nearest
			neighbors of the central atom.
			The angles theta and phi are the standard spherical polar angles
			defining the direction of the bond vector rij\ .
			The second equation defines Ql\ , which is a
			rotationally invariant scalar quantity obtained by summing
			over all the components of degree l\ .

			The optional keyword cutoff defines the distance cutoff
			used when searching for neighbors. The default value, also
			the maximum allowable value, is the cutoff specified
			by the pair style.

			The optional keyword nnn defines the number of nearest
			neighbors used to calculate Ql\ . The default value is 12.
			If the value is NULL, then all neighbors up to the
			specified distance cutoff are used.

			The optional keyword degrees defines the list of order parameters to
			be computed. The first argument nlvalues is the number of order
			parameters. This is followed by that number of integers giving the
			degree of each order parameter. Because Q\ 2 and all odd-degree
			order parameters are zero for atoms in cubic crystals
			(see :ref:`Steinhardt <Steinhardt>`), the default order parameters
			are Q\ 4, Q\ 6, Q\ 8, Q\ 10, and Q\ 12. For the
			FCC crystal with nnn\ =12, Q\ 4 = sqrt(7/3)/8 = 0.19094....
			The numerical values of all order parameters up to Q\ 12
			for a range of commonly encountered high-symmetry structures are given
			in Table I of :ref:`Mickel et al. <Mickel>`.

			The value of Ql 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.

			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.

			.. note::

			If you have a bonded system, then the settings of
			:doc:`special_bonds <special_bonds>` command can remove pairwise
			interactions between atoms in the same bond, angle, or dihedral. This
			is the default setting for the :doc:`special_bonds <special_bonds>`
			command, and means those pairwise interactions do not appear in the
			neighbor list. Because this fix uses the neighbor list, it also means
			those pairs will not be included in the order parameter. This
			difficulty can be circumvented by writing a dump file, and using the
			:doc:`rerun <rerun>` command to compute the order parameter for
			snapshots in the dump file. The rerun script can use a
			:doc:`special_bonds <special_bonds>` command that includes all pairs in
			the neighbor list.

			Output info:

			This compute calculates a per-atom array with nlvalues columns, giving the
			Ql values for each atom, which are real numbers on the range 0 <= Ql <= 1.

			These values can be accessed by any command that uses
			per-atom values from a compute as input. See :ref:`Section_howto 15 <howto_15>` for an overview of LAMMPS output
			options.

			Restrictions
			""""""""""""
			none

			Related commands
			""""""""""""""""

			:doc:`compute coord/atom <compute_coord_atom>`, :doc:`compute centro/atom <compute_centro_atom>`, :doc:`compute hexorder/atom <compute_hexorder_atom>`

			Default
			"""""""

			The option defaults are cutoff = pair style cutoff, nnn = 12, degrees = 5 4 6 8 9 10 12 i.e. Q\ 4, Q\ 6, Q\ 8, Q\ 10, and Q\ 12.


			----------


			.. _Steinhardt:



			.. _Mickel:

			(Steinhardt) P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).


			(Mickel) W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).


			.. _lws: http://lammps.sandia.gov
			.. _ld: Manual.html
			.. _lc: Section_commands.html#comm

lammps/doc/html/_sources/compute_orientorder_atom.txtcaf9483a0a7clammps-icms

compute_orientorder_atom.txtView Options

lammps/doc/html/_sources/compute_orientorder_atom.txt
caf9483a0a7clammps-icms

compute_orientorder_atom.txt
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