forked from lijiext/lammps
122 lines
4.7 KiB
Plaintext
122 lines
4.7 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute orientorder/atom command :h3
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[Syntax:]
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compute ID group-ID orientorder/atom keyword values ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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orientorder/atom = style name of this compute command :l
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one or more keyword/value pairs may be appended :l
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keyword = {cutoff} or {nnn} or {ql}
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{cutoff} value = distance cutoff
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{nnn} value = number of nearest neighbors
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{degrees} values = nlvalues, l1, l2,... :pre
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:ule
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[Examples:]
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compute 1 all orientorder/atom
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compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 :pre
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[Description:]
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Define a computation that calculates a set of bond-orientational
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order parameters {Ql} for each atom in a group. These order parameters
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were introduced by "Steinhardt et al."_#Steinhardt as a way to
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characterize the local orientational order in atomic structures.
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For each atom, {Ql} is a real number defined as follows:
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:c,image(Eqs/orientorder.jpg)
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The first equation defines the spherical harmonic order parameters.
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These are complex number components of the 3D analog of the 2D order
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parameter {qn}, which is implemented as LAMMPS compute
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"hexorder/atom"_compute_hexorder_atom.html.
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The summation is over the {nnn} nearest
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neighbors of the central atom.
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The angles theta and phi are the standard spherical polar angles
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defining the direction of the bond vector {rij}.
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The second equation defines {Ql}, which is a
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rotationally invariant scalar quantity obtained by summing
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over all the components of degree {l}.
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The optional keyword {cutoff} defines the distance cutoff
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used when searching for neighbors. The default value, also
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the maximum allowable value, is the cutoff specified
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by the pair style.
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The optional keyword {nnn} defines the number of nearest
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neighbors used to calculate {Ql}. The default value is 12.
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If the value is NULL, then all neighbors up to the
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specified distance cutoff are used.
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The optional keyword {degrees} defines the list of order parameters to
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be computed. The first argument {nlvalues} is the number of order
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parameters. This is followed by that number of integers giving the
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degree of each order parameter. Because {Q}2 and all odd-degree
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order parameters are zero for atoms in cubic crystals
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(see "Steinhardt"_#Steinhardt), the default order parameters
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are {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12. For the
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FCC crystal with {nnn}=12, {Q}4 = sqrt(7/3)/8 = 0.19094....
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The numerical values of all order parameters up to {Q}12
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for a range of commonly encountered high-symmetry structures are given
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in Table I of "Mickel et al."_#Mickel.
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The value of {Ql} is set to zero for atoms not in the
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specified compute group, as well as for atoms that have less than
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{nnn} neighbors within the distance cutoff.
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The neighbor list needed to compute this quantity is constructed each
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time the calculation is performed (i.e. each time a snapshot of atoms
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is dumped). Thus it can be inefficient to compute/dump this quantity
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too frequently.
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NOTE: If you have a bonded system, then the settings of
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"special_bonds"_special_bonds.html command can remove pairwise
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interactions between atoms in the same bond, angle, or dihedral. This
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is the default setting for the "special_bonds"_special_bonds.html
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command, and means those pairwise interactions do not appear in the
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neighbor list. Because this fix uses the neighbor list, it also means
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those pairs will not be included in the order parameter. This
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difficulty can be circumvented by writing a dump file, and using the
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"rerun"_rerun.html command to compute the order parameter for
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snapshots in the dump file. The rerun script can use a
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"special_bonds"_special_bonds.html command that includes all pairs in
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the neighbor list.
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[Output info:]
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This compute calculates a per-atom array with {nlvalues} columns, giving the
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{Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1.
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These values can be accessed by any command that uses
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per-atom values from a compute as input. See "Section_howto
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15"_Section_howto.html#howto_15 for an overview of LAMMPS output
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options.
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[Restrictions:] none
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[Related commands:]
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"compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html, "compute hexorder/atom"_compute_hexorder_atom.html
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[Default:]
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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.
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:line
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:link(Steinhardt)
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[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
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:link(Mickel)
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[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
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