mirror of https://github.com/lammps/lammps.git
105 lines
3.7 KiB
Plaintext
105 lines
3.7 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 hexorder/atom command :h3
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[Syntax:]
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compute ID group-ID hexorder/atom keyword values ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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hexorder/atom = style name of this compute command :l
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zero or more keyword/value pairs may be appended :l
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keyword = {degree} :l
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{n} value = degree of order parameter :pre
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:ule
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[Examples:]
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compute 1 all hexorder/atom
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compute 1 all hexorder/atom n 4 :pre
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[Description:]
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Define a computation that calculates {qn} the bond-orientational
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order parameter for each atom in a group. The hexatic ({n} = 6) order
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parameter was introduced by "Nelson and Halperin"_#Nelson as a way to detect
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hexagonal symmetry in two-dimensional systems. For each atom, {qn}
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is a complex number (stored as two real numbers) defined as follows:
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:c,image(Eqs/hexorder.jpg)
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where the sum is over the {n} nearest neighbors
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of the central atom. The angle theta
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is formed by the bond vector rij and the {x} axis. theta is calculated
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only using the {x} and {y} components, whereas the distance from the
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central atom is calculated using all three
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{x}, {y}, and {z} components of the bond vector.
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Neighbor atoms not in the group
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are included in the order parameter of atoms in the group.
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The optional keyword {n} sets the degree of the order parameter.
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The default value is 6. For a perfect hexagonal lattice,
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{q}6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3
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depends only on the orientation of the lattice relative to the x axis.
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In an isotropic liquid, local neighborhoods may still exhibit
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weak hexagonal symmetry, but because the orientational correlation
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decays quickly with distance, the value of phi will be different for
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different atoms, and |<{q}6>| << 1.
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The value of {qn} will be zero for atoms not in the
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specified compute group. If the atom has less than {n} neighbors (within
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the potential cutoff), then {qn} is set to zero.
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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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IMPORTANT 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. One way
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to get around this, is to write a dump file, and use the
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"rerun"_rerun.html command to compute the order parameter for snapshots
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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 2 columns, giving the
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real and imaginary parts of {qn}, respectively.
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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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The per-atom array contain pairs of numbers representing the
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real and imaginary parts of {qn}, a complex number subject to the
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constraint |{qn}| <= 1.
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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
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[Default:]
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The option default is {n} = 6.
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:line
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:link(Nelson)
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[(Nelson)] Nelson, Halperin, Phys Rev B, 19, 2457 (1979).
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