4f71701e4e
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14234 f3b2605a-c512-4ea7-a41b-209d697bcdaa
96 lines
3.3 KiB
Plaintext
96 lines
3.3 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 :pre
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ID, group-ID are documented in "compute"_compute.html command
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hexorder/atom = style name of this compute command
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[Examples:]
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compute 1 all hexorder/atom :pre
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[Description:]
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Define a computation that calculates {q}6 the hexatic bond-orientational
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order parameter for each atom in a group. This 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, {q}6
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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 six 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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If the neighbors of the central atom lie on a hexagonal lattice,
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then |{q}6| = 1.
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The complex phase of {q}6 depends on the orientation of the
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lattice relative to the {x} axis. For a liquid in which the
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atomic neighborhood lacks orientational symmetry, |{q}6| << 1.
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The value of all order parameters will be zero for atoms not in the
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specified compute group. If the atom does not have 6 neighbors (within
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the potential cutoff), then its centro-symmetry parameter is set to
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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 {q}6, 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 {q}6, a complex number subject to the
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constraint |{q}6| <= 1.
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[Restrictions:] none
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[Related commands:]
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"compute coord/atom"_compute_coord_atom.html
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[Default:] none
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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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