984132322e
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14232 f3b2605a-c512-4ea7-a41b-209d697bcdaa
119 lines
4.6 KiB
Plaintext
119 lines
4.6 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 cutoff type1 type2 ... :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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cutoff = distance within which to count neighbors (distance units)
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typeN = atom type for Nth order parameter (see asterisk form below) :ul
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[Examples:]
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compute 1 all hexorder/atom 2.0
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compute 1 all hexorder/atom 6.0 1 2
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compute 1 all hexorder/atom 6.0 2*4 5*8 * :pre
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[Description:]
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Define a computation that calculates one or more hexatic bond orientational
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order parameters for each atom in a group. The hexatic bond orientational order
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parameter {q}6 "(Nelson)"_#Nelson for an atom is a complex number (stored as two real numbers).
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It is defined as follows:
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:c,image(Eqs/hexorder.jpg)
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where the sum is over atoms of the specified atom type(s) that are within
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the specified cutoff distance from 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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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 symmettry, |{q}6| << 1.
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The {typeN} keywords allow you to specify which atom types contribute
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to each order parameter. One order parameter is computed for
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each of the {typeN} keywords listed. If no {typeN} keywords are
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listed, a single order parameter is calculated, which includes
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atoms of all types (same as the "*" format, see below).
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The {typeN} keywords can be specified in one of two ways. An explicit
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numeric value can be used, as in the 2nd example above. Or a
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wild-card asterisk can be used to specify a range of atom types. This
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takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
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atom types, then an asterisk with no numeric values means all types
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from 1 to N. A leading asterisk means all types from 1 to n
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(inclusive). A trailing asterisk means all types from n to N
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(inclusive). A middle asterisk means all types from m to n
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(inclusive).
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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. An order parameter for atoms that have no
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neighbors of the specified atom type within the cutoff distance will
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be 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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If single {type1} keyword is specified (or if none are specified),
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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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If multiple {typeN} keywords are specified, this compute calculates
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a per-atom array with 2*N columns, with each consecutive pair of
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columns giving the real and imaginary parts of {q}6.
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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 values will be 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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