compute hexorder/atom command¶
-Syntax¶
-compute ID group-ID hexorder/atom keyword values ...
--
-
- ID, group-ID are documented in compute command -
- hexorder/atom = style name of this compute command -
- zero or more keyword/value pairs may be appended -
- keyword = degree -
-n value = degree of order parameter --
Examples¶
-compute 1 all hexorder/atom
-compute 1 all hexorder/atom n 4
-Description¶
-Define a computation that calculates qn the bond-orientational -order parameter for each atom in a group. The hexatic (n = 6) order -parameter was introduced by Nelson and Halperin as a way to detect -hexagonal symmetry in two-dimensional systems. For each atom, qn -is a complex number (stored as two real numbers) defined as follows:
-
-where the sum is over the n nearest neighbors + + +
+ +
compute hexorder/atom command +
+Syntax: +
+compute ID group-ID hexorder/atom keyword values ... ++
- ID, group-ID are documented in compute command + +
- hexorder/atom = style name of this compute command + +
- one or more keyword/value pairs may be appended
+
+
keyword = n or nnn or cutoff + cutoff value = distance cutoff + nnn value = number of nearest neighbors + n value = degree of order parameter +
+ +
Examples: +
+compute 1 all hexorder/atom +compute 1 all hexorder/atom n 4 nnn 4 cutoff 1.2 ++
Description: +
+Define a computation that calculates qn the bond-orientational +order parameter for each atom in a group. The hexatic (n = 6) order +parameter was introduced by Nelson and Halperin as a way to detect +hexagonal symmetry in two-dimensional systems. For each atom, qn +is a complex number (stored as two real numbers) defined as follows: +
+
+where the sum is over the nnn nearest neighbors of the central atom. The angle theta -is formed by the bond vector rij and the x axis. theta is calculated -only using the x and y components, whereas the distance from the -central atom is calculated using all three -x, y, and z components of the bond vector. -Neighbor atoms not in the group -are included in the order parameter of atoms in the group.
-The optional keyword n sets the degree of the order parameter. -The default value is 6. For a perfect hexagonal lattice, -*q*6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3 -depends only on the orientation of the lattice relative to the x axis. -In an isotropic liquid, local neighborhoods may still exhibit +is formed by the bond vector rij and the x axis. theta is calculated +only using the x and y components, whereas the distance from the +central atom is calculated using all three +x, y, and z components of the bond vector. +Neighbor atoms not in the group +are included in the order parameter of atoms in the group. +
+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 qn. The default value is 6. +If the value is NULL, then all neighbors up to the +distance cutoff are used. +
+The optional keyword n sets the degree of the order parameter. +The default value is 6. For a perfect hexagonal lattice with +nnn = 6, +q6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3 +depends only on the orientation of the lattice relative to the x axis. +In an isotropic liquid, local neighborhoods may still exhibit weak hexagonal symmetry, but because the orientational correlation decays quickly with distance, the value of phi will be different for -different atoms, and |<*q*6>| << 1.
-The value of qn will be zero for atoms not in the -specified compute group. If the atom has less than n neighbors (within -the potential cutoff), then qn is set to zero.
-The neighbor list needed to compute this quantity is constructed each +different atoms, and so when q6 is averaged over all the atoms +in the system, |<q6>| << 1. +
+The value of qn 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.
-Warning
-If you have a bonded system, then the settings of -special_bonds command can remove pairwise +too frequently. +
+IMPORTANT NOTE: If you have a bonded system, then the settings of +special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This -is the default setting for the special_bonds +is the default setting for the 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. One way -to get around this, is to write a dump file, and use the -rerun command to compute the order parameter for snapshots +those pairs will not be included in the order parameter. This difficulty +can be circumvented by writing a dump file, and using the +rerun command to compute the order parameter for snapshots in the dump file. The rerun script can use a -special_bonds command that includes all pairs in -the neighbor list.
-Output info:
-This compute calculates a per-atom array with 2 columns, giving the -real and imaginary parts of qn, respectively.
-These values can be accessed by any command that uses -per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output -options.
-The per-atom array contain pairs of numbers representing the -real and imaginary parts of qn, a complex number subject to the -constraint |*qn*| <= 1.
-Restrictions¶
---none
Default¶
-The option default is n = 6.
--
(Nelson) Nelson, Halperin, Phys Rev B, 19, 2457 (1979).
-Output info: +
+This compute calculates a per-atom array with 2 columns, giving the +real and imaginary parts qn, a complex number restricted to the +unit disk of the complex plane i.e. Re(qn)^2 + Im(qn)^2 <= 1 . +
+These values can be accessed by any command that uses +per-atom values from a compute as input. See Section_howto +15 for an overview of LAMMPS output +options. +
+Restrictions: none +
+Related commands: +
+compute orientorder/atom, compute coord/atom, compute centro/atom +
+Default: +
+The option defaults are n = 6, nnn = 6, cutoff = pair style cutoff +
++ -