compute_centro_atom.txt
bac07b76cef2lammm-master

compute_centro_atom.txt
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			"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

			:link(lws,http://lammps.sandia.gov)
			:link(ld,Manual.html)
			:link(lc,Section_commands.html#comm)

			:line

			compute centro/atom command :h3

			[Syntax:]

			compute ID group-ID centro/atom lattice :pre

			ID, group-ID are documented in "compute"_compute.html command
			centro/atom = style name of this compute command
			lattice = {fcc} or {bcc} or N = # of neighbors per atom to include :ul

			[Examples:]

			compute 1 all centro/atom fcc :pre
			compute 1 all centro/atom 8 :pre

			[Description:]

			Define a computation that calculates the centro-symmetry parameter for
			each atom in the group. In solid-state systems the centro-symmetry
			parameter is a useful measure of the local lattice disorder around an
			atom and can be used to characterize whether the atom is part of a
			perfect lattice, a local defect (e.g. a dislocation or stacking
			fault), or at a surface.

			The value of the centro-symmetry parameter will be 0.0 for atoms not
			in the specified compute group.

			This parameter is computed using the following formula from
			"(Kelchner)"_#Kelchner

			:c,image(Eqs/centro_symmetry.jpg)

			where the {N} nearest neighbors or each atom are identified and Ri and
			Ri+N/2 are vectors from the central atom to a particular pair of
			nearest neighbors. There are N*(N-1)/2 possible neighbor pairs that
			can contribute to this formula. The quantity in the sum is computed
			for each, and the N/2 smallest are used. This will typically be for
			pairs of atoms in symmetrically opposite positions with respect to the
			central atom; hence the i+N/2 notation.

			{N} is an input parameter, which should be set to correspond to the
			number of nearest neighbors in the underlying lattice of atoms. If
			the keyword {fcc} or {bcc} is used, {N} is set to 12 and 8
			respectively. More generally, {N} can be set to a positive, even
			integer.

			For an atom on a lattice site, surrounded by atoms on a perfect
			lattice, the centro-symmetry parameter will be 0. It will be near 0
			for small thermal perturbations of a perfect lattice. If a point
			defect exists, the symmetry is broken, and the parameter will be a
			larger positive value. An atom at a surface will have a large
			positive parameter. If the atom does not have {N} neighbors (within
			the potential cutoff), then its centro-symmetry parameter is set to
			0.0.

			Only atoms within the cutoff of the pairwise neighbor list are
			considered as possible neighbors. Atoms not in the compute group are
			included in the {N} neighbors used in this calculation.

			The neighbor list needed to compute this quantity is constructed each
			time the calculation is performed (e.g. each time a snapshot of atoms
			is dumped). Thus it can be inefficient to compute/dump this quantity
			too frequently or to have multiple compute/dump commands, each with a
			{centro/atom} style.

			[Output info:]

			This compute calculates a per-atom vector, which can be accessed by
			any command that uses per-atom values from a compute as input. See
			"Section_howto 15"_Section_howto.html#howto_15 for an overview of
			LAMMPS output options.

			The per-atom vector values are unitless values >= 0.0. Their
			magnitude depends on the lattice style due to the number of
			contibuting neighbor pairs in the summation in the formula above. And
			it depends on the local defects surrounding the central atom, as
			described above.

			Here are typical centro-symmetry values, from a a nanoindentation
			simulation into gold (FCC). These were provided by Jon Zimmerman
			(Sandia):

			Bulk lattice = 0
			Dislocation core ~ 1.0 (0.5 to 1.25)
			Stacking faults ~ 5.0 (4.0 to 6.0)
			Free surface ~ 23.0 :pre

			These values are not normalized by the square of the lattice
			parameter. If they were, normalized values would be:

			Bulk lattice = 0
			Dislocation core ~ 0.06 (0.03 to 0.075)
			Stacking faults ~ 0.3 (0.24 to 0.36)
			Free surface ~ 1.38 :pre

			For BCC materials, the values for dislocation cores and free surfaces
			would be somewhat different, due to their being only 8 neighbors instead
			of 12.

			[Restrictions:] none

			[Related commands:]

			"compute cna/atom"_compute_cna_atom.html

			[Default:] none

			:line

			:link(Kelchner)
			[(Kelchner)] Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).

lammps/doc/compute_centro_atom.txtbac07b76cef2lammm-master

compute_centro_atom.txtView Options

lammps/doc/compute_centro_atom.txt
bac07b76cef2lammm-master

compute_centro_atom.txt
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