2009-01-20 01:17:01 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>compute cna/atom command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID cna/atom cutoff
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>cna/atom = style name of this compute command
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<LI>cutoff = cutoff distance for nearest neighbors (distance units)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute 1 all cna/atom 3.08
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Define a computation that calculates the CNA (Common Neighbor
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Analysis) pattern for each atom in the group. In solid-state systems
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the CNA pattern is a useful measure of the local crystal structure
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around an atom. The CNA methodology is described in <A HREF = "#Faken">(Faken)</A>
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and <A HREF = "#Tsuzuki">(Tsuzuki)</A>.
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</P>
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<P>Currently, there are five kinds of CNA patterns LAMMPS recognizes:
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</P>
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<UL><LI>fcc = 1
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<LI>hcp = 2
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<LI>bcc = 3
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<LI>icosohedral = 4
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<LI>unknown = 5
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</UL>
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<P>The value of the CNA pattern will be 0 for atoms not in the specified
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2010-01-24 07:20:05 +08:00
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compute group. Note that normally a CNA calculation should only be
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2009-01-20 01:17:01 +08:00
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performed on mono-component systems.
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</P>
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<P>The CNA calculation can be sensitive to the specified cutoff value.
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You should insure the appropriate nearest neighbors of an atom are
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found within the cutoff distance for the presumed crystal strucure.
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E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
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neighbors for perfect BCC crystals. These formulas can be used to
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obtain a good cutoff distance:
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</P>
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<CENTER><IMG SRC = "Eqs/cna_cutoff1.jpg">
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</CENTER>
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<P>where a is the lattice constant for the crystal structure concerned
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and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
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for HCP crystals.
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</P>
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<P>Also note that since the CNA calculation in LAMMPS uses the neighbors
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of an owned atom to find the nearest neighbors of a ghost atom, the
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following relation should also be satisfied:
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</P>
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<CENTER><IMG SRC = "Eqs/cna_cutoff2.jpg">
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</CENTER>
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<P>where Rc is the cutoff distance of the potential, Rs is the skin
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distance as specified by the <A HREF = "neighbor.html">neighbor</A> command, and
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cutoff is the argument used with the compute cna/atom command. LAMMPS
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will issue a warning if this is not the case.
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</P>
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<P>The neighbor list needed to compute this quantity is constructed each
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time the calculation is performed (e.g. 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 or to have multiple compute/dump commands, each with a
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<I>cna/atom</I> style.
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</P>
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<P><B>Output info:</B>
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</P>
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2009-12-05 05:04:00 +08:00
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<P>This compute calculates a per-atom vector, which can be accessed by
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any command that uses per-atom values from a compute as input. See
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2011-12-14 04:43:36 +08:00
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<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
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LAMMPS output options.
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2009-01-20 01:17:01 +08:00
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</P>
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2010-01-24 07:33:48 +08:00
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<P>The per-atom vector values will be a number from 0 to 5, as explained
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above.
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2010-01-24 07:20:05 +08:00
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</P>
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2009-01-20 01:17:01 +08:00
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute_centro_atom.html">compute centro/atom</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Faken"></A>
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<P><B>(Faken)</B> Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
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</P>
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<A NAME = "Tsuzuki"></A>
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<P><B>(Tsuzuki)</B> Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).
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</P>
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</HTML>
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