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< title > compute cna/atom command — LAMMPS documentation< / title >
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2009-01-20 01:17:01 +08:00
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2009-01-20 01:17:01 +08:00
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2009-01-20 01:17:01 +08:00
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2009-01-20 01:17:01 +08:00
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
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< li > compute cna/atom command< / li >
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< a href = "http://lammps.sandia.gov" > Website< / a >
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< span id = "index-0" > < / span > < h1 > compute cna/atom command< a class = "headerlink" href = "#compute-cna-atom-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute ID group-ID cna/atom cutoff
< / pre > < / div >
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< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > command< / li >
< li > cna/atom = style name of this compute command< / li >
< li > cutoff = cutoff distance for nearest neighbors (distance units)< / li >
< / ul >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute 1 all cna/atom 3.08
< / pre > < / div >
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< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< 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
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 class = "reference internal" href = "#faken" > < span > (Faken)< / span > < / a >
and < a class = "reference internal" href = "#tsuzuki" > < span > (Tsuzuki)< / span > < / a > .< / p >
< p > Currently, there are five kinds of CNA patterns LAMMPS recognizes:< / p >
< ul class = "simple" >
< li > fcc = 1< / li >
< li > hcp = 2< / li >
< li > bcc = 3< / li >
< li > icosohedral = 4< / li >
< li > unknown = 5< / li >
< / ul >
< p > The value of the CNA pattern will be 0 for atoms not in the specified
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compute group. Note that normally a CNA calculation should only be
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performed on mono-component systems.< / p >
< 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
found within the cutoff distance for the presumed crystal strucure.
E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
neighbors for perfect BCC crystals. These formulas can be used to
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obtain a good cutoff distance:< / p >
< img alt = "_images/cna_cutoff1.jpg" class = "align-center" src = "_images/cna_cutoff1.jpg" / >
< 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.< / p >
< 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:< / p >
< img alt = "_images/cna_cutoff2.jpg" class = "align-center" src = "_images/cna_cutoff2.jpg" / >
< p > where Rc is the cutoff distance of the potential, Rs is the skin
distance as specified by the < a class = "reference internal" href = "neighbor.html" > < em > neighbor< / em > < / 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.< / p >
< 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
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each with a
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< em > cna/atom< / em > style.< / p >
< p > < strong > Output info:< / strong > < / p >
< 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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< a class = "reference internal" href = "Section_howto.html#howto-15" > < span > Section_howto 15< / span > < / a > for an overview of
LAMMPS output options.< / p >
< p > The per-atom vector values will be a number from 0 to 5, as explained
above.< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< blockquote >
< div > none< / div > < / blockquote >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "compute_centro_atom.html" > < em > compute centro/atom< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
< hr class = "docutils" / >
< p id = "faken" > < strong > (Faken)< / strong > Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).< / p >
< p id = "tsuzuki" > < strong > (Tsuzuki)< / strong > Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).< / p >
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