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< title > compute msd command — LAMMPS 15 May 2015 version documentation< / title >
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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 msd command< / li >
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< a href = "http://lammps.sandia.gov" > Website< / a >
< a href = "Section_commands.html#comm" > Commands< / a >
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< span id = "index-0" > < / span > < h1 > compute msd command< a class = "headerlink" href = "#compute-msd-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 msd keyword values ...
< / 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 > msd = style name of this compute command< / li >
< li > zero or more keyword/value pairs may be appended< / li >
< li > keyword = < em > com< / em > < / li >
< / ul >
< pre class = "literal-block" >
< em > com< / em > value = < em > yes< / em > or < em > no< / em >
< / pre >
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< 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 msd
compute 1 upper msd com yes
< / pre > < / div >
< / 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 mean-squared displacement
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(MSD) of the group of atoms, including all effects due to atoms
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passing thru periodic boundaries. For computation of the non-Gaussian
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parameter of mean-squared displacement, see the < a class = "reference internal" href = "compute_msd_nongauss.html" > < em > compute msd/nongauss< / em > < / a > command.< / p >
< p > A vector of four quantites is calculated by this compute. The first 3
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elements of the vector are the squared dx,dy,dz displacements, summed
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and averaged over atoms in the group. The 4th element is the total
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squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
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averaged over atoms in the group.< / p >
< p > The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms.< / p >
< p > The displacement of an atom is from its original position at the time
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the compute command was issued. The value of the displacement will be
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0.0 for atoms not in the specified compute group.< / p >
< p > If the < em > com< / em > option is set to < em > yes< / em > then the effect of any drift in
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the center-of-mass of the group of atoms is subtracted out before xhe
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displacment of each atom is calcluated.< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > Initial coordinates are stored in “ unwrapped” form, by
using the image flags associated with each atom. See the < a class = "reference internal" href = "dump.html" > < em > dump custom< / em > < / a > command for a discussion of “ unwrapped” coordinates.
See the Atoms section of the < a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > command for a
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discussion of image flags and how they are set for each atom. You can
reset the image flags (e.g. to 0) before invoking this compute by
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using the < a class = "reference internal" href = "set.html" > < em > set image< / em > < / a > command.< / p >
< / div >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > If you want the quantities calculated by this compute
to be continuous when running from a < a class = "reference internal" href = "read_restart.html" > < em > restart file< / em > < / a > ,
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then you should use the same ID for this compute, as in the original
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run. This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
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correctly with time=0 atom coordinates from the restart file.< / p >
< / div >
< p > < strong > Output info:< / strong > < / p >
< p > This compute calculates a global vector of length 4, which can be
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accessed by indices 1-4 by any command that uses global vector values
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from a compute as input. See < a class = "reference internal" href = "Section_howto.html#howto-15" > < span > this section< / span > < / a > for an overview of LAMMPS output
options.< / p >
< p > The vector values are “ intensive” . The vector values will be in
distance^2 < a class = "reference internal" href = "units.html" > < em > units< / em > < / a > .< / 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_msd_nongauss.html" > < em > compute msd/nongauss< / em > < / a > , < a class = "reference internal" href = "compute_displace_atom.html" > < em > compute displace_atom< / em > < / a > , < a class = "reference internal" href = "fix_store_state.html" > < em > fix store/state< / em > < / a > , < a class = "reference internal" href = "compute_msd_chunk.html" > < em > compute msd/chunk< / em > < / a > < / p >
< / div >
< div class = "section" id = "default" >
< h2 > Default< a class = "headerlink" href = "#default" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The option default is com = no.< / p >
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