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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_start.html" > 2. Getting Started< / a > < / li >
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< li > compute msd/nongauss 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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< div class = "section" id = "compute-msd-nongauss-command" >
< span id = "index-0" > < / span > < h1 > compute msd/nongauss command< / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< / h2 >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > compute< / span > < span class = "n" > ID< / span > < span class = "n" > group< / span > < span class = "o" > -< / span > < span class = "n" > ID< / span > < span class = "n" > msd< / span > < span class = "o" > /< / span > < span class = "n" > nongauss< / span > < span class = "n" > keyword< / span > < span class = "n" > values< / span > < span class = "o" > ...< / span >
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< li > ID, group-ID are documented in < a class = "reference internal" href = "compute.html" > < span class = "doc" > compute< / span > < / a > command< / li >
< li > msd/nongauss = style name of this compute command< / li >
< li > zero or more keyword/value pairs may be appended< / li >
< li > keyword = < em > com< / em > < / li >
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< 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< / h2 >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > compute< / span > < span class = "mi" > 1< / span > < span class = "nb" > all< / span > < span class = "n" > msd< / span > < span class = "o" > /< / span > < span class = "n" > nongauss< / span >
< span class = "n" > compute< / span > < span class = "mi" > 1< / span > < span class = "n" > upper< / span > < span class = "n" > msd< / span > < span class = "o" > /< / span > < span class = "n" > nongauss< / span > < span class = "n" > com< / span > < span class = "n" > yes< / span >
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< div class = "section" id = "description" >
< h2 > Description< / h2 >
< p > Define a computation that calculates the mean-squared displacement
(MSD) and non-Gaussian parameter (NGP) of the group of atoms,
including all effects due to atoms passing thru periodic boundaries.< / p >
< p > A vector of three quantites is calculated by this compute. The first
element of the vector is the total squared dx,dy,dz displacements
drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the
fourth power of these displacements drfourth = (dx*dx + dy*dy +
dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the
group. The 3rd component is the nonGaussian diffusion paramter NGP =
3*drfourth/(5*drsquared*drsquared), i.e.< / p >
< img alt = "_images/compute_msd_nongauss.jpg" class = "align-center" src = "_images/compute_msd_nongauss.jpg" / >
< p > The NGP is a commonly used quantity in studies of dynamical
heterogeneity. Its minimum theoretical value (-0.4) occurs when all
atoms have the same displacement magnitude. NGP=0 for Brownian
diffusion, while NGP > 0 when some mobile atoms move faster than
others.< / p >
< p > If the < em > com< / em > option is set to < em > yes< / em > then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calcluated.< / p >
< p > See the < a class = "reference internal" href = "compute_msd.html" > < span class = "doc" > compute msd< / span > < / a > doc page for further important
NOTEs, which also apply to this compute.< / p >
< p > < strong > Output info:< / strong > < / p >
< p > This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
from a compute as input. See < a class = "reference internal" href = "Section_howto.html#howto-15" > < span class = "std std-ref" > this section< / span > < / a > for an overview of LAMMPS output
options.< / p >
< p > The vector values are “ intensive” . The first vector value will be in
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distance^2 < a class = "reference internal" href = "units.html" > < span class = "doc" > units< / span > < / a > , the second is in distance^4 units, and
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the 3rd is dimensionless.< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< / h2 >
< p > This compute is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span class = "std std-ref" > Making LAMMPS< / span > < / a > section for more info.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< / h2 >
< p > < a class = "reference internal" href = "compute_msd.html" > < span class = "doc" > compute msd< / span > < / a > < / p >
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< div class = "section" id = "default" >
< h2 > Default< / h2 >
< p > The option default is com = no.< / p >
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