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lammps/doc/compute_msd_nongauss.txt
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compute_msd_nongauss.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 msd/nongauss command :h3
[Syntax:]
compute ID group-ID msd/nongauss keyword values ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
msd/nongauss = style name of this compute command :l
zero or more keyword/value pairs may be appended :l
keyword = {com} :l
{com} value = {yes} or {no} :pre
:ule
[Examples:]
compute 1 all msd/nongauss
compute 1 upper msd/nongauss com yes :pre
[Description:]
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.
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.
:c,image(Eqs/compute_msd_nongauss.jpg)
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.
If the {com} option is set to {yes} 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.
See the "compute msd"_compute_msd.html doc page for further important
NOTEs, which also apply to this compute.
[Output info:]
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 "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The vector values are "intensive". The first vector value will be in
distance^2 "units"_units.html, the second is in distance^4 units, and
the 3rd is dimensionless.
[Restrictions:]
This compute is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"compute msd"_compute_msd.html
[Default:]
The option default is com = no.
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