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compute_msd_nongauss.txt
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.. index:: compute msd/nongauss
compute msd/nongauss command
============================
Syntax
""""""
.. parsed-literal::
compute ID group-ID msd/nongauss keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* msd/nongauss = style name of this compute command
* zero or more keyword/value pairs may be appended
* keyword = *com*
.. parsed-literal::
*com* value = *yes* or *no*
Examples
""""""""
.. parsed-literal::
compute 1 all msd/nongauss
compute 1 upper msd/nongauss com yes
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.
.. image:: Eqs/compute_msd_nongauss.jpg
:align: center
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 :doc:`compute msd <compute_msd>` 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 :ref:`this section <howto_15>` for an overview of LAMMPS output
options.
The vector values are "intensive". The first vector value will be in
distance^2 :doc:`units <units>`, 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 :ref:`Making LAMMPS <start_3>` section for more info.
Related commands
""""""""""""""""
:doc:`compute msd <compute_msd>`
Default
"""""""
The option default is com = no.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
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