88 lines
2.6 KiB
ReStructuredText
88 lines
2.6 KiB
ReStructuredText
.. index:: compute msd/nongauss
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compute msd/nongauss command
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============================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID msd/nongauss keyword values ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* msd/nongauss = style name of this compute command
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* zero or more keyword/value pairs may be appended
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* keyword = *com*
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.. parsed-literal::
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*com* value = *yes* or *no*
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute 1 all msd/nongauss
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compute 1 upper msd/nongauss com yes
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Description
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"""""""""""
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Define a computation that calculates the mean-squared displacement
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(MSD) and non-Gaussian parameter (NGP) of the group of atoms,
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including all effects due to atoms passing through periodic boundaries.
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A vector of three quantities is calculated by this compute. The first
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element of the vector is the total squared dx,dy,dz displacements
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drsquared = (dx\*dx + dy\*dy + dz\*dz) of atoms, and the second is the
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fourth power of these displacements drfourth = (dx\*dx + dy\*dy +
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dz\*dz)\*(dx\*dx + dy\*dy + dz\*dz), summed and averaged over atoms in the
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group. The third component is the nonGaussian diffusion parameter NGP =
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3\*drfourth/(5\*drsquared\*drsquared), i.e.
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.. math::
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NGP(t) = 3<(r(t)-r(0))^4>/(5<(r(t)-r(0))^2>^2) - 1
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The NGP is a commonly used quantity in studies of dynamical
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heterogeneity. Its minimum theoretical value (-0.4) occurs when all
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atoms have the same displacement magnitude. NGP=0 for Brownian
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diffusion, while NGP > 0 when some mobile atoms move faster than
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others.
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If the *com* option is set to *yes* then the effect of any drift in
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the center-of-mass of the group of atoms is subtracted out before the
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displacement of each atom is calculated.
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See the :doc:`compute msd <compute_msd>` doc page for further important
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NOTEs, which also apply to this compute.
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**Output info:**
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This compute calculates a global vector of length 3, which can be
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accessed by indices 1-3 by any command that uses global vector values
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from a compute as input. See the :doc:`Howto output <Howto_output>` doc
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page for an overview of LAMMPS output options.
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The vector values are "intensive". The first vector value will be in
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distance\^2 :doc:`units <units>`, the second is in distance\^4 units, and
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the third is dimensionless.
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Restrictions
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""""""""""""
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This compute is part of the MISC package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
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Related commands
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""""""""""""""""
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:doc:`compute msd <compute_msd>`
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Default
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"""""""
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The option default is com = no.
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