forked from lijiext/lammps
94 lines
2.6 KiB
Plaintext
94 lines
2.6 KiB
Plaintext
.. 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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.. parsed-literal::
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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 thru periodic boundaries.
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A vector of three quantites 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 3rd component is the nonGaussian diffusion paramter NGP =
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3*drfourth/(5*drsquared*drsquared), i.e.
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.. image:: Eqs/compute_msd_nongauss.jpg
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:align: center
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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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displacment of each atom is calcluated.
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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 :ref:`this section <howto_15>` for an overview of LAMMPS output
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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 3rd 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 LAMMPS
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was built with that package. See the :ref:`Making LAMMPS <start_3>` section 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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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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