forked from lijiext/lammps
91 lines
2.9 KiB
HTML
91 lines
2.9 KiB
HTML
<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>compute msd/nongauss command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID msd/nongauss keyword values ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>msd/nongauss = style name of this compute command
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>com</I>
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<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute 1 all msd/nongauss
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compute 1 upper msd/nongauss com yes
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>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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</P>
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<P>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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</P>
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<CENTER><IMG SRC = "Eqs/compute_msd_nongauss.jpg">
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</CENTER>
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<P>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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</P>
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<P>If the <I>com</I> option is set to <I>yes</I> 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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</P>
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<P>See the <A HREF = "compute_msd.html">compute msd</A> doc page for further IMPORTANT
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NOTES, which also apply to this compute.
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</P>
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<P><B>Output info:</B>
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</P>
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<P>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 <A HREF = "Section_howto.html#howto_15">this
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section</A> for an overview of LAMMPS output
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options.
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</P>
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<P>The vector values are "intensive". The first vector value will be in
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distance^2 <A HREF = "units.html">units</A>, the second is in distance^4 units, and
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the 3rd is dimensionless.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>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 <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute_msd.html">compute msd</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option default is com = no.
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</P>
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</HTML>
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