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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14292 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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5.1 KiB
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128 lines
5.1 KiB
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<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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<HR>
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<H3>compute msd 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 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 = 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> or <I>average</I>
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<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
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<I>average</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
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compute 1 upper msd com yes average 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) of the group of atoms, including all effects due to atoms
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passing thru periodic boundaries. For computation of the non-Gaussian
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parameter of mean-squared displacement, see the <A HREF = "compute_msd_nongauss.html">compute
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msd/nongauss</A> command.
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</P>
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<P>A vector of four quantites is calculated by this compute. The first 3
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elements of the vector are the squared dx,dy,dz displacements, summed
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and averaged over atoms in the group. The 4th element is the total
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squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
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averaged over atoms in the group.
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</P>
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<P>The slope of the mean-squared displacement (MSD) versus time is
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proportional to the diffusion coefficient of the diffusing atoms.
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</P>
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<P>The displacement of an atom is from its reference position. This is
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normally the original position at the time
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the compute command was issued, unless the <I>average</I> keyword is set to <I>yes</I>.
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The value of the displacement will be
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0.0 for atoms not in the specified compute group.
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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 calculated.
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</P>
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<P>If the <I>average</I> option is set to <I>yes</I> then the reference position of
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an atom is based on the average position of that atom,
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corrected for center-of-mass motion if requested.
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The average position
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is a running average over all previous calls to the compute, including the
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current call. So on the first call
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it is current position, on the second call it is the arithmetic average of the
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current position and the position on the first call, and so on.
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Note that when using this option, the precise value of the mean square
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displacement will depend on the number of times the compute is
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called. So, for example, changing the frequency of thermo output may
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change the computed displacement. Also, the precise values will be
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changed if a single simulation is broken up into two parts, using
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either multiple run commands or a restart file. It only makes
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sense to use this option if the atoms are not diffusing, so that
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their average positions relative to the center of mass of the system
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are stationary. The most common case is crystalline solids undergoing
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thermal motion.
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</P>
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<P>IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
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using the image flags associated with each atom. See the <A HREF = "dump.html">dump
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custom</A> command for a discussion of "unwrapped" coordinates.
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See the Atoms section of the <A HREF = "read_data.html">read_data</A> command for a
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discussion of image flags and how they are set for each atom. You can
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reset the image flags (e.g. to 0) before invoking this compute by
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using the <A HREF = "set.html">set image</A> command.
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</P>
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<P>IMPORTANT NOTE: If you want the quantities calculated by this compute
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to be continuous when running from a <A HREF = "read_restart.html">restart file</A>,
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then you should use the same ID for this compute, as in the original
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run. This is so that the fix this compute creates to store per-atom
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quantities will also have the same ID, and thus be initialized
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correctly with atom reference positions from the restart file.
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When <I>average</I> is set to yes, then the atom reference positions
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are restored correctly, but not the number of samples used
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obtain them. As a result, the reference positions from the restart
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file are combined with subsequent positions as if they were from a
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single sample, instead of many, which will change the values of msd
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somewhat.
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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 4, which can be
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accessed by indices 1-4 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 vector values will be in
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distance^2 <A HREF = "units.html">units</A>.
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</P>
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<P><B>Restrictions:</B> none
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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_nongauss.html">compute msd/nongauss</A>, <A HREF = "compute_displace_atom.html">compute
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displace_atom</A>, <A HREF = "fix_store_state.html">fix
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store/state</A>, <A HREF = "compute_msd_chunk.html">compute
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msd/chunk</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 are com = no, average = no.
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</P>
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</HTML>
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