forked from lijiext/lammps
126 lines
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126 lines
5.4 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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<HR>
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<H3>compute msd/chunk 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/chunk chunkID
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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/chunk = style name of this compute command
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<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
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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/chunk molchunk
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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) for multiple chunks of atoms.
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</P>
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<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
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as chunkID. For example, a single chunk could be the atoms in a
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molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
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23</A> for details of how chunks can be
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defined and examples of how they can be used to measure properties of
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a system.
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</P>
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<P>Four quantites are calculated by this compute for each chunk. The
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first 3 quantities are the squared dx,dy,dz displacements of the
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center-of-mass. The 4th component is the total squared displacement,
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i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These
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calculations include all effects due to atoms passing thru periodic
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boundaries.
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</P>
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<P>Note that only atoms in the specified group contribute to the
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calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
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defines its own group; atoms will have a chunk ID = 0 if they are not
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in that group, signifying they are not assigned to a chunk, and will
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thus also not contribute to this calculation. You can specify the
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"all" group for this command if you simply want to include atoms with
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non-zero chunk IDs.
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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 chunks.
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</P>
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<P>The displacement of the center-of-mass of the chunk is from its
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original center-of-mass position, calculated on the timestep this
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compute command was first invoked.
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</P>
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<P>IMPORTANT NOTE: The number of chunks <I>Nchunk</I> calculated by the
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<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command must remain
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constant each time this compute is invoked, so that the displacement
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for each chunk from its original position can be computed
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consistently. If <I>Nchunk</I> does not remain constant, an error will be
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generated. If needed, you can enforce a constant <I>Nchunk</I> by using
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the <I>nchunk once</I> or <I>ids once</I> options when specifying the <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> command.
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</P>
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<P>IMPORTANT NOTE: This compute stores the original position (of the
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center-of-mass) of each chunk. When a displacement is calculated on a
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later timestep, it is assumed that the same atoms are assigned to the
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same chunk ID. However LAMMPS has no simple way to insure this is the
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case, though you can use the <I>ids once</I> option when specifying the
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<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command. Note that if
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this is not the case, the MSD calculation does not have a sensible
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meaning.
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</P>
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<P>IMPORTANT NOTE: The initial coordinates of the atoms in each chunk are
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stored in "unwrapped" form, by using the image flags associated with
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each atom. See the <A HREF = "dump.html">dump custom</A> command for a discussion
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of "unwrapped" coordinates. See the Atoms section of the
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<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and
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how they are set for each atom. You can reset the image flags
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(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
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image</A> command.
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</P>
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<P>IMPORTANT NOTE: Unlike the <A HREF = "compute_msd.html">compute msd</A> command,
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this compute does not store the initial center-of-mass coorindates of
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its molecules in a restart file. Thus you cannot continue the MSD per
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chunk calculation of this compute when running from a <A HREF = "read_restart.html">restart
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file</A>.
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</P>
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<P>The simplest way to output the results of the compute com/msd
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calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
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command, for example:
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</P>
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<PRE>compute cc1 all chunk/atom molecule
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compute myChunk all com/msd cc1
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fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
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</PRE>
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<P><B>Output info:</B>
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</P>
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<P>This compute calculates a global array where the number of rows = the
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number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> command. The number of columns =
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4 for dx,dy,dz and the total displacement. These values can be
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accessed by any command that uses global array values from a compute
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as input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an
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overview of LAMMPS output options.
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</P>
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<P>The array values are "intensive". The array 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.html">compute msd</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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