forked from lijiext/lammps
123 lines
4.6 KiB
HTML
123 lines
4.6 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 gyration/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 gyration/chunk chunkID keyword value ...
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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>gyration/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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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>tensor</I>
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<PRE> <I>tensor</I> value = none
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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 molecule gyration/chunk molchunk
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compute 2 molecule gyration/chunk molchunk tensor
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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 radius of gyration Rg for
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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>This compute calculates the radius of gyration Rg for each chunk,
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which includes all effects due to atoms passing thru periodic
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boundaries.
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</P>
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<P>Rg is a measure of the size of a chunk, and is computed by this
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formula
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</P>
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<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
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</CENTER>
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<P>where M is the total mass of the chunk, Rcm is the center-of-mass
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position of the chunk, and the sum is over all atoms in the
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chunk.
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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>If the <I>tensor</I> keyword is specified, then the scalar Rg value is not
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calculated, but an Rg tensor is instead calculated for each chunk.
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The formula for the components of the tensor is the same as the above
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formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy -
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Rcmy) for the xy component, etc. The 6 components of the tensor are
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ordered xx, yy, zz, xy, xz, yz.
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</P>
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<P>IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
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"unwrapped" form, by using the image flags associated with each atom.
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See the <A HREF = "dump.html">dump custom</A> command for a discussion of
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"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>The simplest way to output the results of the compute gyration/chunk
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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 gyration/chunk 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 vector if the <I>tensor</I> keyword is not
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specified and a global array if it is. The length of the vector or
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number of rows in the array = the number of chunks <I>Nchunk</I> as
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calculated by the specified <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> command. If the <I>tensor</I> keyword
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is specified, the global array has 6 columns. The vector or array can
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be accessed by any command that uses global values from a compute as
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input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
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of LAMMPS output options.
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</P>
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<P>All the vector or array values calculated by this compute are
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"intensive". The vector or array values will be in distance
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<A HREF = "units.html">units</A>, since they are the square root of values
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represented by the formula above.
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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> none
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</P>
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<P><A HREF = "compute_gyration.html">compute gyration</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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