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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13104 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-02-13 20:28:48 +00:00
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doc/Section_howto.html
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@ -2172,7 +2172,7 @@ commands, to calculate various properties of a system:
overviewed. Then some examples are given of how to compute different
properties with chunk commands.
</P>
<H5><A HREF = "compute_chunk_atom.html">Compute chunk/atom</A> command
<H5><A HREF = "compute_chunk_atom.html">Compute chunk/atom</A> command:
</H5>
<P>This compute can assign atoms to chunks of various styles. Only atoms
in the specified group and optional specified region are assigned to a
@ -2213,7 +2213,7 @@ do this. You can also define a <A HREF = "variable.html">per-atom variable</A>
the input script that uses a formula to generate a chunk ID for each
atom.
</P>
<H5><A HREF = "fix_ave_chunk_atom.html">Fix ave/chunk</A> command
<H5><A HREF = "fix_ave_chunk_atom.html">Fix ave/chunk</A> command:
</H5>
<P>This fix takes the ID of a <A HREF = "compute_chunk_atom.html">compute
chunk/atom</A> command as input. For each chunk,
@ -2230,7 +2230,7 @@ values to be time-averaged in various ways, and output to a file. The
fix produces a global array as output with one row of values per
chunk.
</P>
<H5>Compute */chunk commands
<H5>Compute */chunk commands:
</H5>
<P>Currently the following computes operate on chunks of atoms to produce
per-chunk values.
@ -2279,42 +2279,40 @@ largest cluster or fastest diffusing molecule.
<P>Here are eaxmples using chunk commands to calculate various
properties:
</P>
<P>(1) Mimic the deprecated fix ave/spatial command, to average atom
velocity in each spatial bin:
<P>(1) Average velocity in each of 1000 2d spatial bins:
</P>
<P>Old command:
<PRE>compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
</PRE>
<P>(2) Temperature in each spatial bin, after subtracting a flow
velocity:
</P>
<P>fix ave/spatial
<PRE>compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
compute vbias all temp/profile 1 0 0 y 10
fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
</PRE>
<P>(3) Center of mass of each molecule:
</P>
<P>New commands:
<PRE>compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</PRE>
<P>(4) Total force on each molecule and ave/max across all molecules:
</P>
<P>compute chunk/atom
fix ave/chunk
</P>
<P>(2) Mimincing the deprecated compute msd/molecule command
to compute the mean-squared displacement of each molecule:
</P>
<P>Old commands:
</P>
<P>compute molecule/msd
fix ave/time file msd.molecule
</P>
<P>New commands:
</P>
<P>compute chunk/atom style
compute molecule/chunk
fix ave/time file msd.molecule
</P>
<P>(3) print or time ave total force per molecule
average across molecules (variable special functions)
</P>
<P>(4) histogram of cluster sizes (use fix ave/histo)
</P>
<P>(5) count of # of atoms with each coord #
don't need chunking, just fix ave/histo on coord/atom
</P>
<P>(6) ave temperature per bin
<PRE>compute cc1 all chunk/atom molecule
fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
variable xave equal ave(f_1<B>2</B>)
variable xmax equal max(f_1<B>2</B>)
thermo 1000
thermo_style custom step temp v_xave v_xmax
</PRE>
<P>(5) Histogram of cluster sizes:
</P>
<PRE>compute cluster all cluster/atom 1.0
compute cc1 all chunk/atom c_cluster compress yes
compute size all property/chunk cc1 count
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
</PRE>
<HR>
<HR>