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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
parent b8541b66ba
commit f28b0794ce
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56
doc/Section_howto.txt
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@ -2159,7 +2159,7 @@ Here, each of the 3 kinds of chunk-related commands is briefly
overviewed. Then some examples are given of how to compute different
properties with chunk commands.
"Compute chunk/atom"_compute_chunk_atom.html command :h5
"Compute chunk/atom"_compute_chunk_atom.html command: :h5
This compute can assign atoms to chunks of various styles. Only atoms
in the specified group and optional specified region are assigned to a
@ -2198,7 +2198,7 @@ do this. You can also define a "per-atom variable"_variable.html in
the input script that uses a formula to generate a chunk ID for each
atom.
"Fix ave/chunk"_fix_ave_chunk_atom.html command :h5
"Fix ave/chunk"_fix_ave_chunk_atom.html command: :h5
This fix takes the ID of a "compute
chunk/atom"_compute_chunk_atom.html command as input. For each chunk,
@ -2215,7 +2215,7 @@ 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.
Compute */chunk commands :h5
Compute */chunk commands: :h5
Currently the following computes operate on chunks of atoms to produce
per-chunk values.
@ -2264,41 +2264,39 @@ Example calculations with chunks :h5
Here are eaxmples using chunk commands to calculate various
properties:
(1) Mimic the deprecated fix ave/spatial command, to average atom
velocity in each spatial bin:
(1) Average velocity in each of 1000 2d spatial bins:
Old command:
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
fix ave/spatial
(2) Temperature in each spatial bin, after subtracting a flow
velocity:
New commands:
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
compute chunk/atom
fix ave/chunk
(3) Center of mass of each molecule:
(2) Mimincing the deprecated compute msd/molecule command
to compute the mean-squared displacement of each molecule:
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
Old commands:
(4) Total force on each molecule and ave/max across all molecules:
compute molecule/msd
fix ave/time file msd.molecule
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[2])
variable xmax equal max(f_1[2])
thermo 1000
thermo_style custom step temp v_xave v_xmax :pre
New commands:
(5) Histogram of cluster sizes:
compute chunk/atom style
compute molecule/chunk
fix ave/time file msd.molecule
(3) print or time ave total force per molecule
average across molecules (variable special functions)
(4) histogram of cluster sizes (use fix ave/histo)
(5) count of # of atoms with each coord #
don't need chunking, just fix ave/histo on coord/atom
(6) ave temperature per bin
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
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