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add another example to Howto chunk doc page

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Steve Plimpton 2019-08-22 11:37:21 -06:00
parent 82b3fad152
commit c74f5ae416
2 changed files with 47 additions and 8 deletions
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16
doc/src/Howto_chunk.txt
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@ -136,7 +136,9 @@ The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command
spreads per-chunk values to each atom in the chunk, producing per-atom spreads per-chunk values to each atom in the chunk, producing per-atom
values as its output. This can be useful for outputting per-chunk values as its output. This can be useful for outputting per-chunk
values to a per-atom "dump file"_dump.html. Or for using an atom's values to a per-atom "dump file"_dump.html. Or for using an atom's
associated chunk value in an "atom-style variable"_variable.html. associated chunk value in an "atom-style variable"_variable.html. Or
as input to the "fix ave/chunk"_fix_ave_chunk.html command to
spatially average per-chunk values calculated by a per-chunk compute.
The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a
peratom value across the atoms in each chunk to produce a value per peratom value across the atoms in each chunk to produce a value per
@ -184,12 +186,20 @@ compute cc1 all chunk/atom c_cluster compress yes
compute size all property/chunk cc1 count 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 fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
(6) An example of using a per-chunk value to apply per-atom forces to (6) An example for using a per-chunk value to apply per-atom forces to
compress individual polymer chains (molecules) in a mixture, is compress individual polymer chains (molecules) in a mixture, is
explained on the "compute explained on the "compute
chunk/spread/atom"_compute_chunk_spread_atom.html command doc page. chunk/spread/atom"_compute_chunk_spread_atom.html command doc page.
(7) An example of using one set of per-chunk values for molecule (7) An example for using one set of per-chunk values for molecule
chunks, to create a 2nd set of micelle-scale chunks (clustered chunks, to create a 2nd set of micelle-scale chunks (clustered
molecules, due to hydrophobicity), is explained on the "compute molecules, due to hydrophobicity), is explained on the "compute
chunk/reduce"_compute_reduce_chunk.html command doc page. chunk/reduce"_compute_reduce_chunk.html command doc page.
(8) An example for using one set of per-chunk values (dipole moment
vectors) for molecule chunks, spreading the values to each atom in
each chunk, then defining a second set of chunks as spatial bins, and
using the "fix ave/chunk"_fix_ave_chunk.html command to calulate an
average dipole moment vector for each bin. This example is explained
on the "compute chunk/spread/atom"_compute_chunk_spread_atom.html
command doc page.

39
doc/src/compute_chunk_spread_atom.txt
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@ -30,11 +30,18 @@ compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration :pre
[Description:] [Description:]
Define a calculation that "spreads" one or more per-chunk values to Define a calculation that "spreads" one or more per-chunk values to
each atom in the chunk. This can be useful for creating a "dump each atom in the chunk. This can be useful in several scenarios:
file"_dump.html where each atom lists info about the chunk it is in,
e.g. for post-processing purposes. It can also be used in "atom-style For creating a "dump file"_dump.html where each atom lists info about
variables"_variable.html that need info about the chunk each atom is the chunk it is in, e.g. for post-processing purposes. :ulb,l
in. Examples are given below.
To access chunk value in "atom-style variables"_variable.html that
need info about the chunk each atom is in. :l
To use the "fix ave/chunk"_fix_ave_chunk.html command to spatially
average per-chunk values calculated by a per-chunk compute. :l,ule
Examples are given below.
In LAMMPS, chunks are collections of atoms defined by a "compute In LAMMPS, chunks are collections of atoms defined by a "compute
chunk/atom"_compute_chunk_atom.html command, which assigns each atom chunk/atom"_compute_chunk_atom.html command, which assigns each atom
@ -148,6 +155,28 @@ thermo_style custom step etotal press v_ave :pre
:line :line
Here is an example for using one set of chunks, defined for molecules,
to compute the dipole moment vector for each chunk. E.g. for water
molecules. Then spreading those values to each atom in each chunk.
Then defining a second set of chunks based on spatial bins. And
finally, using the "fix ave/chunk"_fix_ave_chunk.html command to
calculate an average dipole moment vector per spatial bin.
compute cmol all chunk/atom molecule
compute dipole all dipole/chunk cmol
compute spread all chunk/spread/atom cmol c_dipole\[1\] c_dipole\[2\] c_dipole\[3\]
compute cspatial all chunk/atom bin/1d z lower 0.1 units reduced
fix ave all ave/chunk 100 10 1000 cspatial c_spread\[*\] :pre
Note that the "fix ave/chunk"_fix_ave_chunk.html command requires
per-atom values as input. That is why the compute chunk/spread/atom
command is used to assign per-chunk values to each atom in the chunk.
If a molecule straddles bin boundaries, each of its atoms contributes
in a weighted manner to the average dipole moment of the spatial bin
it is in.
:line
[Output info:] [Output info:]
This compute calculates a per-atom vector or array, which can be This compute calculates a per-atom vector or array, which can be