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This commit is contained in:
Axel Kohlmeyer
2020-03-10 15:56:11 -04:00
parent e643e88913
commit ae9255e057
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17
doc/src/compute_chunk_spread_atom.rst
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@ -6,7 +6,6 @@ compute chunk/spread/atom command
Syntax
""""""
.. parsed-literal::
compute ID group-ID chunk/spread/atom chunkID input1 input2 ...
@ -24,12 +23,9 @@ Syntax
f_ID = global vector calculated by a fix with ID
f_ID[I] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
Examples
""""""""
.. parsed-literal::
compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration
@ -85,10 +81,8 @@ or fix.
does not check that it is per-chunk data. It only checks that the fix
produces a global vector or array.
----------
Each listed input is operated on independently.
If a bracketed index I is used, it can be specified using a wildcard
@ -105,22 +99,18 @@ had been listed one by one. E.g. these 2 compute chunk/spread/atom
commands are equivalent, since the :doc:`compute com/chunk <compute_com_chunk>` command creates a per-atom array
with 3 columns:
.. parsed-literal::
compute com all com/chunk mychunk
compute 10 all chunk/spread/atom mychunk c_com[*]
compute 10 all chunk/spread/atom mychunk c_com[1] c_com[2] c_com[3]
----------
Here is an example of writing a dump file the with the center-of-mass
(COM) for the chunk each atom is in. The commands below can be added
to the bench/in.chain script.
.. parsed-literal::
compute cmol all chunk/atom molecule
@ -134,7 +124,6 @@ forces for the :doc:`fix addforce <fix_addforce>` command. In this
example the forces act to pull atoms of an extended polymer chain
towards its COM in an attractive manner.
.. parsed-literal::
compute prop all property/atom xu yu zu
@ -155,7 +144,6 @@ bench/in.chain script. Thermo output is shown for 1000 steps, where
the last column is the average radius of gyration over all 320 chains
in the 32000 atom system:
.. parsed-literal::
compute gyr all gyration/chunk cmol
@ -174,10 +162,8 @@ in the 32000 atom system:
900 22.59128 5.0247538 4.5611513
1000 22.586832 4.94697 4.5238362
----------
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.
@ -185,7 +171,6 @@ Then defining a second set of chunks based on spatial bins. And
finally, using the :doc:`fix ave/chunk <fix_ave_chunk>` command to
calculate an average dipole moment vector per spatial bin.
.. parsed-literal::
compute cmol all chunk/atom molecule
@ -201,10 +186,8 @@ 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.
----------
**Output info:**
This compute calculates a per-atom vector or array, which can be