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convert more LAMMPS script examples to use code-block instead of parsed-literal

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This commit is contained in:
Axel Kohlmeyer
2020-03-12 01:11:38 -04:00
parent 2775ebeb9d
commit 7e656b6cea
33 changed files with 89 additions and 89 deletions
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18
doc/src/compute_chunk_spread_atom.rst
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@ -26,7 +26,7 @@ Syntax
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration
@ -99,7 +99,7 @@ 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::
.. code-block:: LAMMPS
compute com all com/chunk mychunk
compute 10 all chunk/spread/atom mychunk c_com[*]
@ -111,7 +111,7 @@ 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::
.. code-block:: LAMMPS
compute cmol all chunk/atom molecule
compute com all com/chunk cmol
@ -124,13 +124,13 @@ 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::
.. code-block:: LAMMPS
compute prop all property/atom xu yu zu
variable k equal 0.1
variable fx atom v_k\*(c_comchunk[1]-c_prop[1])
variable fy atom v_k\*(c_comchunk[2]-c_prop[2])
variable fz atom v_k\*(c_comchunk[3]-c_prop[3])
variable fx atom v_k*(c_comchunk[1]-c_prop[1])
variable fy atom v_k*(c_comchunk[2]-c_prop[2])
variable fz atom v_k*(c_comchunk[3]-c_prop[3])
fix 3 all addforce v_fx v_fy v_fz
Note that :doc:`compute property/atom <compute_property_atom>` is used
@ -171,13 +171,13 @@ 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::
.. code-block:: LAMMPS
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[\*]
fix ave all ave/chunk 100 10 1000 cspatial c_spread[*]
Note that the :doc:`fix ave/chunk <fix_ave_chunk>` command requires
per-atom values as input. That is why the compute chunk/spread/atom