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couple more doc tweaks

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This commit is contained in:
Jacob Gissinger
2024-07-11 19:17:09 -04:00
parent 1a30fe5349
commit 06511a6e77
2 changed files with 9 additions and 9 deletions
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16
doc/src/Howto_chunk.rst
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@ -148,14 +148,14 @@ Example calculations with chunks
Here are examples using chunk commands to calculate various Here are examples using chunk commands to calculate various
properties: properties:
(1) Average velocity in each of 1000 2d spatial bins: 1. Average velocity in each of 1000 2d spatial bins:
.. code-block:: LAMMPS .. code-block:: LAMMPS
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced 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 fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
(2) Temperature in each spatial bin, after subtracting a flow 2. Temperature in each spatial bin, after subtracting a flow
velocity: velocity:
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -164,7 +164,7 @@ velocity:
compute vbias all temp/profile 1 0 0 y 10 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 fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
(3) Center of mass of each molecule: 3. Center of mass of each molecule:
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -172,7 +172,7 @@ velocity:
compute myChunk all com/chunk cc1 compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
(4) Total force on each molecule and ave/max across all molecules: 4. Total force on each molecule and ave/max across all molecules:
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -183,7 +183,7 @@ velocity:
thermo 1000 thermo 1000
thermo_style custom step temp v_xave v_xmax thermo_style custom step temp v_xave v_xmax
(5) Histogram of cluster sizes: 5. Histogram of cluster sizes:
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -192,16 +192,16 @@ velocity:
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 fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
(6) An example for 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 :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page. explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
(7) An example for 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 second set of micelle-scale chunks (clustered chunks, to create a second set of micelle-scale chunks (clustered
molecules, due to hydrophobicity), is explained on the molecules, due to hydrophobicity), is explained on the
:doc:`compute reduce/chunk <compute_reduce_chunk>` command doc page. :doc:`compute reduce/chunk <compute_reduce_chunk>` command doc page.
(8) An example for using one set of per-chunk values (dipole moment 8. An example for using one set of per-chunk values (dipole moment
vectors) for molecule chunks, spreading the values to each atom in vectors) for molecule chunks, spreading the values to each atom in
each chunk, then defining a second set of chunks as spatial bins, and each chunk, then defining a second set of chunks as spatial bins, and
using the :doc:`fix ave/chunk <fix_ave_chunk>` command to calculate an using the :doc:`fix ave/chunk <fix_ave_chunk>` command to calculate an

2
doc/src/read_data.rst
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@ -12,7 +12,7 @@ Syntax
* file = name of data file to read in * file = name of data file to read in
* zero or more keyword/arg pairs may be appended * zero or more keyword/arg pairs may be appended
* keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *group* or *nocoeff* or *fix* * keyword = *add* or *offset* or *shift* or *extra/atom/types* or *extra/bond/types* or *extra/angle/types* or *extra/dihedral/types* or *extra/improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom* or *group* or *nocoeff* or *fix*
.. parsed-literal:: .. parsed-literal::