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add harmonic/cut to python example folder. small tweaks to docs and examples

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Axel Kohlmeyer
2022-03-18 17:58:30 -04:00
parent 6c6a6b7c64
commit a7fce6dc39
18 changed files with 1354 additions and 213 deletions
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doc/src/pair_python.rst
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@ -223,19 +223,21 @@ be explicitly provided. The corresponding python code is:
.. admonition:: Performance Impact
:class: note
The evaluation of scripted python code will slow down the
computation pairwise interactions quite significantly. However, this
can be largely worked around through using the python pair style not
for the actual simulation, but to generate tabulated potentials on the
fly using the :doc:`pair_write <pair_write>` command. Please see below
for an example LAMMPS input of how to build a table file:
The evaluation of scripted python code will slow down the computation
of pairwise interactions quite significantly. However, this performance
penalty can be worked around through using the python pair style not
for the actual simulation, but to generate tabulated potentials using
the :doc:`pair_write <pair_write>` command. This will also enable
GPU or multi-thread acceleration through the GPU, KOKKOS, or OPENMP
package versions of the *table* pair style. Please see below for a
LAMMPS input example demonstrating how to build a table file:
.. code-block:: LAMMPS
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
shell rm -f melt.table
pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj
shell rm -f lj.table
pair_write 1 1 2000 rsq 0.01 2.5 lj.table lj
Note that it is strongly recommended to try to **delete** the potential
table file before generating it. Since the *pair_write* command will
@ -250,7 +252,7 @@ to be assigned to the LAMMPS atom types like this:
.. code-block:: LAMMPS
pair_style table linear 2000
pair_coeff 1 1 melt.table lj
pair_coeff 1 1 lj.table lj
This can also be done for more complex systems. Please see the
*examples/python* folders for a few more examples.