Python Stack in Amsterdam Modeling Suite¶

General¶

The Amsterdam Modeling Suite includes a python stack based on the Enthought Python Distribution.

This python stack is completely separate from any other python installations on the system.

All programs within the Amsterdam Modeling Suite launch python via a special command, amspython.

Included modules¶

Some of the included modules are:

• numpy (1.21.2) and scipy (1.8.0): Big modules with a lot of functionality for math and science, more information on the SciPy website.

• IPython (7.22.0): An improved interactive python shell, more information can be found on the iPython website. Can be started with:

  $AMSBIN/amsipython
  

• ase (3.22.1): ASE (Atomic Simulation Environment) is a python module for atomistic simulations, more information in the ASE documentation.

• matplotlib (3.5.1): A library for plotting data in 2D, more information on the Matplotlib website. We do not ship an interactive backend for matplotlib, so make sure to set a non-interactive backend when using it. For example the Agg backend for PNGs:

  import matplotlib
  matplotlib.use('Agg')
  

• pip (21.3.1): The recommended tool for installing packages from the Python Package Index (PyPI). The pip documentation explains in detail how to use this tool, but for the Python stack shipped with the Amsterdam Modeling Suite all pip commands need to be prefixed with $AMSBIN/amspython -m:

  $AMSBIN/amspython -m pip list
  $AMSBIN/amspython -m pip show scipy
  $AMSBIN/amspython -m pip search rotate-backups
  $AMSBIN/amspython -m pip install rotate-backups
  

• flexmd: A module for running MD simulations with adaptive QM/MM regions. Details can be found in the FlexMD documentation.

• plams: PLAMS (Python Library for Automating Molecular Simulation) is a collection of tools that aim at providing powerful, flexible and easily extendable Python interface to molecular modeling programs. It takes care of input preparation, job execution, file management and output processing as well as helps with building more advanced data workflows. See the PLAMS tutorials and PLAMS documentation for more information.

• autografs: AuToGraFS stands for Automatic Topological Generator for Framework Structures. Information and examples can be found in the AuToGraFS documentation.

Using other modules with the AMS Python Stack¶

You can extend the the AMS Python Stack with other modules. You can use pip (see above) to install additional modules if they are available on the Python Package Index (PyPI). This is the recommended way of installing packages:

$AMSBIN/amspython -m pip install name_of_package

You can also do this for your own packages that you develop, for example:

$AMSBIN/amspython -m pip install -e .

Alternatively, you can add the location of the source to the SCM_PYTHONPATH variable to make the module available in the AMS Python Stack. To avoid collisions with other python installations on the system, we unload PYTHONPATH and PYTHONHOME from the environment when launching the ADF Python Stack and put the content of SCM_PYTHONPATH into PYTHONPATH.

Install and run Jupyter Lab (Jupyter Notebooks)¶

"$AMSBIN/amspython" -m jupyterlab

cat > template.tpl <<EOF
{%- block body %}
{{ nb | json_dumps }}
{% endblock body %}
EOF


"$AMSBIN/amspython" \
    -m nbconvert \
    --to custom \
    --template template.tpl \
    --RegexRemovePreprocessor.patterns='^!' \
    --execute \
    --output output.ipynb \
    notebook.ipynb

Python virtual environment¶

Useful commands¶

• Start a python shell:

  $AMSBIN/amspython
  

• Install new packages via pip:

  $AMSBIN/amspython -m pip install name_of_package
  

• Find out the location of an installed package (e.g. numpy):

  $AMSBIN/amspython -c 'import numpy; print(numpy.__file__)'
  

• Find out which python binary is launched by amspython:

  $AMSBIN/amspython -c 'import sys; print(sys.executable)'
  

• Disable the virtual environment (one-time):

  SCM_PYTHONDIR='' $AMSBIN/amspython