aevmod

aevmod package

This package provides functionality for computing an atomic environment vector (AEV), as well as its Jacobian and Hessian. The AEV is a feature vector that is useful for representing the geometry of a molecule, or simply a set of atoms, in a manner that satisfies rotational and translational invariances. For the i-th atom in the system, its AEV is :math:y_i=f_i(x), where x is a vector of Cartesian coordinates of all atoms in the set. The Jacobian and Hessian are with respect to the :math:x coordinates. Ther package uses pybind11 <http://pybind11.readthedocs.io/en/stable/>_ to expose our C++ AEV library to Python, as a python package aevmod. The package folder includes:

• this README file, which can be viewed in a web browser using restview <https://pypi.python.org/pypi/restview>_. You can use

.. code-block:: shell

# simple invocation in present terminal
restview README.rst &

# or, invocation in a separate xterm terminal
xterm -geometry 100x10-0-0 -e restview README.rst &

• a doc folder containing pdf documentation
• an examples folder containing an example application taev.py
• an include folder containing requisite sacado <https://trilinos.github.io/sacado.html>_ include files for the C++ library
• a pyproject.toml file containing build-system dependencies and other configuration info
• a setup.py file for building and installing the package
• an src folder containing the C++ source code
• a tests folder containing code and data for running tests with pytest <https://docs.pytest.org>_

The aevmod package is compatible with Python 3, and the pybind11 usage requires a C++ compiler that has at least C++11 functionality.

To try out aevmod, under the package folder, do:

.. code-block:: shell

Build and install the package

pip install .

Install pytest so we can run the tests

pip install pytest

You can now run the tests to confirm everything works:

.. code-block:: shell

pytest
====================================== test session starts =======================================
platform darwin -- Python 3.8.10, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
rootdir: /Users/hnnajm/mls/pkg/aev, configfile: setup.cfg, testpaths: tests
plugins: anyio-2.2.0
collected 6 items

tests/test_aev.py .                                                                        [ 16%]
tests/test_ang_indsets.py .                                                                [ 33%]
tests/test_hes.py .                                                                        [ 50%]
tests/test_jac.py .                                                                        [ 66%]
tests/test_rad_indsets.py .                                                                [ 83%]
tests/test_structures.py .                                                                 [100%]

======================================= 6 passed in 0.75s ========================================

You can also run the example code:

.. code-block:: shell

python ./examples/taev.py

If you make a code change you will need to re-build and install. You can do this using pip:

.. code-block:: shell

pip install --upgrade .