aevmod 1.1.0

Compute atomic environment vector (AEV) and its derivatives

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 \(y_i=f_i(x)\), where x is a vector of Cartesian coordinates of all atoms in the set. The Jacobian and Hessian are with respect to the \(x\) coordinates. Ther package uses pybind11 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. You can use

# 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 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

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:

# 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:

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:

python ./examples/taev.py

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

pip install --upgrade .