AndroMolecules

Package containing useful functions for molecular simulations, performing as fast as I could make them.

How to use

Example: compute Lennard-Jones potential of a system of particles in 1D.

import andromolecules as am
import numpy as np

# Create 10 particles randomly over a line 100 armstrongs long
particle_positions = np.random.random(10) * 100

# Define the parameters of the Lennard-Jones potential
epsilon = 1
sigma = 1

# Compute the Lennard-Jones potential of the system
potential_energy = am.lennard_jones_potential(particle_positions, epsilon, sigma)

Contributing

Editing code in developer mode

Use (may require sudo in macOS):

python3 -m pip install -e .

You can also build it with:

python3 setup.py build_ext --inplace

Adding new C extension files

Edit setup.py to add a new Extension under ext_modules:

Extension('andromolecules.submodule.file', ['andromolecules/submodule/file.c'])

And then create the referred C files and headers in the specified location.

Create new source code and wheel

Run:

python3 setup.py sdist bdist_wheel

Upload new build to PyPi

Run:

twine upload dist/*

Style guide

For Python style guides, refer to PEP8, with one exception:

Don't use spaces around the = sign when used to indicate a keyword argument, or when used to indicate a default value for an unannotated function parameter.

Using spaces aroung the = sign in function arguments actually improves readability IMHO.

Useful resources online

NumPy C Code explanations

C Extensions for NumPy Arrays (SciPy cookbook)

NumPy Array API

Python C extension example