Polarizable Embedding Python Tools (pepytools)

The polarizable embedding python tools (pepytools) is a set of executables and a Python API designed to manipulate polarizable embedding (PE) potentials for use in embedded QM/MM calculations in the DALTON quantum chemistry code.

The potentials are typically made from a static charge distribution described by charges, dipoles and quadrupoles placed on atomic sites - for example the atoms of a water molecule - and by a classical, dynamic charge distribution described by (an)isotropic electric dipole-dipole polarizabilities - also placed on atomic sites.

Installing pepytools

pepytools is a python library and installation is quite straight forward

python setup.py install

to install it in the default locations. To install it in a custom location, you can run the following

python setup.py install --prefix=/path/to/custom/installation

Remember to add the installation paths to your environment variables:

export PATH=/path/to/custom/installation/bin:$PATH
export PYTHONPATH=/path/to/custom/installation/lib/python3.7/site-packages:$PYTHONPATH

shown here for a python 3.7 installation example.

Example

The most typical action to use pepytools is to add individual potentials. This is done either through the program supplied with pepytools called pepy_add

shell

pepy_add p1.pot p2.pot > p_new.pot

API

There is of course also access to the API should you choose to make a program that uses potential files in some form. The equivalent of the above example would be something like:

from pepytools import Potential

pot1 = Potential.from_file("p1.pot")
pot2 = Potential.from_file("p2.pot")

pot3 = pot1 + pot2

print(pot3)

The main class of the library, the Potential class, allows you to open potentials from files, add multiple potentials as shown above or even construct potentials from multipole moments, polarizabilities and coordinates and write those potentials back to to a file for later use in your QM/MM calculations.

The polarizable embedding potentials also carry anisotropic polarizabilities at the expansion points and this library also comes with solvers for induced moments.