pyeqeq 0.0.10

Description:

pyeqeq 0.0.10

EQeq
Charge equilibration method for crystal structures.
Modified version, which allows specifying additional parameters:

lambda (default: 1.2) The dielectric screening parameter. Corresponds to eps_eff = 1.67
hI0 (default: -2.0) The electron affinity of hydrogen
chargePrecision (default: 3) Number of digits to use for point charges
method (default: "ewald", alternative: "nonperiodic") Method to compute the Coulombic interaction
mR (default: 2) Number of "expansion" unit cells to consider in periodic calculation ("real space"). 2 => 5x5x5
mK (default: 2) Number of "expansion" unit cells to consider in periodic calculation ("frequency space"). 2 => 5x5x5
eta (default: 50) Ewald splitting parameter
ionizationdata (default: ionizationdata.dat) File with ionization potentials and electron affinities. Default data are
EA: experimental, T.Andersen et al., 1999
IP: experimental, C.E.Moore, 1970
chargecenters (default: chargecenters.dat) File with common oxidation states (lowered, if missing ionizationdata)

Installation
pip install pyeqeq

Usage
Command line interface
To run the HKUST-1 example:
eqeq examples/HKUST1/HKUST1.cif -o examples/HKUST1/HKUST1_w_charge.cif

Python interface
from pyeqeq import run_on_cif
run_on_cif("examples/HKUST1/HKUST1.cif")

Summary
The source code in this program demonstrates the charge equilibration method described
in the accompanying paper. The purpose of the source code provided is to be
minimalistic and do "just the job" described. In practice, you may wish to add various
features to the source code to fit the particular needs of your project.
Major highlights of program:

Obtains charges for atoms in periodic systems without iteration
Can use non-neutral charge centers for more accurate point charges
Designed for speed (but without significant code optimizations)

Features not implemented but that you may want to consider adding:

Spherical cut-offs (for both real-space and reciprocal-space sums)
An iterative loop that guesses the appropriate charge center (so the user does not have to guess)
Ewald parameter auto-optimization
Various code optimizations

Authors
Original implementation by Christopher E. Wilmer, Randall Q. Snurr (advisor), Hansung Kim (car output), Patrick Fuller (streaming functionality), Louis Knapp (json output). Updated by Daniele Ongari.