pyeqeq 0.0.9

Charge equilibration method for crystal structures

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.