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Charge equilibration method for crystal structures. Available from here.
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.
Program expects two input files ionization.dat
and chargecenters.dat
. Please
look at source code to see what the other optional inputs are for (should be
mostly self-explanatory). Compile with something like:
g++ main.cpp -O3 -o eqeq
and run with
./eqeq my_file.cif
To facilitate automation and scaling, this version of EQeq can be operated via Python. To enable, you must build EQeq as a shared library:
g++ -c -fPIC main.cpp -O3 -o eqeq.o
g++ -shared -Wl,-soname,libeqeq.so -O3 -o libeqeq.so eqeq.o
sudo cp libeqeq.so /usr/lib
(for Macs, replace -soname
with -install_name
)
(if you don’t have sudo access, mkdir ~/lib; cp libeqeq.so ~/lib
, then change
the path at the top of eqeq.py
)
From the command line, you can run eqeq.py
:
python eqeq.py --help
python eqeq.py IRMOF-1.cif --output-type mol --method ewald
This includes extensive help documentation on running EQeq, and an easy interface to change individual parameters.
To use globally with Python scripts, you must put the EQeq
directory on your
PYTHONPATH:
export PYTHONPATH:/path/above/EQeq:$PYTHONPATH
Then, you can call EQeq from Python with
import EQeq
EQeq.run("IRMOF-1.cif")
The input takes both filenames and actual data, and outputs either files or strings. This change allows for streaming data, which enables EQeq to be used as part of a broader code pipeline.
import EQeq
# Load a file. In practice, this can come from any source, such as a database
with open("IRMOF-1.cif") as in_file:
data = in_file.read()
charges = EQeq.run(data, output_type="list", method="ewald")
EQeq: An Extended Charge Equilibration Method
EQeq+C: An Empirical Bond-Order-Corrected Extended Charge Equilibration Method