pyEF

A Python package for calculating electric fields, electrostatic potentials (ESP), and electrostatic interactions from quantum mechanical calculations.

Note: This package is under active development as of 2026, if you encounter any issues during use or have any features you would like to see incorporated, please do not hesitate to raise an issue or reach out to the developers at manets12@mit.edu.

Table of Contents

1. Installation
2. Basic Usage

1. Installation

git clone git@github.com:hjkgrp/pyEF.git
cd pyEF
conda env create -f environment.yml
conda activate pyef
pip install -e .

Installing Multiwfn

PyEF requires Multiwfn for charge partitioning and wavefunction analysis.

NOTE: currently Multiwfn is NOT supported on MACOSX, so we recommend using a linux or windows system.

Download and compile:

# Download from http://sobereva.com/multiwfn/
wget http://sobereva.com/multiwfn/misc/Multiwfn_3.8_bin_Linux_noGUI.zip
unzip Multiwfn_3.8_bin_Linux_noGUI.zip 
cd Multiwfn_3.8_bin_Linux_noGUI

#give executable permission to the Multiwfn executable file
chmod +x Multiwfn_noGUI

Add to your PATH (add to ~/.bashrc):

export PATH=/path/to/Multiwfn_3.8_bin_Linux_noGUI/Multiwfn_noGUI:$PATH

Or use the full path when running PyEF (e.g., multiwfn_path: /path/to/Multiwfn_3.8_bin_Linux_noGUI/Multiwfn_noGUI).

2. Basic Usage

Electric Field Calculation

CLI:

# Create jobs.csv
echo "ef, /path/to/structure.molden, /path/to/structure.xyz, (25, 26)" > jobs.csv

# Create config.yaml
cat > config.yaml << EOF
input: jobs.csv
dielectric: 1
multiwfn_path: /path/to/multiwfn
charge_types:
  - Hirshfeld_I
EOF

# Run
pyef -c config.yaml

Python API:

from pyef.analysis import Electrostatics

molden_paths = ['/path/to/structure.molden']
xyz_paths = ['/path/to/structure.xyz']

es = Electrostatics(molden_paths, xyz_paths, dielectric=1.0)
df = es.getEfield('Hirshfeld_I', 'output', '/path/to/multiwfn',
                  input_bond_indices=[(25, 26)])

Electrostatic Potential (ESP) Calculation

CLI:

# Create jobs.csv with metal atom index
echo "esp, /path/to/structure.molden, /path/to/structure.xyz, 30" > jobs.csv

# Run with same config.yaml
pyef -c config.yaml

Python API:

from pyef.analysis import Electrostatics

molden_paths = ['/path/to/structure.molden']
xyz_paths = ['/path/to/structure.xyz']
metal_indices = [30]  # 0-indexed

es = Electrostatics(molden_paths, xyz_paths, lst_of_tmcm_idx=metal_indices, dielectric=1.0)
df = es.getESP(['Hirshfeld_I'], 'output', 'multiwfn', '/path/to/multiwfn')

Electrostatic Stabilization Calculation

CLI:

# Create jobs.csv
echo "estab, /path/to/structure.molden, /path/to/structure.xyz" > jobs.csv

# Create config.yaml with substrate indices
cat > config.yaml << EOF
input: jobs.csv
dielectric: 1
multiwfn_path: /path/to/multiwfn
charge_types:
  - Hirshfeld_I
multipole_order: 2
substrate_idxs: [1, 2, 3, 4, 5]
EOF

# Run
pyef -c config.yaml

Python API:

from pyef.analysis import Electrostatics

molden_paths = ['/path/to/structure.molden']
xyz_paths = ['/path/to/structure.xyz']

es = Electrostatics(molden_paths, xyz_paths, dielectric=1.0)
df = es.getElectrostatic_stabilization('/path/to/multiwfn',
                                        substrate_idxs=[1, 2, 3, 4, 5],
                                        multipole_order=2)

---

Authors: Melissa Manetsch and David W. Kastner