QOSF-FeMoco2020

What is this?

This is the project that Minsik Cho and I worked on during a mentorship program hosted by the Quantum Open Software Foundation (https://qosf.org), over the winter of the year 2020. Our project attempts to apply the Variational Quantum Eigensolver -- an algorithm to estimate energy levels of molecules -- to the FeMo¹ cofactor of nitrogenase. This cluster is responsible for nitrogenase's remarkable ability to break the triple bond of the N_2 molecule at atmospheric temperatures and pressures, and the ability to calculate energies for chemical intermediates of the cluster is critical to understanding the viable reaction pathways.

This is ongoing work, and may be in various states of disarray... be warned.

Visit our Project Webpage for more details.

File Structure

• examples/: Example scripts
• src/: Larger proof-of-concept scripts (less stable)
• lib/: Modified qiskit code
• tests/: Unit tests. Run with pytest tests/
• hdf5_files/: SCF results. Load with QMolecule.load()
• molecules/: Molecular geometries (pulled from the Protein Data Bank)

Setup and Usage Instructions

1. Install conda.
2. Clone this repository and cd to it.
3. Create the environment using:

   conda env create -f environment.yml
   

4. Activate the conda environment:

   conda activate qosf
   

5. Run the test suite:

   pytest tests/
   

6. Run the scripts from the repository root (e.g.):

   python examples/gen_qubit_op_lih.py
   python src/gen_hamiltonian_qiskit.py
   

Special Thanks

Special thanks to Vesselin for providing guidance throughout this project, Michał Stęchły for organizing the mentorship program, and the rest of the folks at the Quantum Open Software Foundation for their work in enabling free and open-source research for quantum computing.

Contact Info

Questions? Reach us at:

• Roy Tu (kroytu [at] berkeley [dot] edu)
• Minsik Cho

Footnotes

1. https://en.wikipedia.org/wiki/FeMoco ↩