OpenQuantumSystems.jl

OpenQuantumSystems.jl is a numerical framework written in Julia that makes it easy to simulate various kinds of open quantum systems with main focus on quantum biology in finite basis. It is inspired by the quantarhei and QuantumOptics.jl.

Installation

You can obtain OpenQuantumSystems using Julia's Pkg REPL-mode (hitting ] as the first character of the command prompt):

(v1.6) pkg> add OpenQuantumSystems

or with using Pkg; Pkg.add("OpenQuantumSystems").

Questions & Contributions

The package is still under development. If you have any questions or need help, see gitter channel and ask away. Also, contributions of any kind are always welcome! If you have any ideas for bug fixes, new features, optimisation or unit tests suggest it straight away or create a pull request.

Motivation

This package is a backbone for calculations for my master thesis supervised by doc. Tomáš Mančal.

Roadmap

What is OpenQuantumSystems.jl capable of right now (v0.5.0)?

• Supports systems with a finite basis.
• Construct Hamiltonians for aggregates of molecules. Bath degrees of freedom are modelled as LHOs with shifted potentials for excited local electronic states.
• Trace over bath degrees of freedom using Franck-Condon factors and reduced density matrix.
• Dynamics solvers:
  • Exact dynamics (U(t) operator)
  • Schrödinger equation
  • Liouville-von Neumann equation
  • Quantum Master Equation — ansatz, iterative, and Redfield variants
• Unified solve() entry point with SimulationResult return type.
• Prepare initial density matrix from a laser-excited pulse.
• Evaluate the bath part of the density matrix using various ansatzes (closed-form QME with RDM).
• Iterative correction of the bath part of the reduced density matrix.
• Memory kernel as superoperator.
• Rate constants from dynamics and memory kernel.
• Physical validation of simulation results (trace, positivity).
• Scoring and comparison of reduced density matrices over time.
• Convenience constructors for common systems (dimer, trimer, linear chain).
• Solver selection guide and API glossary in documentation.

What would be nice to have?

• Loading Hamiltonian and data storage for aggregate.
• Anharmonic oscillators.
• Double excited states.
• Interface with quantarhei, or creating an interface in quantarhei package.

Branches status

Master

Develop

Testing

You can use make.bat or make file for testing, but it will install all the dependencies before executing tests. I advise using jupyter notebook src/local_test.ipynb with julia kernel for tests. Package Revise.jl will load all the functions and by using include("src/test_file.jl") you can quickly debug and add new tests.

Developing

Please use formatting in make.bat or make file. I suggest using Revise.jl with jupyter notebook in src/local.ipynb for adding new features. It will spare you of the painful precompilation time.

Credit

quantarhei - Concepts of aggregate construction, Hamiltonian of aggregate construction and trace over bath degrees of freedom were implemented in quantarhei in python.

QuantumOpticsBase.jl - Provides building elements for this package, such as the implementation of operators and superoperators (and many more).