Jellyfish is a new program for performing and analyzing electron dynamics calculations. Currently, the focus is on the time-dependent configuration interaction method, however, other methods will be implemented in the future. Jellyfish is developed user-friendly by employing a graphical user interface based on a NodeEditor. It also is developer-friendly as modules can be added without the need to edit the Jellyfish core.
JellyfishGUI is the main program in the Program suit. With the help of the user interface, new calculations can be set up, edited, evaluated and executed. Alternatively, all calculations can be performed via a console through JellyfishCMD, for the usage in a HPC environments without graphical output.
JellyfishGUI and JellyfishCMD only provide the user interface, like the file format etc., but not the actual methods/nodes. These are bundled in the form of plugins, compiled externally and then loaded into Jellyfish. Currently, 4 plugins are available, with their code located in the "Plugins" folder.
| Plugin | Description |
|---|---|
| Basics | Contains routines to perform and evaluate time-independent and time-dependent configuration interaction calculations. |
| Visualization | Allows visualization of orbitals, electron densities, and more from stationary and time-dependent calculations. |
| OrcaInterface | Allows to import CIS and LR-TDDFT outputs from the ORCA program. An ORCA input to generate a compatible output is given in the Examples folder for a TDDFT calculation. |
| QuantumCompute | Provides transformation, algorithms and quantum computer simulator to perform electrondynamics calculations with quantum computer simulators. |
More details about the methods implemented so far, the structure of Jellyfish as well as the usage can be found in the publications listed below.
Currently, the easiest way to compile Jellyfish is to use a devcontainer. To do this, Docker and VSCode with the corresponding extension must first be installed. Then the cloned git repository can be opened in a devcontainer, which creates a proper container and compiles and installs all necessary libraries from source. Once the container has been successfully built, Jellyfish can be compiled in VSCode manually or with the
mkdir build && \
cd build && \
cmake .. && \
cmake --build . -j4 && \
mkdir JellyfishGUI/Plugins && \
mkdir JellyfishGUI/basissets && \
cp Plugins/Basics/libBasics.so JellyfishGUI/Plugins && \
cp Plugins/OrcaInterface/libOrcaInterface.so JellyfishGUI/Plugins && \
cp Plugins/Visualization/libVisualization.so JellyfishGUI/Plugins && \
cp Plugins/QuantumComputing/libQuantumComputing.so JellyfishGUI/Plugins && \
mkdir JellyfishCMD/Plugins && \
mkdir JellyfishCMD/basissets && \
cp Plugins/Basics/libBasics.so JellyfishCMD/Plugins && \
cp Plugins/OrcaInterface/libOrcaInterface.so JellyfishCMD/Plugins && \
cp Plugins/Visualization/libVisualization.so JellyfishCMD/Plugins && \
cp Plugins/QuantumComputing/libQuantumComputing.so JellyfishCMD/Plugins
command and then finally executed. The Dockerfile of the devcontainer also serves as a template for a “normal” Docker Jellyfish container.
C++20 compiler
Cmake
Qt (Version 6)
zlib
libzip
eigen (Library for linear algebra; required for all existing plugins)
libcint (Library for calculating GTO integrals; required by Basic, Visualization and QuantumComputing plugin)
muparser (Library for parsing mathematical equations; required for Basic Plugin)
QuEST (Library for simulating quantum computers; required for the QuantumComputing plugin)
VTK (library for visualization; required by VisualizationPlugin)
Libraries for plugins only need to be installed if the corresponding plugins are to be compiled or executed.
In addition, the following modified libraries are directly included in the code: JSON for Modern C++, stduuid, Qt Node Editor, C++ Plugin framework
The "Examples" folder contains the following examples of different types of calculations. The use of the program is quite self-explanatory. Otherwise, more information can be found in the publications and more tutorials will follow.
| Example | Description |
|---|---|
| Guanine excitation | Shows the Orca input of a TDDFT calculation on the example of Guanine, how the output is imported into Jellyfish and a subsequent dynamics calculation and analysis. |
| Quantum dot ionization | Demonstrates the use of even-tempered basis sets and complex absorption potentials to simulate laser ionization in model potentials. |
| H2 HHG | Example of the calculation of high harmonic generation spectra of H2 using complex absorption potentials. |
Issues and pull requests can be submitted via Github. If you develop new plugins we can link them here. For further questions you can write a mail to: [email protected] or [email protected]
If you use Jellyfish please cite the following paper:
Langkabel F, Krause P, Bande A. Jellyfish: A modular code for wave function-based electron dynamics simulations and visualizations on traditional and quantum compute architectures. WIREs Comput Mol Sci. 2024; 14(1):e1696. https://doi.org/10.1002/wcms.1696
This paper also describes the structure and functionality of Jellyfish and introduces the existing plugins.
In addition, Jellyfish was used in the following papers:
Making optical excitations visible – An exciton wavefunction extension to the time-dependent configuration interaction method
Quantum-Compute Algorithm for Exact Laser-Driven Electron Dynamics in Molecules