scine-heron 2.0.0

Graphical user interface for SCINE

Introduction

SCINE Heron is the graphical user interface for all other SCINE modules. It has six main ways of operation:

1) One can explore chemical reactivity immersively and interactively based on first principles in real-time. The graphical user interface of SCINE Heron displays a three-dimensional molecular structure and allows users to interact with it. They can induce structural changes with a computer mouse or a haptic device and perceive the effect of their manipulations immediately through visual and/or haptic feedback. For fast electronic structure calculations, we employ currently different semi-empirical methods, which can deliver properties in the millisecond timescale, while providing a qualitatively correct description of the potential energy surface.

2) One can construct a system-focused atomistic model (SFAM), i.e., a force field parametrized on Hessian calculations on the specific system. SFAM force fields can be employed in the interactive setting either as a stand-alone or in a hybrid QM/MM model. The hybrid model can also be constructed within the graphical user interface either by our automated QM region selection algorithm or by manual selection of the QM region by clicking on the QM atoms.

3) One can launch individual energy calculations and optimization routines, such as transition state searches, with any backend program supported in SCINE, in the ReaDuct tab. The input structures can be read-in from file or stem directly from Interactive or an explored reaction network.

4) One can automaticaly determine the active space for multi-configurational calculations with autoCAS. Based on orbital entanglement measures derived from an approximate DMRG wave function, autoCAS identifies all strongly correlated orbitals to be included in the active space of a final, converged calculation.

5) One can interact with explorations done by SCINE Chemoton. One can visualize the chemical reaction network without drowning in too much information. For example, one can selectively display reactions with a barrier lower than a certain, user-specified threshold. Furthermore, one can analyze all compounds and reactions discovered, e.g., for reactions, one can visualize the trajectory and study the energy along it. It is also possible to search and visualize all pathways between two given compounds. Any compound discovered by Chemoton can be transferred to the interactive part of the GUI, allowing it to be further studied.

6) One can carry out reaction explorations directly in the graphical user interface by either constructing individual Chemoton engines, or by relying on the Steering Wheel mechanism that lets one guide the automated exploration more closely. The exploration can be constrained by additional aggregate and reactive site filters that can also be constructed in the graphical user interface. Almost all of the exploration guidances in Heron support I/O operations which allow to save and reuse individual parts for other explorations or restarts.

License and Copyright Information

For license and copyright information, see the file LICENSE.txt in the source directory.

Further Documentation

For further documentation (e.g., on installation and usage), see https://scine.ethz.ch.

How to Cite

When publishing results obtained with Heron, please cite the corresponding release as archived on Zenodo (please use the DOI of the respective release) and the following paper:

C. H. Müller, M. Steiner, J. P. Unsleber, T. Weymuth, M. Bensberg, K.-S. Csizi, M. Mörchen, P. L. Türtscher, M. Reiher, “Heron: Visualizing and Controlling Chemical Reaction Explorations and Networks”, 2024, arXiv:2406.09541 [physics.chem-ph] (DOI: 10.48550/arXiv.2406.09541).

Additionally, we kindly request you to cite the corresponding software releases of the underlying SCINE modules as archived on Zenodo.

Furthermore, when publishing results obtained with any SCINE module, please cite the following paper:

T. Weymuth, J. P. Unsleber, P. L. Türtscher, M. Steiner, J.-G. Sobez, C. H. Müller, M. Mörchen, V. Klasovita, S. A. Grimmel, M. Eckhoff, K.-S. Csizi, F. Bosia, M. Bensberg, M. Reiher, “SCINE—Software for chemical interaction networks”, J. Chem. Phys., 2024, 160, 222501 (DOI 10.1063/5.0206974).

Known Issues

• The selection of nuclei is broken for vtk>=9.1, we therefore encourage to stay with version 9.0. This version is not available for python>=3.9 on PyPI and requires a manual install.

• Old versions of qt-material may cause overlapping text boxes for newer operating systems such as Ubuntu 22.04.

• An install of PySide2 via PyPI may not be sufficient to have a working Qt installation depending on your system. In this case, it is recommend to first install PySide2 with a package manager (such as apt) before installing it with pip.

• Some PySide2 packages might require additional installs related to pulseaudio such as libpulse-mainloop-glib0

• The start of a steered exploration can become quite slow (~10 seconds) once the protocol gets large (> 20 steps) and issues can occur if you add a new step and immediately start the exploration or start the exploration and immediately click other buttons. Please do not click anything shortly after progressing the protocol. We hope to resolve this by the next release.

Support and Contact

In case you should encounter problems or bugs, please write a short message to [e-mail].