SCINE Heron

Philosophy of SCINE Heron

SCINE Heron is the graphical user interface for all other SCINE modules. It has two main ways of operation. First, one can explore chemical reactivity immersively and interactively based on first principles. SCINE Heron includes the original implementation of real-time quantum chemistry, which was invented in our group. This concept relies on a real-time exploration of the potential energy surface, which is made possible by ultra-fast electronic structure calculations that deliver quantum chemical results instantaneously. 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.

Second, 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. Any compound discovered by Chemoton can be transferred to the interactive part of the GUI, allowing it to be further studied.

Technical Details

Heron is implemented in Python. It can be installed either from source or via PyPI. To work properly, Heron needs a few other SCINE modules:

  • SCINE Database, which is necessary to access a database containing an exploration done with Chemoton,
  • SCINE Sparrow, which allows to do semiempirial calculations, in an interactive fashion, and
  • SCINE Utilities, which is a library of common functionality used across all SCINE modules.
These components do not need to be installed mannually; rather, they are automatically installed when setting up Heron.

Current Features

  • Main Molecular Viewer
    • Real-time calculations of energies and forces (using SCINE Sparrow)
    • Haptic device support
    • Real-time energy plot
    • Basic molecular building/editing
    • Isosurface plots of orbitals and densities
  • Reaction Network Viewer
    • Excerpt view of compounds and reactions
    • Basic filtering options based on reaction energies
    • Navigation around a single centered Compound
    • (Shortest) path searches based on Compound IDs
    • Expansion tab for Compounds (showing contained Structures)
    • Expansion tab for Reactions (showing contained Elementary Steps)
    • SVG export of all graph views
  • SCINE Database Statistics
    • Database content statistics
    • Calculation status statistics
    • Runtime histogram
  • SCINE Database Browser
    • Listing, searching and displaying of individual database entries
    • Reaction and Elementary Steps
    • Compounds and single-molecule Structures
    • Flasks and multi-molecule complexes (also Structures)

Download

SCINE Heron is distributed as an open source code. Visit our GitHub page to download it.

Future Releases

  • Allow setup and steering of explorations with Chemoton

Support

Despite intense testing of the program, questions may arise with respect to the usage of SCINE Heron. Do not hesitate to contact the developers via scine@phys.chem.ethz.ch in case of any questions and suggestions.

References

  • Primary reference for Heron 1.0.0:
    M. Bensberg, Y. Can, M. Del, S. A. Grimmel, M. Mesiti, C. H. Müller, M. Steiner, P. L. Türtscher, J. P. Unsleber, M. Weberndorfer, T. Weymuth, M. Reiher, "qcscine/heron: Release 1.0.0 (Version 1.0.0)", Zenodo, 2022. DOI
  • K. H. Marti, M. Reiher, "Haptic quantum chemistry", J. Comput. Chem., 2009, 30, 2010. DOI
  • M. P. Haag, M. Reiher, "Real‐time quantum chemistry", Int. J. Quantum Chem., 2013, 113, 8. DOI
  • M. P. Haag, M. Reiher, "Studying chemical reactivity in a virtual environment", Faraday Discuss., 2014, 169, 89. DOI
  • M. P. Haag, A. C. Vaucher, M. Bosson, S. Redon, M. Reiher, "Interactive Chemical Reactivity Exploration", ChemPhysChem, 2014, 15, 3301. DOI
  • A. H. Mühlbach, A. C. Vaucher, M. Reiher, "Accelerating Wave Function Convergence in Interactive Quantum Chemical Reactivity Studies", J. Chem. Theory Comput., 2016, 12, 1228. DOI
  • A. C. Vaucher, M. P. Haag, M. Reiher, "Real‐time feedback from iterative electronic structure calculations", J. Comput. Chem., 2016, 37, 805. DOI
  • A. C. Vaucher, M. Reiher, "Molecular Propensity as a Driver for Explorative Reactivity Studies", J. Chem. Inf. Model., 2016, 56, 1470. DOI
  • A. C. Vaucher, M. Reiher, "Steering Orbital Optimization out of Local Minima and Saddle Points Toward Lower Energy", J. Chem. Theory Comput., 2017, 13, 1219. DOI
  • M. A. Heuer, A. C. Vaucher, M. P. Haag, M. Reiher, "Integrated Reaction Path Processing from Sampled Structure Sequences", J. Chem. Theory Comput., 2018, 14, 2052. DOI