SCINE - Swoose

.. image:: resources/swoose_landscape_low_res.png :alt: SCINE Swoose

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Introduction

This repository contains the Swoose module of the SCINE open-source quantum chemistry software. It provides functionalities for treating large molecular systems with self-parametrizing system-focused atomistic models. This includes the automated parametrization of such models and applying them in single point calculations as well as structure optimizations or molecular dynamics simulations. Furthermore, this module also provides QM/MM hybrid models.

License and Copyright Information

This code is licensed under the 3-clause BSD license. Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group. See LICENSE.txt for details.

Installation and Usage

For instructions on how to install and use Swoose as well as for a detailed documentation of the entire functionality of Swoose, please consult the user manual found in the manual directory in the repository. Alternatively the manual can also be found on the official GitHub website and on the SCINE website.

How to Cite

When publishing results obtained with Puffin, please cite the corresponding release as archived on Zenodo <https://doi.org/10.5281/zenodo.5782876>_ (please use the DOI of the respective release).

In addition, we kindly request you to cite the following articles when using the corresponding parts of Swoose:

C. Brunken, M. Reiher, "Self-Parametrizing System-Focused Atomistic Models", J. Chem. Theory Comput., 2020, 16, 1646-1665.

C. Brunken, M. Reiher, "Automated Construction of Quantum-Classical Hybrid Models", J. Chem. Theory Comput., 2021, 17, 3797-3813.

K.-S. Csizi, M. Reiher, "Automated preparation of nanoscopic structures: Graph-based sequence analysis, mismatch detection, and pH-consistent protonation with uncertainty estimates" J. Comput. Chem, 2024, 45, 761-776.

K.-S. Csizi, M. Steiner, M. Reiher, "Nanoscale chemical reaction exploration with a quantum magnifying glass", Nat. Commun., 2024, 15, 5320.

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 <https://doi.org/10.1063/5.0206974>_).

Support and Contact

In case you should encounter problems or bugs, please write a short message to scine@phys.chem.ethz.ch.

Third-Party Libraries Used

SCINE Swoose makes use of the following third-party libraries:

• Boost <https://www.boost.org/>_
• Cereal <https://uscilab.github.io/cereal/>_
• Eigen <http://eigen.tuxfamily.org>_
• Google Test <https://github.com/google/googletest>_
• MongoDB C++ Driver <http://mongocxx.org/>_
• pybind11 <https://github.com/pybind/pybind11>_
• yaml-cpp <https://github.com/jbeder/yaml-cpp>_