SCINE Puffin

Philosophy of SCINE Puffin

SCINE Puffin is a calculation handler for SCINE Chemoton. Thus, it bridges the gap between high level exploration jobs for reaction networks and basic quantum chemical calculations. It provides the means to define and execute jobs that generate new data for reaction networks. SCINE Puffin is designed as an instanced runner that, once bootstrapped, continuously processes requested jobs. It is built to work in containerized environments (Docker, Singularity).

Technical Details

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

• SCINE Database, which is a wrapper for a MongoDB,
• SCINE Molassembler, which is a library to handle molecular structures as graphs,
• SCINE ReaDuct, which is used to carry out "high-level" calculations such as transition state searches,
• SCINE Sparrow, which provides "basic" properties such as electronic energies and nuclear gradients (to be used by ReaDuct) for a range of semiempirical methods, 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 bootstrapping Puffin. Besides Sparrow, other quantum-chemical backend programs are supported:

• Gaussian,
• ORCA,
• Turbomole,
• Serenity (best used via the SCINE Serenity wrapper), and
• xtb (best used via the SCINE xtb wrapper)

Current Features

• Runs as a daemon (with possible graceful timeout/shutdown after a user-defined time, automatic cleaning of failed jobs, and tolerance for database disconnects at the end of jobs)
• Provides a containerized version (usable with Docker, Podman, and Singularity)
• Initial jobs:
• Conformer generation
• Artificial force induced reactions (AFIR) optimization
• Bond order generation
• Geometry optimization
• Hessian generation including thermo chemistry
• IRC scan
• Reactive complex reaction probing (using AFIR, NT1, NT2)
• Single point calculations
• Transition state optimization

Download

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

Future Releases

• Add support for other quantum chemistry backend programs
• Add a gear to generate conformers by molecular dynamics

Documentation

Documentation is provided in the source code; you can also access it here.

Support

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

References

• Primary reference for Puffin 1.3.0:
  M. Bensberg, C. Brunken, K.-S. Csizi, S. A. Grimmel, S. Gugler, J.-G. Sobez, M. Steiner, P. L. Türtscher, J. P. Unsleber, T. Weymuth, M. Reiher, "qcscine/puffin: Release 1.3.0 (Version 1.3.0)", Zenodo, 2023. DOI