scine-serenity-wrapper 3.1.0

A wrapper for Serenity

Introduction

SCINE: Serenity Wrapper is a wrapper around Serenity; it exports the following methods:

• Density Functional Theory (DFT)

• Hartree-Fock (HF)

• (Local) Coupled Cluster (CC, DLPNO-CC)

into the SCINE tool chain. Each method is represented by its own Calculator and the entire wrapper constitutes a SCINE module that can be loaded dynamically at runtime. For more information on these concepts see the Scine::Core repository.

License and Copyright Information

The SCINE Serenity wrapper is distributed under the BSD 3-clause “New” or “Revised” License. For more license and copyright information, see the file LICENSE.txt in the repository.

Note: This license does not cover the original Serenity source code. For the copyright information of the Serenity code please follow the linked git submodule to the developers repository.

Installation and Usage

The wrapper can be built and installed using the following commands:

git submodule update --init
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DSCINE_BUILD_PYTHON_BINDINGS=ON -DCMAKE_INSTALL_PREFIX=<desired path> ..
make -j<number of cores to use>
make install

This will generate and install both the main Serenity code and the wrapper in the form of the file serenity.module.so that can be used in SCINE.

In order to make Serenity available to SCINE the following two environment variables need to be set:

export SERENITY_RESOURCES=<desired path>/share/serenity/data/
export SCINE_MODULE_PATH=$SCINE_MODULE_PATH:<desired path>/lib

Afterwards, SCINE programs such as ReaDuct will pick up Serenity’s existence and it will be possible to request the implemented methods.

The SCINE Serenity wrapper is also available via Python. The underlying SCINE module can be loaded and its implemented calculators accessed using the standard scine_utilities Python bindings. A minimal workflow could look like this:

import scine_utilities as su
import scine_serenity_wrapper

# Generate structure
structure = su.AtomCollection()
structure.elements = [su.ElementType.H, su.ElementType.H]
structure.positions = [[-0.7, 0, 0], [0.7, 0, 0]]

# Get calculator
manager = su.core.ModuleManager.get_instance()
calculator = manager.get('calculator', 'DFT')

# Configure calculator
calculator.structure = structure
calculator.set_required_properties([su.Property.Energy, su.Property.Gradients])

# Calculate
results = calculator.calculate()
print(results.energy)
print(results.gradients)

How to Cite

When publishing results obtained with the SCINE Serenity wrapper, please cite the corresponding release as archived on Zenodo (DOI 10.5281/zenodo.6695038; please use the DOI of the respective release).

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).

This wrapper should also not be mistaken for the actual Serenity code it wraps. For the latter code and its citations, we refer you to the original Serenity repository. There you will find the references of the actual methods used. They are listed in the README.md.

Support and Contact

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