6 Materialchemie
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Automation simplifies the use of computational materials science software and makes it accessible to a wide range of users. This enables high-throughput calcula-tionsand makesiteasier for non-specialists to enter computational materials science. However, in-creasing automation also poses threats that should be considered while interacting with automated procedures.
Automated bonding analysis software has been developed based on Crystal Orbital Hamilton Populations to facilitate high-throughput bonding analysis and machine-learning of bonding features. This work presents the software and discusses its applications to simple and complex materials such as GaN, NaCl, the oxynitrides XTaO2N (X=Ca, Ba, Sr) and Yb14Mn1Sb11.
Invited for this month’s cover are researchers from Bundesanstalt für Materialforschung und -prüfung (Federal Institute for Materials Research and Testing) in Germany, Friedrich Schiller University Jena, Université catholique de Louvain, University of Oregon, Science & Technology Facilities Council, RWTH Aachen University, Hoffmann Institute of Advanced Materials, and Dartmouth College. The cover picture shows a workflow for automatic bonding analysis with Python tools (green python). The bonding analysis itself is performed with the program LOBSTER (red lobster). The starting point is a crystal structure, and the results are automatic assessments of the bonding situation based on Crystal Orbital Hamilton Populations (COHP), including automatic plots and text outputs. Coordination environments and charges are also assessed. More information can be found in the Research Article by J. George, G. Hautier, and co-workers.
The LOBSTER (Deringer et al., 2011;Maintz et al., 2013 ,2016 ;Nelson et al., 2020 ) software aids in extracting quantum-chemical bonding information from materials by projecting the plane-wave based wave functions from density functional theory (DFT) onto an atomic orbital basis. LobsterEnv, a module implemented in pymatgen (Ong et al., 2013) by some of the authors of this package, facilitates the use of quantum-chemical bonding information obtained from LOBSTER calculations to identify neighbors and coordination environments. LobsterPy is a Python package that offers a set of convenient tools to further analyze and summarize the LobsterEnv outputs in the form of JSONs that are easy to interpret and process. These tools enable the estimation of (anti) bonding contributions, generation of textual descriptions, and visualization of LOBSTER computation results. Since its first release, both LobsterPy and LobsterEnv capabilities have been extended significantly. Unlike earlier versions, which could only automatically analyze Crystal Orbital Hamilton Populations (COHPs) (Dronskowski & Blöchl, 1993), both can now also analyze Crystal Orbital Overlap Populations (COOP) (Hughbanks & Hoffmann, 1983) and Crystal Orbital Bond Index (COBI) (Müller et al., 2021). Extracting the information about the most important orbitals contributing to the bonds is optional, and users can enable it as needed. Additionally, bonding-based features for machinelearning (ML) studies can be engineered via the sub-packages “featurize” and “structuregraphs”. Alongside its Python interface, it also provides an easy-to-use command line interface (CLI) that runs automatic analysis of the computations and generates a summary of results and publication-ready figures. LobsterPy has been used to produce the results in Ngo et al. (2023), Chen et al. (2024), Naik et al. (2023), and it is also part of Atomate2 (2023) bonding analysis workflow for generating bonding analysis data in a format compatible with the Materials Project (Jain et al., 2013) API.
We present Jobflow, a domain-agnostic Python package for writing computational workflows tailored for high-throughput computing applications. With its simple decorator-based approach, functions and class methods can be transformed into compute jobs that can be stitched together into complex workflows. Jobflow fully supports dynamic workflows where the full acyclic graph of compute jobs is not known until runtime, such as compute jobs that launch
other jobs based on the results of previous steps in the workflow. The results of all Jobflow compute jobs can be easily stored in a variety of filesystem- and cloud-based databases without the data storage process being part of the underlying workflow logic itself. Jobflow has been intentionally designed to be fully independent of the choice of workflow manager used to dispatch the calculations on remote computing resources. At the time of writing, Jobflow
workflows can be executed either locally or across distributed compute environments via an adapter to the FireWorks package, and Jobflow fully supports the integration of additional workflow execution adapters in the future.