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High-throughput computations are nowadays an established way to suggest new candidate materials for applications to experimentalists. Due to new packages for automation and access to databases of computed materials properties, these studies became more and more complex over the last years. Besides suggesting new candidate materials for applications, they also offer a way to understanding the materials properties based on chemical bonds. For example, we have recently used orbital-based bonding analysis to understand the results of high-throughput studies for spintronic materials, ferroelectric materials and photovoltaic materials in detail. To do so, we have developed Python tools for high-throughput bonding analysis with the programs VASP and Lobster (see www.cohp.de). They are based on the Python packages pymatgen, atomate, and custodian. This implementation will be discussed within the talk. We also expect that these tools offer possibilities to arrive at new descriptors based on chemical bonds for materials properties.
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.
The talk „Automation in computational materials science“ deals with the current state of automation in the field of computational materials science. It illustrates how automation can, for example, be used to speed up the search for new ferroelectric materials and spintronic materials. Furthermore, it lists current tools for automation and challenges in the field.
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.
Chemical bonding and coordination environments are crucial descriptors of material properties. They have previously been applied to creating chemical design guidelines and chemical heuristics. They are currently being used as features in machine learning more and more frequently. I will discuss implementations and algorithms (ChemEnv and LobsterEnv) for identifying these coordination environments based on geometrical characteristics and chemical bond quantum chemical analysis. I'll demonstrate how these techniques helped in testing chemical heuristics like the Pauling rule and thereby improved our understanding of chemistry. I'll also show how these tools can be used to create new design guidelines and a new understanding of chemistry. To use quantum-chemical bonding analysis on a large-scale and for machine-learning approaches, fully automatic workflows and analysis tools have been developed. After presenting the capabilities of these tools, I will also point out how these developments relate to the general trend towards automation in the field of density functional based materials science.
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.
We created a workflow that fully automates bonding analysis using Crystal Orbital Hamilton Populations, which are bond-weighted densities of states. This enables understanding of crystalline material properties based on chemical bonding information. To facilitate data analysis and machine-learning research, our tools include automatic plots, automated text output, and output in machine-readable format.
Understanding and Machine Learning of Materials Properties with Quantum-Chemical Bonding Analysis
(2023)
Bonds and local atomic environments are crucial descriptors for material properties. They have been used to create design rules for materials and are used as features in machine learning of material properties. This talk will show how our recently developed tools, that automatically perform quantum chemical bond analysis and enable the study of chemical bonds and local atomic environments, accelerate and improve the development of such heuristics and machine-learned models for materials properties.
Chemical bonding and coordination environments are crucial descriptors of material properties. They have previously been applied to creating chemical design guidelines and chemical heuristics. They are currently being used as features in machine learning more and more frequently. I will discuss implementations and algorithms (ChemEnv and LobsterEnv) for identifying these coordination environments based on geometrical characteristics and chemical bond quantum chemical analysis. I will demonstrate how these techniques helped in testing chemical heuristics like the Pauling rule and thereby improved our understanding of chemistry. I will also show how these tools can be used to create new design guidelines and a new understanding of chemistry. To use quantum-chemical bonding analysis on a large-scale and for machine-learning approaches, fully automatic workflows and analysis tools have been developed. After presenting the capabilities of these tools, I will also point out how these developments relate to the general trend towards automation in the field of density functional based materials science.
Bonds and local atomic environments are crucial descriptors of material properties. They have been used to create design rules and heuristics and as features in machine learning of materials properties. Implementations and algorithms (e.g., ChemEnv and LobsterEnv) for identifying local atomic environments based on geometrical characteristics and quantum-chemical bonding analysis are nowadays available. Fully automatic workflows and analysis tools have been developed to use quantum-chemical bonding analysis on a large scale. The lecture will demonstrate how our tools, that assess local atomic environments and perform automatic bonding analysis, help to develop new machine learning models and a new intuitive understanding of materials. Furthermore, other recent workflow contributions to the Materials Project software infrastructure (pymatgen, atomate2) related to phonons and machine-learning potentials will be discussed.
Bonds and local atomic environments are crucial descriptors of material properties. They have been used to create design rules and heuristics for materials. More and more frequently, they are used as features in machine learning. Implementations and algorithms (e.g., ChemEnv and LobsterEnv) for identifying these local atomic environments based on geometrical characteristics and quantum-chemical bonding analysis are nowadays available. Fully automatic workflows and analysis tools have been developed to use quantum-chemical bonding analysis on a large scale and for machine-learning approaches. The latter relates to a general trend toward automation in density functional-based materials science. The lecture will demonstrate how our tools, that assess local atomic environments, helped to test and develop heuristics and design rules and an intuitive understanding of materials.
Understanding the chemistry and nature of individual chemical bonds is essential for materials design. Bonding analysis via the LOBSTER software package has provided valuable insights into the properties of materials for thermoelectric and catalysis applications. Thus, the data generated from
bonding analysis becomes an invaluable asset that could be utilized as features in large-scale data analysis and machine learning of material properties. However, no systematic studies exist that conducted high-throughput materials simulations to curate and validate bonding data obtained from LOBSTER. Here we present an approach to constructing such a large database consisting of quantum-chemical bonding information.
Bonds and local atomic environments are crucial descriptors of material properties. They have been used to create design rules and heuristics for materials. More and more frequently, they are used as features in machine learning. Implementations and algorithms (e.g., ChemEnv and LobsterEnv) for identifying these local atomic environments based on geometrical characteristics and quantum-chemical bonding analysis are nowadays available. Fully automatic workflows and analysis tools have been developed to use quantum-chemical bonding analysis on a large scale and for machine-learning approaches. The latter relates to a general trend toward automation in density functional-based materials science. The lecture will demonstrate how our tools, that assess local atomic environments, helped to test and develop heuristics and design rules and an intuitive understanding of materials.
A deep insight into the chemistry and nature of individual chemical bonds is essential for understanding materials. Bonding analysis is expected to provide important features for large-scale data analysis and machine learning of material properties. Such information on chemical bonds can be calculated using the LOBSTER (www.cohp.de) software package, which post-processes data from modern density functional theory computations by projecting plane wave-based wave functions onto a local atomic orbital basis. We have performed bonding analysis on 1520 compounds (insulators and semiconductors) using a fully automated workflow combining the VASP and LOBSTER software packages. We then automatically evaluated the data with LobsterPy (https://github.com/jageo/lobsterpy) and provide results as a database. The projected densities of states and bonding indicators are benchmarked on VASP projections and available heuristics, respectively. Lastly, we illustrate the predictive power of bonding descriptors by constructing a machine-learning model for phononic properties, which shows an increase in prediction accuracies by 27 % (mean absolute errors) compared to a benchmark model differing only by not relying on any quantum-chemical bonding features.
Talk about my recent research on data-driven chemical understanding with geometrical and quantum-chemical bonding analysis.
This database consists of bonding data computed using Lobster for 1520 solid-state compounds consisting of insulators and semiconductors. It consists of two kinds of json files. Smaller lightweight JSONS consists of summarized bonding information for each of the compounds. The files are named as per ID numbers in the materials project database.
Here we provide also the larger computational data json files for 700 compounds. This files consists of all important LOBSTER computation output files data stored as dictionary.
This database consists of bonding data computed using Lobster for 1520 solid-state compounds consisting of insulators and semiconductors. The files are named as per ID numbers in the materials project database.
Here we provide the larger computational data JSON files for the rest of the 820 compounds. This file consists of all important LOBSTER computation output files data stored as a dictionary.
In recent years, many protocols in computational materials science have been automated and made available within software packages (primarily Python-based). This ranges from the automation of simple heuristics (oxidation states, coordination environments) to the automation of protocols, including multiple DFT and post-processing tools such as (an)harmonic phonon computations or bonding analysis. Such developments also shorten the time frames of projects after such developments have been made available and open new possibilities. For example, we can now easily make data-driven tests of well-known rules and heuristics or develop quantum chemistry-based materials descriptors for machine learning approaches. These tests and descriptors can have applications related to magnetic ground state predictions of materials relevant for spintronic applications or for predicting thermal properties relevant for thermal management in electronics. Combining high-throughput ab initio computations with fitting, fine-tuning machine learning models and predictions of such models within complex workflows is also possible and promises further acceleration in the field. In this talk, I will show our latest efforts to link automation with data-driven chemistry and materials science.
Bonds and local atomic environments are crucial descriptors of material properties. They have been used to create design rules and heuristics and as features in machine learning of materials properties. Implementations and algorithms (e.g., ChemEnv and LobsterEnv) for identifying local atomic environments based on geometrical characteristics and quantum-chemical bonding analysis are nowadays available. Fully automatic workflows and analysis tools have been developed to use quantum-chemical bonding analysis on a large scale. The lecture will demonstrate how our tools, that assess local atomic environments and perform automatic bonding analysis, help to develop new machine learning models and a new intuitive understanding of materials.[5,6] Furthermore, the general trend toward automation in density functional-based materials science and some of our recent contributions will be discussed.
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.
Bonds and local atomic environments are crucial descriptors of material properties. They have been used to create design rules and heuristics and as features in machine learning of materials properties. Implementations and algorithms (e.g., ChemEnv and LobsterEnv) for identifying local atomic environments based on geometrical characteristics and quantum-chemical bonding analysis are nowadays available. Fully automatic workflows and analysis tools have been developed to use quantum-chemical bonding analysis on a large scale. The lecture will demonstrate how our tools, that assess local atomic environments and perform automatic bonding analysis, help to develop new machine learning models and a new intuitive understanding of materials. Furthermore, the general trend toward automation in density functional-based materials science and some of our recent contributions will be discussed.
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.
Jobflow is a free, open-source library for writing and executing workflows. Complex workflows can be defined using simple python functions and executed locally or on arbitrary computing resources using the FireWorks workflow manager.
Some features that distinguish jobflow are dynamic workflows, easy compositing and connecting of workflows, and the ability to store workflow outputs across multiple databases.