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| <?xml version="1.0" encoding="utf-8" ?> | ||
| <!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.2 20190208//EN" | ||
| "JATS-publishing1.dtd"> | ||
| <article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other"> | ||
| <front> | ||
| <journal-meta> | ||
| <journal-id></journal-id> | ||
| <journal-title-group> | ||
| <journal-title>Journal of Open Source Software</journal-title> | ||
| <abbrev-journal-title>JOSS</abbrev-journal-title> | ||
| </journal-title-group> | ||
| <issn publication-format="electronic">2475-9066</issn> | ||
| <publisher> | ||
| <publisher-name>Open Journals</publisher-name> | ||
| </publisher> | ||
| </journal-meta> | ||
| <article-meta> | ||
| <article-id pub-id-type="publisher-id">6912</article-id> | ||
| <article-id pub-id-type="doi">10.21105/joss.06912</article-id> | ||
| <title-group> | ||
| <article-title>f3dasm: Framework for Data-Driven Design and Analysis of | ||
| Structures and Materials</article-title> | ||
| </title-group> | ||
| <contrib-group> | ||
| <contrib contrib-type="author"> | ||
| <contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-3602-0452</contrib-id> | ||
| <name> | ||
| <surname>van der Schelling</surname> | ||
| <given-names>M. P.</given-names> | ||
| </name> | ||
| <xref ref-type="aff" rid="aff-1"/> | ||
| </contrib> | ||
| <contrib contrib-type="author"> | ||
| <contrib-id contrib-id-type="orcid">https://orcid.org/0000-0001-5956-3877</contrib-id> | ||
| <name> | ||
| <surname>Ferreira</surname> | ||
| <given-names>B. P.</given-names> | ||
| </name> | ||
| <xref ref-type="aff" rid="aff-2"/> | ||
| </contrib> | ||
| <contrib contrib-type="author" corresp="yes"> | ||
| <contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-6216-0355</contrib-id> | ||
| <name> | ||
| <surname>Bessa</surname> | ||
| <given-names>M. A.</given-names> | ||
| </name> | ||
| <xref ref-type="aff" rid="aff-2"/> | ||
| <xref ref-type="corresp" rid="cor-1"><sup>*</sup></xref> | ||
| </contrib> | ||
| <aff id="aff-1"> | ||
| <institution-wrap> | ||
| <institution>Materials Science & Engineering, Delft University of | ||
| Technology, the Netherlands</institution> | ||
| </institution-wrap> | ||
| </aff> | ||
| <aff id="aff-2"> | ||
| <institution-wrap> | ||
| <institution>School of Engineering, Brown University, United States of | ||
| America</institution> | ||
| </institution-wrap> | ||
| </aff> | ||
| </contrib-group> | ||
| <author-notes> | ||
| <corresp id="cor-1">* E-mail: <email></email></corresp> | ||
| </author-notes> | ||
| <pub-date date-type="pub" publication-format="electronic" iso-8601-date="2024-05-31"> | ||
| <day>31</day> | ||
| <month>5</month> | ||
| <year>2024</year> | ||
| </pub-date> | ||
| <volume>9</volume> | ||
| <issue>100</issue> | ||
| <fpage>6912</fpage> | ||
| <permissions> | ||
| <copyright-statement>Authors of papers retain copyright and release the | ||
| work under a Creative Commons Attribution 4.0 International License (CC | ||
| BY 4.0)</copyright-statement> | ||
| <copyright-year>2022</copyright-year> | ||
| <copyright-holder>The article authors</copyright-holder> | ||
| <license license-type="open-access" xlink:href="https://creativecommons.org/licenses/by/4.0/"> | ||
| <license-p>Authors of papers retain copyright and release the work under | ||
| a Creative Commons Attribution 4.0 International License (CC BY | ||
| 4.0)</license-p> | ||
| </license> | ||
| </permissions> | ||
| <kwd-group kwd-group-type="author"> | ||
| <kwd>Python</kwd> | ||
| <kwd>data-driven</kwd> | ||
| <kwd>materials</kwd> | ||
| <kwd>framework</kwd> | ||
| <kwd>machine learning</kwd> | ||
| </kwd-group> | ||
| </article-meta> | ||
| </front> | ||
| <body> | ||
| <sec id="summary"> | ||
| <title>Summary</title> | ||
| <p><ext-link ext-link-type="uri" xlink:href="https://github.com/bessagroup/f3dasm"><monospace>f3dasm</monospace></ext-link> | ||
| (Framework for Data-driven Design and Analysis of Structures and | ||
| Materials) is a Python project that provides a general and | ||
| user-friendly data-driven framework for researchers and practitioners | ||
| working on the design and analysis of materials and structures. The | ||
| package aims to streamline the data-driven process and make it easier | ||
| to replicate research articles in this field, as well as share new | ||
| work with the community.</p> | ||
| <fig> | ||
| <caption><p>Logo of | ||
| <ext-link ext-link-type="uri" xlink:href="https://github.com/bessagroup/f3dasm"><monospace>f3dasm</monospace></ext-link>. | ||
| <styled-content id="figU003Af3dasm_logo"></styled-content></p></caption> | ||
| <graphic mimetype="image" mime-subtype="png" xlink:href="f3dasm_logo_long.png" /> | ||
| </fig> | ||
| </sec> | ||
| <sec id="statement-of-need"> | ||
| <title>Statement of need</title> | ||
| <p>In the last decades, advancements in computational resources have | ||
| accelerated novel inverse design approaches for structures and | ||
| materials. In particular, data-driven methods leveraging machine | ||
| learning techniques play a major role in shaping our design processes | ||
| today.</p> | ||
| <p>Constructing a large material response database poses practical | ||
| challenges, such as proper data management, efficient parallel | ||
| computing, and integration with third-party software. Because most | ||
| applied fields remain conservative when it comes to openly sharing | ||
| databases and software, a lot of research time is instead being | ||
| allocated to implement common procedures that would be otherwise | ||
| readily available. This lack of shared practices also leads to | ||
| compatibility issues for benchmarking and replication of results by | ||
| violating the FAIR principles.</p> | ||
| <p>In this work we introduce an interface for researchers and | ||
| practitioners working on the design and analysis of materials and | ||
| structures. The package is called | ||
| <ext-link ext-link-type="uri" xlink:href="https://github.com/bessagroup/f3dasm"><monospace>f3dasm</monospace></ext-link> | ||
| (Framework for Data-driven Design and Analysis of Structures and | ||
| Materials). This work generalizes the original closed-source framework | ||
| proposed by Bessa and co-workers | ||
| (<xref alt="Bessa et al., 2017" rid="ref-Bessa2017" ref-type="bibr">Bessa | ||
| et al., 2017</xref>), making it more flexible and adaptable to | ||
| different applications, namely by allowing the integration of | ||
| different choices of software packages needed in the different steps | ||
| of the data-driven process:</p> | ||
| <list list-type="bullet"> | ||
| <list-item> | ||
| <p><bold>design of experiments</bold>, in which input variables | ||
| describing the microstructure, properties and external conditions | ||
| of the system are determined and sampled;</p> | ||
| </list-item> | ||
| <list-item> | ||
| <p><bold>data generation</bold>, typically through computational | ||
| analyses, resulting in the creation of a material response | ||
| database | ||
| (<xref alt="Ferreira et al., 2023" rid="ref-Ferreira2023" ref-type="bibr">Ferreira | ||
| et al., 2023</xref>);</p> | ||
| </list-item> | ||
| <list-item> | ||
| <p><bold>machine learning</bold>, in which a surrogate model is | ||
| trained to fit experimental findings;</p> | ||
| </list-item> | ||
| <list-item> | ||
| <p><bold>optimization</bold>, where we try to iteratively improve | ||
| the design.</p> | ||
| </list-item> | ||
| </list> | ||
| <p><xref alt="[fig:data-driven-process]" rid="figU003Adata-driven-process">[fig:data-driven-process]</xref> | ||
| provides an illustration of the stages in the data-driven process.</p> | ||
| <fig> | ||
| <caption><p>Illustration of the <monospace>f3dasm</monospace> | ||
| data-driven process. | ||
| <styled-content id="figU003Adata-driven-process"></styled-content></p></caption> | ||
| <graphic mimetype="image" mime-subtype="png" xlink:href="data-driven-process.png" /> | ||
| </fig> | ||
| <p><ext-link ext-link-type="uri" xlink:href="https://github.com/bessagroup/f3dasm"><monospace>f3dasm</monospace></ext-link> | ||
| is an | ||
| <ext-link ext-link-type="uri" xlink:href="https://pypi.org/project/f3dasm/">open-source | ||
| Python package</ext-link> compatible with Python 3.8 or later. The | ||
| library includes a suite of benchmark functions, optimization | ||
| algorithms, and sampling strategies to serve as default | ||
| implementations. Furthermore, | ||
| <ext-link ext-link-type="uri" xlink:href="https://github.com/bessagroup/f3dasm"><monospace>f3dasm</monospace></ext-link> | ||
| offers automatic data management for experiments, easy integration | ||
| with high-performance computing systems, and compatibility with the | ||
| hydra configuration manager. Comprehensive | ||
| <ext-link ext-link-type="uri" xlink:href="https://f3dasm.readthedocs.io/en/latest/">online | ||
| documentation</ext-link> is also available to assist users and | ||
| developers of the framework.</p> | ||
| <p>In a similar scope, it is worth mentioning the projects | ||
| <ext-link ext-link-type="uri" xlink:href="https://github.com/jacksund/simmate">simmate</ext-link> | ||
| (<xref alt="Sundberg et al., 2022" rid="ref-Sundberg2022" ref-type="bibr">Sundberg | ||
| et al., 2022</xref>) and | ||
| <ext-link ext-link-type="uri" xlink:href="https://github.com/ICAMS/strucscan">strucscan</ext-link>, | ||
| as they provide tools for the management of materials science | ||
| simulation and databases. However, these projects focus on the | ||
| generation and retrieval of materials properties and do not include | ||
| machine learning or optimization interfaces. In recent years, numerous | ||
| optimization frameworks have been developed to facilitate data-driven | ||
| design. | ||
| <ext-link ext-link-type="uri" xlink:href="https://optuna.org/">Optuna</ext-link> | ||
| is a hyperparameter optimization framework that combines a variety of | ||
| optimization algorithms with dynamically constructed search space | ||
| (<xref alt="Akiba et al., 2019" rid="ref-Akiba2019" ref-type="bibr">Akiba | ||
| et al., 2019</xref>) and | ||
| <ext-link ext-link-type="uri" xlink:href="https://github.com/esa/pagmo2">pygmo</ext-link> | ||
| provides unified interfaces for parallel global optimization | ||
| (<xref alt="Biscani & Izzo, 2020" rid="ref-Biscani2020" ref-type="bibr">Biscani | ||
| & Izzo, 2020</xref>). Interfaces to these and many other | ||
| optimization frameworks have been integrated into a separate package | ||
| <ext-link ext-link-type="uri" xlink:href="https://github.com/bessagroup/f3dasm_optimize"><monospace>f3dasm_optimize</monospace></ext-link>, | ||
| and can be used in conjunction with | ||
| <ext-link ext-link-type="uri" xlink:href="https://github.com/bessagroup/f3dasm"><monospace>f3dasm</monospace></ext-link>.</p> | ||
| </sec> | ||
| <sec id="acknowledgements"> | ||
| <title>Acknowledgements</title> | ||
| <p>We would express our gratitude to Jiaxiang Yi for his contributions | ||
| to writing an interface with the ABAQUS simulation software and to | ||
| Deepesh Toshniwal for providing valuable feedback.</p> | ||
| </sec> | ||
| </body> | ||
| <back> | ||
| <ref-list> | ||
| <title></title> | ||
| <ref id="ref-Bessa2017"> | ||
| <element-citation publication-type="article-journal"> | ||
| <person-group person-group-type="author"> | ||
| <name><surname>Bessa</surname><given-names>Miguel</given-names></name> | ||
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| </person-group> | ||
| <article-title>A framework for data-driven analysis of materials under uncertainty: Countering the curse of dimensionality</article-title> | ||
| <source>Computer Methods in Applied Mechanics and Engineering</source> | ||
| <year iso-8601-date="2017">2017</year> | ||
| <volume>320</volume> | ||
| <issue>April</issue> | ||
| <pub-id pub-id-type="doi">10.1016/j.cma.2017.03.037</pub-id> | ||
| <fpage>633</fpage> | ||
| <lpage>667</lpage> | ||
| </element-citation> | ||
| </ref> | ||
| <ref id="ref-Sundberg2022"> | ||
| <element-citation publication-type="article-journal"> | ||
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| </person-group> | ||
| <article-title>Simmate: A framework for materials science</article-title> | ||
| <source>Journal of Open Source Software</source> | ||
| <publisher-name>The Open Journal</publisher-name> | ||
| <year iso-8601-date="2022">2022</year> | ||
| <volume>7</volume> | ||
| <issue>75</issue> | ||
| <uri>https://doi.org/10.21105/joss.04364</uri> | ||
| <pub-id pub-id-type="doi">10.21105/joss.04364</pub-id> | ||
| <fpage>4364</fpage> | ||
| <lpage></lpage> | ||
| </element-citation> | ||
| </ref> | ||
| <ref id="ref-Biscani2020"> | ||
| <element-citation publication-type="article-journal"> | ||
| <person-group person-group-type="author"> | ||
| <name><surname>Biscani</surname><given-names>Francesco</given-names></name> | ||
| <name><surname>Izzo</surname><given-names>Dario</given-names></name> | ||
| </person-group> | ||
| <article-title>A parallel global multiobjective framework for optimization: pagmo</article-title> | ||
| <source>Journal of Open Source Software</source> | ||
| <publisher-name>The Open Journal</publisher-name> | ||
| <year iso-8601-date="2020">2020</year> | ||
| <volume>5</volume> | ||
| <issue>53</issue> | ||
| <uri>https://doi.org/10.21105/joss.02338</uri> | ||
| <pub-id pub-id-type="doi">10.21105/joss.02338</pub-id> | ||
| <fpage>2338</fpage> | ||
| <lpage></lpage> | ||
| </element-citation> | ||
| </ref> | ||
| <ref id="ref-Akiba2019"> | ||
| <element-citation publication-type="paper-conference"> | ||
| <person-group person-group-type="author"> | ||
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| <name><surname>Sano</surname><given-names>Shotaro</given-names></name> | ||
| <name><surname>Yanase</surname><given-names>Toshihiko</given-names></name> | ||
| <name><surname>Ohta</surname><given-names>Takeru</given-names></name> | ||
| <name><surname>Koyama</surname><given-names>Masanori</given-names></name> | ||
| </person-group> | ||
| <article-title>Optuna: A next-generation hyperparameter optimization framework</article-title> | ||
| <source>Proceedings of the 25th ACM SIGKDD international conference on knowledge discovery & data mining</source> | ||
| <year iso-8601-date="2019">2019</year> | ||
| <uri>https://doi.org/10.1145/3292500.3330701</uri> | ||
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| <fpage>2623</fpage> | ||
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| </element-citation> | ||
| </ref> | ||
| <ref id="ref-Ferreira2023"> | ||
| <element-citation publication-type="article-journal"> | ||
| <person-group person-group-type="author"> | ||
| <name><surname>Ferreira</surname><given-names>Bernardo P.</given-names></name> | ||
| <name><surname>Pires</surname><given-names>F. M. Andrade</given-names></name> | ||
| <name><surname>Bessa</surname><given-names>Miguel A.</given-names></name> | ||
| </person-group> | ||
| <article-title>CRATE: A python package to perform fast material simulations</article-title> | ||
| <source>Journal of Open Source Software</source> | ||
| <publisher-name>The Open Journal</publisher-name> | ||
| <year iso-8601-date="2023">2023</year> | ||
| <volume>8</volume> | ||
| <issue>87</issue> | ||
| <uri>https://doi.org/10.21105/joss.05594</uri> | ||
| <pub-id pub-id-type="doi">10.21105/joss.05594</pub-id> | ||
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| </element-citation> | ||
| </ref> | ||
| </ref-list> | ||
| </back> | ||
| </article> |