TY - JOUR A1 - Ganose, Alex M. A1 - Sahasrabuddhe, Hrushikesh A1 - Asta, Mark A1 - Beck, Kevin A1 - Biswas, Tathagata A1 - Bonkowski, Alexander A1 - Bustamante, Joana A1 - Chen, Xin A1 - Chiang, Yuan A1 - Chrzan, Daryl C. A1 - Clary, Jacob A1 - Cohen, Orion A. A1 - Ertural, Christina A1 - Gallant, Max C. A1 - George, Janine A1 - Gerits, Sophie A1 - Goodall, Rhys E. A. A1 - Guha, Rishabh D. A1 - Hautier, Geoffroy A1 - Horton, Matthew A1 - Inizan, T. J. A1 - Kaplan, Aaron D. A1 - Kingsbury, Ryan S. A1 - Kuner, Matthew C. A1 - Li, Bryant A1 - Linn, Xavier A1 - McDermott, Matthew J. A1 - Mohanakrishnan, Rohith Srinivaas A1 - Naik, Aakash A. A1 - Neaton, Jeffrey B. A1 - Parmar, Shehan M. A1 - Persson, Kristin A. A1 - Petretto, Guido A1 - Purcell, Thomas A. R. A1 - Ricci, Francesco A1 - Rich, Benjamin A1 - Riebesell, Janosh A1 - Rignanese, Gian-Marco A1 - Rosen, Andrew S. A1 - Scheffler, Matthias A1 - Schmidt, Jonathan A1 - Shen, Jimmy-Xuan A1 - Sobolev, Andrei A1 - Sundararaman, Ravishankar A1 - Tezak, Cooper A1 - Trinquet, Victor A1 - Varley, Joel B. A1 - Vigil-Fowler, Derek A1 - Wang, Duo A1 - Waroquiers, David A1 - Wen, Mingjian A1 - Yang, Han A1 - Zheng, Hui A1 - Zheng, Jiongzhi A1 - Zhu, Zhuoying A1 - Jain, Anubhav T1 - Atomate2: Modular workflows for materials science N2 - High-throughput density functional theory (DFT) calculations have become a vital element of computational materials science, enabling materials screening, property database generation, and training of “universal” machine learning models. While several software frameworks have emerged to support these computational efforts, new developments such as machine learned force fields have increased demands for more flexible and programmable workflow solutions. This manuscript introduces atomate2, a comprehensive evolution of our original atomate framework, designed to address existing limitations in computational materials research infrastructure. Key features include the support for multiple electronic structure packages and interoperability between them, along with generalizable workflows that can be written in an abstract form irrespective of the DFT package or machine learning force field used within them. Our hope is that atomate2's improved usability and extensibility can reduce technical barriers for high-throughput research workflows and facilitate the rapid adoption of emerging methods in computational material science. KW - Automation KW - Materials design KW - DFT workflows KW - Phonons KW - Thermal conductivity KW - Bonding analysis PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-635759 DO - https://doi.org/10.1039/d5dd00019j SN - 2635-098X SP - 1 EP - 30 PB - Royal Society of Chemistry (RSC) CY - Cambridge AN - OPUS4-63575 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Ganose, Alex M. A1 - Sahasrabuddhe, Hrushikesh A1 - Asta, Mark A1 - Beck, Kevin A1 - Biswas, Tathagata A1 - Bonkowski, Alexander A1 - Bustamante, Joana A1 - Chen, Xin A1 - Chiang, Yuan A1 - Chrzan, Daryl C. A1 - Clary, Jacob A1 - Cohen, Orion A. A1 - Ertural, Christina A1 - Gallant, Max C. A1 - George, Janine A1 - Gerits, Sophie A1 - Goodall, Rhys E. A. A1 - Guha, Rishabh D. A1 - Hautier, Geoffroy A1 - Horton, Matthew A1 - Inizan, T. J. A1 - Kaplan, Aaron D. A1 - Kingsbury, Ryan S. A1 - Kuner, Matthew C. A1 - Li, Bryant A1 - Linn, Xavier A1 - McDermott, Matthew J. A1 - Mohanakrishnan, Rohith Srinivaas A1 - Naik, Aakash A. A1 - Neaton, Jeffrey B. A1 - Parmar, Shehan M. A1 - Persson, Kristin A. A1 - Petretto, Guido A1 - Purcell, Thomas A. R. A1 - Ricci, Francesco A1 - Rich, Benjamin A1 - Riebesell, Janosh A1 - Rignanese, Gian-Marco A1 - Rosen, Andrew S. A1 - Scheffler, Matthias A1 - Schmidt, Jonathan A1 - Shen, Jimmy-Xuan A1 - Sobolev, Andrei A1 - Sundararaman, Ravishankar A1 - Tezak, Cooper A1 - Trinquet, Victor A1 - Varley, Joel B. A1 - Vigil-Fowler, Derek A1 - Wang, Duo A1 - Waroquiers, David A1 - Wen, Mingjian A1 - Yang, Han A1 - Zheng, Hui A1 - Zheng, Jiongzhi A1 - Zhu, Zhuoying A1 - Jain, Anubhav T1 - Correction: Atomate2: Modular workflows for materials science N2 - Correction for “Atomate2: modular workflows for materials science” by Alex M. Ganose et al., Digital Discovery, 2025, 4, 1944–1973, https://doi.org/10.1039/D5DD00019J. PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-640297 DO - https://doi.org/10.1039/d5dd90036k SN - 2635-098X SP - 1 EP - 2 PB - Royal Society of Chemistry (RSC) CY - Cambridge AN - OPUS4-64029 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Mielke, Johannes A1 - Hanke, F. A1 - Peters, M.V. A1 - Hecht, S. A1 - Persson, M. A1 - Grill, L. T1 - Adatoms underneath single porphyrin molecules on Au(111) N2 - The adsorption of porphyrin derivatives on a Au(111) surface was studied by scanning tunneling microscopy and spectroscopy at low temperatures in combination with density functional theory calculations. Different molecular appearances were found and could be assigned to the presence of single gold adatoms bonded by a coordination bond underneath the molecular monolayer, causing a characteristic change of the electronic structure of the molecules. Moreover, this interpretation could be confirmed by manipulation experiments of individual molecules on and off a single gold atom. This study provides a detailed understanding of the role of metal adatoms in surface–molecule bonding and anchoring and of the appearance of single molecules, and it should prove relevant for the imaging of related molecule–metal systems. PY - 2015 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-324144 UR - http://pubs.acs.org/doi/pdf/10.1021/ja510528x DO - https://doi.org/10.1021/ja510528x SN - 0002-7863 SN - 1520-5126 VL - 137 IS - 5 SP - 1844 EP - 1849 PB - American Chemical Society CY - Washington, DC AN - OPUS4-32414 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Rosen, Andrew S. A1 - Gallant, Max A1 - George, Janine A1 - Riebesell, Janosh A1 - Sahasrabuddhe, Hrushikesh A1 - Shen, Jimmy-Xuan A1 - Wen, Mingjian A1 - Evans, Matthew L. A1 - Petretto, Guido A1 - Waroquiers, David A1 - Rignanese, Gian-Marco A1 - Persson, Kristin A. A1 - Jain, Anubhav A1 - Ganose, Alex M. T1 - Jobflow: Computational Workflows Made Simple N2 - 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. KW - Automation KW - Workflow KW - Computational Materials Science KW - Computations KW - Software PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-593104 DO - https://doi.org/10.21105/joss.05995 VL - 9 IS - 93 SP - 1 EP - 7 PB - The Open Journal AN - OPUS4-59310 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Rosen, Andrew S. A1 - Gallant, Max A1 - George, Janine A1 - Riebesell, Janosh A1 - Sahasrabuddhe, Hrushikesh A1 - Shen, Jimmy-Xuan A1 - Wen, Mingjian A1 - Evans, Matthew L. A1 - Petretto, Guido A1 - Waroquiers, David A1 - Rignanese, Gian-Marco A1 - Persson, Kristin A. A1 - Jain, Anubhav A1 - Ganose, Alex M. T1 - Jobflow: Computational Workflows Made Simple N2 - 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. KW - Automation KW - Workflows KW - Computational Materials Science PY - 2024 DO - https://doi.org/10.5281/zenodo.10466868 PB - Zenodo CY - Geneva AN - OPUS4-59313 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -