24 results on '"Adorf, Carl S."'
Search Results
2. The rule of four: anomalous distributions in the stoichiometries of inorganic compounds
- Author
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Gazzarrini, Elena, Cersonsky, Rose K., Bercx, Marnik, Adorf, Carl S., and Marzari, Nicola
- Published
- 2024
- Full Text
- View/download PDF
3. The rule of four: anomalous stoichiometries of inorganic compounds
- Author
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Gazzarrini, Elena, Cersonsky, Rose K., Bercx, Marnik, Adorf, Carl S., and Marzari, Nicola
- Subjects
Condensed Matter - Materials Science ,Physics - Computational Physics - Abstract
Why are materials with specific characteristics more abundant than others? This is a fundamental question in materials science and one that is traditionally difficult to tackle, given the vastness of compositional and configurational space. We highlight here the anomalous abundance of inorganic compounds whose primitive unit cell contains a number of atoms that is a multiple of four. This occurrence - named here the 'rule of four' - has to our knowledge not previously been reported or studied. Here, we first highlight the rule's existence, especially notable when restricting oneself to experimentally known compounds, and explore its possible relationship with established descriptors of crystal structures, from symmetries to energies. We then investigate this relative abundance by looking at structural descriptors, both of global (packing configurations) and local (the smooth overlap of atomic positions) nature. Contrary to intuition, the overabundance does not correlate with low-energy or high-symmetry structures; in fact, structures which obey the 'rule of four' are characterized by low symmetries and loosely packed arrangements maximizing the free volume. We are able to correlate this abundance with local structural symmetries, and visualize the results using a hybrid supervised-unsupervised machine learning method.
- Published
- 2023
4. AiiDAlab -- an ecosystem for developing, executing, and sharing scientific workflows
- Author
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Yakutovich, Aliaksandr V., Eimre, Kristjan, Schütt, Ole, Talirz, Leopold, Adorf, Carl S., Andersen, Casper W., Ditler, Edward, Du, Dou, Passerone, Daniele, Smit, Berend, Marzari, Nicola, Pizzi, Giovanni, and Pignedoli, Carlo A.
- Subjects
Condensed Matter - Materials Science ,Physics - Computational Physics ,J.2 ,I.6 ,H.4 - Abstract
Cloud platforms allow users to execute tasks directly from their web browser and are a key enabling technology not only for commerce but also for computational science. Research software is often developed by scientists with limited experience in (and time for) user interface design, which can make research software difficult to install and use for novices. When combined with the increasing complexity of scientific workflows (involving many steps and software packages), setting up a computational research environment becomes a major entry barrier. AiiDAlab is a web platform that enables computational scientists to package scientific workflows and computational environments and share them with their collaborators and peers. By leveraging the AiiDA workflow manager and its plugin ecosystem, developers get access to a growing range of simulation codes through a python API, coupled with automatic provenance tracking of simulations for full reproducibility. Computational workflows can be bundled together with user-friendly graphical interfaces and made available through the AiiDAlab app store. Being fully compatible with open-science principles, AiiDAlab provides a complete infrastructure for automated workflows and provenance tracking, where incorporating new capabilities becomes intuitive, requiring only Python knowledge., Comment: Manuscript: 25 pages, 6 figures. Supplementary information: 15 pages, 10 figures
- Published
- 2020
- Full Text
- View/download PDF
5. Materials Cloud, a platform for open computational science
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Talirz, Leopold, Kumbhar, Snehal, Passaro, Elsa, Yakutovich, Aliaksandr V., Granata, Valeria, Gargiulo, Fernando, Borelli, Marco, Uhrin, Martin, Huber, Sebastiaan P., Zoupanos, Spyros, Adorf, Carl S., Andersen, Casper W., Schütt, Ole, Pignedoli, Carlo A., Passerone, Daniele, VandeVondele, Joost, Schulthess, Thomas C., Smit, Berend, Pizzi, Giovanni, and Marzari, Nicola
- Subjects
Condensed Matter - Materials Science ,Physics - Computational Physics ,J.2 ,I.6 ,H.4 - Abstract
Materials Cloud is a platform designed to enable open and seamless sharing of resources for computational science, driven by applications in materials modelling. It hosts 1) archival and dissemination services for raw and curated data, together with their provenance graph, 2) modelling services and virtual machines, 3) tools for data analytics, and pre-/post-processing, and 4) educational materials. Data is citable and archived persistently, providing a comprehensive embodiment of the FAIR principles that extends to computational workflows. Materials Cloud leverages the AiiDA framework to record the provenance of entire simulation pipelines (calculations performed, codes used, data generated) in the form of graphs that allow to retrace and reproduce any computed result. When an AiiDA database is shared on Materials Cloud, peers can browse the interconnected record of simulations, download individual files or the full database, and start their research from the results of the original authors. The infrastructure is agnostic to the specific simulation codes used and can support diverse applications in computational science that transcend its initial materials domain., Comment: 19 pages, 8 figures
- Published
- 2020
- Full Text
- View/download PDF
6. AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance
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Huber, Sebastiaan. P., Zoupanos, Spyros, Uhrin, Martin, Talirz, Leopold, Kahle, Leonid, Häuselmann, Rico, Gresch, Dominik, Müller, Tiziano, Yakutovich, Aliaksandr V., Andersen, Casper W., Ramirez, Francisco F., Adorf, Carl S., Gargiulo, Fernando, Kumbhar, Snehal, Passaro, Elsa, Johnston, Conrad, Merkys, Andrius, Cepellotti, Andrea, Mounet, Nicolas, Marzari, Nicola, Kozinsky, Boris, and Pizzi, Giovanni
- Subjects
Computer Science - Distributed, Parallel, and Cluster Computing ,Condensed Matter - Materials Science - Abstract
The ever-growing availability of computing power and the sustained development of advanced computational methods have contributed much to recent scientific progress. These developments present new challenges driven by the sheer amount of calculations and data to manage. Next-generation exascale supercomputers will harden these challenges, such that automated and scalable solutions become crucial. In recent years, we have been developing AiiDA (http://www.aiida.net), a robust open-source high-throughput infrastructure addressing the challenges arising from the needs of automated workflow management and data provenance recording. Here, we introduce developments and capabilities required to reach sustained performance, with AiiDA supporting throughputs of tens of thousands processes/hour, while automatically preserving and storing the full data provenance in a relational database making it queryable and traversable, thus enabling high-performance data analytics. AiiDA's workflow language provides advanced automation, error handling features and a flexible plugin model to allow interfacing with any simulation software. The associated plugin registry enables seamless sharing of extensions, empowering a vibrant user community dedicated to making simulations more robust, user-friendly and reproducible.
- Published
- 2020
- Full Text
- View/download PDF
7. Virtual Computational Chemistry Teaching Laboratories--Hands-On at a Distance
- Author
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Kobayashi, Rika, Goumans, Theodorus P. M., Carstensen, N. Ole, Soini, Thomas M., Marzari, Nicola, Timrov, Iurii, Ponce´, Samuel, Linscott, Edward B., Sewell, Christopher J., Pizzi, Giovanni, Ramirez, Francisco, Bercx, Marnik, Huber, Sebastiaan P., Adorf, Carl S., and Talirz, Leopold
- Abstract
The COVID-19 pandemic disrupted chemistry teaching practices globally as many courses were forced online, necessitating adaptation to the digital platform. The biggest impact was to the practical component of the chemistry curriculum--the so-called wet lab. Naively, it would be thought that computer-based teaching laboratories would have little problem in making the move. However, this is not the case as there are many unrecognized differences between delivering computer-based teaching in-person and virtually: software issues, technology, and classroom management. Consequently, relatively few "hands-on" computational chemistry teaching laboratories are delivered online. In this paper, we describe these issues in more detail and how they can be addressed, drawing on our experience in delivering a third-year computational chemistry course as well as remote hands-on workshops for the Virtual Winter School on Computational Chemistry and the European BIG-MAP project.
- Published
- 2021
- Full Text
- View/download PDF
8. Inverse Design of Simple Pair Potentials for the Self-Assembly of Complex Structures
- Author
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Adorf, Carl S., Antonaglia, James, Dshemuchadse, Julia, and Glotzer, Sharon C.
- Subjects
Condensed Matter - Soft Condensed Matter - Abstract
The synthesis of complex materials through the self-assembly of particles at the nanoscale provides opportunities for the realization of novel material properties. However, the inverse design process to create experimentally feasible interparticle interaction strategies is uniquely challenging. Standard methods for the optimization of isotropic pair potentials tend toward overfitting, resulting in solutions with too many features and length scales that are challenging to map to mechanistic models. Here we introduce a method for the optimization of simple pair potentials that minimizes the relative entropy of the complex target structure while directly considering only those length scales most relevant for self-assembly. Our approach maximizes the relative information of a target pair distribution function with respect to an ansatz distribution function via an iterative update process. During this process, we filter high frequencies from the Fourier spectrum of the pair potential, resulting in interaction potentials that are smoother and simpler in real space, and therefore likely easier to make. We show that pair potentials obtained by this method assemble their target structure more robustly with respect to optimization method parameters than potentials optimized without filtering., Comment: 11 pages, 6 figures
- Published
- 2017
- Full Text
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9. Simple Data and Workflow Management with the signac Framework
- Author
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Adorf, Carl S., Dodd, Paul M., Ramasubramani, Vyas, and Glotzer, Sharon C.
- Subjects
Computer Science - Databases - Abstract
Researchers in the field of materials science, chemistry, and computational physics are regularly posed with the challenge of managing large and heterogeneous data spaces. The amount of data increases in lockstep with computational efficiency multiplied by the amount of available computational resources, which shifts the bottleneck in the scientific process from data acquisition to data processing and analysis. We present a framework designed to aid in the integration of various specialized data formats, tools and workflows. The signac framework provides all basic components required to create a well-defined and thus collectively accessible and searchable data space, simplifying data access and modification through a homogeneous data interface that is largely agnostic to the data source, i.e., computation or experiment. The framework's data model is designed to not require absolute commitment to the presented implementation, simplifying adaption into existing data sets and workflows. This approach not only increases the efficiency with which scientific results can be produced, but also significantly lowers barriers for collaborations requiring shared data access., Comment: 12 pages, 5 figures
- Published
- 2016
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10. AiiDAlab – an ecosystem for developing, executing, and sharing scientific workflows
- Author
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Yakutovich, Aliaksandr V., Eimre, Kristjan, Schütt, Ole, Talirz, Leopold, Adorf, Carl S., Andersen, Casper W., Ditler, Edward, Du, Dou, Passerone, Daniele, Smit, Berend, Marzari, Nicola, Pizzi, Giovanni, and Pignedoli, Carlo A.
- Published
- 2021
- Full Text
- View/download PDF
11. Simple data and workflow management with the signac framework
- Author
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Adorf, Carl S., Dodd, Paul M., Ramasubramani, Vyas, and Glotzer, Sharon C.
- Published
- 2018
- Full Text
- View/download PDF
12. Inverse design of simple pair potentials for the self-assembly of complex structures.
- Author
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Adorf, Carl S., Antonaglia, James, Dshemuchadse, Julia, and Glotzer, Sharon C.
- Subjects
- *
MATERIALS testing , *PARTICLE interactions , *PARTICLES , *MOLECULAR self-assembly , *ISOTROPIC properties , *CRYSTALLOGRAPHY , *NANOCHEMISTRY - Abstract
The synthesis of complex materials through the self-assembly of particles at the nanoscale provides opportunities for the realization of novel material properties. However, the inverse design process to create experimentally feasible interparticle interaction strategies is uniquely challenging. Standard methods for the optimization of isotropic pair potentials tend toward overfitting, resulting in solutions with too many features and length scales that are challenging to map to mechanistic models. Here we introduce a method for the optimization of simple pair potentials that minimizes the relative entropy of the complex target structure while directly considering only those length scales most relevant for self-assembly. Our approach maximizes the relative information of a target pair distribution function with respect to an ansatz distribution function via an iterative update process. During this process, we filter high frequencies from the Fourier spectrum of the pair potential, resulting in interaction potentials that are smoother and simpler in real space and therefore likely easier to make. We show that pair potentials obtained by this method assemble their target structure more robustly with respect to optimization method parameters than potentials optimized without filtering. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
13. Virtual computational chemistry teaching laboratories – hands-on at a distance
- Author
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Kobayashi, Rika, primary, Goumans, Theodorus P. M., additional, Carstensen, N. Ole, additional, Soini, Thomas M., additional, Marzari, Nicola, additional, Timrov, Iurii, additional, Poncé, Samuel, additional, Linscott, Edward B., additional, Sewell, Christopher J., additional, Pizzi, Giovanni, additional, Ramirez, Francisco, additional, Bercx, Marnik, additional, Huber, Sebastiaan P., additional, Adorf, Carl S., additional, and Talirz, Leopold, additional
- Published
- 2021
- Full Text
- View/download PDF
14. Virtual teaching laboratories – hands-on at a distance
- Author
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Kobayashi, Rika, primary, Goumans, Theodorus P. M., additional, Carstensen, N. Ole, additional, Soini, Thomas M., additional, Marzari, Nicola, additional, Timrov, Iurii, additional, Poncé, Samuel, additional, Linscott, Edward B., additional, Sewell, Christopher J., additional, Pizzi, Giovanni, additional, Ramirez, Francisco, additional, Bercx, Marnik, additional, Huber, Sebastiaan P., additional, Adorf, Carl S., additional, and Talirz, Leopold, additional
- Published
- 2021
- Full Text
- View/download PDF
15. Virtual Computational Chemistry Teaching Laboratories—Hands-On at a Distance
- Author
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UCL - SST/IMCN/MODL - Modelling, Kobayashi, Rika, Goumans, Theodorus P. M., Carstensen, N. Ole, Soini, Thomas M., Marzari, Nicola, Timrov, Iurii, Poncé, Samuel, Linscott, Edward B., Sewell, Christopher J., Pizzi, Giovanni, Ramirez, Francisco, Bercx, Marnik, Huber, Sebastiaan P., Adorf, Carl S., Talirz, Leopold, UCL - SST/IMCN/MODL - Modelling, Kobayashi, Rika, Goumans, Theodorus P. M., Carstensen, N. Ole, Soini, Thomas M., Marzari, Nicola, Timrov, Iurii, Poncé, Samuel, Linscott, Edward B., Sewell, Christopher J., Pizzi, Giovanni, Ramirez, Francisco, Bercx, Marnik, Huber, Sebastiaan P., Adorf, Carl S., and Talirz, Leopold
- Abstract
The COVID-19 pandemic disrupted chemistry teaching practices globally as many courses were forced online, necessitating adaptation to the digital platform. The biggest impact was to the practical component of the chemistry curriculum-the so-called wet lab. Naively, it would be thought that computer-based teaching laboratories would have little problem in making the move. However, this is not the case as there are many unrecognized differences between delivering computer-based teaching in-person and virtually: software issues, technology, and classroom management. Consequently, relatively few “hands-on” computational chemistry teaching laboratories are delivered online. In this paper, we describe these issues in more detail and how they can be addressed, drawing on our experience in delivering a thirdyear computational chemistry course as well as remote hands-on workshops for the Virtual Winter School on Computational Chemistry and the European BIG-MAP project.
- Published
- 2021
16. Data driven analytics of porous battery microstructures
- Author
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Deva, Abhas, primary, Krs, Vojtech, additional, Robinson, Lucas D., additional, Adorf, Carl S., additional, Benes, Bedrich, additional, Glotzer, Sharon C., additional, and García, R. Edwin, additional
- Published
- 2021
- Full Text
- View/download PDF
17. AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance
- Author
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Huber, Sebastiaan P., primary, Zoupanos, Spyros, additional, Uhrin, Martin, additional, Talirz, Leopold, additional, Kahle, Leonid, additional, Häuselmann, Rico, additional, Gresch, Dominik, additional, Müller, Tiziano, additional, Yakutovich, Aliaksandr V., additional, Andersen, Casper W., additional, Ramirez, Francisco F., additional, Adorf, Carl S., additional, Gargiulo, Fernando, additional, Kumbhar, Snehal, additional, Passaro, Elsa, additional, Johnston, Conrad, additional, Merkys, Andrius, additional, Cepellotti, Andrea, additional, Mounet, Nicolas, additional, Marzari, Nicola, additional, Kozinsky, Boris, additional, and Pizzi, Giovanni, additional
- Published
- 2020
- Full Text
- View/download PDF
18. Materials Cloud, a platform for open computational science
- Author
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Talirz, Leopold, primary, Kumbhar, Snehal, additional, Passaro, Elsa, additional, Yakutovich, Aliaksandr V., additional, Granata, Valeria, additional, Gargiulo, Fernando, additional, Borelli, Marco, additional, Uhrin, Martin, additional, Huber, Sebastiaan P., additional, Zoupanos, Spyros, additional, Adorf, Carl S., additional, Andersen, Casper Welzel, additional, Schütt, Ole, additional, Pignedoli, Carlo A., additional, Passerone, Daniele, additional, VandeVondele, Joost, additional, Schulthess, Thomas C., additional, Smit, Berend, additional, Pizzi, Giovanni, additional, and Marzari, Nicola, additional
- Published
- 2020
- Full Text
- View/download PDF
19. Virtual Computational Chemistry Teaching LaboratoriesHands-On at a Distance.
- Author
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Kobayashi, Rika, Goumans, Theodorus P. M., Carstensen, N. Ole, Soini, Thomas M., Marzari, Nicola, Timrov, Iurii, Poncé, Samuel, Linscott, Edward B., Sewell, Christopher J., Pizzi, Giovanni, Ramirez, Francisco, Bercx, Marnik, Huber, Sebastiaan P., Adorf, Carl S., and Talirz, Leopold
- Published
- 2021
- Full Text
- View/download PDF
20. Analysis of Self-Assembly Pathways with Unsupervised Machine Learning Algorithms
- Author
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Adorf, Carl S., primary, Moore, Timothy C., additional, Melle, Yannah J. U., additional, and Glotzer, Sharon C., additional
- Published
- 2019
- Full Text
- View/download PDF
21. How to Professionally Develop Reusable Scientific Software—And When Not To
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Adorf, Carl S., primary, Ramasubramani, Vyas, additional, Anderson, Joshua A., additional, and Glotzer, Sharon C., additional
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- 2019
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22. Analysis of Self-Assembly Pathways with Unsupervised Machine Learning Algorithms
- Author
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Adorf, Carl S., Moore, Timothy C., Melle, Yannah J. U., and Glotzer, Sharon C.
- Abstract
Colloidal and nanoparticle systems display a rich and exciting phase behavior including the self-assembly of highly complex crystal structures. Nucleation and growth pathways toward crystallization have been studied both computationally and experimentally, but the mechanisms for the formation of the precritical nucleus and consequent crystal growth are yet to be fully understood. Recent advances in the application of machine learning algorithms applied to many-particle systems have led to significant breakthroughs in the ability for high-throughput analysis of phase transitions and the identification of crystal structures. We build upon these techniques to identify and analyze pathways for nucleation and growth in supercooled liquids of colloidal systems modeled with isotropic pair potentials. Our study involves the development of unsupervised machine learning models trained on spherical-harmonics-based descriptors. These models allow us to determine clusters of local environments that are present prior to and during crystallization. We analyze these environments to identify prevalent motifs and local order within the supercooled liquid prior to formation of the critical nucleus.
- Published
- 2020
- Full Text
- View/download PDF
23. Virtual Computational Chemistry Teaching Laboratories-Hands-On at a Distance
- Author
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Kobayashi, Rika, Goumans, Theodorus P. M., Carstensen, N. Ole, Soini, Thomas M., Marzari, Nicola, Timrov, Iurii, Ponce, Samuel, Linscott, Edward B., Sewell, Christopher J., Pizzi, Giovanni, Ramirez, Francisco, Bercx, Marnik, Huber, Sebastiaan P., Adorf, Carl S., and Talirz, Leopold
- Subjects
internet/web-based learning ,laboratory instruction ,graduate education/research ,first-year undergraduate/general ,upper-division undergraduate ,ComputingMilieux_COMPUTERSANDEDUCATION ,physical chemistry ,collaborative/cooperative learning ,distance learning/self instruction ,computer-based learning ,hands-on learning/manipulatives - Abstract
The COVID-19 pandemic disrupted chemistry teaching practices globally as many courses were forced online, necessitating adaptation to the digital platform. The biggest impact was to the practical component of the chemistry curriculum-the so-called wet lab. Naively, it would be thought that computer-based teaching laboratories would have little problem in making the move. However, this is not the case as there are many unrecognized differences between delivering computer-based teaching in-person and virtually: software issues, technology, and classroom management. Consequently, relatively few "hands-on" computational chemistry teaching laboratories are delivered online. In this paper, we describe these issues in more detail and how they can be addressed, drawing on our experience in delivering a third-year computational chemistry course as well as remote hands-on workshops for the Virtual Winter School on Computational Chemistry and the European BIG-MAP project.
24. Analysis of Self-Assembly Pathways with Unsupervised Machine Learning Algorithms.
- Author
-
Adorf CS, Moore TC, Melle YJU, and Glotzer SC
- Abstract
Colloidal and nanoparticle systems display a rich and exciting phase behavior including the self-assembly of highly complex crystal structures. Nucleation and growth pathways toward crystallization have been studied both computationally and experimentally, but the mechanisms for the formation of the precritical nucleus and consequent crystal growth are yet to be fully understood. Recent advances in the application of machine learning algorithms applied to many-particle systems have led to significant breakthroughs in the ability for high-throughput analysis of phase transitions and the identification of crystal structures. We build upon these techniques to identify and analyze pathways for nucleation and growth in supercooled liquids of colloidal systems modeled with isotropic pair potentials. Our study involves the development of unsupervised machine learning models trained on spherical-harmonics-based descriptors. These models allow us to determine clusters of local environments that are present prior to and during crystallization. We analyze these environments to identify prevalent motifs and local order within the supercooled liquid prior to formation of the critical nucleus.
- Published
- 2020
- Full Text
- View/download PDF
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