B. Patel, Peter Hill, Liam Pattinson, M. Giacomin, A. Bokshi, Daniel Kennedy, H. Dudding, J. Parisi, Tom F. Neiser, Ajay C. Jayalekshmi, David Dickinson, Juan Ruiz Ruiz
Fusion energy offers the potential for a near limitless source of low-carbon energy and is often regarded as a solution for the world’s long-term energy needs. To realise such a scenario requires the design of high-performance fusion reactors capable of maintaining the extreme conditions necessary to enable fusion. Turbulence is typically the dominant source of transport in magnetically-confined fusion plasmas, accounting for the majority of the particle and heat losses. Gyrokinetic modelling aims to quantify the level of turbulent transport encountered in fusion reactors and can be used to understand the major drivers of turbulence. The realisation of fusion critically depends on understanding how to mitigate turbulent transport, and thus requires high levels of confidence in the predictive tools being employed. Many different gyrokinetic modelling codes are available and Pyrokinetics aims to standardise the analysis of such computationally demanding simulations
{"title":"Pyrokinetics - A Python library to standardise\u0000gyrokinetic analysis","authors":"B. Patel, Peter Hill, Liam Pattinson, M. Giacomin, A. Bokshi, Daniel Kennedy, H. Dudding, J. Parisi, Tom F. Neiser, Ajay C. Jayalekshmi, David Dickinson, Juan Ruiz Ruiz","doi":"10.21105/joss.05866","DOIUrl":"https://doi.org/10.21105/joss.05866","url":null,"abstract":"Fusion energy offers the potential for a near limitless source of low-carbon energy and is often regarded as a solution for the world’s long-term energy needs. To realise such a scenario requires the design of high-performance fusion reactors capable of maintaining the extreme conditions necessary to enable fusion. Turbulence is typically the dominant source of transport in magnetically-confined fusion plasmas, accounting for the majority of the particle and heat losses. Gyrokinetic modelling aims to quantify the level of turbulent transport encountered in fusion reactors and can be used to understand the major drivers of turbulence. The realisation of fusion critically depends on understanding how to mitigate turbulent transport, and thus requires high levels of confidence in the predictive tools being employed. Many different gyrokinetic modelling codes are available and Pyrokinetics aims to standardise the analysis of such computationally demanding simulations","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"21 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140261873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eric Lindgren, Magnus Rahm, Erik Fransson, Fredrik Eriksson, Nicklas Österbacka, Zheyong Fan, Paul Erhart
{"title":"calorine: A Python package for constructing and\u0000sampling neuroevolution potential models","authors":"Eric Lindgren, Magnus Rahm, Erik Fransson, Fredrik Eriksson, Nicklas Österbacka, Zheyong Fan, Paul Erhart","doi":"10.21105/joss.06264","DOIUrl":"https://doi.org/10.21105/joss.06264","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140262432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pierluigi Crescenzi, Emanuele Natale, Aurora Rossi, Paulo Bruno Serafim
{"title":"WorldDynamics.jl: A Julia Package for Developing and\u0000Simulating Integrated Assessment Models","authors":"Pierluigi Crescenzi, Emanuele Natale, Aurora Rossi, Paulo Bruno Serafim","doi":"10.21105/joss.05772","DOIUrl":"https://doi.org/10.21105/joss.05772","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"55 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140264789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"DAPPER: Data Assimilation with Python: a Package for\u0000Experimental Research","authors":"P. Raanes, Yumeng Chen, C. Grudzien","doi":"10.21105/joss.05150","DOIUrl":"https://doi.org/10.21105/joss.05150","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"47 5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140415606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Python module to combine p values arising from\u0000discrete tests.","authors":"Gerrit Ansmann","doi":"10.21105/joss.06096","DOIUrl":"https://doi.org/10.21105/joss.06096","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140413342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Étienne Lac, Guy De Spiegeleer, Adrien Delsalle, Frédéric Collonval, Duc-Trung Lê, Mathias Malandain
{"title":"CoSApp: a Python library to create, simulate and design\u0000complex systems.","authors":"Étienne Lac, Guy De Spiegeleer, Adrien Delsalle, Frédéric Collonval, Duc-Trung Lê, Mathias Malandain","doi":"10.21105/joss.06292","DOIUrl":"https://doi.org/10.21105/joss.06292","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"72 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140415758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The truncated power series algebra (TPSA), also referred to as differential algebra (DA), is a well-established and widely used method in particle accelerator physics and astronomy. The most straightforward usage of TPSA/DA is to calculate the Taylor expansion of a given function at a specific point up to order 𝑛 . In recent years, as the application of TPSA/TA has been extended to other fields, a reusable implementation of TPSA/DA as a modern C++ library or other high level programming language like Python has become desirable. The cppTPSA package implements TPSA/DA in C++11 and provides developers a convenient library with which to build advanced TPSA/DA-based methods. A Python 3 library, pyTPSA, has also been developed based on the C++ lib.
截断幂级数代数（TPSA），也称为微分代数（DA），是粒子加速器物理学和天文学中一种成熟且广泛使用的方法。TPSA/DA 最直接的用法是计算给定函数在特定点的𝑛阶泰勒展开。近年来，随着 TPSA/TA 的应用扩展到其他领域，TPSA/DA 作为现代 C++ 库或其他高级编程语言（如 Python）的可重用实现已变得非常必要。cppTPSA 软件包在 C++11 中实现了 TPSA/DA，为开发人员提供了一个方便的库，用于构建基于 TPSA/DA 的高级方法。基于 C++ 库还开发了 Python 3 库 pyTPSA。
{"title":"cppTPSA/pyTPSA: a C++/Python package for truncated\u0000power series algebra","authors":"He Zhang","doi":"10.21105/joss.04818","DOIUrl":"https://doi.org/10.21105/joss.04818","url":null,"abstract":"The truncated power series algebra (TPSA), also referred to as differential algebra (DA), is a well-established and widely used method in particle accelerator physics and astronomy. The most straightforward usage of TPSA/DA is to calculate the Taylor expansion of a given function at a specific point up to order 𝑛 . In recent years, as the application of TPSA/TA has been extended to other fields, a reusable implementation of TPSA/DA as a modern C++ library or other high level programming language like Python has become desirable. The cppTPSA package implements TPSA/DA in C++11 and provides developers a convenient library with which to build advanced TPSA/DA-based methods. A Python 3 library, pyTPSA, has also been developed based on the C++ lib.","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"30 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140413912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Surjectors: surjection layers for density estimation\u0000with normalizing flows","authors":"Simon Dirmeier","doi":"10.21105/joss.06188","DOIUrl":"https://doi.org/10.21105/joss.06188","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"62 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140415235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Naik, Katharina Ueltzen, C. Ertural, Adam J. Jackson, Janine George
{"title":"LobsterPy: A package to automatically analyze LOBSTER\u0000runs","authors":"A. Naik, Katharina Ueltzen, C. Ertural, Adam J. Jackson, Janine George","doi":"10.21105/joss.06286","DOIUrl":"https://doi.org/10.21105/joss.06286","url":null,"abstract":"","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"20 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140425996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Giulia Crocioni, Dani L. Bodor, Coos Baakman, Farzaneh M. Parizi, Daniel T. Rademaker, Gayatri Ramakrishnan, S. A. van der Burg, Dario F. Marzella, João M. C. Teixeira, Li C. Xue
DeepRank2, a deep
DeepRank2
{"title":"DeepRank2: Mining 3D Protein Structures with Geometric\u0000Deep Learning","authors":"Giulia Crocioni, Dani L. Bodor, Coos Baakman, Farzaneh M. Parizi, Daniel T. Rademaker, Gayatri Ramakrishnan, S. A. van der Burg, Dario F. Marzella, João M. C. Teixeira, Li C. Xue","doi":"10.21105/joss.05983","DOIUrl":"https://doi.org/10.21105/joss.05983","url":null,"abstract":"DeepRank2, a deep","PeriodicalId":503081,"journal":{"name":"Journal of Open Source Software","volume":"13 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140425261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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