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Making digital objects FAIR in high energy physics: An implementation for Universal FeynRules Output (UFO) models 在高能物理中使数字对象公平:通用FeynRules输出(UFO)模型的实现
SciPost Physics Codebases Pub Date : 2022-09-20 DOI: 10.21468/scipostphyscodeb.13
M. Neubauer, Avik Roy, Zijun Wang
{"title":"Making digital objects FAIR in high energy physics: An implementation for Universal FeynRules Output (UFO) models","authors":"M. Neubauer, Avik Roy, Zijun Wang","doi":"10.21468/scipostphyscodeb.13","DOIUrl":"https://doi.org/10.21468/scipostphyscodeb.13","url":null,"abstract":"Research in the data-intensive discipline of high energy physics (HEP) often relies on domain-specific digital contents. Reproducibility of research relies on proper preservation of these digital objects. This paper reflects on the interpretation of principles of Findability, Accessibility, Interoperability, and Reusability (FAIR) in such context and demonstrates its implementation by describing the development of an end-to-end support infrastructure for preserving and accessing Universal FeynRules Output (UFO) models guided by the FAIR principles. UFO models are custom-made python libraries used by the HEP community for Monte Carlo simulation of collider physics events. Our framework provides simple but robust tools to preserve and access the UFO models and corresponding metadata in accordance with the FAIR principles.","PeriodicalId":430271,"journal":{"name":"SciPost Physics Codebases","volume":"32 6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115227632","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}
引用次数: 4
Pychastic: Precise Brownian dynamics using Taylor-Itō integrators in Python Pychastic:在Python中使用taylor - itchi积分器的精确布朗动力学
SciPost Physics Codebases Pub Date : 2022-09-09 DOI: 10.21468/scipostphyscodeb.11
R. Waszkiewicz, Maciej Bartczak, Kamil Kolasa, M. Lisicki
{"title":"Pychastic: Precise Brownian dynamics using Taylor-Itō integrators in Python","authors":"R. Waszkiewicz, Maciej Bartczak, Kamil Kolasa, M. Lisicki","doi":"10.21468/scipostphyscodeb.11","DOIUrl":"https://doi.org/10.21468/scipostphyscodeb.11","url":null,"abstract":"In the last decade, Python-powered physics simulations ecosystem has been growing steadily, allowing greater interoperability, and becoming an important tool in numerical exploration of physical phenomena, particularly in soft matter systems. Driven by the need for fast and precise numerical integration in colloidal dynamics, here we formulate the problem of Brownian Dynamics (BD) in a mathematically consistent formalism of the Itō calculus, and develop a Python package to assist numerical computations. We show that, thanks to the automatic differentiation packages, the classical truncated Taylor-Itō integrators can be implemented without the burden of computing the derivatives of the coefficient functions beforehand. Furthermore, we show how to circumvent the difficulties of BD simulations such as calculations of the divergence of the mobility tensor in the diffusion equation and discontinuous trajectories encountered when working with dynamics on S^2S2 and SO(3)SO(3). The resulting Python package, Pychastic, is capable of performing BD simulations including hydrodynamic interactions at speeds comparable to dedicated implementations in lower-level programming languages, but with a much simpler end-user interface.","PeriodicalId":430271,"journal":{"name":"SciPost Physics Codebases","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114332638","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}
引用次数: 0
pyBumpHunter: A model independent bump hunting tool in Python for high energy physics analyses pyBumpHunter: Python中独立于模型的碰撞搜索工具，用于高能物理分析
SciPost Physics Codebases Pub Date : 2022-08-31 DOI: 10.21468/scipostphyscodeb.15
L. Vaslin, S. Calvet, Vincent Barra, J. Donini
{"title":"pyBumpHunter: A model independent bump hunting tool in Python for high energy physics analyses","authors":"L. Vaslin, S. Calvet, Vincent Barra, J. Donini","doi":"10.21468/scipostphyscodeb.15","DOIUrl":"https://doi.org/10.21468/scipostphyscodeb.15","url":null,"abstract":"The BumpHunter algorithm is widely used in the search for new particles in High Energy Physics analysis. This algorithm offers the advantage of evaluating the local and global p-values of a localized deviation in the observed data without making any hypothesis on the supposed signal. The increasing popularity of the Python programming language motivated the development of a new public implementation of this algorithm in Python, called pyBumpHunter, together with several improvements and additional features. It is the first public implementation of the BumpHunter algorithm to be added to Scikit-HEP. This paper presents in detail the BumpHunter algorithm as well as all the features proposed in this implementation. All these features have been tested in order to demonstrate their behaviour and performance.","PeriodicalId":430271,"journal":{"name":"SciPost Physics Codebases","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122330833","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}
引用次数: 3
Codebase release 1.0 for SpinParser SpinParser的代码库版本1.0
SciPost Physics Codebases Pub Date : 2022-08-24 DOI: 10.21468/scipostphyscodeb.5-r1.0
F. Buessen
{"title":"Codebase release 1.0 for SpinParser","authors":"F. Buessen","doi":"10.21468/scipostphyscodeb.5-r1.0","DOIUrl":"https://doi.org/10.21468/scipostphyscodeb.5-r1.0","url":null,"abstract":"We present the SpinParser open-source software [https://github.com/fbuessen/SpinParser].\u0000The software is designed to perform pseudofermion functional renormalization group (pf-FRG) calculations for frustrated quantum magnets in two and three spatial dimensions. \u0000It aims to make such calculations readily accessible without the need to write specialized program code; instead, custom lattice graphs and microscopic spin models can be defined as plain-text input files. \u0000Underlying symmetries of the model are automatically analyzed and exploited by the numerical core written in C++ in order to optimize the performance across large-scale shared memory and/or distributed memory computing platforms.","PeriodicalId":430271,"journal":{"name":"SciPost Physics Codebases","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125577054","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}
引用次数: 1
Codebase release 3.4 for NetKet NetKet的代码库版本3.4
SciPost Physics Codebases Pub Date : 2022-08-24 DOI: 10.21468/scipostphyscodeb.7-r3.4
F. Vicentini, Damian Hofmann, Attila Szabó, Dian Wu, Christopher Roth, Clemens Giuliani, Gabriel Pescia, J. Nys, Vladimir Vargas-Calderón, N. Astrakhantsev, Giuseppe Carleo
{"title":"Codebase release 3.4 for NetKet","authors":"F. Vicentini, Damian Hofmann, Attila Szabó, Dian Wu, Christopher Roth, Clemens Giuliani, Gabriel Pescia, J. Nys, Vladimir Vargas-Calderón, N. Astrakhantsev, Giuseppe Carleo","doi":"10.21468/scipostphyscodeb.7-r3.4","DOIUrl":"https://doi.org/10.21468/scipostphyscodeb.7-r3.4","url":null,"abstract":"We introduce version 3 of NetKet, the machine learning toolbox for many-body quantum physics.\u0000NetKet is built around neural quantum states and provides efficient algorithms for their evaluation and optimization.\u0000This new version is built on top of JAX, a differentiable programming and accelerated linear algebra framework for the Python programming language.\u0000The most significant new feature is the possibility to define arbitrary neural network ansätze in pure Python code using the concise notation of machine-learning frameworks, which allows for just-in-time compilation as well as the implicit generation of gradients thanks to automatic differentiation.\u0000NetKet 3 also comes with support for GPU and TPU accelerators, advanced support for discrete symmetry groups, chunking to scale up to thousands of degrees of freedom, drivers for quantum dynamics applications, and improved modularity, allowing users to use only parts of the toolbox as a foundation for their own code.","PeriodicalId":430271,"journal":{"name":"SciPost Physics Codebases","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114424467","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}
引用次数: 1
Codebase release 0.5 for HarmonicBalance.jl Codebase release 0.5 for HarmonicBalance.jl
SciPost Physics Codebases Pub Date : 2022-08-24 DOI: 10.21468/scipostphyscodeb.6-r0.5
J. Košata, Javier del Pino, Toni L. Heugel, O. Zilberberg
{"title":"Codebase release 0.5 for HarmonicBalance.jl","authors":"J. Košata, Javier del Pino, Toni L. Heugel, O. Zilberberg","doi":"10.21468/scipostphyscodeb.6-r0.5","DOIUrl":"https://doi.org/10.21468/scipostphyscodeb.6-r0.5","url":null,"abstract":"HarmonicBalance.jl is a publicly available Julia package designed to\u0000simplify and solve systems of periodic time-dependent nonlinear ordinary\u0000differential equations. Time dependence of the system parameters is\u0000treated with the harmonic balance method, which approximates the\u0000system’s behaviour as a set of harmonic terms with slowly-varying\u0000amplitudes. Under this approximation, the set of all possible\u0000steady-state responses follows from the solution of a polynomial system.\u0000In HarmonicBalance.jl, we combine harmonic balance with contemporary\u0000implementations of symbolic algebra and the homotopy continuation method\u0000to numerically determine all steady-state solutions and their associated\u0000fluctuation dynamics. For the exploration of involved steady-state\u0000topologies, we provide a simple graphical user interface, allowing for\u0000arbitrary solution observables and phase diagrams. HarmonicBalance.jl is\u0000a free software available at https://github.com/NonlinearOscillations/HarmonicBalance.jl.","PeriodicalId":430271,"journal":{"name":"SciPost Physics Codebases","volume":"44 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132898713","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}
引用次数: 0
Codebase release 0.1 for jVMC jVMC的代码库release 0.1
SciPost Physics Codebases Pub Date : 2022-08-23 DOI: 10.21468/scipostphyscodeb.2-r0.1
M. Schmitt, M. Reh
{"title":"Codebase release 0.1 for jVMC","authors":"M. Schmitt, M. Reh","doi":"10.21468/scipostphyscodeb.2-r0.1","DOIUrl":"https://doi.org/10.21468/scipostphyscodeb.2-r0.1","url":null,"abstract":"The introduction of Neural Quantum States (NQS) has recently given a new twist to variational Monte Carlo (VMC). The ability to systematically reduce the bias of the wave function ansatz renders the approach widely applicable. However, performant implementations are crucial to reach the numerical state of the art. Here, we present a Python codebase that supports arbitrary NQS architectures and model Hamiltonians. Additionally leveraging automatic differentiation, just-in-time compilation to accelerators, and distributed computing, it is designed to facilitate the composition of efficient NQS algorithms.","PeriodicalId":430271,"journal":{"name":"SciPost Physics Codebases","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125883826","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}
引用次数: 1
Codebase release 1.0 for BlockGen Codebase release 1.0 for BlockGen
SciPost Physics Codebases Pub Date : 2022-08-23 DOI: 10.21468/scipostphyscodeb.3-r1.0
E. Bothmann, W. Giele, S. Höche, J. Isaacson, M. Knobbe
{"title":"Codebase release 1.0 for BlockGen","authors":"E. Bothmann, W. Giele, S. Höche, J. Isaacson, M. Knobbe","doi":"10.21468/scipostphyscodeb.3-r1.0","DOIUrl":"https://doi.org/10.21468/scipostphyscodeb.3-r1.0","url":null,"abstract":"The compute efficiency of Monte-Carlo event generators for the\u0000Large Hadron Collider is expected to become a major bottleneck for\u0000simulations in the high-luminosity phase. Aiming at the development\u0000of a full-fledged generator for modern GPUs, we study the performance\u0000of various recursive strategies to compute multi-gluon tree-level amplitudes.\u0000We investigate the scaling of the algorithms on both CPU and GPU hardware.\u0000Finally, we provide practical recommendations as well as baseline implementations\u0000for the development of future simulation programs. The GPU implementations can be\u0000found at: https://www.gitlab.com/ebothmann/blockgen-archive.","PeriodicalId":430271,"journal":{"name":"SciPost Physics Codebases","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128609137","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}
引用次数: 0
Codebase release 0.3 for ITensor Codebase release 0.3 for tenensor
SciPost Physics Codebases Pub Date : 2022-08-23 DOI: 10.21468/scipostphyscodeb.4-r0.3
M. Fishman, S. White, E. Stoudenmire
{"title":"Codebase release 0.3 for ITensor","authors":"M. Fishman, S. White, E. Stoudenmire","doi":"10.21468/scipostphyscodeb.4-r0.3","DOIUrl":"https://doi.org/10.21468/scipostphyscodeb.4-r0.3","url":null,"abstract":"ITensor is a system for programming tensor network calculations with an interface modeled on \u0000tensor diagrams, allowing users to focus on the connectivity of a tensor network without manually bookkeeping tensor indices. The ITensor interface rules out common programming errors and enables rapid prototyping of algorithms. After discussing the philosophy behind the ITensor approach, we show examples of each part of the interface including Index objects, the ITensor product operator, tensor factorizations, tensor storage types, algorithms for matrix product state (MPS) and matrix product operator (MPO) tensor networks, quantum number conserving block sparse tensors, and the NDTensors library. We also review publications that have used ITensor for quantum many-body physics and for other areas where tensor networks are increasingly applied. To conclude we discuss promising features and optimizations to be added in the future.","PeriodicalId":430271,"journal":{"name":"SciPost Physics Codebases","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115473331","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}
引用次数: 36
Codebase release 2.0 for ALF (Algorithms for Lattice Fermions) ALF (Lattice Fermions算法)代码库2.0版
SciPost Physics Codebases Pub Date : 2022-08-22 DOI: 10.21468/scipostphyscodeb.1-r2.0
F. Assaad, M. Bercx, F. Goth, Anika Götz, J. Hofmann, Emilie Huffman, Zi-Li Liu, F. Parisen Toldin, J. Portela, Jonas Schwab
{"title":"Codebase release 2.0 for ALF (Algorithms for Lattice Fermions)","authors":"F. Assaad, M. Bercx, F. Goth, Anika Götz, J. Hofmann, Emilie Huffman, Zi-Li Liu, F. Parisen Toldin, J. Portela, Jonas Schwab","doi":"10.21468/scipostphyscodeb.1-r2.0","DOIUrl":"https://doi.org/10.21468/scipostphyscodeb.1-r2.0","url":null,"abstract":"The Algorithms for Lattice Fermions package provides a general code\u0000for the finite-temperature and projective auxiliary-field quantum Monte\u0000Carlo algorithm. The code is engineered to be able to simulate any model\u0000that can be written in terms of sums of single-body operators, of\u0000squares of single-body operators and single-body operators coupled to a\u0000bosonic field with given dynamics. The package includes five predefined\u0000model classes: SU(N) Kondo, SU(N) Hubbard, SU(N) t-V and SU(N) models\u0000with long range Coulomb repulsion on honeycomb, square and N-leg\u0000lattices, as well as Z_2Z2\u0000unconstrained lattice gauge theories coupled to fermionic and\u0000Z_2Z2\u0000matter. An implementation of the stochastic Maximum Entropy method is\u0000also provided. One can download the code from our Git instance at\u0000https://git.physik.uni-wuerzburg.de/ALF/ALF/-/tree/ALF-2.0 and sign in\u0000to file issues.","PeriodicalId":430271,"journal":{"name":"SciPost Physics Codebases","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122023847","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}
引用次数: 0
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