Publications

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HarmonicBalance.jl: A Julia suite for nonlinear dynamics using harmonic balance

Jan Košata, Javier del Pino, Toni L. Heugel, Oded Zilberberg

SciPost Phys. Codebases 6 (2022) · published 24 August 2022 | · pdf

HarmonicBalance.jl is a publicly available Julia package designed to simplify and solve systems of periodic time-dependent nonlinear ordinary differential equations. Time dependence of the system parameters is treated with the harmonic balance method, which approximates the system's behaviour as a set of harmonic terms with slowly-varying amplitudes. Under this approximation, the set of all possible steady-state responses follows from the solution of a polynomial system. In HarmonicBalance.jl, we combine harmonic balance with contemporary implementations of symbolic algebra and the homotopy continuation method to numerically determine all steady-state solutions and their associated fluctuation dynamics. For the exploration of involved steady-state topologies, we provide a simple graphical user interface, allowing for arbitrary solution observables and phase diagrams. HarmonicBalance.jl is a free software available at https://github.com/NonlinearOscillations/HarmonicBalance.jl.

4 citations
GrassmannTN: A Python package for Grassmann tensor network computations

Atis Yosprakob

SciPost Phys. Codebases 20 (2023) · published 16 November 2023 | · pdf

We present GrassmannTN, a Python package for the computation of the Grassmann tensor network. The package is built to assist in the numerical computation without the need to input the fermionic sign factor manually. It prioritizes coding readability by designing every tensor manipulating function around the tensor subscripts. The computation of the Grassmann tensor renormalization group and Grassmann isometries using GrassmannTN are given as the use case examples.

3 citations
pyBumpHunter: A model independent bump hunting tool in Python for high energy physics analyses

Louis Vaslin, Samuel Calvet, Vincent Barra, Julien Donini

SciPost Phys. Codebases 15 (2023) · published 14 July 2023 | · pdf

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.

3 citations
Codebase release 2.0 for ALF (Algorithms for Lattice Fermions)

F. F. Assaad, M. Bercx, F. Goth, A. Götz, J. S. Hofmann, E. Huffman, Z. Liu, F. Parisen Toldin, J. S. E. Portela, J. Schwab

SciPost Phys. Codebases 1-r2.0 (2022) · published 22 August 2022 | · src

The Algorithms for Lattice Fermions package provides a general code for the finite-temperature and projective auxiliary-field quantum Monte Carlo algorithm. The code is engineered to be able to simulate any model that can be written in terms of sums of single-body operators, of squares of single-body operators and single-body operators coupled to a bosonic field with given dynamics. The package includes five pre-defined model classes: SU(N) Kondo, SU(N) Hubbard, SU(N) t-V and SU(N) models with long range Coulomb repulsion on honeycomb, square and N-leg lattices, as well as $Z_2$ unconstrained lattice gauge theories coupled to fermionic and $Z_2$ matter. An implementation of the stochastic Maximum Entropy method is also provided. One can download the code from our Git instance at https://git.physik.uni-wuerzburg.de/ALF/ALF/-/tree/ALF-2.0 and sign in to file issues.

3 citations
Nevanlinna.jl: A Julia implementation of Nevanlinna analytic continuation

Kosuke Nogaki, Jiani Fei, Emanuel Gull, Hiroshi Shinaoka

SciPost Phys. Codebases 19 (2023) · published 13 November 2023 | · pdf

We introduce a Julia implementation of the recently proposed Nevanlinna analytic continuation method. The method is based on Nevanlinna interpolants and inherently preserves the causality of a response function due to its construction. For theoretical calculations without statistical noise, this continuation method is a powerful tool to extract real-frequency information from numerical input data on the Matsubara axis. This method has been applied to first-principles calculations of correlated materials. This paper presents its efficient and full-featured open-source implementation of the method including the Hamburger moment problem and smoothing.

2 citations
Pychastic: Precise Brownian dynamics using Taylor-Itō integrators in Python

Radost Waszkiewicz, Maciej Bartczak, Kamil Kolasa, Maciej Lisicki

SciPost Phys. Codebases 11 (2023) · published 3 April 2023 | · pdf

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 $S^2$ and $SO(3)$. 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.

2 citations
LinReTraCe: The linear response transport centre

Matthias Pickem, Emanuele Maggio, Jan M. Tomczak

SciPost Phys. Codebases 16 (2023) · published 17 July 2023 | · pdf

We describe the "Linear Response Transport Centre" (LinReTraCe), a package for the simulation of transport properties of solids. LinReTraCe captures quantum (in)coherence effects beyond semi-classical Boltzmann techniques, while incurring similar numerical costs. The enabling algorithmic innovation is a semi-analytical evaluation of Kubo formulae for resistivities and the coefficients of Hall, Seebeck and Nernst. We detail the program's architecture, its interface and usage with electronic-structure packages such as WIEN2k, VASP, and Wannier90, as well as versatile tight-binding settings.

2 citations
Codebase release 3.4 for NetKet

Filippo Vicentini, Damian Hofmann, Attila Szabó, Dian Wu, Christopher Roth, Clemens Giuliani, Gabriel Pescia, Jannes Nys, Vladimir Vargas-Calderón, Nikita Astrakhantsev, Giuseppe Carleo

SciPost Phys. Codebases 7-r3.4 (2022) · published 24 August 2022 | · src

We introduce version 3 of NetKet, the machine learning toolbox for many-body quantum physics. NetKet is built around neural-network quantum states and provides efficient algorithms for their evaluation and optimization. This new version is built on top of JAX, a differentiable programming and accelerated linear algebra framework for the Python programming language. The 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. NetKet 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.

2 citations
Codebase release 1.0 for Nevanlinna.jl

Kosuke Nogaki, Jiani Fei, Emanuel Gull, Hiroshi Shinaoka

SciPost Phys. Codebases 19-r1.0 (2023) · published 13 November 2023 | · src

We introduce a Julia implementation of the recently proposed Nevanlinna analytic continuation method. The method is based on Nevanlinna interpolants and inherently preserves the causality of a response function due to its construction. For theoretical calculations without statistical noise, this continuation method is a powerful tool to extract real-frequency information from numerical input data on the Matsubara axis. This method has been applied to first-principles calculations of correlated materials. This paper presents its efficient and full-featured open-source implementation of the method including the Hamburger moment problem and smoothing.

1 citation
Codebase release 1.3 for GrassmannTN

Atis Yosprakob

SciPost Phys. Codebases 20-r1.3 (2023) · published 16 November 2023 | · src

We present GrassmannTN, a Python package for the computation of the Grassmann tensor network. The package is built to assist in the numerical computation without the need to input the fermionic sign factor manually. It prioritizes coding readability by designing every tensor manipulating function around the tensor subscripts. The computation of the Grassmann tensor renormalization group and Grassmann isometries using GrassmannTN are given as the use case examples.

1 citation

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