Publications

Order by: publication date number of citations

• Codebase release 0.2 for Pychastic

  Radost Waszkiewicz, Maciej Bartczak, Kamil Kolasa, Maciej Lisicki

  SciPost Phys. Codebases 11-r0.2 (2023) · published 3 April 2023 | Toggle abstract · src

  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.

  1 citation

• 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 | Toggle abstract · 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

• Automatic transformation of irreducible representations for efficient contraction of tensors with cyclic group symmetry

  Yang Gao, Phillip Helms, Garnet Kin-Lic Chan, Edgar Solomonik

  SciPost Phys. Codebases 10 (2023) · published 24 February 2023 | Toggle abstract · pdf

  Tensor contractions are ubiquitous in computational chemistry and physics, where tensors generally represent states or operators and contractions express the algebra of these quantities. In this context, the states and operators often preserve physical conservation laws, which are manifested as group symmetries in the tensors. These group symmetries imply that each tensor has block sparsity and can be stored in a reduced form. For nontrivial contractions, the memory footprint and cost are lowered, respectively, by a linear and a quadratic factor in the number of symmetry sectors. State-of-the-art tensor contraction software libraries exploit this opportunity by iterating over blocks or using general block-sparse tensor representations. Both approaches entail overhead in performance and code complexity. With intuition aided by tensor diagrams, we present a technique, irreducible representation alignment, which enables efficient handling of Abelian group symmetries via only dense tensors, by using contraction-specific reduced forms. This technique yields a general algorithm for arbitrary group symmetric contractions, which we implement in Python and apply to a variety of representative contractions from quantum chemistry and tensor network methods. As a consequence of relying on only dense tensor contractions, we can easily make use of efficient batched matrix multiplication via Intel's MKL and distributed tensor contraction via the Cyclops library, achieving good efficiency and parallel scalability on up to 4096 Knights Landing cores of a supercomputer.

  1 citation

• Codebase release 1.3 for SymTensor

  Yang Gao, Phillip Helms, Garnet Kin-Lic Chan, Edgar Solomonik

  SciPost Phys. Codebases 10-r1.3 (2023) · published 24 February 2023 | Toggle abstract · src

  Tensor contractions are ubiquitous in computational chemistry and physics, where tensors generally represent states or operators and contractions express the algebra of these quantities. In this context, the states and operators often preserve physical conservation laws, which are manifested as group symmetries in the tensors. These group symmetries imply that each tensor has block sparsity and can be stored in a reduced form. For nontrivial contractions, the memory footprint and cost are lowered, respectively, by a linear and a quadratic factor in the number of symmetry sectors. State-of-the-art tensor contraction software libraries exploit this opportunity by iterating over blocks or using general block-sparse tensor representations. Both approaches entail overhead in performance and code complexity. With intuition aided by tensor diagrams, we present a technique, irreducible representation alignment, which enables efficient handling of Abelian group symmetries via only dense tensors, by using contraction-specific reduced forms. This technique yields a general algorithm for arbitrary group symmetric contractions, which we implement in Python and apply to a variety of representative contractions from quantum chemistry and tensor network methods. As a consequence of relying on only dense tensor contractions, we can easily make use of efficient batched matrix multiplication via Intel's MKL and distributed tensor contraction via the Cyclops library, achieving good efficiency and parallel scalability on up to 4096 Knights Landing cores of a supercomputer.

  1 citation

• Efficient and scalable path integral Monte Carlo simulations with worm-type updates for Bose-Hubbard and XXZ models

  Nicolas Sadoune, Lode Pollet

  SciPost Phys. Codebases 9 (2022) · published 29 November 2022 | Toggle abstract · pdf

  We present a novel and open-source implementation of the worm algorithm, which is an algorithm to simulate Bose-Hubbard and sign-positive spin models using a path-integral representation of the partition function. The code can deal with arbitrary lattice structures and assumes spin-exchange terms, or bosonic hopping amplitudes, between nearest-neighbor sites, and local or nearest-neighbor interactions of the density-density type. We explicitly demonstrate the near-linear scaling of the algorithm with respect to the system volume and the inverse temperature and analyze the autocorrelation times in the vicinity of a $U(1)$ second order phase transition. The code is written in such a way that extensions to other lattice models as well as closely-related sign-positive models can be done straightforwardly on top of the provided framework.

  6 citations

• Codebase release 1.0 for Worm Algorithm for Bose-Hubbard and XXZ Models

  Nicolas Sadoune, Lode Pollet

  SciPost Phys. Codebases 9-r1.0 (2022) · published 29 November 2022 | Toggle abstract · src

  We present a novel and open-source implementation of the worm algorithm, which is an algorithm to simulate Bose-Hubbard and sign-positive spin models using a path-integral representation of the partition function. The code can deal with arbitrary lattice structures and assumes spin-exchange terms, or bosonic hopping amplitudes, between nearest-neighbor sites, and local or nearest-neighbor interactions of the density-density type. We explicitly demonstrate the near-linear scaling of the algorithm with respect to the system volume and the inverse temperature and analyze the autocorrelation times in the vicinity of a $U(1)$ second order phase transition. The code is written in such a way that extensions to other lattice models as well as closely-related sign-positive models can be done straightforwardly on top of the provided framework.

  1 citation

• A comprehensive guide to the physics and usage of PYTHIA 8.3

  Christian Bierlich, Smita Chakraborty, Nishita Desai, Leif Gellersen, Ilkka Helenius, Philip Ilten, Leif Lönnblad, Stephen Mrenna, Stefan Prestel, Christian T. Preuss, Torbjörn Sjöstrand, Peter Skands, Marius Utheim, Rob Verheyen

  SciPost Phys. Codebases 8 (2022) · published 10 November 2022 | Toggle abstract · pdf

  This manual describes the Pythia event generator, the most recent version of an evolving physics tool used to answer fundamental questions in particle physics. The program is most often used to generate high-energy-physics collision "events", i.e. sets of particles produced in association with the collision of two incoming high-energy particles, but has several uses beyond that. The guiding philosophy is to produce and re-produce properties of experimentally obtained collisions as accurately as possible. The program includes a wide ranges of reactions within and beyond the Standard Model, and extending to heavy ion physics. Emphasis is put on phenomena where strong interactions play a major role. The manual contains both pedagogical and practical components. All included physics models are described in enough detail to allow the user to obtain a cursory overview of used assumptions and approximations, enabling an informed evaluation of the program output. A number of the most central algorithms are described in enough detail that the main results of the program can be reproduced independently, allowing further development of existing models or the addition of new ones. Finally, a chapter dedicated fully to the user is included towards the end, providing pedagogical examples of standard use cases, and a detailed description of a number of external interfaces. The program code, the online manual, and the latest version of this print manual can be found on the Pythia web page: https://www.pythia.org/.

  172 citations

• Codebase release 8.3 for PYTHIA

  Christian Bierlich, Smita Chakraborty, Nishita Desai, Leif Gellersen, Ilkka Helenius, Philip Ilten, Leif Lönnblad, Stephen Mrenna, Stefan Prestel, Christian T. Preuss, Torbjörn Sjöstrand, Peter Skands, Marius Utheim, Rob Verheyen

  SciPost Phys. Codebases 8-r8.3 (2022) · published 10 November 2022 | Toggle abstract · src

  This manual describes the Pythia event generator, the most recent version of an evolving physics tool used to answer fundamental questions in particle physics. The program is most often used to generate high-energy-physics collision "events", i.e. sets of particles produced in association with the collision of two incoming high-energy particles, but has several uses beyond that. The guiding philosophy is to produce and re-produce properties of experimentally obtained collisions as accurately as possible. The program includes a wide ranges of reactions within and beyond the Standard Model, and extending to heavy ion physics. Emphasis is put on phenomena where strong interactions play a major role. The manual contains both pedagogical and practical components. All included physics models are described in enough detail to allow the user to obtain a cursory overview of used assumptions and approximations, enabling an informed evaluation of the program output. A number of the most central algorithms are described in enough detail that the main results of the program can be reproduced independently, allowing further development of existing models or the addition of new ones. Finally, a chapter dedicated fully to the user is included towards the end, providing pedagogical examples of standard use cases, and a detailed description of a number of external interfaces. The program code, the online manual, and the latest version of this print manual can be found on the Pythia web page: https://www.pythia.org/.

  3 citations

• NetKet 3: Machine Learning Toolbox for Many-Body Quantum Systems

  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 (2022) · published 24 August 2022 | Toggle abstract · pdf

  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.

  38 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 | Toggle abstract · 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