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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
MatsubaraFunctions.jl: An equilibrium Green's function library in the Julia programming language

Dominik Kiese, Anxiang Ge, Nepomuk Ritz, Jan von Delft, Nils Wentzell

SciPost Phys. Codebases 24 (2024) · published 11 January 2024 | · pdf

The Matsubara Green's function formalism stands as a powerful technique for computing the thermodynamic characteristics of interacting quantum many-particle systems at finite temperatures. In this manuscript, our focus centers on introducing MatsubaraFunctions.jl, a Julia library that implements data structures for generalized n-point Green's functions on Matsubara frequency grids. The package's architecture prioritizes user-friendliness without compromising the development of efficient solvers for quantum field theories in equilibrium. Following a comprehensive introduction of the fundamental types, we delve into a thorough examination of key facets of the interface. This encompasses avenues for accessing Green's functions, techniques for extrapolation and interpolation, as well as the incorporation of symmetries and a variety of parallelization strategies. Examples of increasing complexity serve to demonstrate the practical utility of the library, supplemented by discussions on strategies for sidestepping impediments to optimal performance.

1 citation
Codebase release 0.1 for MatsubaraFunctions.jl

Dominik Kiese, Anxiang Ge, Nepomuk Ritz, Jan von Delft, Nils Wentzell

SciPost Phys. Codebases 24-r0.1 (2024) · published 11 January 2024 | · src

The Matsubara Green's function formalism stands as a powerful technique for computing the thermodynamic characteristics of interacting quantum many-particle systems at finite temperatures. In this manuscript, our focus centers on introducing MatsubaraFunctions.jl, a Julia library that implements data structures for generalized n-point Green's functions on Matsubara frequency grids. The package's architecture prioritizes user-friendliness without compromising the development of efficient solvers for quantum field theories in equilibrium. Following a comprehensive introduction of the fundamental types, we delve into a thorough examination of key facets of the interface. This encompasses avenues for accessing Green's functions, techniques for extrapolation and interpolation, as well as the incorporation of symmetries and a variety of parallelization strategies. Examples of increasing complexity serve to demonstrate the practical utility of the library, supplemented by discussions on strategies for sidestepping impediments to optimal performance.

1 citation
Codebase release 2.2 for Pyqcm

Théo N. Dionne, Alexandre Foley, Moïse Rousseau, David Sénéchal

SciPost Phys. Codebases 23-r2.2 (2023) · published 20 December 2023 | · src

Pyqcm is a Python/C++ library that implements a few quantum cluster methods with an exact diagonalization impurity solver. Quantum cluster methods are used in the study of strongly correlated electrons to provide an approximate solution to Hubbard-like models. The methods covered by this library are Cluster Perturbation Theory (CPT), the Variational Cluster Approach (VCA) and Cellular (or Cluster) Dynamical Mean Field Theory (CDMFT). The impurity solver (the technique used to compute the cluster's interacting Green function) is exact diagonalization from sparse matrices, using the Lanczos algorithm and variants thereof. The core library is written in C++ for performance, but the interface is in Python, for ease of use and inter-operability with the numerical Python ecosystem. The library is distributed under the GPL license.

1 citation
Pyqcm: An open-source Python library for quantum cluster methods

Théo N. Dionne, Alexandre Foley, Moïse Rousseau, David Sénéchal

SciPost Phys. Codebases 23 (2023) · published 20 December 2023 | · pdf

Pyqcm is a Python/C++ library that implements a few quantum cluster methods with an exact diagonalization impurity solver. Quantum cluster methods are used in the study of strongly correlated electrons to provide an approximate solution to Hubbard-like models. The methods covered by this library are Cluster Perturbation Theory (CPT), the Variational Cluster Approach (VCA) and Cellular (or Cluster) Dynamical Mean Field Theory (CDMFT). The impurity solver (the technique used to compute the cluster's interacting Green function) is exact diagonalization from sparse matrices, using the Lanczos algorithm and variants thereof. The core library is written in C++ for performance, but the interface is in Python, for ease of use and inter-operability with the numerical Python ecosystem. The library is distributed under the GPL license.

1 citation
Codebase release 2.2 for HEJ

Jeppe R. Andersen, Bertrand Ducloué, Conor Elrick, Hitham Hassan, Andreas Maier, Graeme Nail, Jérémy Paltrinieri, Andreas Papaefstathiou, Jennifer M. Smillie

SciPost Phys. Codebases 21-r2.2 (2023) · published 6 December 2023 | · src

We present version 2.2 of the High Energy Jets (HEJ) Monte Carlo event generator for hadronic scattering processes at high energies. The new version adds support for two further processes of central phenomenological interest, namely the production of a W boson pair with equal charge together with two or more jets and the production of a Higgs boson with at least one jet. Furthermore, a new prediction for charged lepton pair production with high jet multiplicities is provided in the high-energy limit. The accuracy of HEJ 2.2 can be increased further through an enhanced interface to standard predictions based on conventional perturbation theory. We describe all improvements and provide extensive usage examples. HEJ 2.2 can be obtained from https://hej.hepforge.org.

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
Codebase release 0.0 for DFT2kp

João Victor V. Cassiano, Augusto de Lelis Araújo, Paulo E. Faria Junior, Gerson J. Ferreira

SciPost Phys. Codebases 25-r0.0 (2024) · published 5 February 2024 | · src

The $k\cdot p$ method, combined with group theory, is an efficient approach to obtain the low energy effective Hamiltonians of crystalline materials. Although the Hamiltonian coefficients are written as matrix elements of the generalized momentum operator $\pi= p+ p_{SOC}$ (including spin-orbit coupling corrections), their numerical values must be determined from outside sources, such as experiments or ab initio methods. Here, we develop a code to explicitly calculate the Kane (linear in crystal momentum) and Luttinger (quadratic in crystal momentum) parameters of $k\cdot p$ effective Hamiltonians directly from ab initio wavefunctions provided by Quantum ESPRESSO. Additionally, the code analyzes the symmetry transformations of the wavefunctions to optimize the final Hamiltonian. This is an optional step in the code, where it numerically finds the unitary transformation $U$ that rotates the basis towards an optimal symmetry-adapted representation informed by the user. Throughout the paper, we present the methodology in detail and illustrate the capabilities of the code applying it to a selection of relevant materials. Particularly, we show a "hands-on" example of how to run the code for graphene (with and without spin-orbit coupling). The code is open source and available at https://gitlab.com/dft2kp/dft2kp.

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 | · 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
Codebase release r1.4 for CoVVVR

Prasanth Shyamsundar, Jacob L. Scott, Stephen Mrenna, Konstantin T. Matchev, Kyoungchul Kong

SciPost Phys. Codebases 28-r1.4 (2024) · published 4 March 2024 | · src

Monte Carlo (MC) integration is an important calculational technique in the physical sciences. Practical considerations require that the calculations are performed as accurately as possible for a given set of computational resources. To improve the accuracy of MC integration, a number of useful variance reduction algorithms have been developed, including importance sampling and control variates. In this work, we demonstrate how these two methods can be applied simultaneously, thus combining their benefits. We provide a python wrapper, named CoVVVR, which implements our approach in the VEGAS program. The improvements are quantified with several benchmark examples from the literature.

1 citation

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