Related papers: Implementation strategies in phonopy and phono3py
Computational physics increasingly depends on large simulation datasets generated by software that remains under active development for many years. In such settings, reproducibility requires not only well documented data but also explicit…
Here practical aspects of conducting research via computer simulations are discussed. The following issues are addressed: software engineering, object-oriented software development, programming style, macros, make files, scripts, libraries,…
We review results of papers written on the topic of polynomial amoebas with an emphasis on computational aspects of the topic. The polynomial amoebas have a lot of applications in various domains of science. Computation of the amoeba for a…
Many biological and physical systems exhibit behaviour at multiple spatial, temporal or population scales. Multiscale processes provide challenges when they are to be simulated using numerical techniques. While coarser methods such as…
This brief paper: (1) Discusses strategies to generate random test cases that can be used to extensively test any Linear Distance Program (LDP) software. (2) Gives three numerical examples of input cases generated by this strategy that…
Spectroscopy is the most important method for probing the structure of molecules. However, predicting molecular spectra on classical computers is computationally expensive, with the most accurate methods having a cost that grows…
Simulation is a foundational tool for the analysis and testing of cyber-physical systems (CPS), underpinning activities such as algorithm development, runtime monitoring, and system verification. As CPS grow in complexity and scale,…
A hidden Markov process is a well known concept in information theory and is used for a vast range of applications such as speech recognition and error correction. We bridge between two disciplines, experimental physics and advanced…
Effective harmonic methods allow for calculating temperature dependent phonon frequencies by incorporating the anharmonic contributions into an effective harmonic Hamiltonian. The systematic errors arising from such an approximation are…
Significant developments made in quantum hardware and error correction recently have been driving quantum computing towards practical utility. However, gaps remain between abstract quantum algorithmic development and practical applications…
We propose protocols for acquiring speech materials, making them reusable for future investigations, and presenting them for subjective experiments. We also provide means to evaluate existing speech materials' compatibility with target…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
In this letter, we show how the Survey Propagation algorithm can be generalized to include external forcing messages, and used to address selectively an exponential number of glassy ground states. These capabilities can be used to explore…
Probabilistic programming is a growing area that strives to make statistical analysis more accessible, by separating probabilistic modelling from probabilistic inference. In practice this decoupling is difficult. No single inference…
Quantum field theories are the cornerstones of modern physics, providing relativistic and quantum mechanical descriptions of physical systems at the most fundamental level. Simulating real-time dynamics within these theories remains elusive…
We introduce Nosey (Nasalance Open Source Estimation sYstem), a low-cost, customizable, 3D-printed system for recording acoustic nasalance data that we have made available as open-source hardware (http://github.com/phoneticslab/nosey). We…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
We introduce DisCoPy, an open source toolbox for computing with monoidal categories. The library provides an intuitive syntax for defining string diagrams and monoidal functors. Its modularity allows the efficient implementation of…
One of the core research questions in the theory of quantum computing is to find out to what precise extent the classical simulation of a noisy quantum circuits is possible and where potential quantum advantages can set in. In this work, we…
We present results of an extensive test program of a group of pseudorandom number generators which are commonly used in the applications of physics, in particular in Monte Carlo simulations. The generators include public domain programs,…