Related papers: XMDS2: Fast, scalable simulation of coupled stocha…
Multidimensional scaling (MDS) is a popular dimensionality reduction techniques that has been widely used for network visualization and cooperative localization. However, the traditional stress minimization formulation of MDS necessitates…
The family of Multiscale Hybrid-Mixed (MHM) finite element methods has received considerable attention from the mathematics and engineering community in the last few years. The MHM methods allow solving highly heterogeneous problems on…
This is the fourth major release of the xSPDE toolbox, which solves stochastic partial and ordinary differential equations, with applications in biology, chemistry, engineering, medicine, physics and quantum technologies. It computes…
A large part of modern research, especially in the broad field of complex systems, relies on the numerical integration of PDEs, with and without stochastic noise. This is usually done with eiher in-house made codes or external packages like…
HDSDP is a numerical software solving the semidefinite programming problems. The main framework of HDSDP resembles the dual-scaling interior point solver DSDP [BY2008] and several new features, including a dual method based on the…
A template-based generic programming approach was presented in a previous paper that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded…
Partial differential equations (PDEs) are crucial in modeling diverse phenomena across scientific disciplines, including seismic and medical imaging, computational fluid dynamics, image processing, and neural networks. Solving these PDEs at…
Numerical solutions of partial differential equations enable a broad range of scientific research. The Dedalus Project is a flexible, open-source, parallelized computational framework for solving general partial differential equations using…
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…
LIBS2ML is a library based on scalable second order learning algorithms for solving large-scale problems, i.e., big data problems in machine learning. LIBS2ML has been developed using MEX files, i.e., C++ with MATLAB/Octave interface to…
Quantum computing enables parallelism through superposition and entanglement and offers advantages over classical computing architectures. However, due to the limitations of current quantum hardware in the noisy intermediate-scale quantum…
Phase diagrams (PDs) illustrate the relative stability of competing phases under varying conditions, serving as critical tools for synthesizing complex materials. Reliable phase diagrams rely on precise free energy calculations, which are…
Matrix Distributed Processing (MDP) is a C++ library for fast development of efficient parallel algorithms. It constitues the core of FermiQCD. MDP enables programmers to focus on algorithms, while parallelization is dealt with…
This paper introduces PolyDiM, an open-source C++ library tailored for the development and implementation of polytopal discretization methods for partial differential equations. The library provides robust and modular tools to support…
Ordinary differential equation models facilitate the understanding of cellular signal transduction and other biological processes. However, for large and comprehensive models, the computational cost of simulating or calibrating can be…
Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be…
We present an XML-based simulation authoring environment. The proposed description language allows to describe mathematical objects such as systems of ordinary differential equations, partial differential equations in two dimensions, or…
Simflowny is an open platform which automatically generates efficient parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support simultaneously a quite…
Multidimensional scaling (MDS) is a dimensionality reduction tool used for information analysis, data visualization and manifold learning. Most MDS procedures embed data points in low-dimensional Euclidean (flat) domains, such that…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…