相关论文: MeMC: A package for monte-carlo simulations of sph…
Modeling artificial scanning electron microscope (SEM) and scanning ion microscope images has recently become important. This is because of the need to provide repeatable images with a priori determined parameters. Modeled artificial images…
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…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
Monte Carlo simulation is an essential component of experimental particle physics in all the phases of its life-cycle: the investigation of the physics reach of detector concepts, the design of facilities and detectors, the development and…
nimble is an R package for constructing algorithms and conducting inference on hierarchical models. The nimble package provides a unique combination of flexible model specification and the ability to program model-generic algorithms.…
We propose to use a compound of magnetic nanoparticles (20-100 nm) embedded in a flexible polymer (Polydimethylsiloxane PDMS) to filter circulating tumor cells (CTCs). The analysis of CTCs is an emerging tool for cancer biology research and…
A general purpose, self-adapting, Monte Carlo (MC) event generator (simulator) is described. The high efficiency of the MC, that is small maximum weight or variance of the MC weight is achieved by means of dividing the integration domain…
Here we present the derivation, description and results of a Monte Carlo-based algorithm for simulating inelastic scattering of photo-electrons when passing through some scattering medium, such as a gas atmosphere or a solid material. The…
The development of a package for the management of physics data is described: its design, implementation and computational benchmarks. This package improves the data management tools originally developed for Geant4 physics models based on…
A binary format with lists of particle state information, for interchanging particles between various Monte Carlo simulation applications, is presented. Portable C code for file manipulation is made available to the scientific community,…
The Active Matter Evaluation Package (AMEP) is a Python library for analyzing simulation data of particle-based and continuum simulations. It provides a powerful and simple interface for handling large data sets and for calculating and…
Monte Carlo techniques, including MCMC and other methods, are widely used in Bayesian inference to generate sets of samples from a parameter space of interest. The Python GetDist package provides tools for analysing these samples and…
Fidimag is an open-source scientific code for the study of magnetic materials at the nano- or micro-scale using either atomistic or finite difference micromagnetic simulations, which are based on solving the Landau-Lifshitz-Gilbert…
We consider a system where a spherical particle is suspended in a nematic liquid crystal confined between two walls. We calculate the liquid-crystal mediated potential of mean force between the sphere and a substrate by means of Monte Carlo…
SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…
MEG (Mu to Electron Gamma) is an experiment dedicated to search for the $\mu^+ \rightarrow e^+\gamma$ decay that is strongly suppressed in the Standard Model but predicted in several Super Symmetric extensions of it at an accessible rate.…
We design and implement HPMC, a scalable hard particle Monte Carlo simulation toolkit, and release it open source as part of HOOMD-blue. HPMC runs in parallel on many CPUs and many GPUs using domain decomposition. We employ BVH trees…
We present mechanoChemML, a machine learning software library for computational materials physics. mechanoChemML is designed to function as an interface between platforms that are widely used for machine learning on one hand, and others for…
Coronal mass ejections (CMEs) are solar eruptions into interplanetary space of as much as a few billion tons of plasma, with embedded magnetic fields from the Sun's corona. These perturbations play a very important role in…