Search Results for "physics simulations"

The oxDNA code has been moved to https://github.com/lorenzo-rovigatti/oxDNA, please go there for new releases.

RINGS "Rigorous Investigation of Networks Generated using Simulations" is a scientific code developed in Fortran90/MPI to analyze the results of molecular dynamics simulations. Its main feature is the analysis of the connectivity using ring statistics.

WaveTrain is an open-source software for numerical simulations of chain-like quantum systems with nearest-neighbor (NN) interactions only (with or without periodic boundary conditions). This Python package is centered around tensor train (TT, or matrix product) representations of quantum-mechanical Hamiltonian operators and (stationary or time-evolving) state vectors. WaveTrain builds on the Python tensor train toolbox scikit_tt, which provides efficient construction methods, storage...

PUPIL (Program for User Package Interface and Linking), is a software environment that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use...

NESSIE is a modern first-principle calculation software that can adequately address the need for ever-higher levels of numerical accuracy and high-performance in large-scale electronic structure simulations, as well as pioneer the fundamental study of quantum many-body effects in a large number of emerging nanomaterials. NESSIE is an electronic structure code that uses a real-space FEM discretization and domain-decomposition (DD) to perform all-electron ground-state DFT and real-time...

SPARTA is a parallel DSMC code for performing simulations of low-density gases in 2d or 3d. Particles advect through a hierarchical Cartesian grid that overlays the simulation box. The grid is used to group particles by grid cell for purposes of performing collisions and chemistry. Physical objects with triangulated surfaces can be embedded in the grid, creating cut and split grid cells.

I.S.A.A.C.S. Interactive Structure Analysis of Amorphous and Crystalline Systems is a cross-platform software developed to analyze the structural characteristics of three-dimensional models built by computer simulations.

Monte Carlo simulations of various classes of asymmetric exclusion processes (ASEP) with open and periodic boundaries. ASEP is a paradigmatic model of non equilibrium statistical mechanics. It can be utilized to model various non-equilibrium phenomena in Biology such as molecular motor transport and protein synthesis. The code's comments will be gradually expanded upon; if there are mistaken or unclear comments they will be corrected. We cannot give an estimation as to when because...

This program allows to perform a structural cluster analysis of atomic trajectories obtained, e.g., from molecular dynamics simulations. At variance with other approaches, it is possible to analyse also processes in solution, e.g., chemical reactions in liquid water, since the distance metric is based on a Permutation Invariant Vector (PIV) that is symmetric under exchange of identical atoms or molecules, including on the same footing both solute and solvent degrees of freedom. The...

A high-performance simulation package for sampling the chemical and reaction-diffusion master equations. Primarily intended for running stochastic simulations of microbial cells.

PIMC++ is a code designed to perform fully-correlated simulations of quantum systems in continuous space at finite temperature using Path Integral Monte Carlo. It is designed in a modular way to facilitate easy addition of new algorithms.

CHIMP aims to provide a complete suite of tools for the investigation and modeling of chemical systems. It currently is able to parse chemical reaction mechanisms and run kinetic Monte Carlo simulations on the reacting system.

BlochLib is an expression template library of generic data structures and algorithms to perform large scale nuclear magnetic resonance classical and quantum mechanical spin simulations, with many I/O capabilities,and integrated numerical routines.