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The QMol-grid package provides a suite of routines for performing quantum-mechanical simulations in atomic and molecular systems, currently implemented in one spatial dimension. It supports ground- and excited-state calculations for the…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of…
A set of Mathematica functions is presented to model classically two of the most important processes in strong field physics, namely high-order harmonic generation (HHG) and above-threshold ionization (ATI). Our approach is based on the…
Atomistic foundation models (AFMs) have great promise as accurate interatomic potentials, and have enabled data-efficient molecular dynamics simulations with near quantum mechanical accuracy. However, AFMs remain markedly slower at…
This paper documents package for the particle level fast simulation. The package is designed to complete the AcerMC generator framework with the easy-to-use simulation and reconstruction algorithms. The package provides, starting from list…
QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum…
Simulations of quantum chemistry and quantum materials are believed to be among the most important potential applications of quantum information processors, but realizing practical quantum advantage for such problems is challenging. Here,…
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas- and in the condensed phase. Together with recently developed and currently pursued efforts in…
This work describes extensions to existing level-set algorithms developed for application within the field of Atom Probe Tomography (APT). We present a new simulation tool for the simulation of 3D tomographic volumes, using advanced level…
We present the Python Tree Tensor Network package (pyTTN) for the evaluation of dynamical properties of closed and open quantum systems that makes use of Tree Tensor Network (TTN), or equivalently the multi-layer multiconfiguration…
As AI agents move from demos into enterprise deployments, their failure modes become consequential: a misinterpreted tool argument can corrupt production data, a silent reasoning error can go undetected until damage is done, and outputs…
Machine learning has become ubiquitous in materials modelling and now routinely enables large-scale atomistic simulations with quantum-mechanical accuracy. However, developing machine-learned interatomic potentials requires high-quality…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely…
ARC 3.0 is a modular, object-oriented Python library combining data and algorithms to enable the calculation of a range of properties of alkali and divalent atoms. Building on the initial version of the ARC library [N. \v{S}ibali\'c et al,…
Recent advances in both theory and methods have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble-based simulations are used widely to compute a number of individual…
The MeMC is an open-source software package for monte-carlo simulation of elastic shells. It is designed as a tool to interpret the force-distance data generated by indentation of biological nano-vesicles by atomic force microscopes. The…
AMDAT (Amorphous Molecular Dynamics Analysis Toolkit) is an open-source C++ toolkit for post-processing molecular dynamics trajectories, focused on high-performance static and dynamic analyses of amorphous, glassy, and polymer materials,…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…