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We describe the creation of a new Atomic and Molecular Physics science gateway (AMPGateway). The gateway is designed to bring together a subset of the AMP community to work collectively to make their codes available and easier to use by the…
Atoms can be trapped and guided using nano-fabricated wires on surfaces, achieving the scales required by quantum information proposals. These Atom Chips form the basis for robust and widespread applications of cold atoms ranging from atom…
Given an algorithm the quality of the output largely depends on a proper specification of the input parameters. A lot of work has been done to analyze tasks related to using a fixed model [25] and finding a good set of inputs. In this paper…
We present OpenMM-Python-Force, a plugin designed to extend OpenMM's functionality by enabling integration of energy and force calculations from external Python programs via a callback mechanism. During molecular dynamics simulations, data…
Quantum computing's transition from theory to reality has spurred the need for novel software tools to manage the increasing complexity, sophistication, toil, and fallibility of quantum algorithm development. We present Qualtran, an…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Agent-based modeling and network science have been used extensively to advance our understanding of emergent collective behavior in systems that are composed of a large number of simple interacting individuals or agents. With the increasing…
ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and…
Understanding and predicting the properties of inorganic materials is crucial for accelerating advancements in materials science and driving applications in energy, electronics, and beyond. Integrating material structure data with…
This paper introduces EvoCraft, a framework for Minecraft designed to study open-ended algorithms. We introduce an API that provides an open-source Python interface for communicating with Minecraft to place and track blocks. In contrast to…
Atomistic simulations are an important tool in materials modeling. Interatomic potentials (IPs) are at the heart of such molecular models, and the accuracy of a model's predictions depends strongly on the choice of IP. Uncertainty…
The first step in the construction of a regression model or a data-driven analysis, aiming to predict or elucidate the relationship between the atomic scale structure of matter and its properties, involves transforming the Cartesian…
Modeling potential alloys requires the exploration of all possible configurations of atoms. Additionally, modeling the thermal properties of materials requires knowledge of the possible ways of displacing the atoms. One solution to finding…
We present a first-principles computer code package (ABACUS) that is based on density functional theory and numerical atomic basis sets. Theoretical foundations and numerical techniques used in the code are described, with focus on the…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
Atomistic theory holds the promise for the ab initio development of superalloys based on the fundamental principles of quantum mechanics. The last years showed a rapid progress in the field. Results from atomistic modeling enter…
Progress in the atomic-scale modelling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic…
Data-driven schemes that associate molecular and crystal structures with their microscopic properties share the need for a concise, effective description of the arrangement of their atomic constituents. Many types of models rely on…
Large-scale atomistic simulations rely on interatomic potentials providing an efficient representation of atomic energies and forces. Modern machine-learning (ML) potentials provide the most precise representation compared to electronic…
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter…