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Chemellia is an open-source framework for atomistic machine learning in the Julia programming language. The framework takes advantage of Julia's high speed as well as the ability to share and reuse code and interfaces through the paradigm…
MiMiC is a flexible and efficient framework for multiscale simulations in which different subsystems are treated by individual client programs. In this work, we present a new interface with OpenMM to be used as an MM client program and we…
Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…
We describe software and a language for quasibiological computations. Its theoretical basis is a unified theory of complex (adaptive) systems where all laws are regularities of relations between things or agents, and dynamics is made from…
Functional programming languages are seen by many as instrumental to effectively utilizing the computational power of multi-core platforms. As a result, there is growing interest to introduce functional programming and functional thinking…
Based on the previously developed Energy Conserving Semi Implicit Method (ECsim) code, we present its cylindrical implementation, called ECsim-CYL, to be used for axially symmetric problems. The main motivation for the development of the…
Today's world of scientific software for High Energy Physics (HEP) is powered by x86 code, while the future will be much more reliant on accelerators like GPUs and FPGAs. The portable parallelization strategies (PPS) project of the High…
The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle…
We present the first three-dimensional fully kinetic electromagnetic relativistic particle-in-cell simulations of the collision of two interpenetrating plasma shells. The highly accurate plasma-kinetic "particle-in-cell" (with the total of…
A parallelized quantum dynamics package using the Smolyak algorithm for general molecular simulation is introduced in this work. The program has no limitation of the Hamiltonian form and provides high flexibility on the simulation setup to…
Direct studies of intense laser-solid interactions is still of great challenges, because of the many coupled physical mechanisms, such as direct laser heating, ionization dynamics, collision among charged particles, and electrostatic or…
We present Simphony, a free and open-source software toolbox for abstracting and simulating photonic integrated circuits, implemented in Python. The toolbox is both fast and easily extensible; plugins can be written to provide compatibility…
A Monte Carlo code, known as AASI, is developed for simulating energy spectra in alpha spectrometry. The code documented here is a comprehensive package where all the major processes affecting the spectrum are included. A unique feature of…
We present the Fortran code SIMLA, which is designed for the study of charged particle dynamics in laser and other background fields. This can be done classically via the Landau-Lifshitz equation, or alternatively, via the simulation of…
Quantum simulation is a promising near term application for mesoscale quantum information processors, with the potential to solve computationally intractable problems at the scale of just a few dozen interacting quantum systems. Recent…
The design of absorbing boundary conditions (ABC) in a numerical simulation is a challenging task. In the best cases, spurious reflections remain for some angles of incidence or at certain wave lengths. In the worst, ABC are not even…
The formation of biomolecular materials via dynamical interfacial processes such as self-assembly and fusion, for diverse compositions and external conditions, can be efficiently probed using ensemble Molecular Dynamics. However, this…
Scientific applications produce a huge amount of data, which imposes serious management and analysis challenges. In particular, limitations in current database management systems prevent their adoption in simulation applications, in which…
We explore the possibilities of applying structure-preserving numerical methods to a plasma hybrid model with kinetic ions and mass-less fluid electrons satisfying the quasi-neutrality relation. The numerical schemes are derived by finite…
Spacely is an open-source framework for the post-silicon validation of analog, digital, and mixed-signal ASICs (Application-Specific Integrated Circuits) which maximizes the reuse of hardware and software, reducing the time taken to achieve…