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We survey some general-purpose symbolic software packages that implement algorithms from enumerative and analytic combinatorics. Software for the following areas is covered: basic combinatorial objects, symbolic combinatorics, P\'olya…
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…
We present SPARC: Simulation Package for Ab-initio Real-space Calculations. SPARC can perform Kohn-Sham density functional theory calculations for isolated systems such as molecules as well as extended systems such as crystals and surfaces,…
Runko is a new open-source plasma simulation framework implemented in C++ and Python. It is designed to function as an easy-to-extend general toolbox for simulating astrophysical plasmas with different theoretical and numerical models.…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
PCMSolver is an open-source library for continuum electrostatic solvation. It can be combined with any quantum chemistry code and requires a minimal interface with the host program, greatly reducing programming effort. As input, PCMSolver…
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…
By putting together an abstract view on quantum mechanics and a quantum-optics picture of the interactions of an atom with light, we develop a corresponding set of C++ classes that set up the numerical analysis of an atom with an arbitrary…
M2C (Multiphysics Modeling and Computation) is an open-source software for simulating multi-material fluid flows and fluid-structure interactions under extreme conditions, such as high pressures, high temperatures, shock waves, and large…
No quantum system can be considered totally isolated from its environment. In most cases the interaction between the system of interest and the external degrees of freedom deeply changes its dynamics, as described by open quantum system…
Rapid advances in quantum computing technology lead to an increasing need for software simulators that enable both algorithm design and the validation of results obtained from quantum hardware. This includes calculations that aim at probing…
Particle suspensions are ubiquitous in our daily life, but are not well understood due to their complexity. During the last twenty years, various simulation methods have been developed in order to model these systems. Due to varying…
{\tt AbstractSimplicialComplexes.m2} is a computer algebra package written for the computer algebra system {\tt Macaulay2} \cite{M2}. It provides new infrastructure to work with abstract simplicial complexes and related homological…
Accurate models for open quantum systems -- quantum states that have non-trivial interactions with their environment -- may aid in the advancement of a diverse array of fields, including quantum computation, informatics, and the prediction…
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…
Symmetric quantum states are fascinating objects. They correspond to multipartite systems that remain invariant under particle permutations. This symmetry is reflected in their compact mathematical characterisation but also in their unique…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a…
We present QDK/Chemistry, a software toolkit for quantum chemistry workflows targeting quantum computers. The toolkit addresses a key challenge in the field: while quantum algorithms for chemistry have matured considerably, the…
The advent of hybrid computing platforms consisting of quantum processing units integrated with conventional high-performance computing brings new opportunities for algorithm design. By strategically offloading select portions of the…