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We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different…
The OpenMX Viewer (Open source package for Material eXplorer Viewer) is a web-based graphical user interface (GUI) program for visualization and analysis of crystalline and molecular structures and 3D grid data in the Gaussian cube format…
We present a new program able to perform visual structural analysis on 3D particle systems called PASYVAT (PArticle SYstem Visual Analysis Tool). More specifically, it can select multiple interparticle distance ranges from a radial…
Multiscale magnetic simulations, including micromagnetic and atomistic spin dynamics simulations, are widely used in the study of complex magnetic systems over a wide range of spatial and temporal scales. The advances in these simulation…
Despite the popularity of the Graphics Processing Unit (GPU) for general purpose computing, one should not forget about the practicality of the GPU for fast scientific visualisation. As astronomers have increasing access to three…
In non-linear systems, where explicit analytic solutions usually can't be found, visualisation is a powerful approach which can give insights into the dynamical behaviour of models; it is also crucial for teaching this area of mathematics.…
Making quantum mechanical equations and concepts come to life through interactive simulation and visualization are commonplace for augmenting learning and teaching. However, graphical visualizations nearly always exhibit a set of hard-coded…
We report the development of a user-friendly nano-visualization software program which can acquaint high-school students with nanotechnology. The visual introduction to atoms and molecules, which are the building blocks of this technology,…
Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools…
3D visualization is an important data analysis and knowledge discovery tool, however, interactive visualization of large 3D astronomical datasets poses a challenge for many existing data visualization packages. We present a solution to…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Visual analysis is well adopted within the field of oceanography for the analysis of model simulations, detection of different phenomena and events, and tracking of dynamic processes. With increasing data sizes and the availability of…
The growth of computational astrophysics and complexity of multidimensional datasets evidences the need for new versatile visualization tools for both analysis and presentation of the data. In this work we show how to use the open source…
PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design efforts. By harnessing state-of-the-art web technologies…
This work studies machine learning for electron density prediction, which is fundamental for understanding chemical systems and density functional theory (DFT) simulations. To this end, we introduce the Gaussian plane-wave neural operator…
The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing…
WavePacket is an open-source program package for the numerical simulation of quantum-mechanical dynamics. It can be used to solve time-independent or time-dependent linear Schr\"odinger and Liouville-von Neumann-equations in one or more…
We describe TGView3D, an interactive 3D graph viewer optimized for exploring theory graphs. To exploit the three spatial dimensions, it extends a force-directed layout with a hierarchical component. Because of the limitations of regular…
We report an implementation of a program for visualizing complex-valued molecular orbitals. The orbital phase information is encoded on each of the vertices of triangle meshes using the standard color wheel. Using this program, we…
Learning PDE dynamics for fluids increasingly relies on neural operators and Transformer-based models, yet these approaches often lack interpretability and struggle with localized, high-frequency structures while incurring quadratic cost in…