1,928 research outputs found
Computational Physics on Graphics Processing Units
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 on classical molecular dynamics, and on quantum simulations for
electronic structure calculations using the density functional theory, wave
function techniques, and quantum field theory.Comment: Proceedings of the 11th International Conference, PARA 2012,
Helsinki, Finland, June 10-13, 201
Molecular dynamics recipes for genome research
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer. However, variables like the software tool used for modeling and simulation or the size of the molecule under investigation might make one hardware type or configuration more advantageous than another or even make the commodity hardware definitely suitable for MD studies. This work aims to shed lights on this aspect
JDFTx: software for joint density-functional theory
Density-functional theory (DFT) has revolutionized computational prediction
of atomic-scale properties from first principles in physics, chemistry and
materials science. Continuing development of new methods is necessary for
accurate predictions of new classes of materials and properties, and for
connecting to nano- and mesoscale properties using coarse-grained theories.
JDFTx is a fully-featured open-source electronic DFT software designed
specifically to facilitate rapid development of new theories, models and
algorithms. Using an algebraic formulation as an abstraction layer, compact
C++11 code automatically performs well on diverse hardware including GPUs. This
code hosts the development of joint density-functional theory (JDFT) that
combines electronic DFT with classical DFT and continuum models of liquids for
first-principles calculations of solvated and electrochemical systems. In
addition, the modular nature of the code makes it easy to extend and interface
with, facilitating the development of multi-scale toolkits that connect to ab
initio calculations, e.g. photo-excited carrier dynamics combining electron and
phonon calculations with electromagnetic simulations.Comment: 9 pages, 3 figures, 2 code listing
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