Quantum ESPRESSO: a modular and open-source software project for quantum simulations of materials

Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). Quantum ESPRESSO stands for "opEn Source Package for Research in Electronic Structure, Simulation, and Optimization". It is freely available to researchers around the world under the terms of the GNU General Public License. Quantum ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively-parallel architectures, and a great effort being devoted to user friendliness. Quantum ESPRESSO is evolving towards a distribution of independent and inter-operable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.Comment: 36 pages, 5 figures, resubmitted to J.Phys.: Condens. Matte

Simultaneous Image Registration and Monocular Volumetric Reconstruction of a fluid flow

We propose to combine image registration and volumetric reconstruction from a monocular video of a draining off Hele-Shaw cell filled with water. A Hele-Shaw cell is a tank whose depth is small (e.g. 1 mm) compared to the other dimensions (e.g. 400 800 mm2). We use a technique known as molecular tagging which consists in marking by photobleaching a pattern in the fluid and then tracking its deformations. The evolution of the pattern is filmed with a camera whose principal axis coincides with the depth of the cell. The velocity of the fluid along this direction is not constant. Consequently,tracking the pattern cannot be achieved with classical methods because what is observed is the integration of the marked particles over the entire depth of the cell. The proposed approach is built on top of classical direct image registration in which we incorporate a volumetric image formation model. It allows us to accurately measure the motion and the velocity profiles for the entire volume (including the depth of the cell) which is something usually hard to achieve. The results we obtain are consistent with the theoretical hydrodynamic behaviour for this flow which is known as the laminar Poiseuille flow

Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational grids

During the last two years the RealityGrid project has allowed us to be one of the few scientific groups involved in the development of computational grids. Since smoothly working production grids are not yet available, we have been able to substantially influence the direction of software development and grid deployment within the project. In this paper we review our results from large scale three-dimensional lattice Boltzmann simulations performed over the last two years. We describe how the proactive use of computational steering and advanced job migration and visualization techniques enabled us to do our scientific work more efficiently. The projects reported on in this paper are studies of complex fluid flows under shear or in porous media, as well as large-scale parameter searches, and studies of the self-organisation of liquid cubic mesophases. Movies are available at http://www.ica1.uni-stuttgart.de/~jens/pub/05/05-PhilTransReview.htmlComment: 18 pages, 9 figures, 4 movies available, accepted for publication in Phil. Trans. R. Soc. London Series

Analysis of Three-Dimensional Protein Images

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains labor intensive and relies on an expert's ability to derive and evaluate a protein scene model. In this paper, the problem of protein structure determination is formulated as an exercise in scene analysis. A computational methodology is presented in which a 3D image of a protein is segmented into a graph of critical points. Bayesian and certainty factor approaches are described and used to analyze critical point graphs and identify meaningful substructures, such as alpha-helices and beta-sheets. Results of applying the methodologies to protein images at low and medium resolution are reported. The research is related to approaches to representation, segmentation and classification in vision, as well as to top-down approaches to protein structure prediction.Comment: See http://www.jair.org/ for any accompanying file

Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel

A computational pre-processing tool for generating initial configurations of molecules for molecular dynamics simulations in geometries described by a mesh of unstructured arbitrary polyhedra is described. The mesh is divided into separate zones and each can be filled with a single crystal lattice of atoms. Each zone is filled by creating an expanding cube of crystal unit cells, initiated from an anchor point for the lattice. Each unit cell places the appropriate atoms for the user-specified crystal structure and orientation. The cube expands until the entire zone is filled with the lattice; zones with concave and disconnected volumes may be filled. When the mesh is spatially decomposed into portions for distributed parallel processing, each portion may be filled independently, meaning that the entire molecular system never needs to fit onto a single processor, allowing very large systems to be created. The computational time required to fill a zone with molecules scales linearly with the number of cells in the zone for a fixed number of molecules, and better than linearly with the number of molecules for a fixed number of mesh cells. Our tool, molConfig, has been implemented in the open source C++ code OpenFOAM

Accurate ionic forces and geometry optimization in linear-scaling density-functional theory with local orbitals

Linear scaling methods for density-functional theory (DFT) simulations are formulated in terms of localized orbitals in real space, rather than the delocalized eigenstates of conventional approaches. In local-orbital methods, relative to conventional DFT, desirable properties can be lost to some extent, such as the translational invariance of the total energy of a system with respect to small displacements and the smoothness of the potential-energy surface. This has repercussions for calculating accurate ionic forces and geometries. In this work we present results from onetep, our linear scaling method based on localized orbitals in real space. The use of psinc functions for the underlying basis set and on-the-fly optimization of the localized orbitals results in smooth potential-energy surfaces that are consistent with ionic forces calculated using the Hellmann-Feynman theorem. This enables accurate geometry optimization to be performed. Results for surface reconstructions in silicon are presented, along with three example systems demonstrating the performance of a quasi-Newton geometry optimization algorithm: an organic zwitterion, a point defect in an ionic crystal, and a semiconductor nanostructure.<br/

Simulation of the growth of the 3D Rayleigh-Taylor instability in Supernova Remnants using an expanding reference frame

Context: The Rayleigh-Taylor instabilities generated by the deceleration of a supernova remnant during the ejecta-dominated phase are known to produce finger-like structures in the matter distribution which modify the geometry of the remnant. The morphology of supernova remnants is also expected to be modified when efficient particle acceleration occurs at their shocks. Aims: The impact of the Rayleigh-Taylor instabilities from the ejecta-dominated to the Sedov-Taylor phase is investigated over one octant of the supernova remnant. We also study the effect of efficient particle acceleration at the forward shock on the growth of the Rayleigh-Taylor instabilities. Methods: We modified the Adaptive Mesh Refinement code RAMSES to study with hydrodynamic numerical simulations the evolution of supernova remnants in the framework of an expanding reference frame. The adiabatic index of a relativistic gas between the forward shock and the contact discontinuity mimics the presence of accelerated particles. Results: The great advantage of the super-comoving coordinate system adopted here is that it minimizes numerical diffusion at the contact discontinuity, since it is stationary with respect to the grid. We propose an accurate expression for the growth of the Rayleigh-Taylor structures that connects smoothly the early growth to the asymptotic self-similar behaviour. Conclusions: The development of the Rayleigh-Taylor structures is affected, although not drastically, if the blast wave is dominated by cosmic rays. The amount of ejecta that makes it into the shocked interstellar medium is smaller in the latter case. If acceleration occurs at both shocks the extent of the Rayleigh-Taylor structures is similar but the reverse shock is strongly perturbed.Comment: 15 pages, 12 figures, accepted for publication in Astronomy and Astrophysics with minor editorial changes. Version with full resolution images can be found at http://www.lpl.arizona.edu/~ffrasche/~12692.pd