Computational science & discovery最新文献

{"title":"Macro-micro interlocked simulation algorithm: An exemplification for aurora arc evolution","authors":"Tetsuya Sato, H. Hasegawa, N. Ohno","doi":"10.1088/1749-4699/2/1/015007","DOIUrl":"https://doi.org/10.1088/1749-4699/2/1/015007","url":null,"abstract":"Using an innovative holistic simulation algorithm that can self-consistently treat a system that evolves as cooperation between macroscopic and microscopic processes, the evolution of a colorful aurora arc is beautifully reproduced as the result of cooperation between the global field-aligned feedback instability of the coupled magnetosphere–ionosphere system and the ensuing microscopic ion-acoustic instability that generates electric double layers and accelerates aurora electrons. These results are in agreement with rocket and satellite observations. This shows that the proposed holistic algorithm could be a reliable tool to reveal complex real dramatic events and become, in the near future, a viable scientifically secure prediction tool for natural disasters such as earthquakes, landslides and floods caused by typhoons.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"2 1","pages":"015007"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/2/1/015007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SURPRISES: when ab initio meets statistics in extended systems","authors":"S. Taioli, S. Simonucci, M. Dapor","doi":"10.1088/1749-4699/2/1/015002","DOIUrl":"https://doi.org/10.1088/1749-4699/2/1/015002","url":null,"abstract":"The surface photoelectron and inner shell electron spectroscopy (SURPRISES) program suite performs ab initio calculations of photoionization and non-radiative decay spectra in nanoclusters and solid state systems by using a space-energy similarity procedure to reproduce the band-like part of the spectra. This approach provides an extension of Fano resonant multichannel scattering theory dealing with the complexity arising from condensed matter calculations at a computational cost comparable to that of molecules. The bottleneck of electron spectroscopy ab initio calculations in condensed matter is the size of the Hilbert space where the wavefunctions are expanded and the increase in number of final decay states in comparison to that of atoms and molecules. In particular, the diagonalization of the interchannel interaction to take into account the correlation between the double ion and the escaping electron is impracticable when hole delocalization on valence bands and electronic excitations are included in the model. To overcome this problem SURPRISES uses a 'space-energy similarity' approach, which allows the spreading of the Auger probability over the bands without tuning semi-empirical parameters. Furthermore, a completely new feature in the landscape of ab initio resonant decay processes calculations is represented by including energy loss through a statistical approach. Using the calculated lineshape as electron source, a Monte Carlo routine simulates the effect of inelastic losses on the original lineshape. In this process, the computed spectrum can be directly compared with acquired experimental spectra, thus avoiding background subtraction, a procedure not free from uncertainty. The program can exploit the symmetry of the system under investigation to reduce the calculation scaling and may compute photoemission and Auger decay angular distribution patterns including energy loss for the electrons emitted in resonance-affected photoionization processes. In this paper, we present general methods, computational techniques and a number of numerical tests applied to the calculation of Si K–LL and O K–LL Auger spectra from different SiO2 nanoclusters.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"1 1","pages":"015002"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/2/1/015002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High performance parallel computing of flows in complex geometries: II. Applications","authors":"N. Gourdain, L. Gicquel, G. Staffelbach, O. Vermorel, F. Duchaine, J. Boussuge, T. Poinsot","doi":"10.1088/1749-4699/2/1/015004","DOIUrl":"https://doi.org/10.1088/1749-4699/2/1/015004","url":null,"abstract":"Present regulations in terms of pollutant emissions, noise and economical constraints, require new approaches and designs in the fields of energy supply and transportation. It is now well established that the next breakthrough will come from a better understanding of unsteady flow effects and by considering the entire system and not only isolated components. However, these aspects are still not well taken into account by the numerical approaches or understood whatever the design stage considered. The main challenge is essentially due to the computational requirements inferred by such complex systems if it is to be simulated by use of supercomputers. This paper shows how new challenges can be addressed by using parallel computing platforms for distinct elements of a more complex systems as encountered in aeronautical applications. Based on numerical simulations performed with modern aerodynamic and reactive flow solvers, this work underlines the interest of high-performance computing for solving flow in complex industrial configurations such as aircrafts, combustion chambers and turbomachines. Performance indicators related to parallel computing efficiency are presented, showing that establishing fair criterions is a difficult task for complex industrial applications. Examples of numerical simulations performed in industrial systems are also described with a particular interest for the computational time and the potential design improvements obtained with high-fidelity and multi-physics computing methods. These simulations use either unsteady Reynolds-averaged Navier–Stokes methods or large eddy simulation and deal with turbulent unsteady flows, such as coupled flow phenomena (thermo-acoustic instabilities, buffet, etc). Some examples of the difficulties with grid generation and data analysis are also presented when dealing with these complex industrial applications.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"2 1","pages":"015004"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/2/1/015004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A combined theoretical and experimental study of the polymer inter-chain structure in poly(phenylene vinylene) derivatives","authors":"B. Sumpter, M. Drummond, W. Shelton, Edward F. Valeev, M. Barnes","doi":"10.1088/1749-4699/1/1/015006","DOIUrl":"https://doi.org/10.1088/1749-4699/1/1/015006","url":null,"abstract":"The structures and photophysical properties of single molecule MEH-PPV (2-methoxy-5-(2'-ethyl-hexyloxy)-p-phenylenevinylene) and CN-PPV (2,5,2' ,5'-tetrahexyloxy-7,8'-dicyano-p-phenylenevinylene) nanoparticles are investigated using electronic structure theory and high resolution fluorescence experiments. It is shown that electron withdrawing substituents, such as CN, on the vinyl group of the PPV polymer backbone cause substantial change in the π electronic structure which subsequently decreases the inter-chain distance. Not only does CN-PPV have a smaller inter-chain separation compared to MEH-PPV, but also an increased binding energy and more efficient charge transport (carrier mobility) due to larger electronic coupling (charge transfer integrals). These changes help explain the enhanced luminescence quantum yield, photo-stability, and lifetime for CN-PPV versus MEH-PPV observed in experimental high resolution fluorescence imaging of individual single molecule nanoparticles.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"1 1","pages":"015006"},"PeriodicalIF":0.0,"publicationDate":"2008-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/1/1/015006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deterministic point inclusion methods for computational applications with complex geometry","authors":"A. Khamayseh, A. Kuprat","doi":"10.1088/1749-4699/1/1/015004","DOIUrl":"https://doi.org/10.1088/1749-4699/1/1/015004","url":null,"abstract":"A fundamental problem in computation is finding practical and efficient algorithms for determining if a query point is contained within a model of a three-dimensional solid. The solid is modeled using a general boundary representation that can contain polygonal elements and/or parametric patches. We have developed two such algorithms: the first is based on a global closest feature query, and the second is based on a local intersection query. Both algorithms work for two- and three-dimensional objects. This paper presents both algorithms, as well as the spatial data structures and queries required for efficient implementation of the algorithms. Applications for these algorithms include computational geometry, mesh generation, particle simulation, multiphysics coupling, and computer graphics. These methods are deterministic in that they do not involve random perturbations of diagnostic rays cast from the query point in order to avoid 'unclean' or 'singular' intersections of the rays with the geometry. Avoiding the necessity of such random perturbations will become increasingly important as geometries become more convoluted and complex.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"314 1","pages":"015004"},"PeriodicalIF":0.0,"publicationDate":"2008-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/1/1/015004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational aspects of nuclear coupled-cluster theory","authors":"G. Hagen, H. Nam","doi":"10.1143/PTPS.196.102","DOIUrl":"https://doi.org/10.1143/PTPS.196.102","url":null,"abstract":"Coupled-cluster (CC) theory represents an important theoretical tool that we use to solve the quantum many-body problem. CC theory also lends itself to computation in a parallel computing environment. In this paper, we present selected results from ab initio studies of stable and weakly bound nuclei utilizing computational techniques that we employ to solve CC theory. We also outline several perspectives for future research directions in this area.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"1 1","pages":"015008"},"PeriodicalIF":0.0,"publicationDate":"2008-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1143/PTPS.196.102","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64869283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nonlinear turbulent transport in magnetic fusion plasmas","authors":"W. Lee, S. Ethier, R. Kolesnikov, W. Wang, W. Tang","doi":"10.1088/1749-4699/1/1/015010","DOIUrl":"https://doi.org/10.1088/1749-4699/1/1/015010","url":null,"abstract":"For more than a decade, the study of microturbulence driven by ion temperature gradient (ITG) drift instabilities in tokamak devices has been an active area of research in magnetic fusion science for both experimentalists and theorists alike. An important impetus for this avenue of research was the discovery of the radial streamers associated with the ITG modes in the early 1990s using the particle-in-cell (PIC) simulation method. Subsequently, ITG simulations using codes with increasing realism have been made possible by the dramatic increase in computing power. Notable examples were the demonstration of the importance of nonlinearly generated zonal flows in regulating ion thermal transport and the transition from Bohm to gyroBohm scaling with increased device size. In this paper, we will describe an interesting nonlinear physical process, as well as the resulting turbulent transport, that is associated with the interactions between the nonlinear parallel acceleration of the ions and the zonal flow modes. This study was carried out by utilizing a fully parallelized three-dimensional PIC code in global toroidal geometry on the most advanced, modern, massively parallel supercomputers.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"1 1","pages":"015010"},"PeriodicalIF":0.0,"publicationDate":"2008-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/1/1/015010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Terascale direct numerical simulations of turbulent combustion using S3D","authors":"Jacqueline H. Chen, A. Choudhary, B. Supinski, M. Devries, E. Hawkes, S. Klasky, W. Liao, K. Ma, J. Mellor-Crummey, N. Podhorszki, R. Sankaran, S. Shende, C. Yoo","doi":"10.1088/1749-4699/2/1/015001","DOIUrl":"https://doi.org/10.1088/1749-4699/2/1/015001","url":null,"abstract":"Computational science is paramount to the understanding of underlying processes in internal combustion engines of the future that will utilize non-petroleum-based alternative fuels, including carbon-neutral biofuels, and burn in new combustion regimes that will attain high efficiency while minimizing emissions of particulates and nitrogen oxides. Next-generation engines will likely operate at higher pressures, with greater amounts of dilution and utilize alternative fuels that exhibit a wide range of chemical and physical properties. Therefore, there is a significant role for high-fidelity simulations, direct numerical simulations (DNS), specifically designed to capture key turbulence-chemistry interactions in these relatively uncharted combustion regimes, and in particular, that can discriminate the effects of differences in fuel properties. In DNS, all of the relevant turbulence and flame scales are resolved numerically using high-order accurate numerical algorithms. As a consequence terascale DNS are computationally intensive, require massive amounts of computing power and generate tens of terabytes of data. Recent results from terascale DNS of turbulent flames are presented here, illustrating its role in elucidating flame stabilization mechanisms in a lifted turbulent hydrogen/air jet flame in a hot air coflow, and the flame structure of a fuel-lean turbulent premixed jet flame. Computing at this scale requires close collaborations between computer and combustion scientists to provide optimized scaleable algorithms and software for terascale simulations, efficient collective parallel I/O, tools for volume visualization of multiscale, multivariate data and automating the combustion workflow. The enabling computer science, applied to combustion science, is also required in many other terascale physics and engineering simulations. In particular, performance monitoring is used to identify the performance of key kernels in the DNS code, S3D and especially memory intensive loops in the code. Through the careful application of loop transformations, data reuse in cache is exploited thereby reducing memory bandwidth needs, and hence, improving S3D's nodal performance. To enhance collective parallel I/O in S3D, an MPI-I/O caching design is used to construct a two-stage write-behind method for improving the performance of write-only operations. The simulations generate tens of terabytes of data requiring analysis. Interactive exploration of the simulation data is enabled by multivariate time-varying volume visualization. The visualization highlights spatial and temporal correlations between multiple reactive scalar fields using an intuitive user interface based on parallel coordinates and time histogram. Finally, an automated combustion workflow is designed using Kepler to manage large-scale data movement, data morphing, and archival and to provide a graphical display of run-time diagnostics.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"2 1","pages":"015001"},"PeriodicalIF":0.0,"publicationDate":"2008-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/2/1/015001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The nuclear force from Monte Carlo simulations of lattice quantum chromodynamics","authors":"Sinya Aoki, Sinya Aoki, T. Hatsuda, N. Ishii","doi":"10.1088/1749-4699/1/1/015009","DOIUrl":"https://doi.org/10.1088/1749-4699/1/1/015009","url":null,"abstract":"The nuclear force acting between protons and neutrons is studied in the Monte Carlo simulations of the fundamental theory of strong interaction, the quantum chromodynamics defined on the hypercubic space–time lattice. After a brief summary of the empirical nucleon–nucleon (NN) potentials that can fit the NN scattering experiments in high precision, we outline the basic formulation for deriving the potential between the extended objects such as the nucleons composed of quarks. The equal-time Bethe–Salpeter (BS) amplitude is a key ingredient for defining the NN potential on the lattice. We show the results of the numerical simulations on a 324 lattice with lattice spacing a0.137 fm (lattice volume (4.4 fm)4) in the quenched approximation. The calculation was carried out using the massively parallel computer Blue Gene/L at the High Energy Accelerator Research Organization (KEK). We found that the calculated NN potential at low energy has the basic features expected from the empirical NN potentials: attraction at long and medium distances, and the repulsive core at short distances. Various future directions along this line of research are also summarized.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"1 1","pages":"015009"},"PeriodicalIF":0.0,"publicationDate":"2008-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/1/1/015009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The RAGE radiation-hydrodynamic code","authors":"M. Gittings, R. Weaver, M. Clover, T. Betlach, N. Byrne, R. Coker, E. Dendy, R. Hueckstaedt, K. New, Rob Oakes, D. Ranta, Ryan Stefan","doi":"10.1088/1749-4699/1/1/015005","DOIUrl":"https://doi.org/10.1088/1749-4699/1/1/015005","url":null,"abstract":"We describe RAGE, the 'radiation adaptive grid Eulerian' radiation-hydrodynamics code, including its data structures, its parallelization strategy and performance, its hydrodynamic algorithm(s), its (gray) radiation diffusion algorithm, and some of the considerable amount of verification and validation efforts. The hydrodynamics is a basic Godunov solver, to which we have made significant improvements to increase the advection algorithm's robustness and to converge stiffnesses in the equation of state. Similarly, the radiation transport is a basic gray diffusion, but our treatment of the radiation?material coupling, wherein we converge nonlinearities in a novel manner to allow larger timesteps and more robust behavior, can be applied to any multi-group transport algorithm.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"1 1","pages":"015005"},"PeriodicalIF":0.0,"publicationDate":"2008-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/1/1/015005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}