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Synthesis of High-Performance Parallel Programs for a Class of ab Initio Quantum Chemistry Models

G. Baumgartner, A. Auer, D.E. Bernholdt, A. Bibireata, V. Choppella, D. Cociorva, Xiaoyang Gao, R.J. Harrison, S. Hirata, S. Krishnamoorthy, S. Krishnan, Chi-chung Lam (+6 others)
2005 Proceedings of the IEEE  
This paper provides an overview of a program synthesis system for a class of quantum chemistry computations.  ...  The input to the system is a a high-level specification of the computation, from which the system can synthesize high-performance parallel code tailored to the characteristics of the target architecture  ...  This should enable the rapid synthesis of high-performance implementations of sophisticated ab-initio quantum chemistry models, including models that are too tedious for manual development by quantum chemists  ... 
doi:10.1109/jproc.2004.840311 fatcat:gaxrixebifhstbb7ul2gsrpc4m

Optimized materials from first principles simulations: are we there yet?

Giulia Galli, Francois Gygi
2005 Journal of Physics, Conference Series  
We illustrate the progress and successes obtained in recent years in predicting fundamental properties of materials in condensed phases and at the nanoscale, using ab-initio, quantum simulations.  ...  In the past thirty years, the use of scientific computing has become pervasive in all disciplines: collection and interpretation of most experimental data is carried out using computers, and physical models  ...  Acknowledgements This work was performed under the auspices of the U.S. Dept. of Energy at the University of California/ LLNL under contract no. W-7405-Eng-48.  ... 
doi:10.1088/1742-6596/16/1/030 fatcat:n3qpr5cidrdhpd2teyjzoeuxcu

A High-Level Approach to Synthesis of High-Performance Codes for Quantum Chemistry

G. Baumgartner, D.E. Bernholdt, D. Cociorva, R. Harrison, So Hirata, Chi-Chung Lam, M. Nooijen, R. Pitzer, J. Ramanujam, P. Sadayappan
2002 ACM/IEEE SC 2002 Conference (SC'02)  
This paper discusses an approach to the synthesis of high-performance parallel programs for a class of computations encountered in quantum chemistry and physics.  ...  An overview is provided of the synthesis system, that transforms a high-level specification of the computation into high-performance parallel code, tailored to the characteristics of the target architecture  ...  This should enable the rapid synthesis of high-performance implementations of sophisticated ab-initio quantum chemistry models, including models that are too tedious for manual development by quantum chemists  ... 
doi:10.1109/sc.2002.10056 dblp:conf/sc/BaumgartnerBCHHLNPRS02 fatcat:hd4ayjqhofhc5hx6cmovvthw5y

Software Platforms for Electronic/Atomistic/Mesoscopic Modeling: Status and Perspectives

Mikael Christensen, Volker Eyert, Arthur France-Lanord, Clive Freeman, Benoît Leblanc, Alexander Mavromaras, Stephen J Mumby, David Reith, David Rigby, Xavier Rozanska, Hannes Schweiger, Tzu-Ray Shan (+5 others)
2017 Integrating Materials and Manufacturing Innovation  
Perspectives on the evolution of modeling software platforms show the need for fundamental research to improve the predictive power of models as well as coordination and support actions to accelerate industrial  ...  Predicting engineering properties of materials prior to their synthesis enables the integration of their design into the overall engineering process.  ...  Another example is UniChem of Cray Research which provided interoperability between a semi-empirical quantum chemistry program (MNDO91), an ab initio Hartree-Fock program (CADPAC), and a molecular density  ... 
doi:10.1007/s40192-017-0087-2 fatcat:3j4u72qypzdabcxlwmsm7tq4de

Design of Energetic Ionic Liquids

Jerry A. Boatz, Gregory A. Voth, Mark S. Gordon, Sharon Hammes-Schiffer
2010 2010 DoD High Performance Computing Modernization Program Users Group Conference  
A hierarchy of computational approaches is employed, including atomistic, high-level quantum chemical methods applied to individual ions and ion clusters, condensed phase atomistic molecular dynamics simulations  ...  A hierarchy of computational approaches is employed, including atomistic, high-level quantum chemical methods applied to individual ions and ion clusters, condensed phase atomistic molecular dynamics simulations  ...  Acknowledgements The authors gratefully acknowledge grants of computer time at five Department of Defense Supercomputing Resource Centers (the Air Force Research Laboratory, Army Research Laboratory, Engineer  ... 
doi:10.1109/hpcmp-ugc.2010.49 fatcat:iqsjlxx5rvdgvaloriydsneonq

Design of Energetic Ionic Liquids

Jerry A. Boatz, Gregory A. Voth, Mark S. Gordon, Sharon Hammes-Schiffer
2009 2009 DoD High Performance Computing Modernization Program Users Group Conference  
A hierarchy of computational approaches is employed, including atomistic, high-level quantum chemical methods applied to individual ions and ion clusters, condensed phase atomistic molecular dynamics simulations  ...  A hierarchy of computational approaches is employed, including atomistic, high-level quantum chemical methods applied to individual ions and ion clusters, condensed phase atomistic molecular dynamics simulations  ...  Acknowledgements The authors gratefully acknowledge grants of computer time at five Department of Defense Supercomputing Resource Centers (the Air Force Research Laboratory, Army Research Laboratory, Engineer  ... 
doi:10.1109/hpcmp-ugc.2009.30 fatcat:5i2ooxejovdptavvdzg7nvufcu

An extensible global address space framework with decoupled task and data abstractions

Sriram Krishnamoorthy, Umit Catalyurek, Jarek Nieplocha, Atanas Rountev, P. Sadayappan
2006 Proceedings 20th IEEE International Parallel & Distributed Processing Symposium  
The use of the framework for implementation of parallel block-sparse tensor computations in the context of a quantum chemistry application is illustrated.  ...  Although message passing using MPI is the dominant model for parallel programming today, the significant effort required to develop high-performance MPI applications has prompted the development of several  ...  Acknowledgments We thank the National Science Foundation for the support of this research through grants 0121676, 0403342, and 0509467, and the U.S.  ... 
doi:10.1109/ipdps.2006.1639577 dblp:conf/ipps/KrishnamoorthyCNRS06 fatcat:ofshuvpcqbaidmh4tljzvn67aq

A performance optimization framework for compilation of tensor contraction expressions into parallel

G. Baumgartner, D.E. Bernholdt, D. Cociorva, R. Harrison, Chi-Chung Lam, M. Nooijen, J. Ramanujam, P. Sadayappan
2002 Proceedings 16th International Parallel and Distributed Processing Symposium  
This paper discusses a program synthesis system to facilitate the generation of high-performance parallel programs for a class of computations encountered in quantum chemistry and physics.  ...  An overview is provided of the synthesis system under development, that will take as input a high-level specification of the computation and generate high-performance parallel code for a number of target  ...  In this paper, we provide an overview of a project that is developing program synthesis tools to facilitate the development of high-performance parallel programs for a class of scientific computations  ... 
doi:10.1109/ipdps.2002.1016492 dblp:conf/ipps/BaumgartnerBCLRHNS02 fatcat:kteitrzvwrc43aa2tzm5ia6agq

Special Issue on Program Generation, Optimization, and Platform Adaptation

J.M.F. Moura, M. Puschel, D. Padua, J. Dongarra
2005 Proceedings of the IEEE  
This special issue of the PROCEEDINGS OF THE IEEE offers an overview of ongoing efforts to facilitate the development of high-performance libraries and applications for engineers and scientists.  ...  This special issue of the PROCEEDINGS presents an overview of recent research on new methodologies for the design, development, and optimization of high-performance software libraries and applications.  ...  He has served the IEEE in several positions, including Vice-President for Publications for the IEEE Signal Processing Society (SPS) (2000)(2001)(2002), Chair of the IEEE TAB Transactions Committee (2002  ... 
doi:10.1109/jproc.2004.840488 fatcat:qjgvtpeb2rewrenhhjlb2eceve

Empirical Performance-Model Driven Data Layout Optimization [chapter]

Qingda Lu, Xiaoyang Gao, Sriram Krishnamoorthy, Gerald Baumgartner, J. Ramanujam, P. Sadayappan
2005 Lecture Notes in Computer Science  
language for expressing computational models in quantum chemistry.  ...  The performance model with empirically determined cost components is used to perform data layout optimization in the context of the Tensor Contraction Engine, a compiler for a high-level domainspecific  ...  The approach was developed for a program synthesis system targeted at the quantum chemistry domain.  ... 
doi:10.1007/11532378_7 fatcat:rsnop6hjx5fltjrj2ivbfx2mdi

Theory of Gas Phase Scattering and Reactivity for Astrochemistry [article]

Laurent Wiesenfeld, Wing-Fai Thi, Paola Caselli, Alexandre Faure, Luca Bizzocchi, João Brandão, Denis Duflot, Eric Herbst, Stephen J. Klippenstein, Tamiki Komatsuzaki, Cristina Puzzarini, Octavio Roncero, Hiroshi Teramoto (+3 others)
2016 arXiv   pre-print
This report deals with the present status of chemical physics/physical chemistry theory, for the qualitative and quantitative understanding of kinetics of molecular scattering, being it reactive or inelastic  ...  By gathering several types of expertise, from applied mathematics to physical chemistry, dialog is made possible, as a step towards new and more adapted theoretical frameworks, capable of meeting the theoretical  ...  Methods for computing ab initio points a.  ... 
arXiv:1610.00438v1 fatcat:4amrkgtn3bgdhngv3ba3qds6pq

Extending parallel scalability of LAMMPS and multiscale reactive molecular simulations

Yuxing Peng, Lonnie Crosby, Chris Knight, Gregory A. Voth, Philip Blood
2012 Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment on Bridging from the eXtreme to the campus and beyond - XSEDE '12  
However, with a proper implementation of a multi-program (MP) model, large systems can scale to thousands of CPU cores.  ...  Due to the limited scaling of the 3D-FFT in MD simulations, the traditional single-program-multiple-data (SPMD) parallelism model is only able to utilize several hundred CPU cores, even for very large  ...  Thanks to Steve Plimpton and LAMMPS development team for incorporating the MP approach into the main release of the LAMMPS code. AUTHOR AFFILIATIONS  ... 
doi:10.1145/2335755.2335833 fatcat:acf7m64rwvddnk4moslyfia7lu

The virtual chemistry lab for reactions at surfaces: Is it possible? Will it be useful?

Axel Groß
2002 Surface Science  
In this review I will reflect on the question whether ab initio calculations of reactions at surfaces can contribute to the development of, e.g., better catalysts.  ...  Ab initio total-energy calculations based on electronic structure theory have tremendously enlarged our knowledge about the geometrical and electronic structure of clean and adsorbate-covered low-index  ...  Furthermore, I am grateful to again Eckhard Pehlke and Markus Lischka for a careful proofreading of the manuscript.  ... 
doi:10.1016/s0039-6028(01)01526-6 fatcat:3e2cloy54zgcnmq4qqmqcaqotq

Ionic Liquids from a Fragmented Perspective

Justin Conrad, Shinae Kim, Mark Gordon
2019 Physical Chemistry, Chemical Physics - PCCP  
The efficacy of using fragmentation methods, such as the effective fragment potential, the fragment molecular orbital and the effective fragment molecular orbital methods are discussed.  ...  Acknowledgements This work was supported in part by a grant from the U.S. Air Force Office of Scientific Research, Award No.  ...  The authors are very grateful for many important and insightful discussions with Alex Findlater.  ... 
doi:10.1039/c9cp02836f fatcat:7u6yhd737baxva3irt2kzq7e5a

Spontaneous Superlattice Formation in Nanorods Through Partial Cation Exchange

R. D. Robinson, B. Sadtler, D. O. Demchenko, C. K. Erdonmez, L.-W. Wang, A. P. Alivisatos
2007 Science  
Ab initio calculations of the interfacial energy and modeling of strain energies show that these forces drive the self-organization.  ...  In this paper, we demonstrate the application of strain engineering in a colloidal quantum dot system, by introducing a method that spontaneously creates a regularly spaced arrangement of quantum dots  ...  Ab inito modeling: The ab initio calculations of the electronic structure of Ag 2 S and CdS were performed using Vienna Ab-initio Simulation Package (VASP) (S1) and Parallel total Energy The elastic constants  ... 
doi:10.1126/science.1142593 pmid:17641197 fatcat:5blutdcvpvhadoiom5dvnh3hoa
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