Shift‐and‐invert parallel spectral transformation eigensolver: Massively parallel performance for density‐functional based tight‐binding
暂无分享,去创建一个
Hong Zhang | Albert F. Wagner | David A. Dixon | Murat Keçeli | Peter Zapol | D. Dixon | P. Zapol | A. Wagner | M. Keçeli | Hong Zhang
[1] Walter Thiel,et al. Semiempirical quantum–chemical methods , 2014 .
[2] Chao Yang,et al. Parallel eigenvalue calculation based on multiple shift-invert Lanczos and contour integral based spectral projection method , 2014, Parallel Comput..
[3] Patrick Amestoy,et al. Hybrid scheduling for the parallel solution of linear systems , 2006, Parallel Comput..
[4] C. T. Kelley,et al. Parallel implementation of electronic structure eigensolver using a partitioned folded spectrum method , 2015, 1502.07806.
[5] Vipin Kumar,et al. A Parallel Algorithm for Multilevel Graph Partitioning and Sparse Matrix Ordering , 1998, J. Parallel Distributed Comput..
[6] William Gropp,et al. Efficient Management of Parallelism in Object-Oriented Numerical Software Libraries , 1997, SciTools.
[7] Axel Ruhe,et al. The spectral transformation Lánczos method for the numerical solution of large sparse generalized symmetric eigenvalue problems , 1980 .
[8] G. Seifert,et al. Tight-binding density functional theory: an approximate Kohn-Sham DFT scheme. , 2007, The journal of physical chemistry. A.
[9] Joost VandeVondele,et al. Linear Scaling Self-Consistent Field Calculations with Millions of Atoms in the Condensed Phase. , 2012, Journal of chemical theory and computation.
[10] Chao Yang,et al. Accelerating atomic orbital-based electronic structure calculation via pole expansion and selected inversion , 2012, Journal of physics. Condensed matter : an Institute of Physics journal.
[11] R. Bartlett,et al. Coupled-cluster theory in quantum chemistry , 2007 .
[12] James J. P. Stewart,et al. Fast semiempirical calculations , 1982 .
[13] François Pellegrini,et al. PT-Scotch: A tool for efficient parallel graph ordering , 2008, Parallel Comput..
[14] Lexing Ying,et al. SelInv---An Algorithm for Selected Inversion of a Sparse Symmetric Matrix , 2011, TOMS.
[15] J. Poulson. Fast parallel solution of heterogeneous 3D time-harmonic wave equations , 2012 .
[16] Gustavo E. Scuseria,et al. What is the Best Alternative to Diagonalization of the Hamiltonian in Large Scale Semiempirical Calculations , 1999 .
[17] Yousef Saad,et al. A spectrum slicing method for the Kohn-Sham problem , 2012, Comput. Phys. Commun..
[18] Charles H. Ward. Materials Genome Initiative for Global Competitiveness , 2012 .
[19] Yousef Saad,et al. Numerical Methods for Electronic Structure Calculations of Materials , 2010, SIAM Rev..
[20] P. Hohenberg,et al. Inhomogeneous Electron Gas , 1964 .
[21] Emanuel H. Rubensson,et al. Kohn-Sham Density Functional Theory Electronic Structure Calculations with Linearly Scaling Computational Time and Memory Usage. , 2011, Journal of chemical theory and computation.
[22] Stefan Grimme,et al. n-Alkane isodesmic reaction energy errors in density functional theory are due to electron correlation effects. , 2010, Organic letters.
[23] Sándor Suhai,et al. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties , 1998 .
[24] J. Sylvester. XIX. A demonstration of the theorem that every homogeneous quadratic polynomial is reducible by real orthogonal substitutions to the form of a sum of positive and negative squares , 1852 .
[25] Krishnan Raghavachari,et al. Assessment of Gaussian-3 and Density Functional Theories for Enthalpies of Formation of C1−C16 Alkanes† , 2000 .
[26] Chao Yang,et al. Improving the scalability of a symmetric iterative eigensolver for multi‐core platforms , 2014, Concurr. Comput. Pract. Exp..
[27] J. Pople,et al. Approximate Self-Consistent Molecular Orbital Theory. I. Invariant Procedures , 1965 .
[28] Robert A. van de Geijn,et al. Elemental: A New Framework for Distributed Memory Dense Matrix Computations , 2013, TOMS.
[29] Jiali Gao,et al. Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials , 2007 .
[30] J. M. Martínez,et al. Sparse Projected-Gradient Method As a Linear-Scaling Low-Memory Alternative to Diagonalization in Self-Consistent Field Electronic Structure Calculations. , 2013, Journal of chemical theory and computation.
[31] E. Cuthill,et al. Reducing the bandwidth of sparse symmetric matrices , 1969, ACM '69.
[32] Gotthard Seifert,et al. Density functional tight binding , 2014, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
[33] Vipin Kumar,et al. A Fast and High Quality Multilevel Scheme for Partitioning Irregular Graphs , 1998, SIAM J. Sci. Comput..
[34] Foulkes,et al. Tight-binding models and density-functional theory. , 1989, Physical review. B, Condensed matter.
[35] Johannes Grotendorst,et al. Performance of Dense Eigensolvers on BlueGene/Q , 2013, PPAM.
[36] Michael C. Zerner,et al. Triplet states via intermediate neglect of differential overlap: Benzene, pyridine and the diazines , 1976 .
[37] Sergio Pissanetzky,et al. Sparse Matrix Technology , 1984 .
[38] S. Goedecker. Linear scaling electronic structure methods , 1999 .
[39] W. Kohn,et al. Self-Consistent Equations Including Exchange and Correlation Effects , 1965 .
[40] E Weinan,et al. A Fast Parallel Algorithm for Selected Inversion of Structured Sparse Matrices with Application to 2D Electronic Structure Calculations , 2010, SIAM J. Sci. Comput..
[41] Chao Yang,et al. SIESTA-PEXSI: massively parallel method for efficient and accurate ab initio materials simulation without matrix diagonalization , 2014, Journal of physics. Condensed matter : an Institute of Physics journal.
[42] Gerard L. G. Sleijpen,et al. A Jacobi-Davidson Iteration Method for Linear Eigenvalue Problems , 1996, SIAM Rev..
[43] J. Stewart. Optimization of parameters for semiempirical methods I. Method , 1989 .
[44] José E. Román,et al. Strategies for spectrum slicing based on restarted Lanczos methods , 2012, Numerical Algorithms.
[45] Nicolas Renon,et al. A Sparse Self-Consistent Field Algorithm and Its Parallel Implementation: Application to Density-Functional-Based Tight Binding. , 2014, Journal of chemical theory and computation.
[46] M. Yannakakis. Computing the Minimum Fill-in is NP^Complete , 1981 .
[47] C. Lanczos. An iteration method for the solution of the eigenvalue problem of linear differential and integral operators , 1950 .
[48] Michael Sternberg,et al. SIPs: Shift-and-invert parallel spectral transformations , 2007, TOMS.
[49] K. Morokuma,et al. ONIOM: A Multilayered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels−Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative Addition , 1996 .
[50] Vicente Hernández,et al. SLEPc: A scalable and flexible toolkit for the solution of eigenvalue problems , 2005, TOMS.
[51] D R Bowler,et al. Calculations for millions of atoms with density functional theory: linear scaling shows its potential , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.
[52] A. George. Nested Dissection of a Regular Finite Element Mesh , 1973 .
[53] Ernst Schrem,et al. Computer Implementation of the Finite-Element Procedure , 1973 .
[54] James C. Sutherland,et al. Graph-Based Software Design for Managing Complexity and Enabling Concurrency in Multiphysics PDE Software , 2011, TOMS.
[55] M. Dewar,et al. Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters , 1977 .
[56] Yang,et al. Direct calculation of electron density in density-functional theory. , 1991, Physical review letters.
[57] John R. Gilbert,et al. Sparse Matrices in MATLAB: Design and Implementation , 1992, SIAM J. Matrix Anal. Appl..
[58] J. C. Slater,et al. Simplified LCAO Method for the Periodic Potential Problem , 1954 .
[59] Chao Yang,et al. New algorithms for iterative matrix‐free eigensolvers in quantum chemistry , 2015, J. Comput. Chem..
[60] Emanuel H. Rubensson,et al. Systematic sparse matrix error control for linear scaling electronic structure calculations , 2005, J. Comput. Chem..
[61] Thom Vreven,et al. Chapter 3 Hybrid Methods: ONIOM(QM:MM) and QM/MM , 2006 .
[62] A Marek,et al. The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science , 2014, Journal of physics. Condensed matter : an Institute of Physics journal.
[63] E Weinan,et al. Pole-Based approximation of the Fermi-Dirac function , 2009, 0906.1319.
[64] Paolo Bientinesi,et al. High-Performance Solvers for Dense Hermitian Eigenproblems , 2012, SIAM J. Sci. Comput..
[65] Patrick Amestoy,et al. A Fully Asynchronous Multifrontal Solver Using Distributed Dynamic Scheduling , 2001, SIAM J. Matrix Anal. Appl..
[66] T. Frauenheim,et al. DFTB+, a sparse matrix-based implementation of the DFTB method. , 2007, The journal of physical chemistry. A.
[67] Michael C. Zerner,et al. Semiempirical Molecular Orbital Methods , 2007 .