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Journal ArticleDOI

Bringing about matrix sparsity in linear-scaling electronic structure calculations

Emanuel H. Rubensson, +1 more
- 01 May 2011 - 
- Vol. 32, Iss: 7, pp 1411-1423
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TLDR
A novel scheme is proposed that has significantly smaller computational overhead compared with the Euclidean norm‐based truncation scheme of Rubensson et al. while still achieving the desired asymptotic behavior required for linear scaling.
Abstract
The performance of linear-scaling electronic structure calculations depends critically on matrix sparsity. This article gives an overview of different strategies for removal of small matrix elements, with emphasis on schemes that allow for rigorous control of errors. In particular, a novel scheme is proposed that has significantly smaller computational overhead compared with the Euclidean norm-based truncation scheme of Rubensson et al. (J Comput Chem 2009, 30, 974) while still achieving the desired asymptotic behavior required for linear scaling. Small matrix elements are removed while ensuring that the Euclidean norm of the error matrix stays below a desired value, so that the resulting error in the occupied subspace can be controlled. The efficiency of the new scheme is investigated in benchmark calculations for water clusters including up to 6523 water molecules. Furthermore, the foundation of matrix sparsity is investigated. This includes a study of the decay of matrix element magnitude with distance between basis function centers for different molecular systems and different methods. The studied methods include Hartree–Fock and density functional theory using both pure and hybrid functionals. The relation between band gap and decay properties of the density matrix is also discussed. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

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Journal ArticleDOI

O(N) methods in electronic structure calculations.

TL;DR: The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high-performance computers.
Journal ArticleDOI

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals

TL;DR: A systematic infrastructure is described that formalizes concepts implicit in previous work and greatly simplifies computer implementation of reduced-scaling electronic structure methods and the key concept is sparse representation of tensors using chains of sparse maps between two index sets.
Journal ArticleDOI

Applications of large-scale density functional theory in biology.

TL;DR: It is hoped that first principles modelling of biological structure-function relationships are approaching a reality by reviewing some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms.
Journal ArticleDOI

O(N) methods in electronic structure calculations

TL;DR: Linear scaling methods as mentioned in this paper have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the size of atoms.
Journal ArticleDOI

Electrostatic considerations affecting the calculated HOMO–LUMO gap in protein molecules

TL;DR: In this article, a detailed study of energy differences between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO gaps) in protein systems and water clusters is presented.
References
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Journal ArticleDOI

Linear scaling electronic structure methods

TL;DR: In this paper, the physical decay properties of the density matrix were studied for both metals and insulators, and several strategies for constructing O(N) algorithms were presented and critically examined.
Journal ArticleDOI

The Rotation of Eigenvectors by a Perturbation. III

TL;DR: In this article, the difference between the two subspaces is characterized in terms of certain angles through which one subspace must be rotated in order most directly to reach the other, and Sharp bounds upon trigonometric functions of these angles are obtained from the gap and from bounds upon either the perturbation or a computable residual.
Book ChapterDOI

Matrix Perturbation Theory

TL;DR: X is the vector space which acts in the n-dimensional (complex) vector space R.1.1 and is related to Varepsilon by the following inequality.
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