429 research outputs found
Generating optimized Fourier interpolation routines for density function theory using SPIRAL
© 2015 IEEE.Upsampling of a multi-dimensional data-set is an operation with wide application in image processing and quantum mechanical calculations using density functional theory. For small up sampling factors as seen in the quantum chemistry code ONETEP, a time-shift based implementation that shifts samples by a fraction of the original grid spacing to fill in the intermediate values using a frequency domain Fourier property can be a good choice. Readily available highly optimized multidimensional FFT implementations are leveraged at the expense of extra passes through the entire working set. In this paper we present an optimized variant of the time-shift based up sampling. Since ONETEP handles threading, we address the memory hierarchy and SIMD vectorization, and focus on problem dimensions relevant for ONETEP. We present a formalization of this operation within the SPIRAL framework and demonstrate auto-generated and auto-tuned interpolation libraries. We compare the performance of our generated code against the previous best implementations using highly optimized FFT libraries (FFTW and MKL). We demonstrate speed-ups in isolation averaging 3x and within ONETEP of up to 15%
Algebraic Signal Processing Theory: Cooley-Tukey Type Algorithms for DCTs and DSTs
This paper presents a systematic methodology based on the algebraic theory of
signal processing to classify and derive fast algorithms for linear transforms.
Instead of manipulating the entries of transform matrices, our approach derives
the algorithms by stepwise decomposition of the associated signal models, or
polynomial algebras. This decomposition is based on two generic methods or
algebraic principles that generalize the well-known Cooley-Tukey FFT and make
the algorithms' derivations concise and transparent. Application to the 16
discrete cosine and sine transforms yields a large class of fast algorithms,
many of which have not been found before.Comment: 31 pages, more information at http://www.ece.cmu.edu/~smar
Block Circulant and Toeplitz Structures in the Linearized Hartree–Fock Equation on Finite Lattices: Tensor Approach
This paper introduces and analyses the new grid-based tensor approach to
approximate solution of the elliptic eigenvalue problem for the 3D
lattice-structured systems. We consider the linearized Hartree-Fock equation
over a spatial lattice for both periodic and
non-periodic problem setting, discretized in the localized Gaussian-type
orbitals basis. In the periodic case, the Galerkin system matrix obeys a
three-level block-circulant structure that allows the FFT-based
diagonalization, while for the finite extended systems in a box (Dirichlet
boundary conditions) we arrive at the perturbed block-Toeplitz representation
providing fast matrix-vector multiplication and low storage size. The proposed
grid-based tensor techniques manifest the twofold benefits: (a) the entries of
the Fock matrix are computed by 1D operations using low-rank tensors
represented on a 3D grid, (b) in the periodic case the low-rank tensor
structure in the diagonal blocks of the Fock matrix in the Fourier space
reduces the conventional 3D FFT to the product of 1D FFTs. Lattice type systems
in a box with Dirichlet boundary conditions are treated numerically by our
previous tensor solver for single molecules, which makes possible calculations
on rather large lattices due to reduced numerical
cost for 3D problems. The numerical simulations for both box-type and periodic
lattice chain in a 3D rectangular "tube" with up to
several hundred confirm the theoretical complexity bounds for the
block-structured eigenvalue solvers in the limit of large .Comment: 30 pages, 12 figures. arXiv admin note: substantial text overlap with
arXiv:1408.383
Tensor Numerical Methods in Quantum Chemistry: from Hartree-Fock Energy to Excited States
We resume the recent successes of the grid-based tensor numerical methods and
discuss their prospects in real-space electronic structure calculations. These
methods, based on the low-rank representation of the multidimensional functions
and integral operators, led to entirely grid-based tensor-structured 3D
Hartree-Fock eigenvalue solver. It benefits from tensor calculation of the core
Hamiltonian and two-electron integrals (TEI) in complexity using
the rank-structured approximation of basis functions, electron densities and
convolution integral operators all represented on 3D
Cartesian grids. The algorithm for calculating TEI tensor in a form of the
Cholesky decomposition is based on multiple factorizations using algebraic 1D
``density fitting`` scheme. The basis functions are not restricted to separable
Gaussians, since the analytical integration is substituted by high-precision
tensor-structured numerical quadratures. The tensor approaches to
post-Hartree-Fock calculations for the MP2 energy correction and for the
Bethe-Salpeter excited states, based on using low-rank factorizations and the
reduced basis method, were recently introduced. Another direction is related to
the recent attempts to develop a tensor-based Hartree-Fock numerical scheme for
finite lattice-structured systems, where one of the numerical challenges is the
summation of electrostatic potentials of a large number of nuclei. The 3D
grid-based tensor method for calculation of a potential sum on a lattice manifests the linear in computational work, ,
instead of the usual scaling by the Ewald-type approaches
Three real-space discretization techniques in electronic structure calculations
A characteristic feature of the state-of-the-art of real-space methods in
electronic structure calculations is the diversity of the techniques used in
the discretization of the relevant partial differential equations. In this
context, the main approaches include finite-difference methods, various types
of finite-elements and wavelets. This paper reports on the results of several
code development projects that approach problems related to the electronic
structure using these three different discretization methods. We review the
ideas behind these methods, give examples of their applications, and discuss
their similarities and differences.Comment: 39 pages, 10 figures, accepted to a special issue of "physica status
solidi (b) - basic solid state physics" devoted to the CECAM workshop "State
of the art developments and perspectives of real-space electronic structure
techniques in condensed matter and molecular physics". v2: Minor stylistic
and typographical changes, partly inspired by referee comment
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