6,231 research outputs found
New Algebraic Formulation of Density Functional Calculation
This article addresses a fundamental problem faced by the ab initio
community: the lack of an effective formalism for the rapid exploration and
exchange of new methods. To rectify this, we introduce a novel, basis-set
independent, matrix-based formulation of generalized density functional
theories which reduces the development, implementation, and dissemination of
new ab initio techniques to the derivation and transcription of a few lines of
algebra. This new framework enables us to concisely demystify the inner
workings of fully functional, highly efficient modern ab initio codes and to
give complete instructions for the construction of such for calculations
employing arbitrary basis sets. Within this framework, we also discuss in full
detail a variety of leading-edge ab initio techniques, minimization algorithms,
and highly efficient computational kernels for use with scalar as well as
shared and distributed-memory supercomputer architectures
Quantum ESPRESSO: a modular and open-source software project for quantum simulations of materials
Quantum ESPRESSO is an integrated suite of computer codes for
electronic-structure calculations and materials modeling, based on
density-functional theory, plane waves, and pseudopotentials (norm-conserving,
ultrasoft, and projector-augmented wave). Quantum ESPRESSO stands for "opEn
Source Package for Research in Electronic Structure, Simulation, and
Optimization". It is freely available to researchers around the world under the
terms of the GNU General Public License. Quantum ESPRESSO builds upon
newly-restructured electronic-structure codes that have been developed and
tested by some of the original authors of novel electronic-structure algorithms
and applied in the last twenty years by some of the leading materials modeling
groups worldwide. Innovation and efficiency are still its main focus, with
special attention paid to massively-parallel architectures, and a great effort
being devoted to user friendliness. Quantum ESPRESSO is evolving towards a
distribution of independent and inter-operable codes in the spirit of an
open-source project, where researchers active in the field of
electronic-structure calculations are encouraged to participate in the project
by contributing their own codes or by implementing their own ideas into
existing codes.Comment: 36 pages, 5 figures, resubmitted to J.Phys.: Condens. Matte
Computer Architectures to Close the Loop in Real-time Optimization
© 2015 IEEE.Many modern control, automation, signal processing and machine learning applications rely on solving a sequence of optimization problems, which are updated with measurements of a real system that evolves in time. The solutions of each of these optimization problems are then used to make decisions, which may be followed by changing some parameters of the physical system, thereby resulting in a feedback loop between the computing and the physical system. Real-time optimization is not the same as fast optimization, due to the fact that the computation is affected by an uncertain system that evolves in time. The suitability of a design should therefore not be judged from the optimality of a single optimization problem, but based on the evolution of the entire cyber-physical system. The algorithms and hardware used for solving a single optimization problem in the office might therefore be far from ideal when solving a sequence of real-time optimization problems. Instead of there being a single, optimal design, one has to trade-off a number of objectives, including performance, robustness, energy usage, size and cost. We therefore provide here a tutorial introduction to some of the questions and implementation issues that arise in real-time optimization applications. We will concentrate on some of the decisions that have to be made when designing the computing architecture and algorithm and argue that the choice of one informs the other
Second order adjoints for solving PDE-constrained optimization problems
Inverse problems are of utmost importance in many fields of science and engineering. In the
variational approach inverse problems are formulated as PDE-constrained optimization problems,
where the optimal estimate of the uncertain parameters is the minimizer of a certain cost
functional subject to the constraints posed by the model equations. The numerical solution
of such optimization problems requires the computation of derivatives of the model output
with respect to model parameters. The first order derivatives of a cost functional (defined
on the model output) with respect to a large number of model parameters can be calculated
efficiently through first order adjoint sensitivity analysis. Second order adjoint models
give second derivative information in the form of matrix-vector products between the Hessian
of the cost functional and user defined vectors. Traditionally, the construction of second
order derivatives for large scale models has been considered too costly. Consequently, data
assimilation applications employ optimization algorithms that use only first order derivative
information, like nonlinear conjugate gradients and quasi-Newton methods.
In this paper we discuss the mathematical foundations of second order adjoint sensitivity
analysis and show that it provides an efficient approach to obtain Hessian-vector products. We
study the benefits of using of second order information in the numerical optimization process
for data assimilation applications. The numerical studies are performed in a twin experiment
setting with a two-dimensional shallow water model. Different scenarios are considered with
different discretization approaches, observation sets, and noise levels. Optimization algorithms
that employ second order derivatives are tested against widely used methods that require
only first order derivatives. Conclusions are drawn regarding the potential benefits and the
limitations of using high-order information in large scale data assimilation problems
Variational Inference in Nonconjugate Models
Mean-field variational methods are widely used for approximate posterior
inference in many probabilistic models. In a typical application, mean-field
methods approximately compute the posterior with a coordinate-ascent
optimization algorithm. When the model is conditionally conjugate, the
coordinate updates are easily derived and in closed form. However, many models
of interest---like the correlated topic model and Bayesian logistic
regression---are nonconjuate. In these models, mean-field methods cannot be
directly applied and practitioners have had to develop variational algorithms
on a case-by-case basis. In this paper, we develop two generic methods for
nonconjugate models, Laplace variational inference and delta method variational
inference. Our methods have several advantages: they allow for easily derived
variational algorithms with a wide class of nonconjugate models; they extend
and unify some of the existing algorithms that have been derived for specific
models; and they work well on real-world datasets. We studied our methods on
the correlated topic model, Bayesian logistic regression, and hierarchical
Bayesian logistic regression
Feature detection using spikes: the greedy approach
A goal of low-level neural processes is to build an efficient code extracting
the relevant information from the sensory input. It is believed that this is
implemented in cortical areas by elementary inferential computations
dynamically extracting the most likely parameters corresponding to the sensory
signal. We explore here a neuro-mimetic feed-forward model of the primary
visual area (VI) solving this problem in the case where the signal may be
described by a robust linear generative model. This model uses an over-complete
dictionary of primitives which provides a distributed probabilistic
representation of input features. Relying on an efficiency criterion, we derive
an algorithm as an approximate solution which uses incremental greedy inference
processes. This algorithm is similar to 'Matching Pursuit' and mimics the
parallel architecture of neural computations. We propose here a simple
implementation using a network of spiking integrate-and-fire neurons which
communicate using lateral interactions. Numerical simulations show that this
Sparse Spike Coding strategy provides an efficient model for representing
visual data from a set of natural images. Even though it is simplistic, this
transformation of spatial data into a spatio-temporal pattern of binary events
provides an accurate description of some complex neural patterns observed in
the spiking activity of biological neural networks.Comment: This work links Matching Pursuit with bayesian inference by providing
the underlying hypotheses (linear model, uniform prior, gaussian noise
model). A parallel with the parallel and event-based nature of neural
computations is explored and we show application to modelling Primary Visual
Cortex / image processsing.
http://incm.cnrs-mrs.fr/perrinet/dynn/LaurentPerrinet/Publications/Perrinet04tau
Hiding State in CλaSH Hardware Descriptions
Synchronous hardware can be modelled as a mapping from input and state to output and a new state, such mappings are referred to as transition functions. It is natural to use a functional language to implement transition functions. The CaSH compiler is capable of translating transition functions to VHDL. Modelling hardware using multiple components is convenient. Components in CaSH can be considered as instantiations of functions. To avoid packing and unpacking state when composing components, functions are lifted to arrows. By using arrows the chance of making errors will decrease as it is not required to manually (un)pack the state. Furthermore, the Haskell do-syntax for arrows increases the readability of hardware designs. This is demonstrated using a realistic example of a circuit which consists of multiple components
Block Iterative Eigensolvers for Sequences of Correlated Eigenvalue Problems
In Density Functional Theory simulations based on the LAPW method, each
self-consistent field cycle comprises dozens of large dense generalized
eigenproblems. In contrast to real-space methods, eigenpairs solving for
problems at distinct cycles have either been believed to be independent or at
most very loosely connected. In a recent study [7], it was demonstrated that,
contrary to belief, successive eigenproblems in a sequence are strongly
correlated with one another. In particular, by monitoring the subspace angles
between eigenvectors of successive eigenproblems, it was shown that these
angles decrease noticeably after the first few iterations and become close to
collinear. This last result suggests that we can manipulate the eigenvectors,
solving for a specific eigenproblem in a sequence, as an approximate solution
for the following eigenproblem. In this work we present results that are in
line with this intuition. We provide numerical examples where opportunely
selected block iterative eigensolvers benefit from the reuse of eigenvectors by
achieving a substantial speed-up. The results presented will eventually open
the way to a widespread use of block iterative eigensolvers in ab initio
electronic structure codes based on the LAPW approach.Comment: 12 Pages, 5 figures. Accepted for publication on Computer Physics
Communication
Solution of partial differential equations on vector and parallel computers
The present status of numerical methods for partial differential equations on vector and parallel computers was reviewed. The relevant aspects of these computers are discussed and a brief review of their development is included, with particular attention paid to those characteristics that influence algorithm selection. Both direct and iterative methods are given for elliptic equations as well as explicit and implicit methods for initial boundary value problems. The intent is to point out attractive methods as well as areas where this class of computer architecture cannot be fully utilized because of either hardware restrictions or the lack of adequate algorithms. Application areas utilizing these computers are briefly discussed
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