Analytical ray tracing system: Introducing art, a C-library designed for seismic applications

Ray tracing technique is an important tool not only to forward but also for inverse problems in Geophysics, which most of the seismic processing steps depend on. However, implementing ray tracing codes can be very time consuming. This article presents a computer library to trace rays in 2.5D media composed by a stack of layers. The velocity profile inside each layer is such that the eikonal equation can be analytically solved. Therefore, the ray tracing within such profile is made fast and accurate. The great advantage of an analytical ray tracing library is the numerical precision of the quantities computed and the fast execution of the implemented codes. Even though ray tracing programs exist for a long time, for example the seis88 package by ?ervený, most of those programs use a numerical approach to compute the ray. Regardless of the fact that numerical methods can solve more general problems, the analytical ones could be part of a more sophisticated simulation process, where the ray tracing time is completely relevant. We demonstrate the feasibility of our codes using several examples (Miqueles et al., 2013)  [1]. The library can also be used for other applications besides seismic, e.g., optics and tomography.     

MT: A Mathematica package to compute convolutions

We introduce the Mathematica package MT which can be used to compute, both analytically and numerically, convolutions involving harmonic polylogarithms, polynomials or generalized functions. As applications contributions to next-to-next-to-next-to leading order Higgs boson production and the Drell–Yan process are discussed.     

Development of novel statistical reconstruction algorithms for poly-energetic X-ray computed tomography

A beam-hardening effect is a common problem affecting the quantitative aspects of X-ray computed tomography (CT). We have developed two statistical reconstruction algorithms for poly-energetic X-ray CT that can effectively reduce the beam-hardening effect. Phantom tests were used to evaluate our approach in comparison with traditional correction methods. Unlike previous methods, our algorithm utilizes multiple energy-corresponding blank scans to estimate the attenuation map for a particular energy spectrum. Therefore, our algorithm is an energy-selective reconstruction. In addition to benefits over other statistical algorithms for poly-energetic reconstruction, our algorithm has the advantage of not requiring prior knowledge of the object material, the energy spectrum of the source and the energy sensitivity of the detector. The results showed an improvement in coefficient of variation, uniformity and signal-to-noise ratio; overall, this novel approach produces a better beam-hardening correction.     

电容层析成像系统三维图像重建的研究

探讨了电容层析成像(ECT)系统中利用二维断层图像进行三维表面重建并由三维图像求取两相流中离散相体积和观察其空间位置的方法。首先对二维断层图像序列进行轮廓抽取和细线化，然后进行轮廓匹配和轮廓插值并进行表面重建。初步的仿真结果表明，使用的三维重建算法简单、重建精度高、成像速率快。     

Cobra: A package for co-breaking analysis

Cobra, an econometric software package designed for CO-BReaking Analysis, is introduced. Cobra is programmed in Ox, the object-oriented statistical system, and consists of three modules: Firstly, CobraDgp is derived from the Database class and enables the user to generate a multivariate time series that is subject to multiple breaks in its intercept as well as linear trend. Secondly, the Cobra module is derived from the Modelbase class and implements two algorithms for the estimation of co-breaking relationships. Taking advantage of the capabilities provided by Modelbase, Cobra may be loaded into OxPack and used with the GUI GiveWin as front end. Finally, CobraSim is derived from the Simulation class and wrapped around CobraDgp and Cobra to allow a straightforward implementation of Monte Carlo experiments. A brief introduction of the concept of co-breaking is given before Cobra is illustrated by means of an empirical example as well as a simple Monte Carlo. Excerpts of Ox code as well as screenshots are provided.     

HiggsBounds 2.0.0: Confronting neutral and charged Higgs sector predictions with exclusion bounds from LEP and the Tevatron

HiggsBounds 2.0.0 is a computer code which tests both neutral and charged Higgs sectors of arbitrary models against the current exclusion bounds from the Higgs searches at LEP and the Tevatron. As input, it requires a selection of model predictions, such as Higgs masses, branching ratios, effective couplings and total decay widths. HiggsBounds 2.0.0 then uses the expected and observed topological cross section limits from the Higgs searches to determine whether a given parameter scenario of a model is excluded at the 95% C.L. by those searches. Version 2.0.0 represents a significant extension of the code since its first release (1.0.0). It includes now 28/53 LEP/Tevatron Higgs search analyses, compared to the 11/22 in the first release, of which many of the ones from the Tevatron are replaced by updates. As a major extension, the code allows now the predictions for (singly) charged Higgs bosons to be confronted with LEP and Tevatron searches. Furthermore, the newly included analyses contain LEP searches for neutral Higgs bosons (H) decaying invisibly or into (non-flavour tagged) hadrons as well as decay-mode independent searches for neutral Higgs bosons, LEP searches via the production modes τ⁺τ⁻H and , and Tevatron searches via . Also, all Tevatron results presented at the ICHEP?10 are included in version 2.0.0. As physics applications of HiggsBounds 2.0.0 we study the allowed Higgs mass range for model scenarios with invisible Higgs decays and we obtain exclusion results for the scalar sector of the Randall–Sundrum model using up-to-date LEP and Tevatron direct search results.

Program summary

Program title: HiggsBoundsCatalogue identifier: AEFF_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFF_v2_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: GNU General Public Licence version 3No. of lines in distributed program, including test data, etc.: 74 005No. of bytes in distributed program, including test data, etc.: 1 730 996Distribution format: tar.gzProgramming language: Fortran 77, Fortran 90 (two code versions are offered).Classification: 11.1.Catalogue identifier of previous version: AEFF_v1_0Journal reference of previous version: Comput. Phys. Comm. 181 (2010) 138External routines: HiggsBounds requires no external routines/libraries. Some sample programs in the distribution require the programs FeynHiggs 2.7.1 or CPsuperH2.2 to be installed.Does the new version supersede the previous version?: YesNature of problem: Determine whether a parameter point of a given model is excluded or allowed by LEP and Tevatron neutral and charged Higgs boson search results.Solution method: The most sensitive channel from LEP and Tevatron searches is determined and subsequently applied to test this parameter point. The test requires as input, model predictions for the Higgs boson masses, branching ratios and ratios of production cross sections with respect to reference values.Reasons for new version: This version extends the functionality of the previous version.Summary of revisions: List of included Higgs searches has been expanded, e.g. inclusion of (singly) charged Higgs boson searches. The input required from the user has been extended accordingly.Restrictions: Assumes that the narrow width approximation is applicable in the model under consideration and that the model does not predict a significant change to the signature of the background processes or the kinematical distributions of the signal cross sections.Running time: About 0.01 seconds (or less) for one parameter point using one processor of an Intel Core 2 Quad Q6600 CPU at 2.40 GHz for sample model scenarios with three Higgs bosons. It depends on the complexity of the Higgs sector (e.g. the number of Higgs bosons and the number of open decay channels) and on the code version.     

Object-oriented design patterns in Fortran 90/95: mazev1, mazev2 and mazev3

This paper discusses the concept, application, and usefulness of software design patterns for scientific programming in Fortran 90/95. An example from the discipline of object-oriented design patterns, that of a game based on navigation through a maze, is used to describe how some important patterns can be implemented in Fortran 90/95 and how the progressive introduction of design patterns can usefully restructure Fortran software as it evolves. This example is complemented by a discussion of how design patterns have been used in a real-life simulation of Particle-in-Cell plasma physics. The following patterns are mentioned in this paper: Factory, Strategy, Template, Abstract Factory and Facade.

Program summary

Program title: mazev1, mazev2, mazev3Catalogue identifier: AEAI_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAI_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 1958No. of bytes in distributed program, including test data, etc.: 17 100Distribution format: tar.gzProgramming language: Fortran 95Computer: PC/MacOperating system: Unix/Linux/Mac (FreeBSD)/Windows (Cygwin)RAM: These are interactive programs with small (KB) memory requirementsClassification: 6.5, 20Nature of problem: A sequence of programs which demonstrate the use of object oriented design patterns for the restructuring of Fortran 90/95 software. The programs implement a simple maze game similar to that described in [1].Solution method: Restructuring uses versions of the Template, Strategy and Factory design patterns.Running time: Interactive.References:

[1] 

E. Gamma, R. Helm, R. Johnson, J. Vlissides, Design Patterns: Elements of Reusable Object Oriented Software, Addison-Wesley, 1995, ISBN 0201633612.

     

SARAH 4: A tool for (not only SUSY) model builders

We present the new version of the Mathematica package SARAH which provides the same features for a non-supersymmetric model as previous versions for supersymmetric models. This includes an easy and straightforward definition of the model, the calculation of all vertices, mass matrices, tadpole equations, and self-energies. Also the two-loop renormalization group equations for a general gauge theory are now included and have been validated with the independent Python code PyR@TE. Model files for FeynArts, CalcHep/CompHep, WHIZARD and in the UFO format can be written, and source code for SPheno for the calculation of the mass spectrum, a set of precision observables, and the decay widths and branching ratios of all states can be generated. Furthermore, the new version includes routines to output model files for Vevacious for both, supersymmetric and non-supersymmetric, models. Global symmetries are also supported with this version and by linking Susyno the handling of Lie groups has been improved and extended.     

NGluon: A package to calculate one-loop multi-gluon amplitudes

We present a computer library for the numerical evaluation of colour-ordered n-gluon amplitudes at one-loop order in pure Yang–Mills theory. The library uses the recently developed technique of generalised unitarity. Running in double precision the library yields reliable results for up to 14 gluons with only a small fraction of events requiring a re-evaluation using extended floating point arithmetic. We believe that the library presented here provides an important contribution to future LHC phenomenology. The program may also prove useful in cross checking results obtained by other methods. In addition, the code provides a sample implementation which may serve as a starting point for further developments.

Program summary

Program title:NGluonCatalogue identifier: AEIZ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIZ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: GNU Public LicenseNo. of lines in distributed program, including test data, etc.: 30 677No. of bytes in distributed program, including test data, etc.: 334 896Distribution format: tar.gzProgramming language: C++Computer: Any computer platform supported by the GNU compiler suite.Operating system: No specific requirements – tested on Scientific Linux 5.2.RAM: Depending on the complexity, for realistic applications like 10 gluon production in double precision below 10 MB.Classification: 11.5External routines: QCDLoop (http://qcdloop.fnal.gov/), qd (http://crd.lbl.gov/~dhbailey/mpdist/)Nature of problem: Evaluation of next-to-leading order corrections for gluon scattering amplitudes in pure gauge theory.Solution method: Purely numerical approach based on tree amplitudes obtained via Berends–Giele recursion combined with unitarity method.Restrictions: Running in double precision the number of gluons should not exceed 14.Running time: Depending on the number of external gluons between less than a millisecond (4 gluons) up to a 1 s (14 gluons) per phase space point.     

Deterministic solutions to QSAT and Q3SAT by spiking neural P systems with pre-computed resources

In this paper we continue previous studies on the computational efficiency of spiking neural P systems, under the assumption that some pre-computed resources of exponential size are given in advance. Specifically, we give a deterministic solution for each of two well known PSPACE-complete problems: QSAT and Q3SAT. In the case of QSAT, the answer to any instance of the problem is computed in a time which is linear with respect to both the number n of Boolean variables and the number m of clauses that compose the instance. As for Q3SAT, the answer is computed in a time which is at most cubic in the number n of Boolean variables.     

GMIC++: Grouping method in C++: an efficient method to solve large number of Master equations

In typical nucleation, growth and coarsening problems in the study of defect/adatom accumulation in crystalline solids or surfaces, a large number of Master equations are involved to describe the evolution process. As examples, defect clusters nucleate and grow from point defects in solids when subjected to particle irradiation, and atoms depositing on a substrate form clusters leading to film growth. To efficiently solve the large number of master equations, the grouping method was used, which we have coded into a standard C++ program, taking full advantage of the object-oriented programming style supported in the C++ language. Because of the generic nature of this code, it may be of interest to the modeling nucleation and growth processes. As an example to demonstrate the application of this computer code, the Ostwald ripening process of vacancy clustering during aging in metal nickel is calculated.     

一种新的射影重建方法

提出一种新的射影重建方法。它以最小化射影三维空间点的平均二维反投影误差为准则,以奇异值分解为工具,分步线性迭代实现求解过程,避免了传统射影重建方法中复杂的非线性优化过程和基础矩阵计算过程,且不需要任何初始估计,适用于匹配特征点存在“丢失点”的情况,不受相机特殊运动的限制。利用虚拟物体和真实物体图像序列进行了实验,证明该方法具有计算简单、准确性和鲁棒性高等方面的特点,具有较高的实用价值。     

GeoPDEs: A research tool for Isogeometric Analysis of PDEs

GeoPDEs (http://geopdes.sourceforge.net) is a suite of free software tools for applications on Isogeometric Analysis (IGA). Its main focus is on providing a common framework for the implementation of the many IGA methods for the discretization of partial differential equations currently studied, mainly based on B-Splines and Non-Uniform Rational B-Splines (NURBS), while being flexible enough to allow users to implement new and more general methods with a relatively small effort. This paper presents the philosophy at the basis of the design of GeoPDEs and its relation to a quite comprehensive, abstract definition of IGA.     

yambo: An ab initio tool for excited state calculations

yambo is an ab initio code for calculating quasiparticle energies and optical properties of electronic systems within the framework of many-body perturbation theory and time-dependent density functional theory. Quasiparticle energies are calculated within the GW approximation for the self-energy. Optical properties are evaluated either by solving the Bethe-Salpeter equation or by using the adiabatic local density approximation. yambo is a plane-wave code that, although particularly suited for calculations of periodic bulk systems, has been applied to a large variety of physical systems. yambo relies on efficient numerical techniques devised to treat systems with reduced dimensionality, or with a large number of degrees of freedom. The code has a user-friendly command-line based interface, flexible I/O procedures and is interfaced to several publicly available density functional ground-state codes.

Program summary

Program title:yamboCatalogue identifier: AEDH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDH_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GNU General Public Licence v2.0No. of lines in distributed program, including test data, etc.: 149 265No. of bytes in distributed program, including test data, etc.: 2 848 169Distribution format: tar.gzProgramming language: Fortran 95, CComputer: any computer architecture, running any flavor of UNIXOperating system: GNU/Linux, AIX, Irix, OS/XHas the code been vectorised or parallelized?: YesRAM: 10-1000 MbytesClassification: 7.3, 4.4, 7.2External routines:

•

BLAS (http://www.netlib.org/blas/)

•

LAPACK (http://www.netlib.org/lapack/)

•

MPI (http://www-unix.mcs.anl.gov/mpi/) is optional.

•

BLACS (http://www.netlib.org/scalapack/) is optional.

•

SCALAPACK (http://www.netlib.org/scalapack/) is optional.

•

FFTW (http://www.fftw.org/) is optional.

•

netCDF (http://www.unidata.ucar.edu/software/netcdf/) is optional.

Nature of problem: Calculation of excited state properties (quasiparticles, excitons, plasmons) from first principles.Solution method: Many body perturbation theory (Dyson equation, Bethe Salpeter equation) and time-dependent density functional theory. Quasiparticle approximation. Plasmon-pole model for the dielectric screening. Plane wave basis set with norm conserving pseudopotentials.Unusual features: During execution, yambo supplies estimates of the elapsed and remaining time for completion of each runlevel. Very friendly shell-based user-interface.Additional comments:yambo was known as “SELF” prior to GPL release. It belongs to the suite of codes maintained and used by the European Theoretical Spectroscopy Facility (ETSF) [1].Running time: The typical yambo running time can range from a few minutes to some days depending on the chosen level of approximation, and on the property and physical system under study.References:[1] The European Theoretical Spectroscopy Facility, http://www.etsf.eu.     

Vscape V1.1.0. An interactive tool for metastable vacua

Vscape is an interactive tool for studying the one-loop effective potential of an ungauged supersymmetric model of chiral multiplets. The program allows the user to define a supersymmetric model by specifying the superpotential. The F-terms and the scalar and fermionic mass matrices are calculated symbolically. The program then allows you to search numerically for (meta)stable minima of the one-loop effective potential. Additional commands enable you to further study specific minima, by, e.g., computing the mass spectrum for those vacua. Vscape combines the flexibility of symbolic software, with the speed of a numerical package.

Program summary

Program title:Vscape 1.1.1Catalogue identifier: ADZW_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZW_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 80 507No. of bytes in distributed program, including test data, etc.: 6 708 938Distribution format: tar.gzProgramming language: C++Computer: Pentium 4 PC Computers: need (GNU) C++ compiler, Linux standard GNU installation (./configure; make; make install). A precompiled Windows XP version is included in the distribution packageOperating system: Linux, Windows XP using cygwinRAM: 10 MBWord size: 32 bitsClassification: 11.6External routines: GSL (http://www.gnu.org/software/gsl/), CLN (http://www.ginac.de/CLN/), GiNaC (http://directory.fsf.org/GiNaC.html)Nature of problem:Vscape is an interactive tool for studying the one-loop effective potential of an ungauged supersymmetric model of chiral multiplets. The program allows the user to define a supersymmetric model by specifying the superpotential. The F-terms and the scalar and fermionic mass matrices are calculated symbolically. The program then allows you to search numerically for (meta)stable minima of the one-loop effective potential. Additional commands enable you to further study specific minima, by, e.g., computing the mass spectrum for those vacua. Vscape combines the flexibility of symbolic software with the speed of a numerical package.Solution method: Coleman-Weinberg potential is computed using numerical matrix diagonalization. Minima of the one-loop effective potential are found using the Nelder and Mead simplex algorithm. The one-loop effective potential can be studied using numerical differentiation. Symbolic users interface implemented using flex and bison.Restrictions:N=1 supersymmetric chiral models onlyUnusual features: GiNaC (+CLN), GSL, ReadLib (not essential)Running time: Interactive users interface. Most commands execute in a few ms. Computationally intensive commands execute in order of minutes, depending on the complexity of the user defined model.     

基于多重假设的视频压缩感知分层重建

为了改进视频压缩感知方案的性能,提出了一种基于多重假设的视频压缩感知分层重建方案。该重建方案以图像组为单位进行,首先独立重建关键帧,接下来对图像组中的每个非关键帧分配重建层级,并按照层级顺序由低至高逐层重建。每个非关键帧的重建过程逐块进行,需要其时域参考帧及当前帧中的空域数据集为每个重建块做混合多重假设预测,并通过求解全变分最小化问题重建预测残差,最后将预测值与预测残差相加得到重建图像。实验结果表明,在相同采样率下,本文提出的基于多重假设的分层重建方案比已有的方法可以获得最高约3.2dB的峰值信噪比增益。     

wannier90: A tool for obtaining maximally-localised Wannier functions

We present wannier90, a program for calculating maximally-localised Wannier functions (MLWF) from a set of Bloch energy bands that may or may not be attached to or mixed with other bands. The formalism works by minimising the total spread of the MLWF in real space. This is done in the space of unitary matrices that describe rotations of the Bloch bands at each k-point. As a result, wannier90 is independent of the basis set used in the underlying calculation to obtain the Bloch states. Therefore, it may be interfaced straightforwardly to any electronic structure code. The locality of MLWF can be exploited to compute band-structure, density of states and Fermi surfaces at modest computational cost. Furthermore, wannier90 is able to output MLWF for visualisation and other post-processing purposes. Wannier functions are already used in a wide variety of applications. These include analysis of chemical bonding in real space; calculation of dielectric properties via the modern theory of polarisation; and as an accurate and minimal basis set in the construction of model Hamiltonians for large-scale systems, in linear-scaling quantum Monte Carlo calculations, and for efficient computation of material properties, such as the anomalous Hall coefficient. wannier90 is freely available under the GNU General Public License from http://www.wannier.org/.

Program summary

Program title: wannier90Catalogue identifier: AEAK_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAK_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 556 495No. of bytes in distributed program, including test data, etc.: 5 709 419Distribution format: tar.gzProgramming language: Fortran 90, perlComputer: any architecture with a Fortran 90 compilerOperating system: Linux, Windows, Solaris, AIX, Tru64 Unix, OSXRAM: 10 MBWord size: 32 or 64Classification: 7.3External routines:

•

BLAS (http://www/netlib.org/blas).

•

LAPACK (http://www.netlib.org/lapack).

Both available under open-source licenses.Nature of problem: Obtaining maximally-localised Wannier functions from a set of Bloch energy bands that may or may not be entangled.Solution method: In the case of entangled bands, the optimally-connected subspace of interest is determined by minimising a functional which measures the subspace dispersion across the Brillouin zone. The maximally-localised Wannier functions within this subspace are obtained by subsequent minimisation of a functional that represents the total spread of the Wannier functions in real space. For the case of isolated energy bands only the second step of the procedure is required.Unusual features: Simple and user-friendly input system. Wannier functions and interpolated band structure output in a variety of file formats for visualisation.Running time: Test cases take 1 minute.References:

[1] 

N. Marzari, D. Vanderbilt, Maximally localized generalized Wannier functions for composite energy bands, Phys. Rev. B 56 (1997) 12847.

[2] 

I. Souza, N. Marzari, D. Vanderbilt, Maximally localized Wannier functions for entangled energy bands, Phys. Rev. B 65 (2001) 035109.