Linear optical properties of solids within the full-potential linearized augmented planewave method

We present a scheme for the calculation of linear optical properties by the all-electron full-potential linearized augmented planewave (LAPW) method. A summary of the theoretical background for the derivation of the dielectric tensor within the random-phase approximation is provided. The momentum matrix elements are evaluated in detail for the LAPW basis, and the interband as well as the intra-band contributions to the dielectric tensor are given. As an example the formalism is applied to Aluminum. The program is available as a module within the WIEN2k code.     

ATAT@WIEN2k: An interface for cluster expansion based on the linearized augmented planewave method

We have developed an interface between the all-electron density functional theory code WIEN2k, and the MIT Ab-initio Phase Stability (MAPS) code of the Alloy-Theoretic Automated Toolkit (ATAT). WIEN2k is an implementation of the full-potential linearized augmented planewave method which yields highly accurate total energies and optimized geometries for any given structure. The ATAT package consists of two parts. The first one is the MAPS code, which constructs a cluster expansion (CE) in conjunction with a first-principles code. These results form the basis for the second part, which computes the thermodynamic properties of the alloy. The main task of the CE is to calculate the many-body potentials or effective cluster interactions (ECIs) from the first-principles total energies of different structures or supercells using the structure-inversion technique. By linking MAPS seamlessly with WIEN2k we have created a tool to obtain the ECIs for any lattice type of an alloy. We have chosen fcc Al-Ti and bcc W-Re to evaluate our implementation. Our calculated ECIs exhibit all features of a converged CE and compare well with literature results.     

一种节省硬件资源的DFT伪码捕获实现方法

DFT伪码捕获算法在进行伪码搜索的同时估计多普勒频偏,为了满足捕获精度要求,需要增加DFT点数,但随着运算点数的增加硬件实现难度成倍增长.本文提出一种基于FPGA的在不增加DFF点数的前提下实现高精度伪码捕获的方法,详细介绍了如何通过采用查找表和浮动窗等方法在保证系统性能的同时节省资源,通过在FPGA器件中验证表明该方法捕获速度快,精度高,硬件实现简单,占用资源少,有很强的实用价值.     

eHDECAY: An implementation of the Higgs effective Lagrangian into HDECAY

We present eHDECAY, a modified version of the program HDECAY which includes the full list of leading bosonic operators of the Higgs effective Lagrangian with a linear or non-linear realization of the electroweak symmetry and implements two benchmark composite Higgs models.     

The STATFLUX code: a statistical method for calculation of flow and set of parameters, based on the Multiple-Compartment Biokinetical Model

The code STATFLUX, implementing a new and simple statistical procedure for the calculation of transfer coefficients in radionuclide transport to animals and plants, is proposed. The method is based on the general multiple-compartment model, which uses a system of linear equations involving geometrical volume considerations. Flow parameters were estimated by employing two different least-squares procedures: Derivative and Gauss-Marquardt methods, with the available experimental data of radionuclide concentrations as the input functions of time. The solution of the inverse problem, which relates a given set of flow parameter with the time evolution of concentration functions, is achieved via a Monte Carlo simulation procedure.

Program summary

Title of program:STATFLUXCatalogue identifier:ADYS_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYS_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions: noneComputer for which the program is designed and others on which it has been tested:Micro-computer with Intel Pentium III, 3.0 GHzInstallation:Laboratory of Linear Accelerator, Department of Experimental Physics, University of São Paulo, BrazilOperating system:Windows 2000 and Windows XPProgramming language used:Fortran-77 as implemented in Microsoft Fortran 4.0. NOTE: Microsoft Fortran includes non-standard features which are used in this program. Standard Fortran compilers such as, g77, f77, ifort and NAG95, are not able to compile the code and therefore it has not been possible for the CPC Program Library to test the program.Memory required to execute with typical data:8 Mbytes of RAM memory and 100 MB of Hard disk memoryNo. of bits in a word:16No. of lines in distributed program, including test data, etc.:6912No. of bytes in distributed program, including test data, etc.:229 541Distribution format:tar.gzNature of the physical problem:The investigation of transport mechanisms for radioactive substances, through environmental pathways, is very important for radiological protection of populations. One such pathway, associated with the food chain, is the grass-animal-man sequence. The distribution of trace elements in humans and laboratory animals has been intensively studied over the past 60 years [R.C. Pendlenton, C.W. Mays, R.D. Lloyd, A.L. Brooks, Differential accumulation of iodine-131 from local fallout in people and milk, Health Phys. 9 (1963) 1253-1262]. In addition, investigations on the incidence of cancer in humans, and a possible causal relationship to radioactive fallout, have been undertaken [E.S. Weiss, M.L. Rallison, W.T. London, W.T. Carlyle Thompson, Thyroid nodularity in southwestern Utah school children exposed to fallout radiation, Amer. J. Public Health 61 (1971) 241-249; M.L. Rallison, B.M. Dobyns, F.R. Keating, J.E. Rall, F.H. Tyler, Thyroid diseases in children, Amer. J. Med. 56 (1974) 457-463; J.L. Lyon, M.R. Klauber, J.W. Gardner, K.S. Udall, Childhood leukemia associated with fallout from nuclear testing, N. Engl. J. Med. 300 (1979) 397-402]. From the pathways of entry of radionuclides in the human (or animal) body, ingestion is the most important because it is closely related to life-long alimentary (or dietary) habits. Those radionuclides which are able to enter the living cells by either metabolic or other processes give rise to localized doses which can be very high. The evaluation of these internally localized doses is of paramount importance for the assessment of radiobiological risks and radiological protection. The time behavior of trace concentration in organs is the principal input for prediction of internal doses after acute or chronic exposure. The General Multiple-Compartment Model (GMCM) is the powerful and more accepted method for biokinetical studies, which allows the calculation of concentration of trace elements in organs as a function of time, when the flow parameters of the model are known. However, few biokinetics data exist in the literature, and the determination of flow and transfer parameters by statistical fitting for each system is an open problem.Restriction on the complexity of the problem:This version of the code works with the constant volume approximation, which is valid for many situations where the biological half-live of a trace is lower than the volume rise time. Another restriction is related to the central flux model. The model considered in the code assumes that exist one central compartment (e.g., blood) that connect the flow with all compartments, and the flow between other compartments is not included.Typical running time:Depends on the choice for calculations. Using the Derivative Method the time is very short (a few minutes) for any number of compartments considered. When the Gauss-Marquardt iterative method is used the calculation time can be approximately 5-6 hours when ∼15 compartments are considered.     

An insight into the dispersion of changes in cloned and non-cloned code: A genealogy based empirical study

In this paper, we present an in-depth empirical study of a new metric, change dispersion, that measures the extent changes are scattered throughout the code of a software system. Intuitively, highly dispersed changes, the changes that are scattered throughout many software entities (such as files, classes, methods, and variables), should require more maintenance effort than the changes that only affect a few entities. In our research we investigate change dispersion on the code-base of a number of subject systems as a whole, and separately on each system's cloned and non-cloned code. Our central objective is to determine whether cloned code negatively affects software evolution and maintenance. The granularity of our focus is at the method level.Our experimental results on 16 open source subject systems written in four different programming languages (Java, C, C#, and Python) involving two clone detection tools (CCFinderX and NiCad) and considering three major types of clones (Type 1: exact, Type 2: dissimilar naming, and Type 3: some dissimilar code) suggests that change dispersion has a positive and statistically significant correlation with the change-proneness (or instability) of source code. Cloned code, especially in Java and C systems, often exhibits a higher change dispersion than non-cloned code. Also, changes to Type 3 clones are more dispersed compared to changes to Type 1 and Type 2 clones. According to our analysis, a primary cause of high change dispersion in cloned code is that clones from the same clone class often require corresponding changes to ensure they remain consistent.     

An insight into the system dynamics method: a case study in the dynamics of international minerals investment

This paper presents an explanation of the system dynamics method. It is based on the development of a detailed simulation model designed to examine the effectiveness of various environmental, fiscal and corporate policies on the flow of investment funds and mineral resources among a number of simulated mining firms and competing countries. Emphasis is placed on the development process and the reader is referred elsewhere for presentation and discussion of model output.     

Gibbs2: A new version of the quasiharmonic model code. II. Models for solid-state thermodynamics, features and implementation

In the second article of the series, we present the Gibbs2 code, a Fortran90 reimplementation of the original Gibbs program [Comput. Phys. Commun. 158 (2004) 57] for the calculation of pressure–temperature dependent thermodynamic properties of solids under the quasiharmonic approximation. We have taken advantage of the detailed analysis carried out in the first paper to implement robust fitting techniques. In addition, new models to introduce temperature effects have been incorporated, from the simple Debye model contained in the original article to a full quasiharmonic model that requires the phonon density of states at each calculated volume. Other interesting novel features include the empirical energy corrections, that rectify systematic errors in the calculation of equilibrium volumes caused by the choice of the exchange-correlation functional, the electronic contributions to the free energy and the automatic computation of phase diagrams. Full documentation in the form of a user?s guide and a complete set of tests and sample data are provided along with the source code.

Program summary

Program title:Gibbs2Catalogue identifier: AEJI_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJI_v1_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: GNU General Public License, v3No. of lines in distributed program, including test data, etc.: 936 087No. of bytes in distributed program, including test data, etc.: 8 596 671Distribution format: tar.gzProgramming language: Fortran90Computer: Any running Unix/LinuxOperating system: Unix, GNU/LinuxClassification: 7.8External routines: Part of the minpack, pppack and slatec libraries (downloaded from www.netlib.org) are distributed along with the program.Nature of problem: Given the static E(V) curve, and possibly vibrational information such as the phonon density of states, calculate the equilibrium volume and thermodynamic properties of a solid at arbitrary temperatures and pressures in the framework of the quasiharmonic approximation.Additional comments: A detailed analysis concerning the fitting of equations of state has been carried out in the first part of this article, and implemented in the code presented here.Running time: The tests provided only take a few seconds to run.     

An application of the 2-nitrobenzenesulfenyl method to proteomic profiling of human colorectal carcinoma: A novel approach for biomarker discovery

In the development of novel biomarkers, the proteomic approach is advantageous because using it the cancer-associated proteins can be directly identified. We previously developed a 2-nitrobenzenesulfenyl (NBS) method to improve quantitative proteome analysis. Here, we applied this method to proteomic profiling of colorectal carcinoma (CRC) to identify novel proteins with altered expression in CRC. Each pair of tumor and normal tissue specimens from 12 CRC patients was analyzed, and approximately 5000 NBS-labeled paired peaks were quantified. Peaks with altered signal intensities (>1.5-fold) and occurring frequently in the samples (>70%) were selected, and 128 proteins were identified by MS/MS analyses as differentially expressed proteins in CRC tissues. Many proteins were newly revealed to be CRC related; 30 were reported in earlier studies of CRC. Six proteins that were up-regulated in CRC (ZYX, RAN, RCN1, AHCY, LGALS1, and VIM) were further characterized and validated by Western blot and immunohistochemistry. All six were found to be CRC-localized, either in cancer cells or in stroma cells near the cancer cells. These results indicate that the proteins identified in this study are novel candidates for CRC markers, and that the NBS method is useful in proteome mining to discover novel biomarkers.     

An investigation into the characteristics of non-linear frequency response functions. Part 2: New analysis methods based on symbolic expansions and graphical techniques

In Part 1 of this paper the concepts of input and output frequency subdomains were introduced to give insight into the relation between one dimensional and multi-dimensional frequency spaces. The visualisation of both magnitude and phase responses of third order generalized frequency response functions was also presented. In this, the second part, symbolic expansion techniques are introduced and together with the results achieved in Part 1, yield new methods for analysing the properties of generalized frequency response functions. Case studies are included to illustrate the application of the new methods.