Scientific Software Package Research Articles

A parallelization scheme to simulate reactive transport in the subsurface environment with OGS#IPhreeqc 5.5.7-3.1.2

Abstract. The open-source scientific software packages OpenGeoSys and IPhreeqc have been coupled to set up and simulate thermo-hydro-mechanical-chemical coupled processes with simultaneous consideration of aqueous geochemical reactions faster and easier on high-performance computers. In combination with the elaborated and extendable chemical database of IPhreeqc, it will be possible to set up a wide range of multiphysics problems with numerous chemical reactions that are known to influence water quality in porous and fractured media. A flexible parallelization scheme using MPI (Message Passing Interface) grouping techniques has been implemented, which allows an optimized allocation of computer resources for the node-wise calculation of chemical reactions on the one hand and the underlying processes such as for groundwater flow or solute transport on the other. This technical paper presents the implementation, verification, and parallelization scheme of the coupling interface, and discusses its performance and precision.

Crowdsourcing Scientific Software Documentation: A Case Study of the NumPy Documentation Project

Without good documentation, even the most sophisticated and efficient scientific software is difficult to use and maintain. However, due to lack of time, resources, and incentives, scientists who develop software for other scientists aren't keen on writing documentation. Scientific software packages that are freely available and shared within scientific communities often suffer from poor documentation, sometimes making them unusable. This article considers documentation crowdsourcing as a way to address the issue. Using the NumPy documentation project as a case study, the article discusses how to leverage the knowledge about software that resides within the user community. The research looks at technical infrastructure, community engagement, and motivation, and considers benefits, such as expanding the community, and challenges, including maintaining commitment level. The conclusion suggests preliminary guidelines for those thinking about documentation crowdsourcing.

Radiation Physics of a New Electronic Brachytherapy System for Treating Skin Lesions

To commission and analyze a new low energy high dose rate electronic brachytherapy system. Half-value layer (HVL), absolute dose output, beam profiles, and insert factors of an electronic brachytherapy system (EBT) were measured and analyzed. A thimble-shaped parallel-plate ionization chamber was utilized for HVL, absolute output, and insert factor determinations. HVL measurements of the 69.5 keV beam of EBT were conducted using thin aluminum foils in narrow beam geometry. In this setup, the aluminum filters were positioned at a distance of 30 cm from tip of the EBT device and 30 cm from the ion chamber. Absolute calibration of this X-ray beam was carried out based on the AAPM Task Group 61 (TG61) report. Beam profiles and depth ionization curves were measured and analyzed using radiochromic films, a professional scanner, and a scientific software package. The relative output factors of the five standard inserts of this device (10, 15, 20, 25, and 30 mm in diameter) were determined employing the ion chamber in air. Finally, a secondary dose calculation system was developed in a spreadsheet. HVL of the X-ray beam of EBT was measured to be 1.61 mmAl. For TG61-based calibration of this low energy kV beam employing the ion chamber at the SSD of 6 cm, it was determined that for this system Pion, Ppol, backscatter factor, ratio of mass energy absorption coefficient, inverse square correction from the surface to the effective point of measurement, and end-effect are 1.009, 0.995, 1.121, 1.017, 1.061, and 0.997, respectively. Measuring the PDD of this beam was proved difficult. Per TG61 recommendations, PDD values from BJR supplement #25 were employed for translating the measured output at the surface to the depth of 3 mm in tissue. The PDD values from BJR were in agreement with those supplied by the manufacturer to within <0.5%. The absolute dose at the depth of 3 mm was therefore established to be 3.1 Gy, for when the EBT system was programmed to deliver 3 Gy. This agreement level was deemed acceptable for the low-energy and small SSD of this device. Beam profiles showed a relatively flat beam (<5%) with small (1 mm) penumbra. Insert factors varied from 0.95 to 1.01 for the five standard inserts of this EBT device in relations to the 30 mm insert output value. Radiation physics parameters of an EBT X-ray unit were measured to match those claimed by the manufacturer to an accuracy of better than 5%, except HVL. Our measured HVL was 1.61 mm Al, whereas that indicated by the manufacturer is 1.83 mm Al. This discrepancy in HVL has a 0.3% effect on the NK value used for this chamber and less than 2% impact on the PDD employed for determining the absorbed radiation dose at depth. Reproducibility of the radiation beam of this device was on the order of less than 0.3%.

GNSS clock corrections densification at SHAO: from 5 min to 30 s

High frequency multi-GNSS zero-difference applications like Precise Orbit Determination (POD) for Low Earth Orbiters (LEO) and high frequency kinematic positioning require corresponding high-rate GNSS clock corrections. The determination of the GNSS clocks in the orbit determination process is time consuming, especially in the combined GPS/GLONASS processing. At present, a large number of IGS Analysis Centers (AC) provide clock corrections in 5-min sampling and only a few ACs provide clocks in 30-s sampling for both GPS and GLONASS. In this paper, an efficient epoch-difference GNSS clock determination algorithm is adopted based on the algorithm used by the Center for Orbit Determination in Europe (CODE). The clock determination procedure of the GNSS Analysis Center at Shanghai Astronomical Observatory (SHAO) and the algorithm is described in detail. It is shown that the approach greatly speeds up the processing, and the densified 30-s clocks have the same quality as the 5-min clocks estimated based on a zero-difference solution. Comparing the densified 30-s GNSS clocks provided by SHAO with that of IGS and its ACs, results show that our 30-s GNSS clocks are of the same quality as that of IGS. Allan deviation also gives the same conclusion. Further validation of the SHAO 30-s clock product is performed in kinematic PPP and LEO POD. Results indicate that the positions have the same accuracy when using SHAO 30-s GNSS clocks or IGS (and its AC) finals. The robustness of the algorithm and processing approach ensure its extension to provide clocks in 5-s or even higher frequencies. The implementation of the new approach is simple and it could be delivered as a black-box to the current scientific software packages.

QuTiP 2: A Python framework for the dynamics of open quantum systems

We present version 2 of QuTiP, the Quantum Toolbox in Python. Compared to the preceding version [J.R. Johansson, P.D. Nation, F. Nori, Comput. Phys. Commun. 183 (2012) 1760.], we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch–Redfield and Floquet–Markov master equations. Here we introduce these new features, demonstrate their use, and give a summary of the important backward-incompatible API changes introduced in this version. Program SummaryProgram title: QuTiP: The Quantum Toolbox in PythonCatalog identifier: AEMB_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v2_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU General Public License, version 3No. of lines in distributed program, including test data, etc.: 33625No. of bytes in distributed program, including test data, etc.: 410064Distribution format: tar.gzProgramming language: Python.Computer: i386, x86-64.Operating system: Linux, Mac OSX.RAM: 2+ GigabytesClassification: 7.External routines: NumPy, SciPy, Matplotlib, CythonCatalog identifier of previous version: AEMB_v1_0Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 1760Does the new version supercede the previous version?: YesNature of problem: Dynamics of open quantum systemsSolution method: Numerical solutions to Lindblad, Floquet–Markov, and Bloch–Redfield master equations, as well as the Monte Carlo wave function method.Reasons for new version: Compared to the preceding version we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch–Redfield and Floquet–Markov master equations.Restrictions: Problems must meet the criteria for using the master equation in Lindblad, Floquet–Markov, or Bloch–Redfield form.Running time: A few seconds up to several tens of hours, depending on size of the underlying Hilbert space.

Design and Implementation of Scientific Software Components to Enable Multiscale Modeling: The Effective Fragment Potential (QM/EFP) Method.

The design and development of scientific software components to provide an interface to the effective fragment potential (EFP) methods are reported. Multiscale modeling of physical and chemical phenomena demands the merging of software packages developed by research groups in significantly different fields. Componentization offers an efficient way to realize new high performance scientific methods by combining the best models available in different software packages without a need for package readaptation after the initial componentization is complete. The EFP method is an efficient electronic structure theory based model potential that is suitable for predictive modeling of intermolecular interactions in large molecular systems, such as liquids, proteins, atmospheric aerosols, and nanoparticles, with an accuracy that is comparable to that of correlated ab initio methods. The developed components make the EFP functionality accessible for any scientific component-aware software package. The performance of the component is demonstrated on a protein interaction model, and its accuracy is compared with results obtained with coupled cluster methods.

GROMACS—the road ahead

AbstractMolecular dynamics (MD) simulations form a powerful tool that is complementary to experiments and theory. They allow detailed investigations of both biological and chemical systems at the atomic level at timescales ranging from femtoseconds to milliseconds. Mechanisms and processes not accessible to experimental techniques can be followed in ‘real time’, and hypotheses based on experiments or theoretical arguments can be tested. Limits on the accuracy of results are mainly due to the physical models, the ratio of the complexity of the problem and the amount of computer time. Here, we review the state of the art in MD simulations with a focus on imminent challenges for the GROMACS (GROningen MAchine for Chemical Simulation) software. New hardware puts new requirements on software, while the breadth of applications and the amount of physical models implemented are increasing rapidly, highlighting shortcomings in the architecture of the programs. We sketch a road map for a popular scientific software package and discuss some of the choices to be made. © 2011 John Wiley &amp; Sons, Ltd. WIREs Comput Mol Sci 2011 1 710–715 DOI: 10.1002/wcms.50This article is categorized under: Software &gt; Molecular Modeling

LMI parser for NSP Software Package⋆

AbstractIn this paper an extension of SCIYALMIP parser to NSP platform is proposed. SCIYALMIP is language for semidefinite programming problems description on freely distributed SCILAB/SCICOSLAB platforms. This language provides an ability to work with standalone SDP solvers such as CSDP, SDPA, however, many of the effective SDP solvers have been developed as MATLAB toolboxes such as SeDuMi, SDPT3 etc. and are deeply dependent on it. For this reason SCIYALMIP has less possibilities in comparison with well known YALMIP parser for MATLAB. NSP, also known as TUMBI, is a Matlab-like Scientific Software Package developed under the GPL license. NSP emulates the Matlab mex library which is a way to write wrapper code for interfaces. This facility was used to obtain a SeDuMi port from Matlab to NSP. The proposed LMI parser NSPYALMIP is provided a fully free version of famous in control theory computations tool as YALMIP + SeDuMi.

Programming scilab in ARM linux

Scilab is a free and open source alternative to commercial scientific software packages for numerical computations. It provides an open programming environment along with a large number of powerful primitives. To realize the full potential of Scilab in embedded systems, this paper presents programming techniques essential for using Scilab in the ARM Linux environment. The Scilab package that usually runs on general-purpose computers is ported to the embedded Linux platform with an ARM9 processor. The programming of embedded software and hardware drivers using the ported Scilab package is addressed. Examples are given for illustrating the programming techniques. The cost of the embedded platform developed in this work is very low thanks to the free nature of the software packages used. The flexibility of embedded software built on this platform can be maximized since the source code is open.

The dynamic and steady state behavior of a PEM fuel cell as an electric energy source

The main objective of this work is to extract information on the internal behavior of three small polymer electrolyte membrane fuel cells under static and dynamic load conditions. A computational model was developed using Scilab [SCILAB 4, Scilab—a free scientific software package, http://www.scilab.org/, INRIA, France, December, 2005] to simulate the static and dynamic performance [J.M. Correa, A.F. Farret, L.N. Canha, An analysis of the dynamic performance of proton exchange membrane fuel cells using an electrochemical model, in: 27th Annual Conference of IEEE Industrial Electronics Society, 2001, pp. 141–146] of this particular type of fuel cell. This dynamic model is based on electrochemical equations and takes into consideration most of the chemical and physical characteristics of the device in order to generate electric power. The model takes into consideration the operating, design parameters and physical material properties. The results show the internal losses and concentration effects behavior, which are of interest for power engineers and researchers.

Gompertz: A Scilab Program for Estimating Gompertz Curve Using Gauss-Newton Method of Least Squares

A computer program for estimating Gompertz curve using Gauss-Newton method of least squares is described in detail. It is based on the estimation technique proposed in Reddy (1985). The program is developed using Scilab (version 3.1.1), a freely available scientific software package that can be downloaded from http://www.scilab.org/. Data is to be fed into the program from an external disk file which should be in Microsoft Excel format. The output will contain sample size, tolerance limit, a list of initial as well as the final estimate of the parameters, standard errors, value of Gauss-Normal equations namely GN₁ GN₂ and GN₃, No. of iterations, variance(σ²), Durbin-Watson statistic, goodness of fit measures such as R², D value, covariance matrix and residuals. It also displays a graphical output of the estimated curve vis a vis the observed curve. It is an improved version of the program proposed in Dastidar (2005).

Deformation Monitoring and Analysis Using Victorian Regional CORS Data

This paper investigates the feasibility using continuously operating reference stations (CORS) in Victoria (termed GPSnet) for deformation monitoring and analysis. A number of critical issues associated with the suitability, geological stability, data quality of the GPS networks system, the precision and reliability of the GPSnet solution are investigated using geological information. Appropriate strategies for GPS data processing and deformation analysis are investigated. The absolute and relative displacement of selected GPSnet stations are analysed using chronological GPS CORS data and dedicated high precision scientific GPS data processing software packages. The latest International Terrestrial Reference Frame is used for deformation analyses. Detailed data-processing strategies and results of deformation analyses are presented and some useful conclusions are drawn. Results show that the methodology of deformation analysis and data processing based on the regional CORS network data is feasible and effective. It is concluded that high-precision continuous tracking data from GPSnet is a very valuable asset and can provide a technicallyadvanced and cost-effective geoscientific infrastructure for deformation monitoring analysis. By mining the data from the GPSnet, not only reliable and high precision deformation information can be potentially obtained, but also high expenditure required for establishing dedicated deformation monitoring networks in this area can also be spared.

Parallel Computation of the Regional Ocean Modeling System

The Regional Ocean Modeling System (ROMS) is a regional ocean general circulation modeling system solving the free surface, hydrostatic, primitive equations over varying topography. It is free software distributed worldwide for studying both complex coastal ocean problems and the basin-to-global scale ocean circulation. The original ROMS code could only be run on shared-memory systems. With the increasing need to simulate larger model domains with finer resolutions and on a variety of computer platforms, there is a need in the ocean-modeling community to have a ROMS code that can be run on any parallel computer ranging from 10 to hundreds of processors. Recently, we have explored parallelization for ROMS using the Message-Passing Interface (MPI) programming model. In this paper, we present an efficient parallelization strategy for such a large-scale scientific software package, based on an existing shared-memory computing model. In addition, we discuss scientific applications and data-performance issues on a couple of SGI systems, including Columbia, the world's third-fastest supercomputer.

Evaluation of a generalized regression artificial neural network for extending cadmium?s working calibration range in graphite furnace atomic absorption spectrometry

A generalized regression artificial neural network (GRANN) was developed and evaluated for modeling cadmium's nonlinear calibration curve in order to extend its upper concentration limit from 4.0 microg L-1 up to 22.0 microg L-1. This type of neural network presents important advantages over the more popular backpropagation counterpart which are worth exploiting in analytical applications, namely, (1) a smaller number of variables have to be optimized, with the subsequent reduction in "development hassle"; and, (2) shorter development times, thanks to the fact that the adjustment of the weights (the artificial synapses) is a non-iterative, one-pass process. A backpropagation artificial neural network (BPANN), a second-order polynomial, and some less frequently employed polynomial and exponential functions (e.g., Gaussian, Lorentzian, and Boltzmann), were also evaluated for comparison purposes. The quality of the fit of the various models, assessed by calculating the root mean square of the percentage deviations, was as follows: GRANN>Boltzmann>second-order polynomial>BPANN>Gauss>Lorentz. The accuracy and precision of the models were further estimated through the determination of cadmium in the certified reference material "Trace Metals in Drinking Water" (High Purity Standards, Lot No. 490915), which has a cadmium certified concentration (12.00+/-0.06 microg L-1) that lies in the nonlinear regime of the calibration curve. Only the models generated by the GRANN and BPANN accurately predicted the concentrations of a series of solutions, prepared by serial dilution of the CRM, with cadmium concentrations below and above the maximum linear calibration limit (4.0 microg L-1). Extension of the working range by using the proposed methodology represents an attractive alternative from the analytical point of view, since it results in less specimen manipulation and consequently reduced contamination risks without compromising either the accuracy or the precision of the analyses. The implementation of artificial neural networks also helps to reduce the trial-and-error task of looking for the right mathematical model from among the many possibilities currently available in the various scientific and statistic software packages.

Development of courseware for introduction of nonlinear frame analysis using free scientific software package

The courseware for introduction of nonlinear frame analysis was developed with a free scientific software package called Scilab. This courseware is configured on Scilab interpreter with newly developed functions specialized for matrix structural analysis. With this courseware, the students can learn basic concepts of matrix structural analysis semi-interactively. © 2004 Wiley Periodicals, Inc. Comput Appl Eng Educ 12: 224–231, 2004; Published online in Wiley InterScience (www.interscience.wiley.com); DOI 10.1002/cae.20017

Using digital image processing for the assessment of postural changes and movement patterns in bodywork clients

A number of scientific/research quality software packages exist for the capture, display and analysis of digital images. This article discusses the use of a high resolution video camera and a desktop computer coupled with the freeware scientific visualization software package NIH Image to visually represent and record posture and movement protocols in the clinical, research or educational setting. Existing digital image processing techniques and tools can be extrapolated to the purposes of research, data gathering and clinical application in the field of bodywork.

Algebraic Java classes for numerical optimization

Our software, Jest, comprises a general and extendible library for numerical optimization for science and engineering, Jam, and a particular extension of that framework for seismic image processing, Jag. Jest successfully separates optimization and application software without imposing limitations on an application's vector representation, on an application's operator implementation, or on a solver's ability to manipulate vectors and operators. To ensure the compatibility of solver and application, Jest includes a set of simple interfaces that define method invocations for the fundamental mathematical objects of numerical optimization, such as vectors, vector spaces, operators, and solvers. Jest's solvers are implemented in terms of these mathematical objects and consequently possess the generality of the original abstract mathematical algorithm. Jest's seismic imaging library, Jag, demonstrates that Jest incurs no restrictions and little or no programming overhead for scientific or engineering software packages. While generally implemented in Java, Jest links some computationally intensive applications to C-routines to improve performance. Once Jest is integrated in our laboratory's electronic book, our research becomes reproducible by the push of a button in any World Wide Web browser. © 1998 John Wiley & Sons, Ltd.

Algebraic Java classes for numerical optimization

Our software, Jest, comprises a general and extendible library for numerical optimization for science and engineering, Jam, and a particular extension of that framework for seismic image processing, Jag. Jest successfully separates optimization and application software without imposing limitations on an application's vector representation, on an application's operator implementation, or on a solver's ability to manipulate vectors and operators. To ensure the compatibility of solver and application, Jest includes a set of simple interfaces that define method invocations for the fundamental mathematical objects of numerical optimization, such as vectors, vector spaces, operators, and solvers. Jest's solvers are implemented in terms of these mathematical objects and consequently possess the generality of the original abstract mathematical algorithm. Jest's seismic imaging library, Jag, demonstrates that Jest incurs no restrictions and little or no programming overhead for scientific or engineering software packages. While generally implemented in Java, Jest links some computationally intensive applications to C-routines to improve performance. Once Jest is integrated in our laboratory's electronic book, our research becomes reproducible by the push of a button in any World Wide Web browser. © 1998 John Wiley & Sons, Ltd.

Using Computer Simulation Models of Physiological and Metabolic Processes in Laboratory Animals.

Kinetic analysis and integrated systems modeling have contributed significantly to our understanding of the physiology and pathophysiology of metabolic systems in humans and animals. With the advent of personal computers and scientific software packages, a growing number of experimental biologists are using mathematical modeling techniques in their experimental design. At the same time many of these users recognize that the discipline of kinetic analysis requires its own expertise in order to develop and maintain state-ofthe-art modeling tools in such a way that the power of modeling is maximized. With the development of sophisticated systems models, questions are arising about the boundary between the use of these models and laboratory experimentation. This is particularly important when an experimental design calls for laboratory animals as models for human physiology and pathophysiology. These questions arise primarily because the development, testing, and application of mathematical models are poorly appreciated. In particular, robust mathematical models obtained by using the power of mathematics to bind together diverse pieces of physiological information lead to the formulation of specific hypotheses that can only be tested through further experimentation. Model development and laboratory experimentation is thus a cyclical process. Against this background, the purpose of this article is to describe the modeling process and the purposes for which models can be used. Examples will be given to illustrate specific situations. In this light, the limitations of a model's utilitarian values can be discussed, and the boundary between simulating and performing experiments will become clearer. We will illustrate 2 case studies in which laboratory experimentation and modeling are used together: one uses an animal model for a human disease (atherosclerosis), and the other uses an animal model to understand the physiology of that particular species (water metabolism).

Evaluating elementary functions in a numerical coprocessor based on rational approximations

A different approach to hardware evaluation of elementary functions for high-precision floating-point numbers (in particular, the extended double precision format of the IEEE standard P754) is examined. The evaluation is based on rational approximations of the elementary functions, a method which is commonly used in scientific software packages. A hardware model is presented of a floating-point numeric coprocessor consisting of a fast adder and a fast multiplier, and the minimum hardware required for evaluation of the elementary functions is added to it. Next, rational approximations for evaluating the elementary functions and testing the accuracy of the results are derived. The calculation time of these approximations in the proposed numeric processor is then estimated. It is concluded that rational approximations can successfully complete with previously used methods when execution time and silicon area are considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>