SUSE Linux Research Articles

BetheSF: Efficient computation of the exact tagged-particle propagator in single-file systems via the Bethe eigenspectrum

Single-file diffusion is a paradigm for strongly correlated classical stochastic many-body dynamics and has widespread applications in soft condensed matter and biophysics. However, exact results for single-file systems are sparse and limited to the simplest scenarios. We present an algorithm for computing the non-Markovian time-dependent conditional probability density function of a tagged-particle in a single-file of N particles diffusing in a confining external potential. The algorithm implements an eigenexpansion of the full interacting many-body problem obtained by means of the coordinate Bethe ansatz. While formally exact, the Bethe eigenspectrum involves the generation and evaluation of permutations, which becomes unfeasible for single-files with an increasing number of particles N. Here we exploit the underlying exchange symmetries between the particles to the left and to the right of the tagged-particle and show that it is possible to reduce the complexity of the algorithm from the worst case scenario O(N!) down to O(N). A C++ code to calculate the non-Markovian probability density function using this algorithm is provided. Solutions for simple model potentials are readily implemented including single-file diffusion in a flat and a ‘tilted’ box, as well as in a parabolic potential. Notably, the program allows for implementations of solutions in arbitrary external potentials under the condition that the user can supply solutions to the respective single-particle eigenspectra. Program summaryProgram Title: BetheSFCPC Library link to program files:http://dx.doi.org/10.17632/3bs74vf72n.1Licensing provisions: MITProgramming language: C++ (C++17 support required)Supplementary material: makefile, README, SingleFileBluePrint.hppNature of problem: Diffusive single-files are mathematical models of effectively one-dimensional strongly correlated many-body systems. While the dynamics of the full system is Markovian, the diffusion of a tracer-particle in a single-file is an example of non-Markovian and anomalous diffusion. The many-body Fokker–Planck equation governing the system’s dynamics can be solved using the coordinate Bethe ansatz. A naïve implementation of such a solution runs in non-polynomial time since it requires the generation of permutations of the elements of a multiset.Solution method: In this paper we show how, exploiting the exchange symmetries of the system, it is possible to reduce the complexity of the algorithm to evaluate the solution, using a permutation-generation algorithm, from O(N!) in the worst case scenario to O(N) in the best case scenario, which corresponds to tagging the first or the last particle, where N stands for the number of particles in the single-file.Additional comments including restrictions and unusual features: The code may overflow for large single-files N≥170. All the benchmarks ran on the following CPU: Intel Xeon E3-1270 v2 3.50 GHz 4 cores. The compiler used is g++ 7.3.1 (SUSE Linux) with the optimization-O3 turned on. The code to produce all the data in the figures is included in the files: figure2.cpp, figure3.cpp, figure4.cpp, figure5a.cpp and figure5b.cpp

POTLIB2Math: A Mathematica interface to the potential energy surface library for chemical systems

The theoretical description of molecular dynamics proceeds from the specification of an appropriate Born–Oppenheimer potential energy surface (PES) or surfaces. For many chemical systems, such surfaces are incorporated within a repository of standardized FORTRAN codes known as POTLIB. The present work describes a Mathematica package that uses a MathLink interface to interactively call POTLIB subroutines from within a Mathematica session. This allows for rapid prototyping and deployment of new algorithms and is useful for both pedagogical and research applications in chemical physics. We present basic usage of the package functions and several simple applications for illustration. Program summaryProgram title: POTLIB2MathCatalogue identifier: AEQJ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQJ_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.: 63859No. of bytes in distributed program, including test data, etc.: 1481706Distribution format: tar.gzProgramming language: C, FORTRAN, and Mathematica.Computer: Developed and tested on GNU/Linux PC, Macintosh, and Windows PC platforms running Mathematica version 8 or higher.Operating system: Tested on MacOSX, SUSE Linux, and WindowsXP/7/8.RAM: Varies depending on user-defined applications.Classification: 16.8.External routines: GNU make, gcc, gfortran, Mathematica, and MathLink DeveloperKitSubprograms used:Cat IdTitleReferenceADPJ_v1_0POTLIB 2001CPC 144(2002)169Nature of problem:POTLIB [1, 2] is a collection of FORTRAN subprograms that calculate potential energy surfaces and gradients for various chemical systems as a function of molecular geometry. The objective of this work is to develop an interface that allows users to interactively execute POTLIB subprograms from within a Mathematica session.Solution method:POTLIB2Math is a fully-documented Mathematica package that uses a MathLink interface for passing data between Mathematica and POTLIB subprograms. GNU make and C/FORTRAN compilers are used to automate building the executables on various platforms.Running time:The examples included in the distribution file take just a few minutes to run.

Structure of Dimeric F1F0-ATP Synthase

The structure of the dimeric ATP synthase from yeast mitochondria was analyzed by transmission electron microscopy and single particle image analysis. In addition to the previously reported side views of the dimer, top view and intermediate projections served to resolve the arrangement of the rotary c(10) ring and the other stator subunits at the F(0)-F(0) dimeric interface. A three-dimensional reconstruction of the complex was calculated from a data set of 9960 molecular images at a resolution of 27 Å. The structural model of the dimeric ATP synthase shows the two monomers arranged at an angle of ∼45°, consistent with our earlier analysis of the ATP synthase from bovine heart mitochondria (Minauro-Sanmiguel, F., Wilkens, S., and Garcia, J. J. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 12356-12358). In the ATP synthase dimer, the two peripheral stalks are located near the F(1)-F(1) interface but are turned away from each other so that they are not in contact. Based on the three-dimensional reconstruction, a model of how dimeric ATP synthase assembles to form the higher order oligomeric structures that are required for mitochondrial cristae biogenesis is discussed.

MCNP output data analysis with ROOT (MODAR)

MCNP Output Data Analysis with ROOT (MODAR) is a tool based on CERN's ROOT software. MODAR has been designed to handle time-energy data issued by MCNP simulations of neutron inspection devices using the associated particle technique. MODAR exploits ROOT's Graphical User Interface and functionalities to visualize and process MCNP simulation results in a fast and user-friendly way. MODAR allows to take into account the detection system time resolution (which is not possible with MCNP) as well as detectors energy response function and counting statistics in a straightforward way. New version program summary Program title: MODAR Catalogue identifier: AEGA_v1_1 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEGA_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 150 927 No. of bytes in distributed program, including test data, etc.: 4 981 633 Distribution format: tar.gz Programming language: C++ Computer: Most Unix workstations and PCs Operating system: Most Unix systems, Linux and windows, provided the ROOT package has been installed. Examples where tested under Suse Linux and Windows XP. RAM: Depends on the size of the MCNP output file. The example presented in the article, which involves three two dimensional 139 × 740 bins histograms, allocates about 60 MB. These data are running under ROOT and include consumption by ROOT itself. Classification: 17.6 Catalogue identifier of previous version: AEGA_v1_0 Journal reference of previous version: Comput. Phys. Comm. 181 (2010) 1161 External routines: ROOT version 5.24.00 ( http://root.cern.ch/drupal/) Does the new version supersede the previous version?: Yes Nature of problem: The output of a MCNP simulation is an ascii file. The data processing is usually performed by copying and pasting the relevant parts of the ascii file into Microsoft Excel. Such an approach is satisfactory when the quantity of data is small but is not efficient when the size of the simulated data is large, for example when time-energy correlations are studied in detail such as in problems involving the associated particle technique. In addition, since the finite time resolution of the simulated detector cannot be modeled with MCNP, systems in which time-energy correlation is crucial cannot be described in a satisfactory way. Finally, realistic particle energy deposit in detectors is calculated with MCNP in a two step process involving type-5 then type-8 tallies. In the first step, the photon flux energy spectrum associated to a time region is selected and serves as a source energy distribution for the second step. Thus, several files must be manipulated before getting the result, which can be time consuming if one needs to study several time regions or different detectors performances. In the same way, modeling counting statistics obtained in a limited acquisition time requires several steps and can also be time consuming. Solution method: In order to overcome the previous limitations, the MODAR C++ code has been written to make use of CERN's ROOT data analysis software. MCNP output data are read from the MCNP output file with dedicated routines. Two dimensional histograms are filled and can be handled efficiently within the ROOT framework. To keep a user friendly analysis tool, all processing and data display can be done by means of ROOT Graphical User Interface. Specific routines have been written to include detectors finite time resolution and energy response function as well as counting statistics in a straightforward way. Reasons for new version: For applications involving the Associate Particle Technique, a large number of gamma rays are produced by the fast neutrons interactions. To study the energy spectra, it is useful to identify the gamma-ray energy peaks in a straightforward way. Therefore, the possibility to show gamma rays corresponding to specific reactions has been added in MODAR. Summary of revisions: It is possible to use a gamma ray database to better identify in the energy spectra gamma ray peaks with their first and second escapes. Histograms can be scaled by the number of source particle to evaluate the number of counts that is expected without statistical uncertainties. Additional comments: The possibility of adding tallies has also been incorporated in MODAR in order to describe systems in which the signal from several detectors can be summed. Moreover, MODAR can be adapted to handle other problems involving two dimensional data. Running time: The CPU time needed to smear a two dimensional histogram depends on the size of the histogram. In the presented example, the time-energy smearing of one of the 139 × 740 two dimensional histograms takes 3 minutes with a DELL computer equipped with INTEL Core 2.

MCNP Output Data Analysis with ROOT (MODAR)

MCNP Output Data Analysis with ROOT (MODAR) is a tool based on CERN's ROOT software. MODAR has been designed to handle time–energy data issued by MCNP simulations of neutron inspection devices using the associated particle technique. MODAR exploits ROOT's Graphical User Interface and functionalities to visualize and process MCNP simulation results in a fast and user-friendly way. MODAR allows to take into account the detection system time resolution (which is not possible with MCNP) as well as detectors energy response function and counting statistics in a straightforward way. Program summary Program title: MODAR Catalogue identifier: AEGA_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEGA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 155 373 No. of bytes in distributed program, including test data, etc.: 14 815 461 Distribution format: tar.gz Programming language: C++ Computer: Most Unix workstations and PC Operating system: Most Unix systems, Linux and windows, provided the ROOT package has been installed. Examples where tested under Suse Linux and Windows XP. RAM: Depends on the size of the MCNP output file. The example presented in the article, which involves three two-dimensional 139 × 740 bins histograms, allocates about 60 MB. These data are running under ROOT and include consumption by ROOT itself. Classification: 17.6 External routines: ROOT version 5.24.00 ( http://root.cern.ch/drupal/) Nature of problem: The output of an MCNP simulation is an ASCII file. The data processing is usually performed by copying and pasting the relevant parts of the ASCII file into Microsoft Excel. Such an approach is satisfactory when the quantity of data is small but is not efficient when the size of the simulated data is large, for example when time–energy correlations are studied in detail such as in problems involving the associated particle technique. In addition, since the finite time resolution of the simulated detector cannot be modeled with MCNP, systems in which time–energy correlation is crucial cannot be described in a satisfactory way. Finally, realistic particle energy deposit in detectors is calculated with MCNP in a two-step process involving type-5 then type-8 tallies. In the first step, the photon flux energy spectrum associated to a time region is selected and serves as a source energy distribution for the second step. Thus, several files must be manipulated before getting the result, which can be time consuming if one needs to study several time regions or different detectors performances. In the same way, modeling counting statistics obtained in a limited acquisition time requires several steps and can also be time consuming. Solution method: In order to overcome the previous limitations, the MODAR C++ code has been written to make use of CERN's ROOT data analysis software. MCNP output data are read from the MCNP output file with dedicated routines. Two-dimensional histograms are filled and can be handled efficiently within the ROOT framework. To keep a user friendly analysis tool, all processing and data display can be done by means of ROOT Graphical User Interface. Specific routines have been written to include detectors finite time resolution and energy response function as well as counting statistics in a straightforward way. Additional comments: The possibility of adding tallies has also been incorporated in MODAR in order to describe systems in which the signal from several detectors can be summed. Moreover, MODAR can be adapted to handle other problems involving two-dimensional data. Running time: The CPU time needed to smear a two-dimensional histogram depends on the size of the histogram. In the presented example, the time–energy smearing of one of the 139 × 740 two-dimensional histograms takes 3 minutes with a DELL computer equipped with INTEL Core 2.

Maple procedures for the coupling of angular momenta. An up-date of the Racah module

An up-date of the Racah module is presented, adopted to Maple 11 and 12, which supports both, algebraic manipulations of expressions from Racah's algebra as well as numerical computations of many functions and symbols from the theory of angular momentum. The functions that are known to the program include the Wigner rotation matrices and n-j symbols, Clebsch–Gordan and Gaunt coefficients, spherical harmonics of various kinds as well as several others.

ASPIN: An all spin scattering code for atom–molecule rovibrationally inelastic cross sections

We present in this work a new computational code for the quantum calculation of integral cross sections for atom–molecule (linear) scattering processes. The atom is taken to be structureless while the molecule can be in its singlet, doublet, or triplet spin states and can be treated as either a rigid rotor or a rovibrational target. All the relevant state-to-state integral cross sections, and their sums over final states, can be calculated with the present code, for which we also describe in detail the various component routines. Program summary Program title: ASPIN Catalogue identifier: AEBO_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEBO_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 99 596 No. of bytes in distributed program, including test data, etc.: 1 267 615 Distribution format: tar.gz Programming language: Fortran/MPI Computer: AMD OPTERON COMPUTING SYSTEMS, model TYAN GX28 (B2882) Operating system: SuSE LINUX Professional 9 RAM: 128 GB Classification: 2.6 External routines: LAPACK/BLAS Nature of problem: Scattering of a diatomic molecule in its Σ 1 , Σ 2 , or Σ 3 spin states with an atom in its S 1 state. Partial and integral cross sections. Solution method: The coupled channel equations that describe the scattering process are solved through the propagation of the reactance K matrix employing a modification of the Variable Phase Method [1–3]. Restrictions: Depending on the vib-rotational base used the problem may or may not fit into available RAM memory because all the runtime relevant quantities are stored on RAM memory instead of on disk. Additional comments: Both serial and parallel implementations of the program are provided. The CPC Librarian was not able to successfully run the parallel version. Running time: For simple and converged calculations a usual running time is in the order of a few minutes in the computer mentioned above, being shorter for the singlet and longer for the triplet.

The grasp2K relativistic atomic structure package

This paper describes grasp2K, a general-purpose relativistic atomic structure package. It is a modification and extension of the GRASP92 package by [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249]. For the sake of continuity, two versions are included. Version 1 retains the GRASP92 formats for wave functions and expansion coefficients, but no longer requires preprocessing and more default options have been introduced. Modifications have eliminated some errors, improved the stability, and simplified interactive use. The transition code has been extended to cases where the initial and final states have different orbital sets. Several utility programs have been added. Whereas Version 1 constructs a single interaction matrix for all the J's and parities, Version 2 treats each J and parity as a separate matrix. This block structure results in a reduction of memory use and considerably shorter eigenvectors. Additional tools have been developed for this format. The CPU intensive parts of Version 2 have been parallelized using MPI. The package includes a “make” facility that relies on environment variables. These make it easier to port the application to different platforms. The present version supports the 32-bit Linux and ibmSP environments where the former is compatible with many Unix systems. Descriptions of the features and the program/data flow of the package will be given in some detail in this report.

User data persistence in physical memory

In this paper we present the results of experiments we conducted on Suse Linux and Windows XP systems to determine the age of user process data in physical memory. To be able to measure the age of pages we used an artificial load program which time-stamps data segment and block device cache pages. Our goal was to compare the behaviour of both systems and to determine whether the rate of decay for user data depends on the demand for physical memory. Our findings show that Windows and Linux systems preserve almost the same number of pages with user data, and the age distribution of these pages does not change significantly with the level of demand.

Simulation of n-qubit quantum systems. III. Quantum operations

During the last decade, several quantum information protocols, such as quantum key distribution, teleportation or quantum computation, have attracted a lot of interest. Despite the recent success and research efforts in quantum information processing, however, we are just at the beginning of understanding the role of entanglement and the behavior of quantum systems in noisy environments, i.e. for nonideal implementations. Therefore, in order to facilitate the investigation of entanglement and decoherence in n-qubit quantum registers, here we present a revised version of the Feynman program for working with quantum operations and their associated (Jamiołkowski) dual states. Based on the implementation of several popular decoherence models, we provide tools especially for the quantitative analysis of quantum operations. Apart from the implementation of different noise models, the current program extension may help investigate the fragility of many quantum states, one of the main obstacles in realizing quantum information protocols today. Program summary Title of program: Feynman Catalogue identifier: ADWE_v3_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADWE_v3_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: None Operating systems: Any system that supports Maple; tested under Microsoft Windows XP, SuSe Linux 10 Program language used: Maple 10 Typical time and memory requirements: Most commands that act upon quantum registers with five or less qubits take ⩽10 seconds of processor time (on a Pentium 4 processor with ⩾ 2 GHz or equivalent) and 5–20 MB of memory. Especially when working with symbolic expressions, however, the memory and time requirements critically depend on the number of qubits in the quantum registers, owing to the exponential dimension growth of the associated Hilbert space. For example, complex (symbolic) noise models (with several Kraus operators) for multi-qubit systems often result in very large symbolic expressions that dramatically slow down the evaluation of measures or other quantities. In these cases, Maple's assume facility sometimes helps to reduce the complexity of symbolic expressions, but often only numerical evaluation is possible. Since the complexity of the Feynman commands is very different, no general scaling law for the CPU time and memory usage can be given. No. of bytes in distributed program including test data, etc.: 799 265 No. of lines in distributed program including test data, etc.: 18 589 Distribution format: tar.gz Reasons for new version: While the previous program versions were designed mainly to create and manipulate the state of quantum registers, the present extension aims to support quantum operations as the essential ingredient for studying the effects of noisy environments. Does this version supersede the previous version: Yes Nature of the physical problem: Today, entanglement is identified as the essential resource in virtually all aspects of quantum information theory. In most practical implementations of quantum information protocols, however, decoherence typically limits the lifetime of entanglement. It is therefore necessary and highly desirable to understand the evolution of entanglement in noisy environments. Method of solution: Using the computer algebra system Maple, we have developed a set of procedures that support the definition and manipulation of n-qubit quantum registers as well as (unitary) logic gates and (nonunitary) quantum operations that act on the quantum registers. The provided hierarchy of commands can be used interactively in order to simulate and analyze the evolution of n-qubit quantum systems in ideal and nonideal quantum circuits.

Debris disk radiative transfer simulation tool (DDS)

A WWW interface for the simulation of spectral energy distributions of optically thin dust configurations with an embedded radiative source is presented. The density distribution, radiative source, and dust parameters can be selected either from an internal database or defined by the user. This tool is optimized for studying circumstellar debris disks where large grains ( a grain ≫ 1 μ m ) are expected to determine the far-infrared through millimeter dust reemission spectral energy distribution. The tool is available at http://aida28.mpia-hd.mpg.de/~swolf/dds. Program summary Title of program:Debris Disk Radiative Transfer Simulator (DDS) Catalogue identifier:ADVV Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADVV Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions:none Computers:PC with Intel(R) XEON(TM) 2.80 GHz processor Operating systems or monitors under which the program has been tested:SUSE Linux 9.1 Programming language used:Fortran 90 (for the main program; furthermore Perl, CGI and HTML) Memory required to execute with typical data:10 8 words No. of bits in a word:8 No. of lines in distributed program, including test data, etc.:44 636 No. of bytes in distributed program, including test data, etc.: 4 806 280 Distribution format:tar.gz Nature of the physical problem:Simulation of scattered light and thermal reemission in arbitrary optically dust distributions with spherical, homogeneous grains where the dust parameters (optical properties, sublimation temperature, grain size) and SED of the illuminating/heating radiative source can be arbitrarily defined (example application: [S. Wolf, L.A. Hillenbrand, Astrophys. J. 596 (2003) 603]). The program is optimized for studying circumstellar debris disks where large grains (i.e. with large size parameters) are expected to determine the far-infrared through millimeter dust reemission spectral energy distribution. Method of solution:Calculation of the dust temperature distribution and dust reemission and scattering spectrum in the optically thin limit. Restrictions on the complexity of the problem:(1) The approach to calculate dust temperatures and dust reemission spectra is only valid in the optically thin regime. The validity of this constraint is verified for each model during the runtime of the code. (2) The relative abundances of different grains can be arbitrarily chosen, but must be constant outside the dust sublimation region, i.e. the shape of the (arbitrary) radial dust density distribution outside the dust sublimation region is the same for all grain sizes and chemistries. (3) The size of upload files (such as the dust density distribution, optical data of the dust grains, stellar spectral energy distribution, etc.) is limited (see http://aida28.mpia-hd.mpg.de/~swolf/dds/ for current file size limits). However, the resulting limitation to the complexity of possible model definitions is marginal only. Typical running time:3 sec–30 min (depending on the complexity of the model). Unusual features of the program:The program as provided through the CPC Program Library is equipped with an HTML user interface. It is installed and available at http://aida28.mpia-hd.mpg.de/~swolf/dds.

Mie scattering by ensembles of particles with very large size parameters

We present a computer program for the simulation of Mie scattering in case of arbitrarily large size parameters. The elements of the scattering matrix, efficiency factors as well as the corresponding cross-sections, the albedo and the scattering asymmetry parameter are calculated. Single particles as well as particle ensembles consisting of several components and particle size distributions can be considered. Program summary Title of program: miex Catalogue identifier: ADUD Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADUD Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Computers: Any machine running standard FORTRAN 90; miex has been tested on an Intel Celeron processor (Redhat Linux 9.0, Intel Fortran Compiler 7.1), an Intel XEON processor (SuSE Linux 9.0, Intel Fortran Compiler 8.0), and a Sun-Blade-1000 (OS 8.5, Sun Workshop Compiler Fortran 90 2.0). Installations: standard Operating systems or monitors under which the program has been tested: Redhat Linux 9.0, SuSE Linux 9.0, Sun OS 8.5 Programming language used: Fortran 90 Memory required to execute with typical data: 1 MByte – several 100 MByte (see Appendix A for examples) No. of bits in a word: 8 No. of processors used: 1 Has the code been vectorized or parallelized?: No No. of lines in distributed program, including test data, etc.: 78 238 No. of bytes in distributed program, including test data, etc.: 1 015 805 Distributed format: tar.gz Nature of the physical problem: Among a variety of applications, Mie scattering is of essential importance for the continuum radiative transfer in cosmic dust configurations. In this particular case, Mie theory describes the interaction of electromagnetic radiation with spherical dust grains on the basis of their complex refractive index and size parameter. Both, broad grain size distributions (radii a: nanometers–millimeters) and a very wide wavelength range ( λ≈10 −10– 10 −2 m ) of the interacting radiation are considered. Previous numerical solutions to the Mie scattering problem are not appropriate to consider size parameters x=2 πa/ λ>10 4–10 5. In contrast to this, the presented code allows to consider arbitrary size parameters. It will be useful not only for applications in astrophysics but also in other fields of science (atmospheric and ocean optics, biophysics, etc.) and industry (particle sizing, ecology control measurements, etc.). Method of solution: Calculations of Mie scattering coefficients and efficiency factors as outlined by Voshchinnikov (2004), combined with standard solutions of the scattering amplitude functions. Single scattering by particle ensembles is calculated by proper averaging of the respective parameters. Restrictions on the complexity of the problem: Single scattering Typical running time: Seconds to minutes Unusual features of the program: None

GEOSSAV: a simulation tool for subsurface applications

Geostatistical Environment fOr Subsurface Simulation And Visualization (GEOSSAV) is a tool for the integration of hard and soft data into stochastic simulation and visualization of distributions of geological structures and hydrogeological properties in the subsurface. GEOSSAV, as an interface to selected geostatistical modules (bicalib, gamv, vargplt, and sisim) from the Geostatistical Software LIBrary, GSLIB (GSLIB: Geostatistical Software Library and User's Guide, 2nd Edition, Oxford University Press, Oxford, 1998, 369pp), can be used for data analysis, variogram computation of regularly or irregularly spaced data, and sequential indicator simulation of subsurface heterogeneities. Sequential indicator simulation, based on various kriging techniques (simple, ordinary, and Bayesian), is suitable for the simulation of continuous variables such as hydraulic conductivity of an aquifer or chemical concentrations at a contaminated site, and categorical variables which indicate the presence or absence of a particular lithofacies. The software integration platform and development environment of GEOSSAV is Tool command language (Tcl) with its graphical user interface, Toolkit (Tk), and a number of Tcl/Tk extensions. The standard Open Graphics Library application programming interface is used for rendering three-dimensional (3D) data distributions and for slicing perpendicular to the main coordinate axis. Export options for finite-difference groundwater models allow either files that characterize single model layers (which are saved in ASCII matrix format) or files that characterize the complete 3D flow model setup for MODFLOW-based groundwater simulation systems (which are saved in block-centered flow package files (User's documentation for MODFLOW-96, an update to the US Geological Survey modular finite-difference ground-water flow model, Geological Survey Open-File Report 96-485, Reston, VA, 1996, 56pp)). GEOSSAV can be used whenever stochastic solutions are preferred to solve site-specific heterogeneity problems, e.g., in the field of hydrology, groundwater, groundwater and/or soil contamination, site remediation, air pollution, and ecology. An example from the Rhine/Wiese aquifer near Basel demonstrates the application of GEOSSAV on geostatistical data analysis and subsurface visualization. GEOSSAV has been successfully tested on Microsoft Windows NT 4.0/2000/XP and on SuSE Linux 7.3. The current version is available at http://www.unibas.ch/earth/pract.

Evaluation of a miniature electromagnetic position tracker.

The advent of miniaturized electromagnetic digitizers opens a variety of potential clinical applications for computer aided interventions using flexible instruments; endoscopes or catheters can easily be tracked within the body. With respect to the new applications, the systematic distortions induced by various materials such as closed metallic loops, wire guides, catheters, and ultrasound scan heads were systematically evaluated in this paper for a new commercial tracking system. We employed the electromagnetic tracking system Aurora (Mednetix/CH, NDI/Can); data were acquired using the serial port of a PC running SuSE Linux 7.1 (SuSE, Gmbh, Nürnberg). Objects introduced into the digitizer volume included wire loops of different diameters, wire guides, optical tracking tools, an ultrasonic (US) scan head, an endoscope with radial ultrasound scan head and various other objects used in operating rooms and interventional suites. Beyond this, we determined the influence of a C-arm fluoroscopy unit. To quantify the reliability of the system, the miniaturized sensor was mounted on a nonmetallic measurement rack while the transmitter was fixed at three different distances within the digitizer range. The tracker was shown to be more sensitive to distortions caused by materials close to the emitter (average distortion error 13.6 mm +/- 16.6 mm for wire loops positioned at a distance between 100 mm and 200 mm from the emitter). Distortions caused by materials near the sensor (distances smaller than 100 mm) are small (typical error 2.2 mm +/- 1.9 mm). The C-arm fluoroscopy unit caused considerable distortions and limits the reliability of the tracker (distortion error 18.6 mm +/- 24.9 mm). Distortions resulting from the US scan head are high at distances smaller than about 100 mm from the emitter. The distortions also increase when the scan head is positioned horizontally and close to the sensor (average error 4.1 mm +/- 1.5 mm when the scan head is positioned within a distance of 100 mm from the sensor). The distortions are slightly higher when the ultrasound machine is switched on. We also evaluated the influence of common medical instruments on distance measurements. For these measurements the average deviation from the known distance of 200 mm amounted to 3.0 mm +/- 1.5 mm (undistorted distance measurement 1.5 mm +/- 0.3 mm). The deviations also depend on the relative orientation between emitter and sensor. The results demonstrate that the miniature tracking system opens up new perspectives with regard to surgery applications where a flexible instrument is to be tracked within the body. Significant distortions caused by metallic objects only occur in the worst cases, for example, in the presence of a closed, unisiolated wire loop or a C-arm fluorescence unit close to the emitter and which can be avoided by suitable usage.