Reflection and time-dependent computing: Experiences with the R2 architecture

In this paper we present an application of computational reflection in the programming oftime-dependent systems. A time-dependent system performs its tasks according to timing specifications specified within the system or imposed from outside the system. Reflective techniques can be applied to programming time-dependent systems because (1) some application programs require the introduction of a new language construct for specifying timing requirements and (2) different applications may require domain-specific scheduling algorithms. To allow a programmer to add or modify language constructs or scheduling algorithms, however, a clear reflective architecture and program interfaces must be provided. This paper proposes a concurrent object-based reflective architecture (R ² architecture) for time-dependent computing. This architecture is based on anindividual reflection scheme and introduces new meta-level objects (real-time meta objects) that are responsible for time-dependent capabilities. An alarm-clock object and a scheduler object are introduced, and message protocols between them and real-time meta objects are defined. We implemented this architecture on ABCL/R2 and created the Sampled Sound Player program as an application. With this application we provided three different scheduler objects and measured the impact of different scheduling algorithms on sound playback. The measured results show that a scheduler with more complex computations at the meta level exhibited less scheduling overhead, thus was capable of better sound playback. The other example, Time-dependent Graceful Degradation Scheme, demonstrates the programming of functionality degradation triggered by failure to satisfy timing specifications.     

Time-dependent analysis of segmental bridges

The computer program TIMEDEP is presented for the time-dependent analysis of segmental bridges. Loadings considered at each stage of construction include self-weight, time-dependent effects, temperature, and construction loads. The program is intended to be used for routine day-to-day design and operates on the IBM Personal Computer as well as on most other mainframe computers. Five numerical examples illustrate the usefulness of the program. Documentation, sample input and output, and a FORTRAN source listing are also provided.     

A FORTRAN program for multivariate survival analysis on the personal computer

In this paper a FORTRAN program is presented for multivariate survival or life table regression analysis in a competing risks' situation. The relevant failure rate (for example, a particular disease or mortality rate) is modelled as a log-linear function of a vector of (possibly time-dependent) explanatory variables. The explanatory variables may also include the variable time itself, which is useful for parameterizing piecewise exponential time-to-failure distributions in a Gompertz-like or Weibull-like way as a more efficient alternative to Cox's proportional hazards model. Maximum likelihood estimates of the coefficients of the log-linear relationship are obtained from the iterative Newton-Raphson method. The program runs on a personal computer under DOS; running time is quite acceptable, even for large samples.     

A wave-packet technique to simulate resonant X-ray scattering cross sections

This article describes algorithms and a program implementation for wave packet calculations of resonant X-ray scattering cross sections of molecules with one active internal degree of freedom. The program uses a time-dependent formalism and a grid representation of the wave packets. The potentials of ground, core-excited and final states can be specified by analytical expressions or by discrete sets of energies on arbitrary grids allowing for interfacing with electronic structure packages. The theory on which the program is founded is briefly reviewed. The implemented numerical algorithm is described in detail together with usage instructions and a sample application.     

ANALYSIS: Software for Graphical Analysis of Multidimensional Flow Cytometric List Mode Data

A computer program for graphical analysis of multidimensional flow cytometric list mode data is described. The program offers one-, two-, and three-dimensional inspection of an amount of data that is only limited by disk space. Subpopulations within the original data set can be identified by setting one or more two-dimensional AND gates around them. The order of measurement can be used as a parameter for evaluation of time-dependent processes. Other new parameters can be made by zooming in on a parameter, logarithmic transformation, or division of two parameters. The program is written in Turbo Pascal and it can run on any MS-DOC PC with an EGA/VGA resolution screen.     

Ion trajectory modelling in time-dependent potential fields: Applicaion to RF-only quadrupoles

IONISM, a program to model ion trajectories in time-dependent potential fields, is described. The program uses the standard over-relaxation to create a     

Time-dependent service-load behavior of wood floors: analytical model

A preceding companion paper[1] examined the experimental time-dependent service-load response of wood joist floor systems, including an assessment of time-dependent deflections and load distribution. The results of the experimental program are used herein to develop an analytical model for the time-dependent response of wood joist floors. Time-dependent component (i.e. joist, sheathing and connection) models are developed from component tests. These component models are then integrated into a system model. The focus of this paper is to present the theoretical basis for the time-dependent system model, and illustrate its predictive capabilities. The system model approximates the time-dependent system creep of parallel-member wood systems to an acceptable degree of accuracy. Moreover, the model requires relatively little computer time, thus making it suitable for use in a Monte Carlo simulation     

On the application of boundary conditions to time dependent computations for quasi one-dimensional fluid flows

A study is made of the influence of boundary and initial conditions on time-dependent finite-difference solutions of quasi-one-dimensional duct flows. Several questions are addressed: (1) Under what conditions will a time-dependent solution converge to a steady-state supersonic flow, (2) Under what conditions will it converge to subsonic flow and (3) What conditions are necessary to insure a particular unique solution for subsonic flows. The results provide an orientation, or way of thinking, about the role of such conditions in time-dependent solutions of steady-state flows. The results also show that supersonic solutions are readily obtained by holding only pressure and temperature fixed at the duct inlet, and allowing velocity to float. However, subsonic solutions require pressure, temperature and velocity to be fixed at both the duct inlet and exit. If no conditions are held fixed at the exit, the results always converge to the supersonic solution, even if the fixed inlet mass flow is less than critical. In such a case, the program appears to generate additional mass flow between the inlet and throat, sufficient to choke the flow. These results also have some impact on two- and three-dimensional time-dependent solutions where subsonic flow is present on some or all portions of the flow boundaries.     

Beyond software performance visualization

Performance visualization tools of the past decade have yielded new insights into the behavior of sequential, parallel and distributed programs. However, they have three inherent limitations: (1) they only display what happened in one execution of a program (this is dangerous when analyzing concurrent applications, which are prone to non-deterministic behavior); (2) a human uses one or more bandwidth-limited senses with a visualization tool (this limits the scalability of a visualization tool); (3) the relationship of ‘interesting’ program events is often separated in time by other events; thus discerning time-dependent behavior often hinges on finding the ‘right’ visualization—a possibly time-consuming activity. CHITRA93 complements visualization systems, while alleviating these limitations, and analyzes a set (or ensemble) of traces by combining the visualization of a few traces with a statistical analysis of the entire ensemble (overcoming (1)). It reduces the ensemble to empirical models that capture the time-dependent relationships of ‘interesting’ program events through application, programming language and computer architecture independent analysis techniques (addressing (2) and (3)). It also incorporates the following transforms, such as aggregation, that simplify the ensemble and reduce the state-space size of the models generated; a user interface that allows certain transforms to be selected by editing the visualization with a mouse; homogeneity tests that allow partitioning of an ensemble; an efficient semi-Markov model generation algorithm whose computation time is linear in the sum of the lengths of the traces comprising the ensemble; and a CHAID-based model that can fathom non-Markovian relationships among transitions in the traces. The use of CHITRA93 is demonstrated by partitioning ten parallel database traces with nearly 8,000 states into two homogeneous subsets, each modeled by an irreducible, periodic and hierarchical stochastic process with as few as four states.     

A computer program for an illness-death process with time-dependent covariates

This paper presents a computer program for estimating transition probabilities between states in a stochastic model for an illness-death process which incorporates time-dependent covariates. Parameters are estimated by the method of maximum likelihood using the Newton-Raphson iterative procedure. The program provides the standard normal deviate statistics as well as the value of the maximum of the likelihood function which can be used on repeated applications to test hypotheses concerning coefficients associated with covariates. Although this program is demonstrated by using a model with two ‘illness’ states and two ‘death’ states, it is also suitable for analyzing data with models involving fewer states, such as the analysis of survival time with covariates assuming a proportional hazard model.     

Qprop: A Schrödinger-solver for intense laser-atom interaction

The Qprop package is presented. Qprop has been developed to study laser-atom interaction in the nonperturbative regime where nonlinear phenomena such as above-threshold ionization, high order harmonic generation, and dynamic stabilization are known to occur. In the nonrelativistic regime and within the single active electron approximation, these phenomena can be studied with Qprop in the most rigorous way by solving the time-dependent Schrödinger equation in three spatial dimensions. Because Qprop is optimized for the study of quantum systems that are spherically symmetric in their initial, unperturbed configuration, all wavefunctions are expanded in spherical harmonics. Time-propagation of the wavefunctions is performed using a split-operator approach. Photoelectron spectra are calculated employing a window-operator technique. Besides the solution of the time-dependent Schrödinger equation in single active electron approximation, Qprop allows to study many-electron systems via the solution of the time-dependent Kohn-Sham equations.

Program summary

Program title:QPROPCatalogue number:ADXBProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXBProgram obtainable from:CPC Program Library, Queen's University of Belfast, N. IrelandComputer on which program has been tested:PC Pentium IV, AthlonOperating system:LinuxProgram language used:C++Memory required to execute with typical data:Memory requirements depend on the number of propagated orbitals and on the size of the orbitals. For instance, time-propagation of a hydrogenic wavefunction in the perturbative regime requires about 64 KB RAM (4 radial orbitals with 1000 grid points). Propagation in the strongly nonperturbative regime providing energy spectra up to high energies may need 60 radial orbitals, each with 30000 grid points, i.e. about 30 MB. Examples are given in the article.No. of bits in a word:Real and complex valued numbers of double precision are usedNo. of lines in distributed program, including test data, etc.:69 995No. of bytes in distributed program, including test data, etc.: 2 927 567Peripheral used:Disk for input-output, terminal for interaction with the userCPU time required to execute test data:Execution time depends on the size of the propagated orbitals and the number of time-stepsDistribution format:tar.gzNature of the physical problem:Atoms put into the strong field of modern lasers display a wealth of novel phenomena that are not accessible to conventional perturbation theory where the external field is considered small as compared to inneratomic forces. Hence, the full ab initio solution of the time-dependent Schrödinger equation is desirable but in full dimensionality only feasible for no more than two (active) electrons. If many-electron effects come into play or effective ground state potentials are needed, (time-dependent) density functional theory may be employed. Qprop aims at providing tools for (i) the time-propagation of the wavefunction according to the time-dependent Schrödinger equation, (ii) the time-propagation of Kohn-Sham orbitals according to the time-dependent Kohn-Sham equations, and (iii) the energy-analysis of the final one-electron wavefunction (or the Kohn-Sham orbitals).Method of solution:An expansion of the wavefunction in spherical harmonics leads to a coupled set of equations for the radial wavefunctions. These radial wavefunctions are propagated using a split-operator technique and the Crank-Nicolson approximation for the short-time propagator. The initial ground state is obtained via imaginary time-propagation for spherically symmetric (but otherwise arbitrary) effective potentials. Excited states can be obtained through the combination of imaginary time-propagation and orthogonalization. For the Kohn-Sham scheme a multipole expansion of the effective potential is employed. Wavefunctions can be analyzed using the window-operator technique, facilitating the calculation of electron spectra, either angular-resolved or integratedRestrictions onto the complexity of the problem:The coupling of the atom to the external field is treated in dipole approximation. The time-dependent Schrödinger solver is restricted to the treatment of a single active electron. As concerns the time-dependent density functional mode of Qprop, the Hartree-potential (accounting for the classical electron-electron repulsion) is expanded up to the quadrupole. Only the monopole term of the Krieger-Li-Iafrate exchange potential is currently implemented. As in any nontrivial optimization problem, convergence to the optimal many-electron state (i.e. the ground state) is not automatically guaranteedExternal routines/libraries used:The program uses the well established libraries blas, lapack, and f2c     

Fortran programs for the time-dependent Gross-Pitaevskii equation in a fully anisotropic trap

Here we develop simple numerical algorithms for both stationary and non-stationary solutions of the time-dependent Gross-Pitaevskii (GP) equation describing the properties of Bose-Einstein condensates at ultra low temperatures. In particular, we consider algorithms involving real- and imaginary-time propagation based on a split-step Crank-Nicolson method. In a one-space-variable form of the GP equation we consider the one-dimensional, two-dimensional circularly-symmetric, and the three-dimensional spherically-symmetric harmonic-oscillator traps. In the two-space-variable form we consider the GP equation in two-dimensional anisotropic and three-dimensional axially-symmetric traps. The fully-anisotropic three-dimensional GP equation is also considered. Numerical results for the chemical potential and root-mean-square size of stationary states are reported using imaginary-time propagation programs for all the cases and compared with previously obtained results. Also presented are numerical results of non-stationary oscillation for different trap symmetries using real-time propagation programs. A set of convenient working codes developed in Fortran 77 are also provided for all these cases (twelve programs in all). In the case of two or three space variables, Fortran 90/95 versions provide some simplification over the Fortran 77 programs, and these programs are also included (six programs in all).

Program summary

Program title: (i) imagetime1d, (ii) imagetime2d, (iii) imagetime3d, (iv) imagetimecir, (v) imagetimesph, (vi) imagetimeaxial, (vii) realtime1d, (viii) realtime2d, (ix) realtime3d, (x) realtimecir, (xi) realtimesph, (xii) realtimeaxialCatalogue identifier: AEDU_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDU_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.: 122 907No. of bytes in distributed program, including test data, etc.: 609 662Distribution format: tar.gzProgramming language: FORTRAN 77 and Fortran 90/95Computer: PCOperating system: Linux, UnixRAM: 1 GByte (i, iv, v), 2 GByte (ii, vi, vii, x, xi), 4 GByte (iii, viii, xii), 8 GByte (ix)Classification: 2.9, 4.3, 4.12Nature of problem: These programs are designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in one-, two- or three-space dimensions with a harmonic, circularly-symmetric, spherically-symmetric, axially-symmetric or anisotropic trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Solution method: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation, in either imaginary or real time, over small time steps. The method yields the solution of stationary and/or non-stationary problems.Additional comments: This package consists of 12 programs, see “Program title”, above. FORTRAN77 versions are provided for each of the 12 and, in addition, Fortran 90/95 versions are included for ii, iii, vi, viii, ix, xii. For the particular purpose of each program please see the below.Running time: Minutes on a medium PC (i, iv, v, vii, x, xi), a few hours on a medium PC (ii, vi, viii, xii), days on a medium PC (iii, ix).

Program summary (1)

Title of program: imagtime1d.FTitle of electronic file: imagtime1d.tar.gzCatalogue identifier:Program summary URL:Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: PC/Linux, workstation/UNIXMaximum RAM memory: 1 GByteProgramming language used: Fortran 77Typical running time: Minutes on a medium PCUnusual features: NoneNature of physical problem: This program is designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in one-space dimension with a harmonic trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Method of solution: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation in imaginary time over small time steps. The method yields the solution of stationary problems.

Program summary (2)

Title of program: imagtimecir.FTitle of electronic file: imagtimecir.tar.gzCatalogue identifier:Program summary URL:Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: PC/Linux, workstation/UNIXMaximum RAM memory: 1 GByteProgramming language used: Fortran 77Typical running time: Minutes on a medium PCUnusual features: NoneNature of physical problem: This program is designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in two-space dimensions with a circularly-symmetric trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Method of solution: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation in imaginary time over small time steps. The method yields the solution of stationary problems.

Program summary (3)

Title of program: imagtimesph.FTitle of electronic file: imagtimesph.tar.gzCatalogue identifier:Program summary URL:Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: PC/Linux, workstation/UNIXMaximum RAM memory: 1 GByteProgramming language used: Fortran 77Typical running time: Minutes on a medium PCUnusual features: NoneNature of physical problem: This program is designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in three-space dimensions with a spherically-symmetric trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Method of solution: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation in imaginary time over small time steps. The method yields the solution of stationary problems.

Program summary (4)

Title of program: realtime1d.FTitle of electronic file: realtime1d.tar.gzCatalogue identifier:Program summary URL:Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: PC/Linux, workstation/UNIXMaximum RAM memory: 2 GByteProgramming language used: Fortran 77Typical running time: Minutes on a medium PCUnusual features: NoneNature of physical problem: This program is designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in one-space dimension with a harmonic trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Method of solution: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation in real time over small time steps. The method yields the solution of stationary and non-stationary problems.

Program summary (5)

Title of program: realtimecir.FTitle of electronic file: realtimecir.tar.gzCatalogue identifier:Program summary URL:Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: PC/Linux, workstation/UNIXMaximum RAM memory: 2 GByteProgramming language used: Fortran 77Typical running time: Minutes on a medium PCUnusual features: NoneNature of physical problem: This program is designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in two-space dimensions with a circularly-symmetric trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Method of solution: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation in real time over small time steps. The method yields the solution of stationary and non-stationary problems.

Program summary (6)

Title of program: realtimesph.FTitle of electronic file: realtimesph.tar.gzCatalogue identifier:Program summary URL:Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: PC/Linux, workstation/UNIXMaximum RAM memory: 2 GByteProgramming language used: Fortran 77Typical running time: Minutes on a medium PCUnusual features: NoneNature of physical problem: This program is designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in three-space dimensions with a spherically-symmetric trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Method of solution: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation in real time over small time steps. The method yields the solution of stationary and non-stationary problems.

Program summary (7)

Title of programs: imagtimeaxial.F and imagtimeaxial.f90Title of electronic file: imagtimeaxial.tar.gzCatalogue identifier:Program summary URL:Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: PC/Linux, workstation/UNIXMaximum RAM memory: 2 GByteProgramming language used: Fortran 77 and Fortran 90Typical running time: Few hours on a medium PCUnusual features: NoneNature of physical problem: This program is designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in three-space dimensions with an axially-symmetric trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Method of solution: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation in imaginary time over small time steps. The method yields the solution of stationary problems.

Program summary (8)

Title of program: imagtime2d.F and imagtime2d.f90Title of electronic file: imagtime2d.tar.gzCatalogue identifier:Program summary URL:Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: PC/Linux, workstation/UNIXMaximum RAM memory: 2 GByteProgramming language used: Fortran 77 and Fortran 90Typical running time: Few hours on a medium PCUnusual features: NoneNature of physical problem: This program is designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in two-space dimensions with an anisotropic trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Method of solution: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation in imaginary time over small time steps. The method yields the solution of stationary problems.

Program summary (9)

Title of program: realtimeaxial.F and realtimeaxial.f90Title of electronic file: realtimeaxial.tar.gzCatalogue identifier:Program summary URL:Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: PC/Linux, workstation/UNIXMaximum RAM memory: 4 GByteProgramming language used: Fortran 77 and Fortran 90Typical running time Hours on a medium PCUnusual features: NoneNature of physical problem: This program is designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in three-space dimensions with an axially-symmetric trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Method of solution: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation in real time over small time steps. The method yields the solution of stationary and non-stationary problems.

Program summary (10)

Title of program: realtime2d.F and realtime2d.f90Title of electronic file: realtime2d.tar.gzCatalogue identifier:Program summary URL:Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: PC/Linux, workstation/UNIXMaximum RAM memory: 4 GByteProgramming language used: Fortran 77 and Fortran 90Typical running time: Hours on a medium PCUnusual features: NoneNature of physical problem: This program is designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in two-space dimensions with an anisotropic trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Method of solution: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation in real time over small time steps. The method yields the solution of stationary and non-stationary problems.

Program summary (11)

Title of program: imagtime3d.F and imagtime3d.f90Title of electronic file: imagtime3d.tar.gzCatalogue identifier:Program summary URL:Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: PC/Linux, workstation/UNIXMaximum RAM memory: 4 GByteProgramming language used: Fortran 77 and Fortran 90Typical running time: Few days on a medium PCUnusual features: NoneNature of physical problem: This program is designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in three-space dimensions with an anisotropic trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Method of solution: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation in imaginary time over small time steps. The method yields the solution of stationary problems.

Program summary (12)

Title of program: realtime3d.F and realtime3d.f90Title of electronic file: realtime3d.tar.gzCatalogue identifier:Program summary URL:Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandDistribution format: tar.gzComputers: PC/Linux, workstation/UNIXMaximum Ram Memory: 8 GByteProgramming language used: Fortran 77 and Fortran 90Typical running time: Days on a medium PCUnusual features: NoneNature of physical problem: This program is designed to solve the time-dependent Gross-Pitaevskii nonlinear partial differential equation in three-space dimensions with an anisotropic trap. The Gross-Pitaevskii equation describes the properties of a dilute trapped Bose-Einstein condensate.Method of solution: The time-dependent Gross-Pitaevskii equation is solved by the split-step Crank-Nicolson method by discretizing in space and time. The discretized equation is then solved by propagation in real time over small time steps. The method yields the solution of stationary and non-stationary problems.     

A generalized effective exposure modeling program for assessing dose-response in epidemiologic investigations

The computer program OCMAP (occupational cohort mortality analysis program) has been extended to allow exposure indices for person-years to be calculated as time-dependent covariates rather than as the usual cumulative indices. The article develops a general formula for weighting exposures and describes the cumulative index, the lag, partial weight, and the lognormal models as specific examples. The implementation in OCMAP is flexible in that it permits these specific models or any other user-specified weighting scheme to be used. Several example schemes are applied to a cohort of workers exposed to arsenic.     

MKVPCI: a computer program for Markov models with piecewise constant intensities and covariates

We present a computer program for fitting Markov models with piecewise constant intensities and for estimating the effect of covariates on transition intensities. The basic idea of the proposed approach is to introduce artificial time-dependent covariates in the data to represent the time dependence of the transition intensities, and to use a modified time-homogeneous Markov model to estimate the baseline transition intensities and the regression coefficients. The program provides the maximum likelihood estimates of the parameters together with their estimated standard errors, and allows testing various statistical hypotheses. To illustrate the use of the program, we present a three-state model for analyzing the smoking habits of school children.     

Chitra: visual analysis of parallel and distributed programs in thetime, event, and frequency domains

Chitra analyzes a program execution sequence (PES) collected during execution of a program and produces a homogeneous, semi-Markov chain model fitting the PES. The PES represents the evolution of a program state vector in time. Therefore Chitra analyzes the time-dependent behavior of a program. The authors describe a set of transforms that map a PES to a simplified PES. Because the transforms are program-independent. Chitra can be used with any program. Chitra provides a visualization of PESs and transforms, to allow a user to visually guide transform selection in an effort to generate a simple yet accurate semi-Markov chain model. The resultant chain can predict performance at program parameters different than those used in the input PES, and the chain structure can diagnose performance problems     

Resonant coherent excitation of hydrogen-like ions planar channeled in a crystal; Transition into the first excited state

The presented program is designed to simulate the characteristics of resonant coherent excitation of hydrogen-like ions planar-channeled in a crystal. The program realizes the numerical algorithm to solve the Schrödinger equation for the ion-bound electron at a special resonance excitation condition. The calculated wave function of the bound electron defines probabilities for the ion to be in the either ground or first excited state, or to be ionized. Finally, in the outgoing beam the fractions of ions in the ground state, in the first excited state, and ionized by collisions with target electrons, are defined. The program code is written on C++ and is designed for multiprocessing systems (clusters). The output data are presented in the table.Program summaryProgram title: RCE_H-like_1Catalogue identifier: AEKX_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEKX_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.: 2813No. of bytes in distributed program, including test data, etc.: 34 667Distribution format: tar.gzProgramming language: C++ (g++, icc compilers)Computer: Multiprocessor systems (clusters)Operating system: Any OS based on LINUX; program was tested under Novell SLES 10Has the code been vectorized or parallelized?: Yes. Contains MPI directivesRAM: <1 MB per processorClassification: 2.1, 2.6, 7.10External routines: MPI library for GNU C++, Intel C++ compilersNature of problem: When relativistic hydrogen-like ion moves in the crystal in the planar channeling regime, in the ion rest frame the time-periodic electric field acts on the bound electron. If the frequency of this field matches the transition frequency between electronic energy levels, the resonant coherent excitation can take place. Therefore, ions in the different states may be observed in the outgoing beam behind the crystal. To get the probabilities for the ion to be in the ground state or in the first excited state, or to be ionized, the Schrödinger equation is solved for the electron of ion. The numerical solving of the Schrödinger equation is carried out taking into account the fine structure of electronic energy levels, the Stark effect due to the influence of the crystal electric field on electronic energy levels and the ionization of ion due to the collisions with crystal electrons.Solution method: The wave function of the electron of ion is the superposition of the wave functions of stationary states with time-dependent coefficients. These stationary wave functions and corresponding energies are defined from the stationary Schrödinger equation. The equation is reduced to the problem of the eigen values and vectors of Hermitian matrix. The corresponding matrix equation is considered as the linear equation system. Then the time-dependent coefficients of the electron wave function are defined from the Schrödinger equation, with a time-periodic crystal field. The time-periodic field is responsible for the transitions between the stationary states. The final time-dependent Schrödinger equation represents the matrix equation which has been solved by means of the QR-algorithm.Restrictions: As expected the program gives the correct results for relativistic hydrogen-like ions with the kinetic energies up to 1 GeV/u and at the crystal thicknesses of 1–100 μm. The restrictions are: first, the program might give inadequate results, when the ion kinetic energy is too large (>10 GeV/u); second, the unaccounted physical factors may be significant at specific conditions. For example, the spontaneous emission by exited highly charged ions, as well as both energy and angular spread of the incident beam, could lead to additional broadening of the resonance. The medium polarization by the electric field of ion can influence the electronic energy levels of the ion in the non-relativistic case. The role of these factors was discussed in the references. Also, the large crystal thickness may require large computational time.Running time: In general, the running time depends on the number of processors. In our tests we used the crystal thickness up to 100 μm and the number of 2.66 GHz processors was up to 100. The running time was about 1 hour in these conditions.     

MASAS—A user-friendly simulation tool for modeling the fate of anthropogenic substances in lakes

MASAS is a computer simulation tool to investigate anthropogenic organic compounds in lakes. Models included are based on a dynamic one-dimensional vertical lake model describing the time-dependent concentration of a compound in the water column and in the sediment. Provision of data is ensured by library files. Interactive specification of transport and transformation processes yields models of different complexity, suitable for the initial assessment of chemicals and for chemodynamic studies. A hypothetical spill of an insecticide (disulfoton) serves as an illustration. Aspects relevant to the development of user-friendly software in the environmental sciences are discussed. User-friendliness is found to depend more on program concepts than on a particular user interface. The management of data sets on lakes and compounds, and the implementation of transport and transformation processes in MASAS exemplify the significance of modularization, program data structures, the use of metaphors, and the distinction between automatic and user-controlled program functions.     

Finite element simulation of polymer behaviour using a three-dimensional, finite deformation constitutive model

This paper presents a phenomenological three-dimensional viscoelastic–plastic constitutive model for polymers. The model is based on the assumption that stress can be decomposed into two parts, namely viscoelastic and elastic–plastic. The proposed rate-dependent nonlinear model is then implemented in a finite element program. The validity of the code is assessed by the data from experiments on a specific polymer. The data from three types of tests, namely uniaxial compression, creep, and relaxation, are used to evaluate the validity of the model. Comparisons show that the proposed constitutive model could satisfactorily represent the time-dependent mechanical behaviour of polymers. The model is then used to study the effect of friction in the compression test and the behaviour of polymers under cyclic loading.     

Prediction of time-dependent structural behaviour with recurrent neural networks for fuzzy data

In the paper, an approach is described which permits the numerical, model-free prediction of uncertain time-dependent structural responses. Uncertain time-dependent structural actions and responses are modelled by means of fuzzy processes. The prediction approach is based on recurrent neural networks for fuzzy data trained by time-dependent results of measurements or numerical analyses. An efficient solution for network training and prediction is developed utilizing α-cuts and fuzzy arithmetic. The approach is verified using a fractional rheological model. The capability of the approach is demonstrated by predicting the long-term structural behaviour of reinforced concrete plates strengthened by textile reinforced concrete layers.