A parallel 3D Poisson solver for space charge simulation in cylindrical coordinates

This paper presents the development of a parallel three-dimensional Poisson solver in cylindrical coordinate system for the electrostatic potential of a charged particle beam in a circular tube. The Poisson solver uses Fourier expansions in the longitudinal and azimuthal directions, and Spectral Element discretization in the radial direction. A Dirichlet boundary condition is used on the cylinder wall, a natural boundary condition is used on the cylinder axis and a Dirichlet or periodic boundary condition is used in the longitudinal direction. A parallel 2D domain decomposition was implemented in the (r,θ) plane. This solver was incorporated into the parallel code PTRACK for beam dynamics simulations. Detailed benchmark results for the parallel solver and a beam dynamics simulation in a high-intensity proton LINAC are presented. When the transverse beam size is small relative to the aperture of the accelerator line, using the Poisson solver in a Cartesian coordinate system and a Cylindrical coordinate system produced similar results. When the transverse beam size is large or beam center located off-axis, the result from Poisson solver in Cartesian coordinate system is not accurate because different boundary condition used. While using the new solver, we can apply circular boundary condition easily and accurately for beam dynamic simulations in accelerator devices.     

A 3D model for ion beam formation and transport simulation

In this paper, we present a three-dimensional model for self consistently modeling ion beam formation from plasma ion sources and transporting in low energy beam transport systems. A multi-section overlapped computational domain has been used to break the original transport system into a number of weakly coupled subsystems. Within each subsystem, macro-particle tracking is used to obtain the charge density distribution in this subdomain. The three-dimensional Poisson equation is solved within the subdomain after each particle tracking to obtain the self-consistent space-charge forces and the particle tracking is repeated until the solution converges. Two new Poisson solvers based on a combination of the spectral method and the finite difference multigrid method have been developed to solve the Poisson equation in cylindrical coordinates for the straight beam transport section and in Frenet-Serret coordinates for the bending magnet section. This model can have important application in design and optimization of the low energy beam line optics of the proposed Rare Isotope Accelerator (RIA) front end.     

REACH: A program for coarse-grained biomolecular simulation

REACH (Realistic Extension Algorithm viaCovariance Hessian) is a program package for residue-scale coarse-grained biomolecular simulation. The program calculates the force constants of a residue-scale elastic network model in single-domain proteins using the variance-covariance matrix obtained from atomistic molecular dynamics simulation. Secondary-structure dependence of the force constants is integrated. The method involves self-consistent, direct mapping of atomistic simulation results onto a coarse-grained force field in an efficient automated procedure without requiring iterative fits and avoiding system dependence.

Program summary

Program title: REACHCatalogue identifier: AEDA_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDA_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.: 42 244No. of bytes in distributed program, including test data, etc.: 3 682 118Distribution format: tar.gzProgramming language: FORTRAN 77Computer: x86 PCOperating system: GNU/Linux, SUSE and Red HatRAM: Depends on the system size to be calculatedWord size: 32 or 64 bitsClassification: 3External routines: LAPACK, BLASNature of problem: A direct calculation of force field for residue-scale coarse-grained biomolecular simulation derived from atomistic molecular dynamics trajectory.Solution method: A variance-covariance matrix and the associated Hessian (second-derivative) matrix are calculated from an atomistic molecular dynamics trajectory of single-domain protein internal motion and the off-diagonal Hessian matrix is fitted to that of a residue-scale elastic network model. The resulting force constants for the residue pair interactions are expressed as model functions as a function of pairwise distance.Running time: Depends on the system size and the number of MD trajectory frames used. The test run provided with the distribution takes only a few seconds to execute.     

A geometry modeling system for ray tracing or particle transport Monte Carlo simulation

The principles of a geometry modeling system for ray tracing or Monte Carlo particle transport simulation are presented. The model uses the boundary representation of volumes and was developed using object oriented programming. The surface is adopted as the basic element in the model. Complex structures are described using the derived concept of compound surfaces. Particle tracking exceptions caused by floating point rounding errors are discussed and robust algorithms that use geometrical reasoning to address these problems are presented.     

QUBIT4MATLAB V3.0: A program package for quantum information science and quantum optics for MATLAB

A program package for MATLAB is introduced that helps calculations in quantum information science and quantum optics. It has commands for the following operations: (i) Reordering the qudits of a quantum register, computing the reduced state of a quantum register. (ii) Defining important quantum states easily. (iii) Formatted input and output for quantum states and operators. (iv) Constructing operators acting on given qudits of a quantum register and constructing spin chain Hamiltonians. (v) Partial transposition, matrix realignment and other operations related to the detection of quantum entanglement. (vi) Generating random state vectors, random density matrices and random unitaries.

Program summary

Program title:QUBIT4MATLAB V3.0Catalogue identifier:AEAZ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAZ_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.:5683No. of bytes in distributed program, including test data, etc.: 37 061Distribution format:tar.gzProgramming language:MATLAB 6.5; runs also on OctaveComputer:Any which supports MATLAB 6.5Operating system:Any which supports MATLAB 6.5; e.g., Microsoft Windows XP, LinuxClassification:4.15Nature of problem: Subroutines helping calculations in quantum information science and quantum optics.Solution method: A program package, that is, a set of commands is provided for MATLAB. One can use these commands interactively or they can also be used within a program.Running time:10 seconds-1 minute     

Code OK1—Simulation of multi-beam irradiation on a spherical target in heavy ion fusion

Code OK1 is a fast and precise three-dimensional computer program designed for simulations of heavy ion beam (HIB) irradiation on a direct-driven spherical fuel pellet in heavy ion fusion (HIF). OK1 provides computational capabilities of a three-dimensional energy deposition profile on a spherical fuel pellet and the HIB irradiation non-uniformity evaluation, which are valuables for optimizations of the beam parameters and the fuel pellet structure, as well for further HIF experiment design. The code is open and complete, and can be easily modified or adapted for users' purposes in this field.

Program summary

Title of program: OK1Catalogue identifier: ADSTProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSTProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer: PC (Pentium 4, ∼1 GHz or more recommended)Operating system: Windows or UNIXProgram language used: C++Memory required to execute with typical data: 911 MBNo. of bits in a word: 32No. of processors used: 1 CPUHas the code been vectorized or parallelized: NoNo. of bytes in distributed program, including test data: 16 557Distribution format: tar gzip fileKeywords: Heavy ion beam, inertial confinement fusion, energy deposition, fuel pelletNature of physical problem: Nuclear fusion energy may have attractive features as one of our human energy resources. In this paper we focus on heavy ion inertial confinement fusion (HIF). Due to a favorable energy deposition behavior of heavy ions in matter [J.J. Barnard et al., UCRL-LR-108095, 1991; C. Deutsch et al., J. Plasma Fusion Res. 77 (2001) 33; T. Someya et al., Fusion Sci. Tech. (2003), submitted] it is expected that heavy ion beam (HIB) would be one of energy driver candidates to operate a future inertial confinement fusion power plant. For a successful fuel ignition and fusion energy release, a stringent requirement is imposed on the HIB irradiation non-uniformity, which should be less than a few percent [T. Someya et al., Fusion Sci. Tech. (2003), submitted; M.H. Emery et al., Phys. Rev. Lett. 48 (1982) 253; S. Kawata et al., J. Phys. Soc. Jpn. 53 (1984) 3416]. In order to meet this requirement we need to evaluate the non-uniformity of a realistic HIB irradiation and energy deposition pattern. The HIB irradiation and non-uniformity evaluations are sophisticated and difficult to calculate analytically. Based on our code one can numerically obtain a three-dimensional profile of energy deposition and evaluate the HIB irradiation non-uniformity onto a spherical target for a specific HIB parameter value set in HIF.Method of solution: OK1 code is based on the stopping power of ions in matter [J.J. Barnard et al., UCRL-LR-108095, 1991; C. Deutsch et al., J. Plasma Fusion Res. 77 (2001) 33; T. Someya et al., Fusion Sci. Tech. (2003), submitted; M.H. Emery et al., Phys. Rev. Lett. 48 (1982) 253; S. Kawata et al., J. Phys. Soc. Jpn. 53 (1984) 3416; T. Mehlhorn, SAND80-0038, 1980; H.H. Andersen, J.F. Ziegler, Pergamon Press, 1977, p. 3]. The code simulates a multi-beam irradiation, obtains the 3D energy deposition profile of the fuel pellet and evaluates the deposition non-uniformity.Restrictions on the complexity of the problem: NoTypical running time: The execution time depends on the number of beams in the simulated irradiation and its characteristics (beam radius on the pellet surface, beam subdivision, projectile particle energy and so on). In almost of the practical running tests performed, the typical running time for one beam deposition is less than 2 s on a PC with a CPU of Pentium 4, 2.2 GHz (e.g., in Test 2 when the number of beams is 600, the running time is about 18 minutes).Unusual features of the program: No     

A stabilized finite element method for modeling of gas discharges

An efficient stabilized finite element method for modeling of gas discharge plasmas is represented which provides wiggle-free solutions without introducing much artificial diffusion. The stabilization is achieved by modifying the standard Galerkin test functions by means of a weighted quadratic term that results in a consistent Petrov-Galerkin formulation of the charge carriers in the plasma. Using the example of a glow discharge plasma in argon, it is shown that this efficient method provides more accurate results on the same spatial grid than the widely used finite difference approach proposed by Scharfetter-Gummel if the weighting factor is determined in dependence on the local Péclet number and the modified test functions are consistently applied to all terms of the governing equations.     

A transport simulation code for inertial confinement fusion relevant laser-plasma interaction

We present a code for the simulation of laser-plasma interaction processes relevant for applications in inertial confinement fusion. The code consists of a fully nonlinear hydrodynamics in two spatial dimensions using a Lagrangian, discontinuous Galerkin-type approach, a paraxial treatment of the laser field and a spectral treatment of the dominant non-local transport terms. The code is fully parallelized using MPI in order to be able to simulate macroscopic plasmas.One example of a fully nonlinear evolution of a laser beam in an underdense plasma is presented for the conditions previewed for the future MegaJoule laser project.     

Nonlinear feedback-based control of the distribution of total energy between the degrees of freedom of a mechanical system. A quantum approach

The closed mechanical system capable of spontaneous redistribution of its total energy between the degrees of freedom was shown to manifest the quantum properties.     

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

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

Program summary

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

A B-spline Galerkin method for the Dirac equation

The B-spline Galerkin method is first investigated for the simple eigenvalue problem, y^″=−λ²y, that can also be written as a pair of first-order equations y^′=λz, z^′=−λy. Expanding both y(r) and z(r) in the Bk basis results in many spurious solutions such as those observed for the Dirac equation. However, when y(r) is expanded in the Bk basis and z(r) in the dBk/dr basis, solutions of the well-behaved second-order differential equation are obtained. From this analysis, we propose a stable method (Bk,Bk±1) basis for the Dirac equation and evaluate its accuracy by comparing the computed and exact R-matrix for a wide range of nuclear charges Z and angular quantum numbers κ. When splines of the same order are used, many spurious solutions are found whereas none are found for splines of different order. Excellent agreement is obtained for the R-matrix and energies for bound states for low values of Z. For high Z, accuracy requires the use of a grid with many points near the nucleus. We demonstrate the accuracy of the bound-state wavefunctions by comparing integrals arising in hyperfine interaction matrix elements with exact analytic expressions. We also show that the Thomas-Reiche-Kuhn sum rule is not a good measure of the quality of the solutions obtained by the B-spline Galerkin method whereas the R-matrix is very sensitive to the appearance of pseudo-states.     

A program for the simulation and analysis of open atmospheric balloon soundings

The equation of motion for a balloon in an atmosphere is generalized but placed in proper context by taking into account some fluid theory results and a few factors not considered in previous works. The design of a computer program becomes necessary to find solutions. A code that allows to perform 2D simulations of open balloons flights is developed. The coupled integrodifferential nature of the problem represented a significant challenge for a satisfactory implementation.     

A new version of Scilab software package for the study of dynamical systems

This work presents a new version of a software package for the study of chaotic flows, maps and fractals [1]. The codes were written using Scilab, a software package for numerical computations providing a powerful open computing environment for engineering and scientific applications. It was found that Scilab provides various functions for ordinary differential equation solving, Fast Fourier Transform, autocorrelation, and excellent 2D and 3D graphical capabilities. The chaotic behaviors of the nonlinear dynamics systems were analyzed using phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropy. Various well-known examples are implemented, with the capability of the users inserting their own ODE or iterative equations.

New version program summary

Program title: Chaos v2.0Catalogue identifier: AEAP_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAP_v2_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.: 1275No. of bytes in distributed program, including test data, etc.: 7135Distribution format: tar.gzProgramming language: Scilab 5.1.1. Scilab 5.1.1 should be installed before running the program. Information about the installation can be found at http://wiki.scilab.org/howto/install/windows.Computer: PC-compatible running Scilab on MS Windows or LinuxOperating system: Windows XP, LinuxRAM: below 150 MegabytesClassification: 6.2Catalogue identifier of previous version: AEAP_v1_0Journal reference of previous version: Comput. Phys. Comm. 178 (2008) 788Does the new version supersede the previous version?: YesNature of problem: Any physical model containing linear or nonlinear ordinary differential equations (ODE).Solution method:

1.

Numerical solving of ordinary differential equations for the study of chaotic flows. The chaotic behavior of the nonlinear dynamical system is analyzed using Poincare sections, phase-space maps, autocorrelation functions, power spectra, Lyapunov exponents and Kolmogorov-Sinai entropies.

2.

Numerical solving of iterative equations for the study of maps and fractals.

Reasons for new version: The program has been updated to use the new version 5.1.1 of Scilab with new graphical capabilities [2]. Moreover, new use cases have been added which make the handling of the program easier and more efficient.Summary of revisions:

1.

A new use case concerning coupled predator-prey models has been added [3].

2.

Three new use cases concerning fractals (Sierpinsky gasket, Barnsley's Fern and Tree) have been added [3].

3.

The graphical user interface (GUI) of the program has been reconstructed to include the new use cases.

4.

The program has been updated to use Scilab 5.1.1 with the new graphical capabilities.

Additional comments: The program package contains 12 subprograms.

•

interface.sce - the graphical user interface (GUI) that permits the choice of a routine as follows

•

1.sci - Lorenz dynamical system

•

2.sci - Chua dynamical system

•

3.sci - Rosler dynamical system

•

4.sci - Henon map

•

5.sci - Lyapunov exponents for Lorenz dynamical system

•

6.sci - Lyapunov exponent for the logistic map

•

7.sci - Shannon entropy for the logistic map

•

8.sci - Coupled predator-prey model

•

1f.sci - Sierpinsky gasket

•

2f.sci - Barnsley's Fern

•

3f.sci - Barnsley's Tree

Running time: 10 to 20 seconds for problems that do not involve Lyapunov exponents calculation; 60 to 1000 seconds for problems that involve high orders ODE, Lyapunov exponents calculation and fractals.References:

[1]

C.C. Bordeianu, C. Besliu, Al. Jipa, D. Felea, I. V. Grossu, Comput. Phys. Comm. 178 (2008) 788.

[2]

S. Campbell, J.P. Chancelier, R. Nikoukhah, Modeling and Simulation in Scilab/Scicos, Springer, 2006.

[3]

R.H. Landau, M.J. Paez, C.C. Bordeianu, A Survey of Computational Physics, Introductory Computational Science, Princeton University Press, 2008.

     

A quantum full adder for a scalable nuclear spin quantum computer

We demonstrate a strategy for implementation a quantum full adder in a spin chain quantum computer. As an example, we simulate a quantum full adder in a chain containing 201 spins. Our simulations also demonstrate how one can minimize errors generated by non-resonant effects.     

A lattice Boltzmann model for the Korteweg-de Vries equation with two conservation laws

A lattice Boltzmann model for the Korteweg-de Vries (KdV) equation is presented by using the higher-order moment method. In contrast to the previous lattice Boltzmann model to the KdV equation, our method has higher-order accuracy. Two key steps in the development of this model are the addition of a momentum conservation condition, and the construction of a correlation between the first conservation law and the second conservation law. The numerical example shows the higher-order moment method can be used to raise the truncation error of the lattice Boltzmann scheme.     

Numerical simulation on the dynamics of photoinduced cooperative phenomena in molecular crystals

We develop a new simulation method to study the dynamics of initial nucleation processes of photoinduced structural change of molecular crystals. In order to describe the nonadiabatic transition in each molecule, we employ a model of localized electrons coupled with a fully quantized phonon mode, and the time-dependent Schrödinger equation for the model is numerically solved. By applying a mean-field approximation in solving the Schrödinger equation, the calculation method is quite efficient on parallel computing systems. We show that coherently driven molecular distortion plays an important role in the successive conversion of electronic states which leads to photoinduced cooperative phenomena.     

A new simulation code for particle diffusion in anisotropic, large-scale and turbulent magnetic fields

A new Monte Carlo code is presented that simulates the scattering processes of energetic particles in turbulent magnetic fields. The growing number of analytical models for anisotropic turbulence geometries gives rise to the need of fast and adaptable simulation codes that, in order to be able to judge the accuracy of the results, calculate the estimated mean errors of the transport parameters. Furthermore, the need to understand the interplay of scattering in anisotropic large-scale (such as the solar magnetic field) and turbulent (such as the Maltese cross-like structured solar wind turbulence) magnetic fields is accounted for with the calculation of the off-diagonal elements of the diffusion tensor.     

The stationary phase auxiliary field Monte Carlo method: a new strategy for reducing the sign problem of auxiliary field methodologies

In this paper we focus on a new computational procedure, which permits an efficient calculation within the classical auxiliary field methodology. As has been previously reported, the method suffers from a sign problem, typically encountered in methodologies based on a field-theoretical approach. To ameliorate its statistical convergence, the efforts have so far exclusively been concentrated on the development of efficient analytical integral transformation techniques, such as the method of Gaussian equivalent representation of Efimov et al. In the present work we reformulate the classical auxiliary field methodology according to the concepts of the stationary phase Monte Carlo method of Doll et al., a numerical strategy originally developed for the simulation with real-time path integrals. The procedure, which is here employed for the first time for auxiliary field computation, utilizes an importance sampling strategy, to identify the regions of configuration space that contribute most strongly to the functional integral averages. Its efficiency is here compared to the method of Gaussian equivalent representation.     

SIMULHOLE: A computer program for three-dimensional simulation of a disseminated gold deposit

A three-dimensional simulation model was used to study spatial variability of grade values for a disseminated gold deposit for mine-planning purposes. After a review of fundamentals of the technique, the paper presents a case history of a disseminated gold deposit (Québec, Canada) in an application of the SIMULHOLE program. Real and simulated histograms, as well as geological sections transverse and longitudinal to the orebody with grades simulated for each synthetic hole, are given as output of the SIMULHOLE program.