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  • 1.
    Bessarab, Pavel F.
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. St. Petersburg State University, Russian Federation.
    Uzdin, Valery M.
    Jonsson, Hannes
    Method for finding mechanism and activation energy of magnetic transitions, applied to skyrmion and antivortex annihilation2015In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 196, p. 335-347Article in journal (Refereed)
    Abstract [en]

    A method for finding minimum energy paths of transitions in magnetic systems is presented. The path is optimized with respect to orientation of the magnetic vectors while their magnitudes are fixed or obtained from separate calculations. The curvature of the configuration space is taken into account by: (1) using geodesics to evaluate distances and displacements of the system during the optimization, and (2) projecting the path tangent and the magnetic force on the tangent space of the manifold defined by all possible orientations of the magnetic vectors. The method, named geodesic nudged elastic band (GNEB), and its implementation are illustrated with calculations of complex transitions involving annihilation and creation of skyrmion and antivortex states. The lifetime of the latter was determined within harmonic transition state theory using a noncollinear extension of the Alexander-Anderson model.

  • 2. Blennow, Mattias
    et al.
    Fernandez Martinez, Enrique
    Neutrino oscillation parameter sampling with MonteCUBES2010In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 181, no 1, p. 227-231Article in journal (Refereed)
    Abstract [en]

    We present MonteCUBES ("Monte Carlo Utility Based Experiment Simulator"), a software package designed to sample the neutrino oscillation parameter space through Markov Chain Monte Carlo algorithms. MonteCUBES makes use of the GLoBES software so that the existing experiment definitions for GLoBES, describing long baseline and reactor experiments. can be used with MonteCUBES. MonteCUBES consists of two main parts: The first is a C library, written as a plug-in for GLoBES, implementing the Markov Chain Monte Carlo algorithm to sample the parameter space. The second part is a user-friendly graphical Matlab interface to easily read, analyze, plot and export the results of the parameter space sampling.

  • 3. Brickner, R.G
    et al.
    Baillie, C.F
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    QCD on the Connection Machine: Beyond-Lisp1991In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 65, p. 39-51Article in journal (Refereed)
    Abstract [en]

     We report on the status of code development for a simulation of quantum chromodynamics (QCD) with dynamical Wilson fermions on the Connection Machine model CM-2. Our original code, written in * Lisp, gave performance in the near-GFLOPS range. We have rewritten the most time-consuming parts of the code in the low-level programming system CMIS, including the matrix multiply and the communication. Current versions of the code run at approximately 3.6 GFLOPS for the fermion matrix inversion, and we expect the next version to reach or exceed 5 GFLOPS.

  • 4.
    Davis, Sergio
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Belonoshko, Anatoly
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Johansson, Börje
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    SearchFill: A stochastic optimization code for detecting atomic vacancies in crystalline and non-crystalline systems2011In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 182, no 5, p. 1105-1110Article in journal (Refereed)
    Abstract [en]

    We present an implementation of a stochastic optimization algorithm applied to location of atomic vacancies. Our method labels an empty point in space as a vacancy site, if the total spatial overlap of a "virtual sphere", centered around the point, with the surrounding atoms (and other vacancies) falls below a tolerance parameter. A Metropolis-like algorithm displaces the vacancies randomly, using an "overlap temperature" parameter to allow for acceptance of moves into regions with higher overlap, thus avoiding local minima. Once the algorithm has targeted a point with low overlap, the overlap temperature is decreased, and the method works as a steepest descent optimization.

    Our method, with only two free parameters, is able to detect the correct number and coordinates of vacancies in a wide spectrum of condensed-matter systems, from crystals to amorphous solids, in fact in any given set of atomic coordinates, without any need of comparison with a reference initial structure.

  • 5.
    Höök, L. Josef
    et al.
    KTH, School of Electrical Engineering (EES), Fusion Plasma Physics.
    Johnson, Thomas
    KTH, School of Electrical Engineering (EES), Fusion Plasma Physics.
    Composition schemes for the stochastic differential equation describing collisional pitch-angle diffusion2014In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 185, no 2, p. 590-594Article in journal (Refereed)
    Abstract [en]

    Two new second order accurate Monte Carlo integration schemes are derived for the stochastic differential equation describing pitch-angle scattering by Coulomb collisions in magnetized plasmas. Here the pitch-angle is the angle between the magnetic field and the particle velocity vectors. Mathematically this collision process corresponds to diffusion in the polar angle of a spherical coordinate system. The schemes are simple to implement, they are naturally bounded to the solution domain and their convergences are shown to compare favourably against commonly used alternative integration schemes.

  • 6. Innocenti, M. E.
    et al.
    Beck, A.
    Ponweiser, T.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Lapenta, G.
    Introduction of temporal sub-stepping in the Multi-Level Multi-Domain semi-implicit Particle-In-Cell code Parsek2D-MLMD2015In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 189, p. 47-59Article in journal (Refereed)
    Abstract [en]

    In this paper, the introduction of temporal sub-stepping in Multi-Level Multi-Domain (MLMD) simulations of plasmas is discussed. The MLMD method addresses the multi-scale nature of space plasmas by simulating a problem at different levels of resolution. A large-domain "coarse grid" is simulated with low resolution to capture large-scale, slow processes. Smaller scale, local processes are obtained through a "refined grid" which uses higher resolution. Very high jumps in the resolution used at the different levels can be achieved thanks to the Implicit Moment Method and appropriate grid interlocking operations. Up to now, the same time step was used at all the levels. Now, with temporal sub-stepping, the different levels can also benefit from the use of different temporal resolutions. This saves further resources with respect to "traditional" simulations done using the same spatial and temporal stepping on the entire domain. It also prevents the levels from working at the limits of the stability condition of the Implicit Moment Method. The temporal sub-stepping is tested with simulations of magnetic reconnection in space. It is shown that, thanks to the reduced costs of MLMD simulations with respect to single-level simulations, it becomes possible to verify with realistic mass ratios scaling laws previously verified only for reduced mass ratios. Performance considerations are also provided.

  • 7.
    Jaun, André
    et al.
    KTH, Superseded Departments, Alfvén Laboratory.
    Blomqvist, K.
    Bondeson, A.
    Rylander, T.
    Iterative solution of global electromagnetic wavefields with finite elements2001In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 135, no 1, p. 74-81Article in journal (Refereed)
    Abstract [en]

    The time-independent Maxwell equations are solved iteratively in 2D geometry fur 3D global waves in plasma physics. Krylov space methods, such as the generalized- or the quasi-minimal residuals (GMRES or QMR), are applied together with an incomplete factorization (ILU) preconditioning to a formulation using nodal elements for the electromagnetic scalar and vector potentials. The plasma response is represented as a complex, frequency dependent, dielectric tensor operator and can be used for a variety of applications involving low frequency waves in a tokamak. The iterative approach does not only result in considerable memory savings, but it is also more efficient than a direct solution and paves the way for the parallelization of global wave and stability codes.

  • 8.
    Johnsson, Lennart
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Cyclic Reduction on a Binary Tree1985In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 37, no 1-3, p. 195-203Article in journal (Refereed)
    Abstract [en]

    Ensembles of large numbers of processors tightly coupled into networks are of increasing interest. Binary tree interconnect has many favourable characteristics from a construction point of view, though the limited communication bandwidth between arbitrary processors poses a potential bottleneck. In this paper we present an algorithm for odd-even cyclic reduction on a binary tree for which the limited bandwidth does not increase the order of the computational complexity, compared to an ideal parallel machine. The complexity is 2 log2N with respect to arithmetic operations, and 3 log2N with respect to communication. The communication complexity compares favourably with the best previously published result, O(log22N). We also show that the benefits of truncated cyclic reduction are much greater for parallel reduction algorithms than for sequential algorithms. A reduction in the computational complexity proportional to the reduction in the number of reduction steps is possible.

  • 9. Jucker, M.
    et al.
    Graves, J. P.
    Cooper, W. A.
    Mellet, N.
    Johnson, Thomas
    KTH, School of Electrical Engineering (EES), Fusion Plasma Physics.
    Brunner, S.
    Integrated modeling for ion cyclotron resonant heating in toroidal systems2011In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 182, no 4, p. 912-925Article in journal (Refereed)
    Abstract [en]

    An integrated model capable of self-consistent Ion Cyclotron Resonant Heating (ICRH) simulations has been developed. This model includes both full shaping and pressure effects, warm contributions to the dielectric tensor, pressure anisotropy and finite orbit width. It evolves the equilibrium, wave field and full hot particle distribution function until a self-consistent solution is found. This article describes the workings of the three codes VMEC, LEMan and VENUS and how they are linked for iterated computations in a code package we have named SCENIC. The package is thoroughly tested and it is demonstrated that a number of iterations have to be performed in order to find a consistent solution. Since the formulation of the problem can treat general 3D systems, we show a quasi-axisymmetric stellarator low power test case, and then concentrate on experimentally relevant Joint European Torus (JET) 2D configurations.

  • 10.
    Leetmaa, M.a
    et al.
    Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden.
    Skorodumova, Natalia
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Multiscale Materials Modelling. Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden.
    KMCLib 1.1: Extended random number support and technical updates to the KMCLib general framework for kinetic Monte-Carlo simulations2015In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 196, p. 611-613Article in journal (Refereed)
    Abstract [en]

    We here present a revised version, v1.1, of the KMCLib general framework for kinetic Monte-Carlo (KMC) simulations. The generation of random numbers in KMCLib now relies on the C++11 standard library implementation, and support has been added for the user to choose from a set of C++11 implemented random number generators. The Mersenne-twister, the 24 and 48 bit RANLUX and a ’minimal-standard’ PRNG are supported. We have also included the possibility to use true random numbers via the C++11 std::random-device generator. This release also includes technical updates to support the use of an extended range of operating systems and compilers. New version program summary Program title: KMCLib v1.1 Catalogue identifier: AESZ-v1-1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AESZ-v1-1.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 49,398 No. of bytes in distributed program, including test data, etc.: 1,536,855 Distribution format: tar.gz Programming language: Python and C++. Computer: Any computer that can run a C++11 compatible C++ compiler and a Python 2.7 interpreter. Operating system: Tested on Ubuntu 14.4 LTS, Ubuntu 12.4 LTS, CentOS 6.6, Mac OSX 10.10.3, Mac OSX 10.9.5 and Mac OSX 10.8.2 but should run on any system that can have a C++11 compatible C++ compiler and a Python 2.7 interpreter. Has the code been vectorized or parallelized?: Yes, with MPI. From one to hundreds of processors may be used depending on the type of input and simulation. RAM: From a few megabytes to several gigabytes depending on input parameters and the size of the system to simulate. Catalogue identifier of previous version: AESZ-v1-0 Journal reference of previous version: Comput. Phys. Comm. 185 (2014) 2340 Classification: 4.13, 16.13. External routines: To run the serial version of KMCLib no external libraries are needed other than the standard C++ runtime library and a Python 2.7 interpreter with support for numpy. For running the parallel version an MPI implementation is needed, such as e.g. MPICH from http://www.mpich.org or Open-MPI from http://www.open-mpi.org. SWIG (obtainable from http://www.swig.org/) and CMake (obtainable from http://www.cmake.org/) are both needed for building the backend module, while Sphinx (obtainable from http://sphinx-doc.org) is needed for building the documentation. CPPUNIT (obtainable from http://sourceforge.net/projects/cppunit/, also included in the KMCLib distribution) is needed for building the C++ unit tests Does the new version supersede the previous version?: Yes Nature of problem: Atomic scale simulation of slowly evolving dynamics is a great challenge in many areas of computational materials science and catalysis. When the rare-events dynamics of interest is orders of magnitude slower than the typical atomic vibrational frequencies a straight-forward propagation of the equations of motions for the particles in the simulation cannot reach time scales of relevance for modeling the slow dynamics. Solution method: KMCLib provides an implementation of the kinetic Monte Carlo (KMC) method that solves the slow dynamics problem by utilizing the separation of time scales between fast vibrational motion and the slowly evolving rare-events dynamics. Only the latter is treated explicitly and the system is simulated as jumping between fully equilibrated local energy minima on the slow-dynamics potential energy surface. Reasons for new version: The v1.1 revision increases the reliability and flexibility of the random number generation options in KMCLib, which is a central part of the KMC algorithm. The new release also comes with extended support for additional compilers and updates to the build system to simplify the installation procedure on some widely used platforms. Summary of revisions:Enough time has passed since the introduction of the <random> header in the C++ standard runtime library with the C++11 standard, that most installed compilers today have support to enable the use of C++11 specific language features in C+++. The <random> standard header comes with a set of well-defined pseudo random number generators (PRNG). Using standard library routines in favor of custom implementations has the obvious advantage of being more reliable and with guaranteed support over a longer time. From the v1.1 revision, KMCLib therefore relies on the C++11 standard library <random> header to produce pseudo-random numbers. This also makes it easier to enable support for several different PRNG:s for the user to choose from. From previously only supporting a Mersenne-twister implementation, KMCLib now has support for using the Mersenne-twister [1], the 24 and 48-bit RANLUX [2] generators, as well as a ’minimal-standard’ PRNG [3].For machines with a random device installed, KMCLib v1.1 can run simulations with true random numbers. This is enabled by using the std::random-device generator in C++. If the random device is properly installed the true random numbers are available to KMCLib out of the box and the user only needs to specify the use of the random device with an input flag in the same way as she chooses any of the available PRNG:s.The v1.1 revision includes major updates to the build system. The build system has no effect on the outcome of the simulations, but has a great impact on how easy it is to install the program. The Intel compiler is widely available on super computer clusters and support for this compiler widely extends the number of systems where KMCLib can be easily setup and run. The popularity of the Mac platform also makes smooth installation and compilation with clang desirable. With version v1.1 the make system for KMClib now includes support for the clang compiler on Mac and support for both the Intel compiler and the gcc compiler on Linux. See the reference manual for details of which versions of the operating systems and compilers have been tested.Restrictions: KMCLib implements the lattice KMC method and is as such, restricted to geometries that can be expressed on a grid in space. See the original paper describing KMCLib [4] for further details. Unusual features: KMCLib has been designed to be easily customized, to allow for user-defined functionality and integration with other codes. The user can define her own on-the-fly rate calculator via a Python API, so that site-specific elementary process rates, or rates depending on long-range interactions or complex geometrical features can easily be included. KMCLib also allows for on-the-fly analysis with user-defined analysis modules. KMCLib can keep track of individual particle movements and includes tools for mean square displacement analysis based on the algorithm described in Ref. [5], and is therefore particularly well suited for studying diffusion processes at surfaces and in solids. With the release of v1.1 KMCLib now supports several different pseudo random number generators, but can also, if a random device is installed on the machine, use true random numbers via the std::random-device generator. Additional comments: The full documentation of the program is distributed with the code and can also be found online at http://leetmaa.github.io/KMCLib/manual-v1.1/. Running time: From a few seconds to several days depending on the type of simulation and input parameters. References:M. Matsumoto and T. Nishimura, "Mersenne Twister: A 623- dimensionally equidistributed uniform pseudorandom number generator", ACM Trans. on Modeling and Computer Simulation, 8 (1998) 3.M. Lscher, "A portable high-quality random number generator for lattice field theory calculations", Computer Physics Communications, 79 (1994) 100110.S. K. Park, K. W. Miller and P K. Stockmeyer, "Technical correspondence", Communications of the ACM, 36 (1993) 105.M. Leetmaa and N. V. Skorodumova, "KMCLib: A general framework for lattice kinetic Monte Carlo (KMC) simulations", Computer Physics Communications, 185 (2014) 2340.M. Leetmaa and N. V. Skorodumova, "Mean square displacements with error estimates from non-equidistant time-step kinetic Monte Carlo simulations", Computer Physics Communications, 191 (2015) 119.

  • 11.
    Leetmaa, Mikael
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Multiscale Materials Modelling.
    Skorodumova, Natalia V.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Multiscale Materials Modelling. Department of Physics and Astronomy, Uppsala University.
    KMCLib: A general framework for lattice kinetic Monte Carlo (KMC) simulations2014In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 185, no 9, p. 2340-2349Article in journal (Refereed)
    Abstract [en]

    KMCLib is a general framework for lattice kinetic Monte Carlo (KMC) simulations. The program can handle simulations of the diffusion and reaction of millions of particles in one, two, or three dimensions, and is designed to be easily extended and customized by the user to allow for the development of complex custom KMC models for specific systems without having to modify the core functionality of the program. Analysis modules and on-the-fly elementary step diffusion rate calculations can be implemented as plugins following a well-defined API. The plugin modules are loosely coupled to the core KMCLib program via the Python scripting language. KMCLib is written as a Python module with a backend C++ library. After initial compilation of the backend library KMCLib is used as a Python module; input to the program is given as a Python script executed using a standard Python interpreter. We give a detailed description of the features and implementation of the code and demonstrate its scaling behavior and parallel performance with a simple one-dimensional A-B-C lattice KMC model and a more complex three-dimensional lattice KMC model of oxygen-vacancy diffusion in a fluorite structured metal oxide. KMCLib can keep track of individual particle movements and includes tools for mean square displacement analysis, and is therefore particularly well suited for studying diffusion processes at surfaces and in solids. Program summary Program title: KMCLib Catalogue identifier: AESZ_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AESZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 49 064 No. of bytes in distributed program, including test data, etc.: 1 575 172 Distribution format: tar.gz Programming language: Python and C++. Computer: Any computer that can run a C++ compiler and a Python interpreter. Operating system: Tested on Ubuntu 12.4 LTS, CentOS release 5.9, Mac OSX 10.5.8 and Mac OSX 10.8.2, but should run on any system that can have a C++ compiler, MPI and a Python interpreter. Has the code been vectorized or parallelized?: Yes. From one to hundreds of processors depending on the type of input and simulation. RAM: From a few megabytes to several gigabytes depending on input parameters and the size of the system to simulate. Classification: 4.13, 16.13. External routines: KMCLib uses an external Mersenne Twister pseudo random number generator that is included in the code. A Python 2.7 interpreter and a standard C++ runtime library are needed to run the serial version of the code. For running the parallel version an MPI implementation is needed, such as e.g. MPICH from http://www.mpich.org or Open-MPI from http://www.open-mpi.org. SWIG (obtainable from http://www.swig.org/) and CMake (obtainable from http://www.cmake.org/) are needed for building the backend module, Sphinx (obtainable from http://sphinx-doc.org) for building the documentation and CPPUNIT (obtainable from http://sourceforge.net/projects/cppunit/) for building the C++ unit tests. Nature of problem: Atomic scale simulation of slowly evolving dynamics is a great challenge in many areas of computational materials science and catalysis. When the rare-events dynamics of interest is orders of magnitude slower than the typical atomic vibrational frequencies a straight-forward propagation of the equations of motions for the particles in the simulation cannot reach time scales of relevance for modeling the slow dynamics. Solution method: KMCLib provides an implementation of the kinetic Monte Carlo (KMC) method that solves the slow dynamics problem by utilizing the separation of time scales between fast vibrational motion and the slowly evolving rare-events dynamics. Only the latter is treated explicitly and the system is simulated as jumping between fully equilibrated local energy minima on the slow-dynamics potential energy surface. Restrictions: KMCLib implements the lattice KMC method and is as such restricted to geometries that can be expressed on a grid in space. Unusual features: KMCLib has been designed to be easily customized, to allow for user-defined functionality and integration with other codes. The user can define her own on-the-fly rate calculator via a Python API, so that site-specific elementary process rates, or rates depending on long-range interactions or complex geometrical features can easily be included. KMCLib also allows for on-the-fly analysis with user-defined analysis modules. KMCLib can keep track of individual particle movements and includes tools for mean square displacement analysis, and is therefore particularly well suited for studying diffusion processes at surfaces and in solids. Additional comments: The full documentation of the program is distributed with the code and can also be found at http://www.github.com/leetmaa/KMCLib/manual Running time: From a few seconds to several days depending on the type of simulation and input parameters.

  • 12.
    Leetmaa, Mikael
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Multiscale Materials Modelling. Uppsala University, Sweden.
    Skorodumova, Natalia V.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Multiscale Materials Modelling. Uppsala University, Sweden.
    Mean square displacements with error estimates from non-equidistant time-step kinetic Monte Carlo simulations2015In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 191, p. 119-124Article in journal (Refereed)
    Abstract [en]

    We present a method to calculate mean square displacements (MSD) with error estimates from kinetic Monte Carlo (KMC) simulations of diffusion processes with non-equidistant time-steps. An analytical solution for estimating the errors is presented for the special case of one moving particle at fixed rate constant. The method is generalized to an efficient computational algorithm that can handle any number of moving particles or different rates in the simulated system. We show with examples that the proposed method gives the correct statistical error when the MSD curve describes pure Brownian motion and can otherwise be used as an upper bound for the true error.

  • 13.
    Persson, Clas
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Ambrosch-Draxl, Claudia
    A full-band FPLAPW plus k center dot p-method for solving the Kohn-Sham equation2007In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 177, no 3, p. 280-287Article in journal (Refereed)
    Abstract [en]

    We have implemented a full-band k . p-approach into a full-potential linearized augmented plane wave (FPLAPW) code in order to more efficiently-and still accurately - calculate the electronic and optical properties of periodic crystalline solids within the Kohn-Sham singleelectron formalism. The validity of this full-band k - p-method is discussed as well as the convergence of the eigenvalues and eigenvectors with respect to basis set and k-mesh, with applications to the semiconductor ZnO and the metal Al. Moreover, the accuracy of the FPLAPW + k - p-method for computing the band structure and the dielectric function is demonstrated for the more complex materials YBa2Cu3O7 and poly(paraphenylene). For these structures, the full-band k - p-approach reduces the computational time by as much as 90%.

  • 14.
    Páll, Szilard
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    A flexible algorithm for calculating pair interactions on SIMD architectures2013In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 184, no 12, p. 2641-2650Article in journal (Refereed)
    Abstract [en]

    Calculating interactions or correlations between pairs of particles is typically the most time-consuming task in particle simulation or correlation analysis. Straightforward implementations using a double loop over particle pairs have traditionally worked well, especially since compilers usually do a good job of unrolling the inner loop. In order to reach high performance on modern CPU and accelerator architectures, single-instruction multiple-data (SIMD) parallelization has become essential. Avoiding memory bottlenecks is also increasingly important and requires reducing the ratio of memory to arithmetic operations. Moreover, when pairs only interact within a certain cut-off distance, good SIMD utilization can only be achieved by reordering input and output data, which quickly becomes a limiting factor. Here we present an algorithm for SIMD parallelization based on grouping a fixed number of particles, e.g. 2, 4, or 8, into spatial clusters. Calculating all interactions between particles in a pair of such clusters improves data reuse compared to the traditional scheme and results in a more efficient SIMD parallelization. Adjusting the cluster size allows the algorithm to map to SIMD units of various widths. This flexibility not only enables fast and efficient implementation on current CPUs and accelerator architectures like GPUs or Intel MIC, but it also makes the algorithm future-proof. We present the algorithm with an application to molecular dynamics simulations, where we can also make use of the effective buffering the method introduces.

  • 15.
    Salek, Pawel
    KTH, Superseded Departments, Biotechnology.
    A wave-packet technique to simulate resonant X-ray scattering cross sections2003In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 150, no 2, p. 85-98Article in journal (Refereed)
    Abstract [en]

    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.

  • 16.
    Scheffel, Jan
    et al.
    KTH, School of Electrical Engineering (EES), Fusion Plasma Physics.
    Lindvall, Kristoffer
    KTH, School of Electrical Engineering (EES), Fusion Plasma Physics.
    Yik, H. F.
    A time-spectral approach to numerical weather prediction2018In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 226, p. 127-135Article in journal (Refereed)
    Abstract [en]

    Finite difference methods are traditionally used for modelling the time domain in numerical weather prediction (NWP). Time-spectral solution is an attractive alternative for reasons of accuracy and efficiency and because time step limitations associated with causal CFL-like criteria, typical for explicit finite difference methods, are avoided. In this work, the Lorenz 1984 chaotic equations are solved using the time-spectral algorithm GWRM (Generalized Weighted Residual Method). Comparisons of accuracy and efficiency are carried out for both explicit and implicit time-stepping algorithms. It is found that the efficiency of the GWRM compares well with these methods, in particular at high accuracy. For perturbative scenarios, the GWRM was found to be as much as four times faster than the finite difference methods. A primary reason is that the GWRM time intervals typically are two orders of magnitude larger than those of the finite difference methods. The GWRM has the additional advantage to produce analytical solutions in the form of Chebyshev series expansions. The results are encouraging for pursuing further studies, including spatial dependence, of the relevance of time-spectral methods for NWP modelling. Program summary: Program Title: Time-adaptive GWRM Lorenz 1984 Program Files doi: http://dx.doi.org/10.17632/4nxfyjj7nv.1 Licensing provisions: MIT Programming language: Maple Nature of problem: Ordinary differential equations with varying degrees of complexity are routinely solved with numerical methods. The set of ODEs pertaining to chaotic systems, for instance those related to numerical weather prediction (NWP) models, are highly sensitive to initial conditions and unwanted errors. To accurately solve ODEs such as the Lorenz equations (E. N. Lorenz, Tellus A 36 (1984) 98–110), small time steps are required by traditional time-stepping methods, which can be a limiting factor regarding the efficiency, accuracy, and stability of the computations. Solution method: The Generalized Weighted Residual Method, being a time-spectral algorithm, seeks to increase the time intervals in the computation without degrading the efficiency, accuracy, and stability. It does this by postulating a solution ansatz as a sum of weighted Chebyshev polynomials, in combination with the Galerkin method, to create a set of linear/non-linear algebraic equations. These algebraic equations are then solved iteratively using a Semi Implicit Root solver (SIR), which has been chosen due to its enhanced global convergence properties. Furthermore, to achieve a desired accuracy across the entire domain, a time-adaptive algorithm has been developed. By evaluating the magnitudes of the Chebyshev coefficients in the time dimension of the solution ansatz, the time interval can either be decreased or increased.

  • 17. Shen, L. F.
    et al.
    He, Sailing
    KTH, Superseded Departments, Electromagnetic Theory.
    Xiao, S. S.
    A finite-difference eigenvalue algorithm for calculating the band structure of a photonic crystal2002In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 143, no 3, p. 213-221Article in journal (Refereed)
  • 18.
    Tholerus, Emmi
    et al.
    KTH, School of Electrical Engineering (EES), Fusion Plasma Physics.
    Johnson, Thomas
    KTH, School of Electrical Engineering (EES), Fusion Plasma Physics.
    Hellsten, Torbjörn
    KTH, School of Electrical Engineering (EES), Fusion Plasma Physics.
    FOXTAIL: Modeling the nonlinear interaction between Alfven eigenmodes and energetic particles in tokamaks2017In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 214, p. 39-51Article in journal (Refereed)
    Abstract [en]

    FOXTAIL is a new hybrid magnetohydrodynamic-kinetic code used to describe interactions between energetic particles and Alfven eigenmodes in tokamaks with realistic geometries. The code Simulates the nonlinear dynamics of the amplitudes of individual eigenmodes and of a set of discrete markers in five dimensional phase space representing the energetic particle distribution. Action angle coordinates of the equilibrium system are used for efficient tracing of energetic particles, and the particle acceleration by the wave fields of the eigenmodes is Fourier decomposed in the same angles. The eigenmodes are described using temporally constant eigenfunctions with dynamic complex amplitudes. Possible applications of the code are presented, e.g., making a quantitative validity evaluation of the one-dimensional bump-on-tail approximation of the system. Expected effects of the fulfillment of the Chirikov criterion in two-mode scenarios have also been verified.

  • 19.
    Tholerus, Emmi
    et al.
    KTH, School of Electrical Engineering (EES), Fusion Plasma Physics.
    Johnson, Thomas
    KTH, School of Electrical Engineering (EES), Fusion Plasma Physics.
    Hellsten, Torbjörn
    KTH, School of Electrical Engineering (EES), Fusion Plasma Physics.
    FOXTAIL: Modeling the nonlinear interaction between Alfvén eigenmodes and energetic particles in tokamaks2016In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944Article in journal (Refereed)
    Abstract [en]

    FOXTAIL is a new hybrid magnetohydrodynamic-kinetic code used to describe interactions between energetic particles and Alfvén eigenmodes in tokamaks with realistic geometries. The code simulates the nonlinear dynamics of the amplitudes of individual eigenmodes and of a set of discrete markers in five-dimensional phase space representing the energetic particle distribution. Action-angle coordinates of the equilibrium system are used for efficient tracing of energetic particles, and the particle acceleration by the wave fields of the eigenmodes is Fourier decomposed in the same angles. The eigenmodes are described using temporally constant eigenfunctions with dynamic complex amplitudes. Possible applications of the code are presented, e.g., making a quantitative validity evaluation of the one-dimensional bump-on-tail approximation of the system. Expected effects of the fulfillment of the Chirikov criterion in two-mode scenarios have also been verified.

  • 20. Wiklund, H. S.
    et al.
    Lindstrom, Stefan B.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Uesaka, T.
    Boundary condition considerations in lattice Boltzmann formulations of wetting binary fluids2011In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 182, no 10, p. 2192-2200Article in journal (Refereed)
    Abstract [en]

    We propose a new lattice Boltzmann numerical scheme for binary-fluid surface interactions. The new scheme combines the existing binary free energy lattice Boltzmann method [Swift et al., Phys. Rev. E 54 (1996)] and a new wetting boundary condition for diffuse interface methods in order to eliminate spurious variations in the order parameter at solid surfaces. We use a cubic form for the surface free energy density and also take into account the contribution from free energy in the volume when discretizing the wetting boundary condition. This allows us to eliminate the spurious variation in the order parameter seen in previous implementations. With the new scheme a larger range of equilibrium contact angles are possible to reproduce and capillary intrusion can be simulated at higher accuracy at lower resolution.

1 - 20 of 20
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