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1.
  • Brickner, R.G, et al. (författare)
  • QCD on the Connection Machine: Beyond-Lisp
  • 1991
  • Ingår i: Computer Physics Communications. - 0010-4655 .- 1879-2944. ; 65, s. 39-51
  • Tidskriftsartikel (refereegranskat)abstract
    •  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.
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2.
  • Edvardsson, Sverker, et al. (författare)
  • An atomic program for energy levels of equivalent electrons: lanthanides and actinides
  • 2001
  • Ingår i: Computer Physics Communications. - 0010-4655 .- 1879-2944. ; 133:2/3, s. 396-406
  • Tidskriftsartikel (refereegranskat)abstract
    • A program written in C is presented to carry out brute force calculations in order to derive energy levels for an equivalent electronic configuration. Relativistic effects are partly neglected except for the spin-orbit interaction. Since the main relativistic effects are indirect, i.e. causing a contraction of the core which in turn causes the outer shells to expand, they are included to a high degree through the use of appropriate Slater integrals. The program is especially useful for primarily unfilled f-shells of the rare-earth or actinide ions. Modifications of the program to include spin−spin, spin−other orbit, Breit interaction etc. is straight forward. The program is also general in the sense that there is no need to find out or generate any Racah coefficients of fractional parentage. The complete energy matrix is diagonalized with all operators interacting simultaneously thus allowing mixing of all quantum numbers. This result in all energy eigenvalues and eigenvectors that in turn for example are partly responsible for the polarized dipole, quadrupole, … transitions within the unfilled shell. Free ion configuration interaction is accounted for through the use of standard CI operators. The Stark splitting can be studied via the standard crystal field Hamiltonian. Magnetic field influence on the energy levels may also be studied.
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3.
  • Ishio, H., et al. (författare)
  • Wave function statistics for mesoscopic transport through chaotic open billiards : Time reversibility, space reciprocity breaking and statistical crossover
  • 2001
  • Ingår i: Computer Physics Communications. - 0010-4655 .- 1879-2944. ; 142:1-3, s. 64-70
  • Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
    • We investigate the probability distributions and spatial correlations of the local densities of electron wave functions for ballistic transport through mesoscopic chaotic open billiards. By quantitative comparison between our accurate fully-quantal calculations with theoretical expressions, we find wave-statistical behaviors intrinsically different from those in closed systems. It is shown that chaotic-scattering wave functions in open systems can be universally interpreted in terms of statistically independent real and imaginary random fields together with breaking of the endowed space reciprocity, resulting in the same wave function statistics as in the time-reversal symmetry-breaking crossover regime in closed systems. © 2001 Elsevier Science B.V. All rights reserved.
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4.
  • Jaun, André, et al. (författare)
  • Iterative solution of global electromagnetic wavefields with finite elements
  • 2001
  • Ingår i: Computer Physics Communications. - 0010-4655 .- 1879-2944. ; 135:1, s. 74-81
  • Tidskriftsartikel (refereegranskat)abstract
    • 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.
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5.
  • Johnsson, Lennart (författare)
  • Cyclic Reduction on a Binary Tree
  • 1985
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 37:1-3, s. 195-203
  • Tidskriftsartikel (refereegranskat)abstract
    • 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.
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6.
  • Jönsson, Per, et al. (författare)
  • A program for computing weak and intermediate field Zemman splittings from MCHF wave functions
  • 2002
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 144:2, s. 188-199
  • Tidskriftsartikel (refereegranskat)abstract
    • Given electronic wave functions generated by the MCHF_CI program (LSJ format), this program calculates diagonal Landé g factors that determine separations of magnetic sublevels in weak external magnetic fields. In addition the program computes off-diagonal Landé g factors and constructs the total interaction matrix for an atom in a magnetic field. By diagonalizing the interaction matrix and plotting the eigenvalues as functions of the magnetic field, Zeeman structures beyond the weak field limit are obtained.
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7.
  • Levitina, Tatiana, et al. (författare)
  • On the Schrödinger equation in ellipsoidal coordinates
  • 2000
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 126:1-2, s. 107-113
  • Tidskriftsartikel (refereegranskat)abstract
    • Quantum scattering by a potential separable in ellipsoidal coordinates is investigated. If the potential vanishes at infinity fast enough, its scattering data – S-matrix, far field amplitude, and total cross-section – are expanded in perturbed Lamé wave functions.
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8.
  • Salek, Pawel (författare)
  • A wave-packet technique to simulate resonant X-ray scattering cross sections
  • 2003
  • Ingår i: Computer Physics Communications. - 0010-4655 .- 1879-2944. ; 150:2, s. 85-98
  • Tidskriftsartikel (refereegranskat)abstract
    • 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.
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9.
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10.
  • Thibert-Plante, Xavier, 1980-, et al. (författare)
  • A simple spectral algorithm for solving large-scale Poisson equation in 2D
  • 2003
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 154:2, s. 89-97
  • Tidskriftsartikel (refereegranskat)abstract
    • We show that it is possible with easy-to-program algorithms to reach spatial resolutions of the order of 108 grid points for computing the electric potential on 2D periodic lattices, such as the Si(111)7×7 surface. We have used a spectral Fourier technique and parallelized FFTs with OPEN_MP on SGI machines. This method can be easily extended to 3D.
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11.
  • Abbasi, R., et al. (författare)
  • LeptonInjector and LeptonWeighter : A neutrino event generator and weighter for neutrino observatories
  • 2021
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 266
  • Tidskriftsartikel (refereegranskat)abstract
    • We present a high-energy neutrino event generator, called LeptonInjector, alongside an event weighter, called LeptonWeighter. Both are designed for large-volume Cherenkov neutrino telescopes such as IceCube. The neutrino event generator allows for quick and flexible simulation of neutrino events within and around the detector volume, and implements the leading Standard Model neutrino interaction processes relevant for neutrino observatories: neutrino-nucleon deep-inelastic scattering and neutrino-electron annihilation. In this paper, we discuss the event generation algorithm, the weighting algorithm, and the main functions of the publicly available code, with examples.
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12.
  • Alber, Lukas, et al. (författare)
  • NTMpy : An open source package for solving coupled parabolic differential equations in the framework of the three-temperature model
  • 2021
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 265
  • Tidskriftsartikel (refereegranskat)abstract
    • The NTMpy code package allows for simulating the one-dimensional thermal response of multilayer samples after optical excitation, as in a typical pump-probe experiment. Several Python routines are combined and optimized to solve coupled heat diffusion equations in one dimension, on arbitrary piecewise homogeneous material stacks, in the framework of the so-called three-temperature model. The energy source deposited in the material is modelled as a light pulse of arbitrary cross-section and temporal profile. A transfer matrix method enables the calculation of realistic light absorption in presence of scattering interfaces as in multilayer samples. The open source code is fully object-oriented to enable a user-friendly and intuitive interface for adjusting the physically relevant input parameters. Here, we describe the mathematical background of the code, we lay out the workflow, and we validate the functionality of our package by comparing it to commercial software, as well as to experimental transient reflectivity data recorded in a pump-probe experiment with femtosecond light pulses.
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13.
  • Andersson, Martin, et al. (författare)
  • HFSZEEMAN - A program for computing weak and intermediate field fine and hyperfine structure Zeeman splittings from MCDHF wave functions
  • 2008
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 178:2, s. 156-170
  • Tidskriftsartikel (refereegranskat)abstract
    • Given electronic wave functions generated by the grasp2K relativistic atomic structure package, this program calculates diagonal magnetic dipole A(J) and electric quadrupole B-J hyperfine interaction constants and Lande g(J) factors. In addition the program computes diagonal and off-diagonal reduced hyperfine and Zeeman matrix elements and constructs the total interaction matrix for an atom in an external magnetic field. By diagonalizing the interaction matrix and plotting eigenvalues as functions of the magnetic field, Zeeman splittings of hyperfine levels are obtained. The method is applicable in the weak and intermediate field regions and yields results that are useful when analyzing spectra from e.g. EBIT sources and magnetic stars. The program can also be used in the field free limit to calculate mixing coefficients that determine rates of hyperfine induced transitions. For atoms with zero nuclear spin I the program computes splittings of the fine-structure levels. Program summary Program title: HFSZEEMAN Catalogue identifier: ADZS_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADZS-v1-0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1528 No. of bytes in distributed program, including test data, etc.: 294 664 Distribution format: tar.gz Programming language: Fortran, Matlab Computer: IBM-compatible PC, unix workstation Operating system: Unix, Linux Classification: 11.6 Subprograms used: Cat Id: ADZL_v1_0; Title: grasp2K v1.0; Reference: CPC 177 (2007) 597 Nature of problem: Prediction of weak and intermediate field Zeeman splittings of fine- and hyperfine structure levels using multiconfiguration Dirac-Hartree-Fock wave functions. Solution method: The electronic wave function for a state labeled Gamma JM is expanded in terms of jj-coupled configuration state functions vertical bar Gamma JM > = Sigma(gamma)c(gamma)vertical bar gamma JM >. In this representation the reduced matrix elements used to construct the interaction matrix can be computed as sums over one-particle radial integrals. By diagonalizing the interaction matrix and plotting eigenvalue as functions of the magnetic field, Zeeman splittings of fine- and hyperfine structure levels are obtained. Restrictions: The complexity of the cases that can be handled is entirely determined by the grasp2K package [P. Jonsson, H. Xe, C. Froese Fischer, I.P. Grant, Comput. Phys. Commun. 177 (2007) 597] used for the generation of the electronic wave functions. Running time: CPU time required to execute test cases: a few seconds.
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14.
  • Appel, L. C., et al. (författare)
  • Equilibrium reconstruction in an iron core tokamak using a deterministic magnetisation model
  • 2018
  • Ingår i: Computer Physics Communications. - : ELSEVIER. - 0010-4655 .- 1879-2944. ; 223, s. 1-17
  • Tidskriftsartikel (refereegranskat)abstract
    • In many tokamaks ferromagnetic material, usually referred to as an iron-core, is present in order to improve the magnetic coupling between the solenoid and the plasma. The presence of the iron core in proximity to the plasma changes the magnetic topology with consequent effects on the magnetic field structure and the plasma boundary. This paper considers the problem of obtaining the free-boundary plasma equilibrium solution in the presence of ferromagnetic material based on measured constraints. The current approach employs, a model described by O'Brien et al. (1992) in which the magnetisation currents at the iron-air boundary are represented by a set of free parameters and appropriate boundary conditions are enforced via a set of quasi-measurements on the material boundary. This can lead to the possibility of overfitting the data and hiding underlying issues with the measured signals. Although the model typically achieves good fits to measured magnetic signals there are significant discrepancies in the inferred magnetic topology compared with other plasma diagnostic measurements that are independent of the magnetic field. An alternative approach for equilibrium reconstruction in iron-core tokamaks, termed the deterministic magnetisation model is developed and implemented in EFIT++. The iron is represented by a boundary current with the gradients in the magnetisation dipole state generating macroscopic internal magnetisation currents. A model for the boundary magnetisation currents at the iron-air interface is developed using B-Splines enabling continuity to arbitrary order; internal magnetisation currents are allocated to triangulated regions within the iron, and a method to enable adaptive refinement is implemented. The deterministic model has been validated by comparing it with a synthetic 2-D electromagnetic model of JET. It is established that the maximum field discrepancy is less than 1.5 mT throughout the vacuum region enclosing the plasma. The discrepancies of simulated magnetic probe signals are accurate to within 1% for signals with absolute magnitude greater than 100 mT; in all other cases agreement is to within 1 mT. The effect of neglecting the internal magnetisation currents increases the maximum discrepancy in the vacuum region to >20 mT, resulting in errors of 5%-10% in the simulated probe signals. The fact that the previous model neglects the internal magnetisation currents (and also has additional free parameters when fitting the measured data) makes it unsuitable for analysing data in the absence of plasma current. The discrepancy of the poloidal magnetic flux within the vacuum vessel is to within 0.1 Wb. Finally the deterministic model is applied to an equilibrium force-balance solution of a JET discharge using experimental data. It is shown that the discrepancies of the outboard separatrix position, and the outer strike-point position inferred from Thomson Scattering and Infrared camera data are much improved beyond the routine equilibrium reconstruction, whereas the discrepancy of the inner strike-point position is similar.
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15.
  • Araujo, M. V., et al. (författare)
  • Lorenzetti Showers- A general-purpose framework for supporting signal reconstruction and triggering with calorimeters
  • 2023
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 286
  • Tidskriftsartikel (refereegranskat)abstract
    • Calorimeters play an important role in high-energy physics experiments. Their design includes electronic instrumentation, signal processing chain, computing infrastructure, and also a good understanding of their response to particle showers produced by the interaction of incoming particles. This is usually supported by full simulation frameworks developed for specific experiments so that their access is restricted to the collaboration members only. Such restrictions limit the general-purpose developments that aim to propose innovative approaches to signal processing, which may include machine learning and advanced stochastic signal processing models. This work presents the Lorenzetti Showers, a general-purpose framework that mainly targets supporting novel signal reconstruction and triggering strategies using segmented calorimeter information. This framework fully incorporates developments down to the signal processing chain level (signal shaping, energy estimation, and noise mitigation techniques) to allow advanced signal processing approaches in modern calorimetry and triggering systems. The developed framework is flexible enough to be extended in different directions. For instance, it can become a tool for the phenomenology community to go beyond the usual detector design and physics process generation approaches. Program summary Program Title: Lorenzetti Showers CPC Library link to program files: https://doi .org /10 .17632 /sy64367452 .1 Developer's repository link: https://github .com /lorenzetti -hep /lorenzetti Licensing provisions: GPLv3 Programming language: Python, C++. Nature of problem: In experimental high-energy physics, simulation is essential for experiment preparation, design and interpretations of ongoing acquisitions. Especially for calorimeters, an accurate simulation that can describe detector geometry, behavior to different physics processes and signal generation close to the readout electronics and data acquisition levels is required to properly develop signal processing and computational methods. Such detectors may face very challenging demands arising from the new designs, such as pileup mitigation and noise reduction tasks under unprecedented levels. In this sense, simulation requirements continuously increase in complexity and performance, because new physics searches require large datasets and accurate modeling to experimental effects. Solution method: The Lorenzetti Showers is an integrated software framework that provides complete calorimeter information close enough to the electronic readout chain. Thus, the proposed framework allows users to access cell readout values, configurable sensor pulse-shapes, crosstalk modeling, and different energy estimation methods. It aims at supporting designs that target low or high pileup operation conditions in an easy-to-use modular structure. The developed framework is based on Pythia 8 (particle generation) and Geant4 (interactions with the calorimeter technique under analysis). An efficient data recording structure was used to allow full access to the Lorenzetti Showers outputs. In summary, the Lorenzetti Showers tool provides to the scientific community a user-friendly, flexible, user-oriented, and low-level calorimeter simulation framework. Additional comments including restrictions and unusual features: The framework current version provides the implementation of a generic segmented calorimeter (electromagnetic and hadronic sections), which may be modified by the user, if desired. It allows the generation of particles interactions using Pythia 8 (native) or any generator compatible with the HepMC format (which may be integrated using an external input file) and propagation through a user-configurable calorimeter using Geant4.
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16.
  • Barrio, Roberto, et al. (författare)
  • A database of rigorous and high-precision periodic orbits of the Lorenz model
  • 2015
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 194, s. 76-83
  • Tidskriftsartikel (refereegranskat)abstract
    • A benchmark database of very high-precision numerical and validated initial conditions of periodic orbits for the Lorenz model is presented. This database is a "computational challenge" and it provides the initial conditions of all periodic orbits of the Lorenz model up to multiplicity 10 and guarantees their existence via computer-assisted proofs methods, The orbits are computed using high-precision arithmetic and mixing several techniques resulting in 1000 digits of precision on the initial conditions of the periodic orbits, and intervals of size 10100 that prove the existence of each orbit. Program summary Program title: Lorenz-Database Catalogue identifier: AEWM_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEWM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 8515 No. of bytes in distributed program, including test data, etc.: 6964501 Distribution format: tar.gz Programming language: Data. Computer: Any computer. Operating system: Any. RAM: Database, no requirements Classification: 4.3, 4.12. Nature of problem: Database of all periodic orbits of the Lorenz model up to multiplicity 10 with 1000 precision digits. Solution method: Advanced search methods for locating unstable periodic orbits combined with the Taylor series method for multiple precision integration of ODEs and interval methods for providing Computer-Assisted proofs of the periodic orbits. Unusual features: The database gives 100 digits rigorously proved using Computer-Assisted techniques and 1000 digits using an optimal adaptive Taylor series method. Running time: Not Applicable.
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17.
  • Béland, Laurent Karim, et al. (författare)
  • Accurate classical short-range forces for the study of collision cascades in Fe-Ni-Cr
  • 2017
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 219, s. 11-19
  • Tidskriftsartikel (refereegranskat)abstract
    • The predictive power of a classical molecular dynamics simulation is largely determined by the physical validity of its underlying empirical potential. In the case of high-energy collision cascades, it was recently shown that correctly modeling interactions at short distances is necessary to accurately predict primary damage production. An ab initio based framework is introduced for modifying an existing embedded atom method FeNiCr potential to handle these short-range interactions. Density functional theory is used to calculate the energetics of two atoms approaching each other, embedded in the alloy, and to calculate the equation of state of the alloy as it is compressed. The pairwise terms and the embedding terms of the potential are modified in accordance with the ab initio results. Using this reparametrized potential, collision cascades are performed in Ni50Fe50, Ni80Cr20 and Ni33Fe33Cr33. The simulations reveal that alloying Ni and NiCr to Fe reduces primary damage production, in agreement with some previous calculations. Alloying Ni and NiFe to Cr does not reduce primary damage production, in contradiction with previous calculations.
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18.
  • Bessarab, Pavel F., et al. (författare)
  • Method for finding mechanism and activation energy of magnetic transitions, applied to skyrmion and antivortex annihilation
  • 2015
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 196, s. 335-347
  • Tidskriftsartikel (refereegranskat)abstract
    • 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.
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19.
  • Bezshyyko, Oleg, et al. (författare)
  • PETAG01 : A Program for the Direct Simulation of a Pellet Target
  • 2008
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 178:2, s. 144-155
  • Tidskriftsartikel (refereegranskat)abstract
    • We describe a numerical model of an internal pellet target to study the beam dynamics in storage rings, where the nuclear experiments with such type of target are planned. In this model the Monte Carlo algorithm is applied to evaluate the particle coordinates and momentum deviation depending on time and parameters of the target. One has to mention that due to statistical character of the pellet distribution in the target the analytical techniques are not applicable. This is also true for the particle distribution in the stored beam, which is influenced by various effects (such as a cooling process, intra-beam scattering, betatron oscillation, space charge effect). In this case only the Monte Carlo technique to model energy straggling in combination with the pellet distribution in the target should be considered. Program summary Program title: PETAG01 Catalogue identifier: ADZV_v1_0 Program summary URL: http://cpc.es.qub.ac.uk/summaries/ADZV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1068 No. of bytes in distributed program, including test data, etc.: 11314 Distribution format: tar.gz Programming language: Fortran 77, C/C++ Computer: Platform independent Operating system: MS Windows 95/2000/XP, Linux (Unix) RAM: 128 MB Classification: 11.10 Nature of problem: Particle beam dynamics with use of the pellet target. Solution method: Monte Carlo with analytical approximation. Running time: dozens of seconds
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20.
  • Blennow, Mattias, 1980-, et al. (författare)
  • Neutrino oscillation parameter sampling with MonteCUBES
  • 2010
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 181:1, s. 227-231
  • Tidskriftsartikel (refereegranskat)abstract
    • 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.
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21.
  • Brändas, Erkki J., et al. (författare)
  • Filter Diagonalization : filtering and postprocessing with prolates.
  • 2009
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 180:9, s. 1448-1457
  • Tidskriftsartikel (refereegranskat)abstract
    • A detailed account is given of a recent modification of the Filter Diagonalization technique that serves to analyze a signal spectrum within a selected energy range. Our approach employs for filtering the eigenfunctions of the Finite Fourier Transform, or prolates, which are superior to other filters due to their special properties. In particular, prolates are simultaneously band-limited and highly concentrated at a finite time-interval, producing filters with optimal accuracy. In addition both features are acquired by the convolution of a band-limited function with a prolate, that permits the latter to be interpolated via the Walter and Shen sampling formula, which essentially simplifies the supplementary computations. Rigorous filtering error estimates are obtained. Test calculations illustrate the facilities of the presented modification.
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22.
  • Bzowski, Adam (författare)
  • TripleK : A Mathematica package for evaluating triple-K integrals and conformal correlation functions
  • 2021
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 258
  • Tidskriftsartikel (refereegranskat)abstract
    • I present a Mathematica package designed for manipulations and evaluations of triple-K integrals and conformal correlation functions in momentum space. Additionally, the program provides tools for evaluation of a large class of 2- and 3-point massless multi-loop Feynman integrals with generalized propagators. The package is accompanied by five Mathematica notebooks containing detailed calculations of numerous conformal 3-point functions in momentum space.
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23.
  • Crialesi-Esposito, Marco, et al. (författare)
  • FluTAS : A GPU-accelerated finite difference code for multiphase flows
  • 2023
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 284
  • Tidskriftsartikel (refereegranskat)abstract
    • We present the Fluid Transport Accelerated Solver, FluTAS, a scalable GPU code for multiphase flows with thermal effects. The code solves the incompressible Navier-Stokes equation for two-fluid systems, with a direct FFT-based Poisson solver for the pressure equation. The interface between the two fluids is represented with the Volume of Fluid (VoF) method, which is mass conserving and well suited for complex flows thanks to its capacity of handling topological changes. The energy equation is explicitly solved and coupled with the momentum equation through the Boussinesq approximation. The code is conceived in a modular fashion so that different numerical methods can be used independently, the existing routines can be modified, and new ones can be included in a straightforward and sustainable manner. FluTAS is written in modern Fortran and parallelized using hybrid MPI/OpenMP in the CPU-only version and accelerated with OpenACC directives in the GPU implementation. We present different benchmarks to validate the code, and two large-scale simulations of fundamental interest in turbulent multiphase flows: isothermal emulsions in HIT and two-layer Rayleigh-Bénard convection. FluTAS is distributed through a MIT license and arises from a collaborative effort of several scientists, aiming to become a flexible tool to study complex multiphase flows. Program summary: Program Title: : Fluid Transport Accelerated Solver, FluTAS. CPC Library link to program files: https://doi.org/10.17632/tp6k8wky8m.1 Developer's repository link: https://github.com/Multiphysics-Flow-Solvers/FluTAS.git. Licensing provisions: MIT License. Programming language: Fortran 90, parallelized using MPI and slab/pencil decomposition, GPU accelerated using OpenACC directives. External libraries/routines: FFTW, cuFFT. Nature of problem: FluTAS is a GPU-accelerated numerical code tailored to perform interface resolved simulations of incompressible multiphase flows, optionally with heat transfer. The code combines a standard pressure correction algorithm with an algebraic volume of fluid method, MTHINC [1]. Solution method: the code employs a second-order-finite difference discretization and solves the two-fluid Navier-Stokes equation using a projection method. It can be run both on CPU-architectures and GPU-architectures.
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24.
  • Crialesi-Esposito, Marco, et al. (författare)
  • FluTAS: A GPU-accelerated finite difference code for multiphase flows
  • Ingår i: Computer Physics Communications. - 0010-4655 .- 1879-2944.
  • Tidskriftsartikel (refereegranskat)abstract
    • We present the Fluid Transport Accelerated Solver, FluTAS, a scalable GPU code for multiphase flows with thermal effects. The code solves the incompressible Navier-Stokes equation for two-fluid systems, with a direct FFT-based Poisson solver for the pressure equation. The interface between the two fluids is represented with the Volume of Fluid (VoF) method, which is mass conserving and well suited for complex flows thanks to its capacity of handling topological changes. The energy equation is explicitly solved and coupled with the momentum equation through the Boussinesq approximation. The code is conceived in a modular fashion so that different numerical methods can be used independently, the existing routines can be modified, and new ones can be included in a straightforward and sustainable manner. FluTAS is written in modern Fortran and parallelized using hybrid MPI/OpenMP in the CPU-only version and accelerated with OpenACC directives in the GPU implementation. We present different benchmarks to validate the code, and two large-scale simulations of fundamental interest in turbulent multiphase flows: isothermal emulsions in HIT and two-layer Rayleigh-Bénard convection. FluTAS is distributed through a MIT license and arises from a collaborative effort of several scientists, aiming to become a flexible tool to study complex multiphase flows.
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25.
  • Davidsson, Joel, 1989-, et al. (författare)
  • ADAQ : Automatic workflows for magneto-optical properties of point defects in semiconductors
  • 2021
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 269
  • Tidskriftsartikel (refereegranskat)abstract
    • Automatic Defect Analysis and Qualification (ADAQ) is a collection of automatic workflows developed for high-throughput simulations of magneto-optical properties of point defects in semiconductors. These workflows handle the vast number of defects by automating the processes to relax the unit cell of the host material, construct supercells, create point defect clusters, and execute calculations in both the electronic ground and excited states. The main outputs are the magneto-optical properties which include zero-phonon lines, zero-field splitting, and hyperfine coupling parameters. In addition, the formation energies are calculated. We demonstrate the capability of ADAQ by performing a complete characterization of the silicon vacancy in silicon carbide in the polytype 4H (4H-SiC).
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26.
  • Davis, Sergio, et al. (författare)
  • SearchFill : A stochastic optimization code for detecting atomic vacancies in crystalline and non-crystalline systems
  • 2011
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 182:5, s. 1105-1110
  • Tidskriftsartikel (refereegranskat)abstract
    • 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.
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27.
  • De Vanna, Francesco, et al. (författare)
  • URANOS-2.0: Improved performance, enhanced portability, and model extension towards exascale computing of high-speed engineering flows
  • 2024
  • Ingår i: Computer Physics Communications. - : Elsevier B.V.. - 0010-4655 .- 1879-2944. ; 303
  • Tidskriftsartikel (refereegranskat)abstract
    • We present URANOS-2.0, the second major release of our massively parallel, GPU-accelerated solver for compressible wall flow applications. This latest version represents a significant leap forward in our initial tool, which was launched in 2023 (De Vanna et al. [1]), and has been specifically optimized to take full advantage of the opportunities offered by the cutting-edge pre-exascale architectures available within the EuroHPC JU. In particular, URANOS-2.0 emphasizes portability and compatibility improvements with the two top-ranked supercomputing architectures in Europe: LUMI and Leonardo. These systems utilize different GPU architectures, AMD and NVIDIA, respectively, which necessitates extensive efforts to ensure seamless usability across their distinct structures. In pursuit of this objective, the current release adheres to the OpenACC standard. This choice not only facilitates efficient utilization of the full potential inherent in these extensive GPU-based architectures but also upholds the principles of vendor neutrality, a distinctive characteristic of URANOS solvers in the CFD solvers' panorama. However, the URANOS-2.0 version goes beyond the goals of improving usability and portability; it introduces performance enhancements and restructures the most demanding computational kernels. This translates into a 2× speedup over the same architecture. In addition to its enhanced single-GPU performance, the present solver release demonstrates very good scalability in multi-GPU environments. URANOS-2.0, in fact, achieves strong scaling efficiencies of over 80% across 64 compute nodes (256 GPUs) for both LUMI and Leonardo. Furthermore, its weak scaling efficiencies reach approximately 95% and 90% on LUMI and Leonardo, respectively, when up to 256 nodes (1024 GPUs) are considered. These significant performance advancements position URANOS-2.0 as a state-of-the-art supercomputing platform tailored for compressible wall turbulence applications, establishing the solver as an integrated tool for various aerospace and energy engineering applications, which can span from direct numerical simulations, wall-resolved large eddy simulations, up to most recent wall-modeled large eddy simulations. Program summary: Program title: Unsteady Robust All-around Navier-StOkes Solver (URANOS) CPC Library link to program files: https://doi.org/10.17632/pw5hshn9k6.2 Developer's repository link: https://github.com/uranos-gpu/uranos-gpu, https://github.com/uranos-gpu/uranos-gpu/tree/v2.0 Licensing provisions: BSD License 2.0 Programming language: Modern Fortran, OpenACC, MPI Nature of problem: Solving the compressible Navier-Stokes equations in a three-dimensional Cartesian framework. Solution method: Convective terms are treated with high-resolution shock-capturing schemes. The system dynamics is advanced in time with a three-stage Runge-Kutta method. Parallelization adopts MPI+OpenACC.
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28.
  • Dion, Claude, et al. (författare)
  • Ground state of the time-independent Gross–Pitaevskii equation
  • 2007
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 177:10, s. 787-798
  • Tidskriftsartikel (refereegranskat)abstract
    • We present a suite of programs to determine the ground state of the time-independent Gross–Pitaevskii equation, used in the simulation of Bose–Einstein condensates. The calculation is based on the Optimal Damping Algorithm, ensuring a fast convergence to the true ground state. Versions are given for the one-, two-, and three-dimensional equation, using either a spectral method, well suited for harmonic trapping potentials, or a spatial grid.
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29.
  • Dion, Claude, 1970-, et al. (författare)
  • Program for quantum wave-packet dynamics with time-dependent potentials
  • 2014
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 185:1, s. 407-414
  • Tidskriftsartikel (refereegranskat)abstract
    • We present a program to simulate the dynamics of a wave packet interacting with a time-dependent potential. The time-dependent Schrödinger equation is solved on a one-, two-, or three-dimensional spatial grid using the split operator method. The program can be compiled for execution either on a single processor or on a distributed-memory parallel computer.
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30.
  • Dion, Claude (författare)
  • Program for quantum wave-packet dynamics with time-dependent potentials (new version announcement)
  • 2023
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 291
  • Tidskriftsartikel (refereegranskat)abstract
    • Wavepacket is a program to simulate the dynamics of a wave packet interacting with a time-dependent potential, with the time-dependent Schrödinger equation being solved on a one-, two-, or three-dimensional spatial grid using the split operator method. This new version fixes bugs present in the original program.
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31.
  • Dolfi, Michele, et al. (författare)
  • Matrix Product State applications for the ALPS project
  • 2014
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 185:12, s. 3430-3440
  • Tidskriftsartikel (refereegranskat)abstract
    • The density-matrix renormalization group method has become a standard computational approach to the low-energy physics as well as dynamics of low-dimensional quantum systems. In this paper, we present a new set of applications, available as part of the ALPS package, that provide an efficient and flexible implementation of these methods based on a matrix product state (MPS) representation. Our applications implement, within the same framework, algorithms to variationally find the ground state and low-lying excited states as well as simulate the time evolution of arbitrary one-dimensional and two-dimensional models. Implementing the conservation of quantum numbers for generic Abelian symmetries, we achieve performance competitive with the best codes in the community. Example results are provided for (i) a model of itinerant fermions in one dimension and (ii) a model of quantum magnetism. PROGRAM SUMMARY Program title: ALPS MPS Catalogue identifier: AEUL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEUL_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Use of ‘mps optim’, ‘mps tevol’, ‘mps meas’ or ‘mps overlap’ requires citation of this paper. Use of any ALPS program requires citation of the ALPS [1] paper. No. of lines in distributed program, including test data, etc.: 373799 No. of bytes in distributed program, including test data, etc.: 2019043 Distribution format: tar.gz Programming language: C++, OpenMP for parallelization. Computer: PC, HPC cluster. Operating system: Any, tested on Linux, Mac OS X and Windows. Has the code been vectorized or parallelized?: Parallelized using OpenMP 1 to 24 processors used. RAM: 100 MB–100 GB. Classification: 7.7. External routines: ALPS [1, 2], BLAS/LAPACK, HDF5. Nature of problem: Solution of quantum many-body systems is generally a hard problem. The many-body Hilbert space grows exponentially with the system size which limits exact diagonalization results to only 20–40 spins, and the fermionic negative sign problem limits the Quantum Monte Carlo methods to a few special cases. Solution method: The matrix product states ansatz provides a controllable truncation of the Hilbert space which makes it currently the method of choice to investigate low-dimensional systems in condensed matter physics. Our implementation allows simulation of arbitrary one-dimensional and two-dimensional models and achieves performance competitive with the best codes in the community. We implement conservation of quantum numbers for generic Abelian symmetries. Running time: 10 s–8h per sweep. References: [1] B. Bauer, et al. (ALPS Collaboration), The ALPS project release 2.0: open source software for strongly correlated systems, J. Stat. Mech. 2011 (05) (2011) P05001. http://dx.doi.org/10.1088/1742-5468/2011/05/P05001. [2] http://alps.comp-phys.org.
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32.
  • Edvardsson, Sverker, et al. (författare)
  • A program for accurate solutions of two-electron atoms
  • 2004
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 165:3, s. 260-270
  • Tidskriftsartikel (refereegranskat)abstract
    • We present a comprehensible computer program capable of treating non-relativistic ground and excited states for a twoelectron atom having infinite nuclear mass. An iterative approach based on the implicitly restarted Arnoldi method (IRAM) is employed. The Hamiltonian matrix is never explicitly computed. Instead the action of the Hamiltonian operator on discrete pair functions is implemented. The finite difference method is applied and subsequent extrapolations gives the continuous grid result. The program is written in C and is highly optimized. All computations are made in double precision. Despite this relatively low degree of floating point precision (48 digits are not uncommon), the accuracy in the results can reach about 10 significant figures. Both serial and parallel versions are provided. The parallel program is particularly suitable for shared memory machines such as the Sun Starcat series. The serial version is simple to compile and should run on any platform.
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33.
  • Edvardsson, Sverker, et al. (författare)
  • corr3p_tr : A particle approach for the general three-body problem
  • 2016
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 200, s. 259-273
  • Tidskriftsartikel (refereegranskat)abstract
    • This work presents a convenient way to solve the non-relativistic Schrodinger equation numerically for a general three-particle system including full correlation and mass polarization. Both Coulombic and non-Coulombic interactions can be studied. The eigensolver is based on a second order dynamical system treatment (particle method). The Hamiltonian matrix never needs to be realized. The wavefunction evolves towards the steady state solution for which the Schrodinger equation is fulfilled. Subsequent Richardson extrapolations for several meshes are then made symbolically in matlab to obtain the continuum solution. The computer C code is tested under Linux 64 bit and both double and extended precision versions are provided. Test runs are exemplified and, when possible, compared with corresponding values in the literature. The computer code is small and self contained making it unusually simple to compile and run on any system. Both serial and parallel computer runs are straight forward. Program summary Program title: corr3p_tr Catalogue identifier: AEYR_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEYR_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.ukilicence/licence.html No. of lines in distributed program, including test data, etc.: 15025 No. of bytes in distributed program, including test data, etc.: 156430 Distribution format: tar.gz Programming language: ANSI C. Computer: Linux 64bit PC. Operating system: Linux 64bit. RAM: 300 M bytes Classification: 2.7, 2.8, 2.9. Nature of problem: The Schrodinger equation for an arbitrary three -particle system is solved using finite differences and a fast particle method for the eigenvalue problem [20, 21, 23]. Solution method: A fast eigensolver is applied (see Appendix). This solver works for both symmetrical and nonsymmetrical matrices (which opens up for more accurate nonsymmetrical finite difference expressions to be applied at the boundaries). The three-particle Schrodinger equation is transformed in two major steps. First step is to introduce the function Q(r(1), (r)2, mu) = r(1)r(2)(1 - mu(2))phi(r(1), r(2), mu), where mu = cos (0(12)). The cusps (r(1) = r(2), mu = 1) are then transformed into boundary conditions. The derivatives of Qare then continuous in the whole computational space and thus the finite difference expressions are well defined. Three-particle coalescence (r(1) = r(2) = 0, mu) is treated in the same way. The second step is to replace Q(r(1), r(2), mu) with (2,root x(1)x(2))(-1)Q(x(1) x(2), mu). The space (x(1), x(2), mu) is much more appropriate for a finite difference approach since the square roots x(1) = root r(1), x(2) = root r(2) allow the boundaries to be much further out. The non-linearity of the x-grid also leads to a finer description near the nucleus and a coarser one further out thus resulting in a saving of grid points. Also, in contrast to the usual variable r(12), we have instead used mu which is an independent variable. This simplifies the mathematics and numerical treatments. Several different grids can naturally run completely independent of each other thus making parallel computations trivial. From several grid results the physical property of interest is extrapolated to continuum space. The extrapolations are made in a matlab m-script where all computations can be made symbolically so the loss of decimal figures are minimized during this process. The computer code, including correlation effects and mass polarization, is highly optimized and deals with either triangular or quadratic domains in (x(1), x(2)). Restrictions: The amount of CPU time may become unreasonable for states needing boundary conditions very far beyond the origin. Also if the condition number of the corresponding Hamiltonian matrix is very high, the number of iterations will grow. The use of double precision computations also puts a limit on the accuracy of extrapolated results to about 6-7 decimal figures. Unusual features: The numerical solver is based on a particle method presented in [20, 21, 23]. In the Appendix we provide specific details of dealing with eigenvalue problems. The program uses a 64 bit environment (Linux 64bit). Parallel runs can be made conveniently through a simple bash script. Additional comments: The discretized wavefunction is complete on every given grid. New interactions can therefore conveniently be added to the Hamiltonian without the need to seek for an appropriate basis set. Running time: Given a modern CPU such as Intel core i5 and that the outer boundary conditions of r(1) and r(2) is limited to, say 16 atomic units, the total CPU time of totally 10 grids of a serial run is typically limited to a few minutes. One can then expect about 6-7 correct figures in the extrapolated eigenvalue. A single grid of say h(1) = h(2) = h(3) = 1/16 converges in less than 1 s (with an error in the eigenvalue of about 1 percent). Parallel runs are possible and can further minimize CPU times for more demanding tasks. References: [20] S. Edvardsson, M. Gulliksson, and J. Persson.). Appl. Mech. ASME, 79 (2012) 021012. [21] S. Edvardsson, M. Neuman, P Edstrom, and H. Olin. Comp. Phys. Commun. 197 (2015) 169. [23] M. Neuman, S. Edvardsson, P. Edstrom, Opt. Lett. 40 (2015) 4325.
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34.
  • Edvardsson, Sverker, et al. (författare)
  • Solving equations through particle dynamics
  • 2015
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 197, s. 169-181
  • Tidskriftsartikel (refereegranskat)abstract
    • The present work evaluates a recently developed particle method (DFPM). The basic idea behind this method is to utilize a Newtonian system of interacting particles that through dissipation solves mathematical problems. We find that this second order dynamical system results in an algorithm that is among the best methods known. The present work studies large systems of linear equations. Of special interest is the wide eigenvalue spectrum. This case is common as the discretization of the continuous problem becomes dense. The convergence rate of DFPM is shown to be in parity with that of the conjugate gradient method, both analytically and through numerical examples. However, an advantage with DFPM is that it is cheaper per iteration. Another advantage is that it is not restricted to symmetric matrices only, as is the case for the conjugate gradient method. The convergence properties of DFPM are shown to be superior to the closely related approach utilizing only a first order dynamical system, and also to several other iterative methods in numerical linear algebra. The performance properties are understood and optimized by taking advantage of critically damped oscillators in classical mechanics. Just as in the case of the conjugate gradient method, a limitation is that all eigenvalues (spring constants) are required to be of the same sign. DFPM has no other limitation such as matrix structure or a spectral radius as is common among iterative methods. Examples are provided to test the particle algorithm’s merits and also various performance comparisons with existent numerical algorithms are provided.
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35.
  • Ekman, Jörgen, et al. (författare)
  • RIS4 : A program for relativistic isotope shift calculations
  • 2019
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 235, s. 433-446
  • Tidskriftsartikel (refereegranskat)abstract
    • Spectral lines from different isotopes display a small separation in energy, commonly referred to as the line isotope shift. The program RIS4 (Relativistic Isotope Shift) calculates normal and specific mass shift parameters as well as field shift electronic factors from relativistic multiconfiguration Dirac-Hartree-Fock wave functions. These quantities, together with available nuclear data, determine isotope-dependent energy shifts. Using a reformulation of the field shift, it is possible to study, in a model-independent way, the atomic energy shifts arising from changes in nuclear charge distributions, e.g. deformations. (C) 2018 Published by Elsevier B.V.
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36.
  • Ekstedt, Andreas, et al. (författare)
  • DRalgo : A package for effective field theory approach for thermal phase transitions
  • 2023
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 288, s. 108725-
  • Tidskriftsartikel (refereegranskat)abstract
    • DRalgo is an algorithmic implementation that constructs an effective, dimensionally reduced, high-temperature field theory for generic models. The corresponding Mathematica package automatically performs the matching to next-to-leading order. This includes two-loop thermal corrections to scalar and Debye masses as well as one-loop thermal corrections to couplings. DRalgo also allows for integrating out additional heavy scalars. Along the way, the package provides leading-order beta functions for general gauge-charges and fermion-families; both in the fundamental and in the effective theory. Finally, the package computes the finite-temperature effective potential within the effective theory. The article explains the theory of the underlying algorithm while introducing the software on a pedagogical level.
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37.
  • Ekstrand, Joel (författare)
  • Lambda : A Mathematica-package for operator product expansions in vertex algebras
  • 2011
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 182:2, s. 409-418
  • Tidskriftsartikel (refereegranskat)abstract
    • We give an introduction to the Mathematica package Lambda, designed for calculating λ-brackets in both vertex algebras, and in SUSY vertex algebras. This is equivalent to calculating operator product expansions in two-dimensional conformal field theory. The syntax of λ-brackets is reviewed, and some simple examples are shown, both in component notation, and in N = 1 superfield notation.
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38.
  • Eliasson, Bengt (författare)
  • A nonuniform nested grid method for simulations of RF induced ionospheric turbulence
  • 2007
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 178, s. 8-14
  • Tidskriftsartikel (refereegranskat)abstract
    • We present a numerical scheme to simulate radio-frequency (RF) induced ionospheric turbulence, in which an electromagnetic wave is injected into the overhead ionospheric plasma. At the turning point of the ordinary mode, the electromagnetic wave undergoes linear mode-conversion to electrostatic Langmuir and upper hybrid waves that can have a much shorter wavelength than the electromagnetic wave. In order to resolve both the electromagnetic and electrostatic waves, avoiding severe restrictions on the time step due to the Courant–Friedrich–Lewy (CFL) condition, the equation of motion for the plasma particles is solved on a denser grid than that for the Maxwell equations near the mode-conversion region. An interpolation scheme is employed to calculate the electromagnetic field in the equation of motion of the plasma particles, and an averaging scheme is used to calculate the current density acting as a source in the Maxwell equation. Special care has to be taken to reduce numerical recurrence effects when the wavelength of the electrostatic wave is of the same order or shorter than the coarse grid spacing of the electromagnetic wave.
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39.
  • Eriksson, David, et al. (författare)
  • 2HDMC - two-Higgs-doublet model calculator
  • 2010
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 181:1, s. 189-205
  • Tidskriftsartikel (refereegranskat)abstract
    • We describe the public C++ code 2HDMC which can be used to perform calculations in a general, CP-conserving, two-Higgs-doublet model (2HDM). The program features simple conversion between different parametrizations of the 2HDM potential, a flexible Yukawa sector specification with choices of different Z_2-symmetries or more general couplings, a decay library including all two-body - and some three-body - decay modes for the Higgs bosons, and the possibility to calculate observables of interest for constraining the 2HDM parameter space, as well as theoretical constraints from positivity and unitarity. The latest version of the 2HDMC code and full documentation is available from: http://www.isv.uu.se/thep/MC/2HDMC.
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40.
  • Eriksson, Jacob, et al. (författare)
  • Calculating fusion neutron energy spectra from arbitrary reactant distributions
  • 2016
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 199, s. 40-46
  • Tidskriftsartikel (refereegranskat)abstract
    • The Directional Relativistic Spectrum Simulator (DRESS) code can perform Monte-Carlo calculations of reaction product spectra from arbitrary reactant distributions, using fully relativistic kinematics. The code is set up to calculate energy spectra from neutrons and alpha particles produced in the D(d, n)3He and T(d, n)4He fusion reactions, but any two-body reaction can be simulated by including the corresponding cross section. The code has been thoroughly tested. The kinematics calculations have been benchmarked against the kinematics module of the ROOT Data Analysis Framework. Calculated neutron energy spectra have been validated against tabulated fusion reactivities and against an exact analytical expression for the thermonuclear fusion neutron spectrum, with good agreement. The DRESS code will be used as the core of a detailed synthetic diagnostic framework for neutron measurements at the JET and MAST tokamaks.
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41.
  • Fan, Wenyuan, et al. (författare)
  • varRhoTurbVOF : A new set of volume of fluid solvers for turbulent isothermal multiphase flows in OpenFOAM
  • 2020
  • Ingår i: Computer Physics Communications. - : Elsevier B.V.. - 0010-4655 .- 1879-2944. ; 247
  • Tidskriftsartikel (refereegranskat)abstract
    • The volume of fluid (VOF) method is a popular approach for multiphase flow modeling. The open-source computational fluid dynamics (CFD) software, OpenFOAM, implements a variety of VOF-based solvers and provides users a wide range of turbulence models. Since isothermal multiphase flows under the VOF framework belong to the variable-density incompressible flow category, the isothermal VOF-based solvers in OpenFOAM fail to use the correct turbulence models. varRhoTurbVOF is designed to solve this issue and with the hope to replace all the corresponding existing solvers in the future. With the object-oriented paradigm, varRhoTurbVOF guarantees the usability, reusability and maintainability of the codes. Aside from turbulence modeling, all other features in the original solvers are preserved in varRhoTurbVOF. Program summary: Program Title: varRhoTurbVOF Program Files doi: http://dx.doi.org/10.17632/4t8z8vzyvs.1 Licensing provisions: GPLv3 Programming language: C++ Supplementary material: http://dx.doi.org/10.17632/7mp25kyb4p.4 Nature of problem: Under the VOF framework, the flow of the isothermal mixture belongs to the variable-density incompressible flow category. For such flows, VOF-based solvers of OpenFOAM fail to construct the correct governing equations for turbulence modeling. varRhoTurbVOF contains a set of newly designed VOF-based solvers which could use the desired governing equations for turbulence quantities. Solution method: varRhoTurbVOF creates a new class for variable-density incompressible turbulence models, which allows reusing the existing turbulence model template classes. A set of VOF-based solvers are then created to be able to construct variable-density incompressible turbulence models.
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42.
  • Fan, Wenyuan, et al. (författare)
  • varRhoTurbVOF 2 : Modified OpenFOAM volume of fluid solvers with advanced turbulence modeling capability
  • 2020
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 256
  • Tidskriftsartikel (refereegranskat)abstract
    • varRhoTurbVOF contains a set of OpenFOAM volume of fluid (VOF) solvers for turbulent isothermal multiphase flows, which are variable-density incompressible. Unlike their official counterparts, where Favre-averaged and Reynolds-averaged velocities coexist in different equations, new solvers use Favre-averaged velocities consistently in all equations. This major update introduces three main improvements to the previous version of varRhoTurbVOF. First, the implementation is extended to VOF solvers for isothermal and non-isothermal phase change two-phase flows, where the flow is no longer incompressible. Second, in order to introduce backward compatibility and to avoid code duplication, the turbulence model construction procedure is redesigned such that solvers can determine whether the variable-density effect is considered or not in the turbulence modeling part based on the input file at run time. Third, the Egorov turbulence damping model for omega-based turbulence models is implemented with its most recent developments. Plus, an extension to epsilon-based turbulence models is developed and implemented. Program summary Program Title: varRhoTurbVOF CPC Library link to program files: http://dx.doi.org/10.17632/4t8z8vzyvs.2 Developer's repository link: https://github.com/wenyuan- fan/varRhoTurbVOF_2 Licensing provisions: GPLv3 Programming language: C++ Journal reference of previous version: Wenyuan Fan, Henryk Anglart, 2020. varRhoTurbVOF: A new set of volume of fluid solvers for turbulent isothermal multiphase flows in OpenFOAM, Computer Physics Communications, 247, 106876. Does the new version supersede the previous version?: Yes Reasons for the new version: Implementation of new solvers and models; code redesign to maintain backward compatibility. Summary of revisions: The updated version mainly has three new features in comparison with the previous version: The issue addressed in [1] exists in all OpenFOAM VOF solvers where the variable-density effect is neglected in the turbulence modeling. In order to solve this issue for phase change VOF solvers, two additional solvers, namely, varRhoInterPhaseChangeFoam and varRhoInter CondensatingEvaporatingFoam, are implemented based on their official counterparts. The procedure of constructing the turbulence model inside individual solvers is redesigned. Using the new design, solvers will construct turbulence models with or without the variable-density effect being considered based on the user input. When the latter mode is activated, solvers will behave just like their official counterparts. In such a way, the backward compatibility of the code is achieved without introducing code duplications. The Egorov turbulence damping model [2], which is a popular approach to phenomenologically modify turbulence behaviors near a two-phase interface, is implemented. In addition to the original model, recent modifications, e.g., a new length scale calculation and asymmetric damping treatments [3], are implemented as well. The Egorov model only works with.-based turbulence models. In the new release, the model is extended to.-based turbulence models following the idea proposed in [4] such that the turbulence damping model is applicable to commonly used turbulence models. Nature of problem: Within the VOF framework, the mixture has a density changing with phases. However, in quite a few OpenFOAM VOF solvers, the variable-density effect is considered in the momentum equation but neglected in the turbulence modeling. As a result, Favre-averaged velocities and Reynolds-averaged velocities are used in the momentum equation and turbulence quantity equations, respectively and simultaneously, introducing a severe self-inconsistency. Solutions to this problem have been proposed in [1] with no backward compatibility support. Also, no phase change solvers are supported in the previous version. Another issue with turbulent VOF simulations is that, even with the correct implementation, certain modifications are still needed to correct the turbulence behavior around the interface. Solution method: The extension to phase change VOF solvers is straightforward according to [1]. Regarding the construction of turbulence models, two additional fields, namely, rhoTurb and rhoPhiTurb, are created and used in turbulence models. If the user chooses to use the variable-density turbulence models, real two-phase density rho and mass flux rhoPhi will be assigned to rhoTurb and rhoPhiTurb, respectively. Otherwise, rhoTurb and rhoPhiTurb will use unity and volume flux phi, respectively. This run time selection design enables solvers to operate in two modes, which guarantees the backward compatibility and avoids code duplications. The implementation of the turbulence damping model also takes the backward compatibility into account. At run time, the code will automatically determine whether the mixture density should be included in the turbulence damping model by checking the dimension of the corresponding equation. Additional comments: A manual is provided to introduce how the turbulence damping modeled is formulated and how to use the model. It should be emphasized that the Egorov damping model is a phenomenological model. Model parameters should be carefully selected for any given mesh and flow condition.
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43.
  • Fischer, Charlotte Froese, et al. (författare)
  • GRASP2018-A Fortran 95 version of the General Relativistic Atomic Structure Package
  • 2019
  • Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 237, s. 184-187
  • Tidskriftsartikel (refereegranskat)abstract
    • The present GRASP2018 is an updated Fortran 95 version of the recommended block versions of programs from GRASP2K Version 1_1 for large-scale calculations Jonsson et al. (2013). MPI programs are included so that all major tasks can be executed using parallel computers. Tools have been added that simplify the generation of configuration state function expansions for the multireference single- and double computational model. Names of programs have been changed to accurately reflect the task performed by the code. Modifications to the relativistic self-consistent field program have been made that, in some instances, greatly reduce the number of iterations needed for determining the requested eigenvalues and the memory required. Changes have been made to the relativistic configuration interaction program to substantially cut down on the time for constructing the Hamiltonian matrix for configuration state function expansions based on large ,orbital sets. In the case of a finite nucleus the grid points have been changed so that the first non-zero point is Z-dependent as for the point nucleus. A number of tools have been developed to generate LaTeX tables of eigenvalue composition, energies, transition data and lifetimes. Tools for plotting and analyzing computed properties along an iso-electronic sequence have also been added. A number of minor errors have been corrected. A detailed manual is included that describes different aspects of the package as well as the steps needed in order to produce reliable results. Program summary Program Title: GRAsp2018 Program Files doi: http://dx.doi.org/10.17632/x574wpp2vg.1 Licensing provisions: MIT license Programming language: Fortran 95. Nature of problem: Prediction of atomic properties - atomic energy levels, isotope shifts, oscillator strengths, radiative decay rates, hyperfine structure parameters, specific mass shift parameters, Zeeman effects - using a multiconfiguration Dirac-Hartree-Fock approach. Solution method: The computational method is the same as in the previous GRASP2K [1,2] version except that only the latest recommended versions of certain routines are included. Restrictions: All calculations are for bound state solutions. Instead of relying on packing algorithms for specifying arguments of arrays of integrals, orbitals are designated by a "short integer" requiring one byte of memory for a maximum of 127 orbitals. The tables of reduced coefficients of fractional parentage used in this version are limited to sub-shells with j <= 9/2 [3]; occupied sub-shells with j > 9/2 are, therefore, restricted to a maximum of two electrons. Some other parameters, such as the maximum number of orbitals are determined in a parameter_def _M.f 90 file that can be modified prior to compile time. Unusual features: Parallel versions are available for several applications. References [1] P. Jonsson, X. He, C. Froese Fischer, and I. P. Grant, Comput. Phys. Commun. 176, 597 (2007). [2] P. Jonsson, G. Gaigalas, J. Bieron, C. Froese Fischer, and I. P. Grant, Comput. Phys. Commun. 184, 2197 (2013). [3] G. Gaigalas, S. Fritzsche, Z. Rudzikas, Atomic Data and Nuclear Data Tables 76, 235 (2000). (C) 2018 Elsevier B.V. All rights reserved.
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44.
  • Galler, Anna, et al. (författare)
  • The AbinitioD Gamma A Project v1.0 : Non-local correlations beyond and susceptibilities within dynamical mean-field theory
  • 2019
  • Ingår i: Computer Physics Communications. - : ELSEVIER. - 0010-4655 .- 1879-2944. ; 245
  • Tidskriftsartikel (refereegranskat)abstract
    • The ab initio extension of the dynamical vertex approximation (D Gamma A) method allows for realistic materials calculations that include non-local correlations beyond GW and dynamical mean-field theory. Here, we discuss the AbinitioD Gamma A algorithm, its implementation and usage in detail, and make the program package available to the scientific community.Program summary: Program Title: AbinitioD Gamma A Program Files: doi: http : //dx doi org/10 17632/h3k3f g6szb. 1 Licensing provisions: GNU General Public License v3 Programming language: Fortran95 and Python Required dependencies: MPI, LAPACK, BLAS, HDF5 (>= 1.8.12), Python (> 2.7), h5py (>= 2.5.0), numpy (>= 1.9.1) Optional dependencies: pip, matplotlib (>= 1.5.1), scipy (>= 0.14.0) Supplementary material: Test case files and step-by-step instructions. Nature of problem: Realistic materials calculations including non-local correlations beyond dynamical mean-field theory (DMFT) as well as non-local interactions. Solving the Bethe-Salpeter equation for multiple orbitals. Determining momentum-resolved susceptibilities in DMFT.Solution method: Ab initio dynamical vertex approximation: starting from the local two-particle vertex and constructing from it the local DMFT correlations, the GW diagrams, and further non-local correlations, e.g., spin fluctuations. Efficient solution of the Bethe-Salpeter equation, avoiding divergencies in the irreducible vertex in the particle-hole channel by reformulating the problem in terms of the full vertex. Parallelization with respect to the bosonic frequency and transferred momentum. Additional comments including restrictions and unusual features: As input, a Hamiltonian derived, e.g., from density functional theory and a DM Gamma T solution thereof is needed including a local two-particle vertex calculated at DMFT self-consistency. Hitherto the AbinitioD Gamma A program package is restricted to SU(2) symmetric problems. A so-called lambda correction or self-consistency is not yet implemented in the AbinitioD Gamma A code. Susceptibilities are so far only calculated within DM Gamma T, not the dynamical vertex approximation. 
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45.
  • Gao, Jiacheng, et al. (författare)
  • Irvsp : To obtain irreducible representations of electronic states in the VASP
  • 2021
  • Ingår i: Computer Physics Communications. - : ELSEVIER. - 0010-4655 .- 1879-2944. ; 261
  • Tidskriftsartikel (refereegranskat)abstract
    • We present an open-source program irvsp, to compute irreducible representations of electronic states for all 230 space groups with an interface to the Vienna ab-initio Simulation Package. This code is fed with plane-wave-based wavefunctions (e.g. WAVECAR) and space group operators (listed in OUTCAR), which are generated by the VASP package. This program computes the traces of matrix presentations and determines the corresponding irreducible representations for all energy bands and all the k-points in the three-dimensional Brillouin zone. It also works with spin-orbit coupling (SOC), i.e., for double groups. It is in particular useful to analyze energy bands, their connectivities, and band topology, after the establishment of the theory of topological quantum chemistry. Accordingly, the associated library -irrep_bcs.a - is developed, which can be easily linked to by other ab-initio packages. In addition, the program has been extended to orthogonal tight-binding (TB) Hamiltonians, e.g. electronic or phononic TB Hamiltonians. A sister program is presented as well. Program summary Program title: irvsp CPC Library link to program files: http://doi.org/10.1763/y9ds5nnm2f.1 Licensing provisions: GNU Lesser General Public License Programming language: Fortran 90/77 Nature of problem: Determining irreducible representations for all energy bands and all the k-points in 230 space groups. It is in particular useful to analyze energy bands, their connectivities, and band topology. Solution method: By computing the traces of matrix presentations of space group operators for the eigen-wavefunctions at a certain k-point in a given space group, one can determine irreducible representations for them.
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46.
  • Gariazzo, S., et al. (författare)
  • PArthENoPE revolutions
  • 2022
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 271
  • Tidskriftsartikel (refereegranskat)abstract
    • This paper presents the main features of a new and updated version of the program PArthENoPE, which the community has been using for many years for computing the abundances of light elements produced during Big Bang Nucleosynthesis. This is the third release of the PArthENoPE code, after the 2008 and the 2018 ones, and will be distributed from the code's website, http://parthenope.na.infn.it. Apart from minor changes, the main improvements in this new version include a revisited implementation of the nuclear rates for the most important reactions of deuterium destruction, 2H(p,γ)3He, 2H(d, n)3He and 2H(d, p)3H, and a re-designed GUI, which extends the functionality of the previous one. The new GUI, in particular, supersedes the previous tools for running over grids of parameters with a better management of parallel runs, and it offers a brand-new set of functions for plotting the results.
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47.
  • Georgoudis, Alessandro, et al. (författare)
  • AZURITE : An algebraic geometry based package for finding bases of loop integrals
  • 2017
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 221, s. 203-215
  • Tidskriftsartikel (refereegranskat)abstract
    • For any given Feynman graph, the set of integrals with all possible powers of the propagators spans a vector space of finite dimension. We introduce the package AZURITE (A ZURich-bred method for finding master InTEgrals), which efficiently finds a basis of this vector space. It constructs the needed integration by-parts (IBP) identities on a set of generalized-unitarity cuts. It is based on syzygy computations and analyses of the symmetries of the involved Feynman diagrams and is powered by the computer algebra systems SINGULAR and MATHEMATICA. It can moreover analytically calculate the part of the IBP identities that is supported on the cuts. In some cases, the basis obtained by AZURITE may be slightly overcomplete.Program summaryProgram Title: AZURITELicensing provisions: GNU General Public License (GPL)Programming language: Wolfram MATHEMATICA version 10.0 or higherSupplementary material: A manual in the form of a MATHEMATICA notebookNature of problem: Determination of a basis of the space of loop integrals spanned by a given Feynman diagram and all of its subdiagramsSolution method: MATHEMATICA implementation.
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48.
  • Gonoskov, Ivan, et al. (författare)
  • Single-step propagators for calculation of time evolution in quantum systems with arbitrary interactions
  • 2016
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 202, s. 211-215
  • Tidskriftsartikel (refereegranskat)abstract
    • We propose and develop a general method of numerical calculation of the wave function time evolution in a quantum system which is described by Hamiltonian of an arbitrary dimensionality and with arbitrary interactions. For this, we obtain a general n-order single-step propagator in closed-form, which could be used for the numerical solving of the problem with any prescribed accuracy. We demonstrate the applicability of the proposed approach by considering a quantum problem with non-separable time-dependent Hamiltonian: the propagation of an electron in focused electromagnetic field with vortex electric field component.
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49.
  • Guan, Xin, et al. (författare)
  • An iterative approach for the exact solution of the pairing Hamiltonian
  • 2022
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 275
  • Tidskriftsartikel (refereegranskat)abstract
    • A new iterative algorithm is established for the exact solution of the standard pairing problem, based on the Richardson-Gaudin method using the polynomial approach. It provides efficient and robust solutions for both spherical and deformed systems at a large scale. The key to its success is that the initial guess for the solutions of such a large set of the non-linear equations is provided in a physically meaningful and controllable manner. Moreover, one reduces the large-dimensional problem to a one-dimensional Monte Carlo sampling procedure, which improves the algorithm's efficiency and avoids the non-solutions and numerical instabilities that persist in most existing approaches. We calculated the ground state and low-lying excited states of equally spaced systems at different pairing strengths G. We then applied the model to study the quantum phase transitional Sm isotopes and the actinide nuclei Pu isotopes, where an excellent agreement with experimental data is obtained. Program summary Program Title: IterV1.m CPC Library link to program files: https://doi.org/10.17632/rjnbhgk2p6.1 Licensing provisions: GPLv3 Programming language: Mathematica Nature of problem: The program calculates exact pairing energies based on a new iterative algorithm. The key is the procedure of determining the initial guesses for the large-set non-linear equations involved in a controllable and physically motivated manner. It provides an efficient and robust solver for both spherical and deformed systems in super large model spaces. Solution method: The new iterative algorithm approach starts with simple systems with knucleon pairs and n = klevels, which can be solved iteratively by including one pair and one level at each step using the Newton-Raphson algorithm with a Monte Carlo sampling procedure. Then it takes the solutions of those systems as initial values and obtain the converged results for the full space by gradually adding the remaining levels. In this way, one reduces the k-dimensional Monte Carlo sampling procedure to a one-dimensional sampling, which improves the efficiency of the algorithm and avoids the non-solutions and numerical instabilities.
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50.
  • Hua, Weijie (författare)
  • MCNOX : A code for computing and interpreting ultrafast nonlinear X-ray spectra of molecules at the multiconfigurational level
  • 2024
  • Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 296
  • Tidskriftsartikel (refereegranskat)abstract
    • This work describes a program for computing and analyzing the ultrafast (attosecond and femtosecond) nonlinear X-ray spectra of molecules at the multiconfigurational quantum chemistry level, called MCNOX. It is aimed at cutting-edge current and future photochemistry/photophysics applications enabled by X-ray free-electron lasers and high harmonic generation light sources. It can compute steady-state X-ray absorption spectroscopy (XAS) and three types of ultrafast nonlinear X-ray spectra: transient XAS, all-X-ray four-wave mixing, and stimulated Raman spectra. It is especially capable of picking out major electronic transitions, and further computing the natural transition orbitals for these transitions, which help finally yield the physical and chemical insights from complex signals. Following a research paradigm of "electronic structure-*molecular dynamics-*signal", in this paper, methods for the former two steps are reviewed, and then the theory, implementations, and technical details for signal simulations are presented along illustrative examples on uracil.
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