| 1. |
- Acharya, S, et al.
(author)
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Real-time data processing in the ALICE High Level Trigger at the LHC
- 2019
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In: Computer Physics Communications. - : Elsevier BV. - 0010-4655. ; 242, s. 25-48
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Journal article (peer-reviewed)abstract
- At the Large Hadron Collider at CERN in Geneva, Switzerland, atomic nuclei are collided at ultra-relativistic energies. Many final-state particles are produced in each collision and their properties are measured by the ALICE detector. The detector signals induced by the produced particles are digitized leading to data rates that are in excess of 48 GB/s. The ALICE High Level Trigger (HLT) system pioneered the use of FPGA- and GPU-based algorithms to reconstruct charged-particle trajectories and reduce the data size in real time. The results of the reconstruction of the collision events, available online, are used for high level data quality and detector-performance monitoring and real-time time-dependent detector calibration. The online data compression techniques developed and used in the ALICE HLT have more than quadrupled the amount of data that can be stored for offline event processing.
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| 2. |
- Appel, L. C., et al.
(author)
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Equilibrium reconstruction in an iron core tokamak using a deterministic magnetisation model
- 2018
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In: Computer Physics Communications. - : ELSEVIER. - 0010-4655 .- 1879-2944. ; 223, s. 1-17
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Journal article (peer-reviewed)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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| 3. |
- Barrio, Roberto, et al.
(author)
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A database of rigorous and high-precision periodic orbits of the Lorenz model
- 2015
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In: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 194, s. 76-83
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Journal article (peer-reviewed)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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| 4. |
- Béland, Laurent Karim, et al.
(author)
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Accurate classical short-range forces for the study of collision cascades in Fe-Ni-Cr
- 2017
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In: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 219, s. 11-19
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Journal article (peer-reviewed)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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| 5. |
- Bessarab, Pavel F., et al.
(author)
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Method for finding mechanism and activation energy of magnetic transitions, applied to skyrmion and antivortex annihilation
- 2015
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In: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 196, s. 335-347
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Journal article (peer-reviewed)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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| 6. |
- Cantwell, C. D., et al.
(author)
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Nektar plus plus : An open-source spectral/hp element framework
- 2015
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In: Computer Physics Communications. - : Elsevier BV. - 0010-4655. ; 192, s. 205-219
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Journal article (peer-reviewed)abstract
- Nektar++ is an open-source software framework designed to support the development of high-performance scalable solvers for partial differential equations using the spectral/hp element method. High-order methods are gaining prominence in several engineering and biomedical applications due to their improved accuracy over low-order techniques at reduced computational cost for a given number of degrees of freedom. However, their proliferation is often limited by their complexity, which makes these methods challenging to implement and use. Nektar++ is an initiative to overcome this limitation by encapsulating the mathematical complexities of the underlying method within an efficient C++ framework, making the techniques more accessible to the broader scientific and industrial communities. The software supports a variety of discretisation techniques and implementation strategies, supporting methods research as well as application-focused computation, and the multi-layered structure of the framework allows the user to embrace as much or as little of the complexity as they need. The libraries capture the mathematical constructs of spectral/hp element methods, while the associated collection of pre-written PDE solvers provides out-of-the-box application-level functionality and a template for users who wish to develop solutions for addressing questions in their own scientific domains. Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland No. of lines in distributed program, including test data, etc.: 1052456 No. of bytes in distributed program, including test data, etc.: 42851367 External routines: Boost, PFTW, MPI, BLAS, LAPACK and METIS (www.cs.umn.edu) Nature of problem: The Nektar++ framework is designed to enable the discretisation and solution of time-independent or time-dependent partial differential equations. Running time: The tests provided take a few minutes to run. Runtime in general depends on mesh size and total integration time.
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| 7. |
- Edvardsson, Sverker, et al.
(author)
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corr3p_tr : A particle approach for the general three-body problem
- 2016
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In: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 200, s. 259-273
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Journal article (peer-reviewed)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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| 8. |
- Edvardsson, Sverker, et al.
(author)
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Solving equations through particle dynamics
- 2015
-
In: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 197, s. 169-181
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Journal article (peer-reviewed)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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| 9. |
- Ekman, Jörgen, et al.
(author)
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RIS4 : A program for relativistic isotope shift calculations
- 2019
-
In: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 235, s. 433-446
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Journal article (peer-reviewed)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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| 10. |
- Eriksson, Jacob, et al.
(author)
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Calculating fusion neutron energy spectra from arbitrary reactant distributions
- 2016
-
In: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 199, s. 40-46
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Journal article (peer-reviewed)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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