Hostname: page-component-745bb68f8f-b95js Total loading time: 0 Render date: 2025-01-12T09:48:41.079Z Has data issue: false hasContentIssue false
  • English
  • Français

BOUT++: Recent and current developments

Part of: Focus on Fusion Culham Thesis Prize Winners

Published online by Cambridge University Press:  15 October 2014

B. D. Dudson ,
A. Allen ,
G. Breyiannis ,
E. Brugger ,
J. Buchanan ,
L. Easy ,
S. Farley ,
I. Joseph ,
M. Kim  and
A. D. McGann
...Show all authors
B. D. Dudson*
Affiliation:
York Plasma Institute, Department of Physics, University of York, Heslington, York, YO10 5DD, UK
A. Allen
Affiliation:
York Plasma Institute, Department of Physics, University of York, Heslington, York, YO10 5DD, UK
G. Breyiannis
Affiliation:
Japan Atomic Energy Agency, Rokkasho Fusion Institute, Rokkasho-mura, 039-3212, Japan
E. Brugger
Affiliation:
Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
J. Buchanan
Affiliation:
CCFE, Culham Science Centre, Abingdon, OX14 3DB, UK
L. Easy
Affiliation:
York Plasma Institute, Department of Physics, University of York, Heslington, York, YO10 5DD, UK CCFE, Culham Science Centre, Abingdon, OX14 3DB, UK
S. Farley
Affiliation:
Mathematics Department, Illinois Institute of Technology, Chicago, IL 60616, USA
I. Joseph
Affiliation:
Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
M. Kim
Affiliation:
Department of Physics, POSTECH, Pohang, Gyeongbuk 790-784, Korea
A. D. McGann
Affiliation:
York Plasma Institute, Department of Physics, University of York, Heslington, York, YO10 5DD, UK
J. T. Omotani
Affiliation:
CCFE, Culham Science Centre, Abingdon, OX14 3DB, UK
M. V. Umansky
Affiliation:
Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
N. R. Walkden
Affiliation:
York Plasma Institute, Department of Physics, University of York, Heslington, York, YO10 5DD, UK CCFE, Culham Science Centre, Abingdon, OX14 3DB, UK
T. Xia
Affiliation:
Lawrence Livermore National Laboratory, Livermore, CA 94551, USA Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, China
X. Q. Xu
Affiliation:
Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
*
†Email address for correspondence: benjamin.dudson@york.ac.uk
Get access Rights & Permissions [Opens in a new window]

Abstract

BOUT++ is a 3D nonlinear finite-difference plasma simulation code, capable of solving quite general systems of Partial Differential Equations (PDEs), but targeted particularly on studies of the edge region of tokamak plasmas. BOUT++ is publicly available, and has been adopted by a growing number of researchers worldwide. Here we present improvements which have been made to the code since its original release, both in terms of structure and its capabilities. Some recent applications of these methods are reviewed, and areas of active development are discussed. We also present algorithms and tools which have been developed to enable creation of inputs from analytic expressions and experimental data, and for processing and visualisation of output results. This includes a new tool Hypnotoad for the creation of meshes from experimental equilibria. Algorithms have been implemented in BOUT++ to solve a range of linear algebraic problems encountered in the simulation of reduced Magnetohydrodynamics (MHD) and gyro-fluid models: A preconditioning scheme is presented which enables the plasma potential to be calculated efficiently using iterative methods supplied by the PETSc library (the Portable, Extensible Toolkit for Scientific Computation) (Balay et al. 2014), without invoking the Boussinesq approximation. Scaling studies are also performed of a linear solver used as part of physics-based preconditioning to accelerate the convergence of implicit time-integration schemes.

Type
Research Article
Information
Journal of Plasma Physics , Volume 81 , Issue 1 , January 2015 , 365810104
Copyright
Copyright © Cambridge University Press 2014 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

Aho, A. V., Lam, M. S., Sethi, R. and Ullman, J. D. 2006 Compilers: Principles, Techniques, and Tools, Addison-Wesley.Google Scholar
Angus, J. R. and Umansky, M. V. 2014 Phys. Plasmas 21, 012 514.Google Scholar
Angus, J. R., Umansky, M. V. and Krasheninnikov, S. I. 2012a 3d blob modelling with bout++. Contrib. Plasma Phys. 52, 348–352.CrossRefGoogle Scholar
Angus, J. R., Umansky, M. V. and Krasheninnikov, S. I. 2012b Effect of drift waves on plasma blob dynamics. Phys. Rev. Lett. 108, 215 002.CrossRefGoogle ScholarPubMed
Austin, T. M., Berndt, M. and Moulton, J. D. 2004 Technical Report LA-UR 03-4149. LANL, USA.Google Scholar
Balay, S., Gropp, W. D., McInnes, L. C. and Smith, B. F. 1997 In: Modern Software Tools in Scientific Computing (ed. Arge, E., Bruaset, A. M. and Langtangen, H. P.). Birkhauser Press, pp. 163–202.CrossRefGoogle Scholar
Balay, S. et al. 2010 Technical Report ANL-95/11 - Revision 3.1. Argonne National Laboratory.Google Scholar
Balay, S. et al. 2014 PETSc Web page. http://www.mcs.anl.gov/petsc.Google Scholar
Beer, M. A. et al. 1997 Phys. Plasmas 4 (5), 1792–1799.Google Scholar
Catto, P. J. and Simakov, A. N. 2004 A drift ordered short mean free path description for magnetized plasma allowing strong spatial anisotropy. Phys. Plasmas 11 (1), 90–102.Google Scholar
Chacón, L., Knoll, D. A. and Finn, J. M. 2002 J. Comput. Phys. 178 (1), 15–36.Google Scholar
Dimits, A. M., Joseph, I. and Umansky, M. V. 2013 A fast non-Fourier method for Landau-fluid operators. Phys. Plasmas 21 (5), 055 907.CrossRefGoogle Scholar
D'Ippolito, D. A., Myra, J. R. and Zweben, S. J. 2011 Phys. Plasmas 18, 060 501.Google Scholar
Dudson, B., Farley, S. and Curfmann McInnes, L. 2012 arXiv:1209.2054.Google Scholar
Dudson, B. D. et al. 2009 Comput. Phys. Commun. 180, 1467–1480.CrossRefGoogle Scholar
Friedman, B., Carter, T. A., Umansky, M. V., Schaffner, D. and Dudson, D. 2012 Phys. Plasmas 19, 102 307.Google Scholar
Fundamenski, W et al. 2001 J. Nucl. Mater. 290–293, 593.Google Scholar
Gamma, E., Helm, R., Johnson, R. and Vlissides, J. 1995 Design Patterns: Elements of Reusable Object-Oriented Software, Addison-Wesley.Google Scholar
Garcia, O. E. et al. 2007 J. Nucl. Mater. 363, 575.Google Scholar
Gekelman, W. et al. 1991 Rev. Sci. Instrum. 62, 2875.Google Scholar
Gendrih, Ph et al. 2012 J. Phys.: Conf. Ser. 401, 012 007.Google Scholar
General Atomics 2014 G EQDSK file format. https://fusion.gat.com/theory/Efitgeqdsk.Google Scholar
Golub, G. H. and Van Loan, C. F. 2013 Matrix Computations, The Johns Hopkins University Press.CrossRefGoogle Scholar
Goswami, R. et al. 2001 Phys. Plasmas 8, 857.Google Scholar
Hammett, G. W. and Perkins, F. W. 1990 Phys. Rev. Lett. 64, 3019.Google Scholar
Hazeltine, R. D. and Meiss, J. D. 2003 Plasma Confinement, Dover publications.Google Scholar
Heroux, M. A. et al. 2005 ACM Trans. Math. Softw. 31 (3), 397–423.Google Scholar
Hindmarsh, A. C. 1983 Scientific Computing, (ed. Stepleman, R. S. et al.). (IMACS Transactions on Scientific Computation, 1). Amsterdam: North-Holland, pp. 55–64.Google Scholar
Hindmarsh, A. C. et al. 2005 SUNDIALS: suite of nonlinear and differential/algebraic equation solvers. ACM Trans. Math. Softw. 31 (3), 363–396.CrossRefGoogle Scholar
Hockney, R. W. 1965 J. Assoc. Comput. Mach. 12, 95.CrossRefGoogle Scholar
Iserles, A. 2009 A First Course in the Numerical Analysis of Differential Equations, Cambridge University Press, ISBN: 978-0-521-73490-5.Google Scholar
Ji, J. Y., Held, E. D. and Sovinec, C. R. 2009 Phys. Plasmas 16 (2), 022 312.CrossRefGoogle Scholar
Jones, E. et al. 2001 – SciPy: open source scientific tools for Python.Google Scholar
Karniadakis, G. E., Israeli, M. and Orszag, S. A. 1991 J. Comput. Phys. 97, 414.Google Scholar
Kawashima et al. 2006 Plasma Fusion Res. 1, 31.Google Scholar
Knepley, M. G. 2012 arXiv:1209.1711.Google Scholar
Knoll, D. A. et al. 2001 SIAM J. Sci. Comput. 23 (2), 381.Google Scholar
Lao, L. L., St. John, H., Stambaugh, R. D., Kellman, A. G. and Pfeiffer, W. 1985 Reconstruction of current profile parameters and plasma shapes in tokamaks. Nucl. Fusion 25, 1611–22.Google Scholar
Lao, L. L. et al. 2005 MHD equilibrium reconstruction in the DIII-D tokamak. Fusion Sci. Technol. 48, 968.Google Scholar
LLVM Project 2014 Implementing a language with LLVM. http://llvm.org/docs/tutorial/.Google Scholar
Ma, J. F., Xu, X. Q. and Dudson, B. D. 2014 54, 033 011.Google Scholar
Marchand, R. and Dumberry, M. 1996 CARRE: a quasi-orthogonal mesh generator for 2D edge plasma modelling. Comput. Phys. Commun. 96, 232–246.Google Scholar
Mousseau, V. A., Knoll, D. A. and Rider, W. J. 2000 J. Comput. Phys. 160, 743.Google Scholar
Nakamura, M. 2011 J. Nucl. Mater. 415, S553.CrossRefGoogle Scholar
Naulin, V. et al. 2007 J. Nucl. Mater. 24, 363–365.Google Scholar
Omotani, J. T. and Dudson, B D 2013 Plasma Phys. Control. Fusion 55, 055 009.Google Scholar
Ottaviani, M. and Manfredi, G 1999 Phys. Plasmas 6, 3267.Google Scholar
Park, S and Schowengerdt, R 1983 Comput. Vis., Graph. and Image Process. 23, 256.Google Scholar
Radhakrishnan, K. and Hindmarsh, A. C. 1993 Technical Report. LLNL, http://computation.llnl.gov/casc/nsde/pubs/u113855.pdf.Google Scholar
Ricci, P. et al. 2012 Plasma Phys. Control Fusion 54, (124 047).Google Scholar
Ricci, P. and Rogers, B. N. 2013 Phys. Plasmas 20, 010, 702.Google Scholar
Roache, P. J. 1998 Verification and Validation in Computational Science and Engineering, Albuquerque NM: Hermosa Publishers.Google Scholar
Rognlien, T. D. et al. 1992 J. Nucl. Mater. 196–198, 347.Google Scholar
Rognlien, T. D., Xu, X. Q. and Hindmarsh, A. C. 2002 Application of parallel implicit methods to edge-plasma numerical simulations. J. Comput. Phys. 175, 249–268.Google Scholar
Salari, K. and Knupp, P. 2000 Code verification by the method of manufactured solutions. Technical Report. SAND2000-1444. Sandia National Laboratories.Google Scholar
Schneider, R. et al. 2006 Contrib. Plasma Phys. 46, 3–191.Google Scholar
Scott, B. 2003 Plasma Phys. Control Fusion 45, A385–398.Google Scholar
Scott, B. 2005a Phys. Plasmas 12, 102 307.Google Scholar
Scott, B. D. 2002 New J. Phys. 4, 52.1–52.30.Google Scholar
Scott, B. D. 2005b GEM - an energy conserving electromagnetic gyrofluid model. arXiv:physics/0501124.Google Scholar
Stangeby, P. C. 2000 The Plasma Boundary of Magnetic Fusion Devices, IoP.Google Scholar
Tamain, P. et al. 2010 TOKAM-3D: a 3D fluid code for transport and turbulence in the edge plasma of Tokamaks. J. Comput. Phys. 229 (2), 361–378.Google Scholar
Tarditi, A. et al. 1996 Contrib. Plasma Phys. 36, 132.Google Scholar
Temperton, C. 1975 Algorithms for the solution of cyclic tridiagonal systems. J. Comput. Phys. 19 (3), 317–323.Google Scholar
Tskhakaya, D. 2012 Contrib. Plasma Phys. 52 (5–6), 490–499.Google Scholar
Tskhakaya, D., Subba, F., Bonnin, X., Coster, D. P., Fundamenski, W., Pitts, R. A. and Contributors, JET EFDA 2008 On kinetic effects during parallel transport in the sol. Contrib. Plasma Phys. 48 (1–3), 89–93.Google Scholar
Umansky, M. V., Rognlien, T. D., Xu, X. Q., Dudson, B. D. and Kirk, A. 2006 Modelling of edge plasma turbulence in a spherical tokamak.Google Scholar
Walkden, N. R., Dudson, B. D. and Fishpool, G. 2013 Characterization of 3d filament dynamics in a mast sol flux tube geometry. Plasma Phys. Control Fusion 55, 105 005.Google Scholar
Wesson, J. A., ed. 1997 Tokamaks, 2nd edn. Clarendon Press.Google Scholar
Wolfram Research, Inc. 2014 Mathematica. Champaign, Illinois.Google Scholar
Xi, P. W., Xu, X. Q., Xia, T. Y., Nevins, W. M. and Kim, S. S. 2013 53 (11), 113 020.Google Scholar
Xia, T. Y., Xu, X. Q., Dudson, B. D. and Li, J. 2012 Contrib. Plasma Phys. 52, 353–359.Google Scholar
Xu, X. et al. 2013 Phys. Plasmas 20, 056 113.Google Scholar
Xu, X. Q., Cohen, R. H., Porter, G. D., Myra, J. R., D'Ippolito, D. A. and Moyer, R. 1999 Turbulence in boundary plasmas. J. Nucl. Mater. 266–269, 993–996.CrossRefGoogle Scholar
Xu, X. Q., Cohen, R. H., Porter, G. D., Rognlien, T. D., Ryutov, D. D., Myra, J. R., D'Ippolito, D. A., Moyer, R. A. and Groebner, R. J. 2000 Turbulence studies in tokamak boundary plasmas with realistic divertor geometry. Nucl. Fusion 40 (3Y), 731–736.Google Scholar
Xu, X. Q., Umansky, M. V., Dudson, B. and Snyder, P. B. 2008 Boundary plasma turbulence simulations for tokamaks. Commun. Comput. Phys. 4 (5), 949–979.Google Scholar
Xu, X. Q. et al. 2010 Phys. Rev. Lett. 105, 175 005.Google Scholar
Yu, G. Q., Krasheninnikov, S. I. and Guzdar, P. N. 2006 Phys. Plasmas 13, 042 508.Google Scholar
Zohm, H. 1996 Plasma Phys. Control Fusion 38, 105–128.CrossRefGoogle Scholar