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Developing of Scientific Software Applications in Python. [Part] 1, Transformation of Hubbard Hamiltonian into the Matrix and its Diagonalization

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In order to perform larger scale physics research in the area of superconductivity, we have developed an application that can transform the Hubbard Hamiltonian into a matrix and diagonalize it to find the selected model’s energy spectrum. For that purpose we have used the Python language and its wide ecosystem. This paper proves that selected tools are capable of creating scientific applications in a general sense. After a short introduction into the physics problem and the designed algorithm we will present the computer science problems and their solutions in creating usual scientific programs, in particular: performance and parallelization issues, storage of input data and the results, bottlenecks detections, as well as optimization and testing. The most interesting examples of the developing cycle will be described to give a prepared solution for implementing the other scientific software.
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  • Institute of Physics, Jan Długosz University Al. Armii Krajowej 13/15, 42-200 Częstochowa, Poland
  • Institute of Physics, Jan Długosz University Al. Armii Krajowej 13/15, 42-200 Częstochowa, Poland
  • Institute of Physics, Częstochowa University of Technology Al. Armii Krajowej 19, 42-200 Częstochowa, Poland
  • Institute of Physics, Częstochowa University of Technology Al. Armii Krajowej 19, 42-200 Częstochowa, Poland
Bibliografia
  • [1] T.E. Oliphant, Python for Scientific Computing, Computing in Science & Engineering 9, 10-20 (2007).
  • [2] D.M. Beazley, P.S. Lomdahl, Extensible Message Passing Application Development and Debugging with Python, Proceedings 11th International Parallel Processing Symposium, 650-655 (1997).
  • [3] J. Spałek, Wstęp do fizyki materii skondensowanej, Wydawnictwo Naukowe PWN, Warszawa 2015.
  • [4] H. Fangohr, Python for Computational Science and Engineering, Faculty of Engineering and the Environment University of Southampton, Southampton 2014.
  • [5] Python Software Foundation, Python Documentation, https://docs.python.org, 2015. Developing of Scientific Software Applications in Python 189
  • [6] D.M. Beazley, Scientific Computing with Python, Astronomical Data Analysis Software and Systems IX ASP Conference Series 216, San Francisco 2000.
  • [7] D.M. Beazley, P.S. Lomdahl, Building Flexible Large-Scale Scientific Computing Applications with Scripting Languages, 8th SIAM Conference on Parallel Processing for Scientific Computing, Minnesota 1997.
  • [8] X. Cai, H. P. Langtangen, H. Moe, On the Performance of the Python Programming Language for Serial and Parallel Scientific Computations, Scientific Programming 13, 31-56 (2005).
  • [9] R.B. Lehoucq, D.C. Sorensen, C.Yang, ARPACK Users’Guide: Solution of Large-Scale Eigenvalue Problems with Implicitly Restarted Arnoldi Methods, University of Leeds, 1997.
  • [10] S. Behnel, R. Bradshaw, C. Citro, L. Dalcin, D. S. Seljebotn, K. Smith, Cython: The Best of Both Worlds, Computing in Science and Engineering 13, 31-39 (2011).
  • [11] A. S. Szalay, J. A. Blakeley, Gray’s laws: database-centric computing in science, [in:] T. Hey (ed.), S. Tansley (ed.), K. Tolle (ed.), The Fourth Paradigm: Data-Intensive Scientific Discovery, Redmond, p. 5-11, 2009.
  • [12] P. Buneman, Why Don’t Scientists Use Databases?, Microsoft PowerPoint Presentation to National e-Science Centre, (2002).
  • [13] A. Noreen, K. Olaussen, A Python Class for Higher-Dimensional Schroedinger Equations, arXiv:1503.04607 [physics.comp-ph], (2015).
  • [14] M.R B. Kristensen, B. Vinter, Numerical Python for scalable architectures, Proceedings of the Fourth Conference on Partitioned Global Address Space Programming Model, New York, art. 15 2010.
  • [15] J.K. Nilsen, X. Cai, B. Høyland, H. P. Langtangen, Simplifying the parallelization of scientific codes by a function-centric approach in Python, Computational Science & Discovery 3, (2010).
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