Design patterns for multiphysics modeling in Fortran 2003 and C++

ACM Transactions on Mathematical Software

Volumn 37, Issue 1, 2010, Pages

  Rouson, Damian W I ^a   Adalsteinsson, Helgi ^a   Xia, Jim ^b  

^a SANDIA NATIONAL LABORATORIES   (United States)

^b IBM TORONTO LAB   (Canada)

Author keywords

Design patterns; Lorenz equations; Multiphysics modeling

Indexed keywords

ABSTRACT DATA TYPES; ARCHITECTURAL DESCRIPTIONS; ARCHITECTURAL ELEMENT; AUTOMATED MEMORY MANAGEMENT; COMPILE TIME; CONTROL LOGIC; COUPLED DIFFERENTIAL EQUATIONS; DESIGN PATTERNS; FORTRAN; LANGUAGE FEATURES; LORENZ EQUATION; MATHEMATICAL NOTATIONS; MULTI-PHYSICS; MULTI-PHYSICS MODELING; MULTIPHYSICS PHENOMENA; NAVIER-STOKES SOLVER; NONLINEAR TERMS; NUMERICAL SOFTWARE; OBJECT-ORIENTED SOFTWARE DESIGNS; OPERATOR OVERLOADING; PRIVATE DATA; RUNTIMES; SYSTEM EVOLUTION;

ABSTRACTING; DESIGN; DIFFERENTIAL EQUATIONS; DYNAMICAL SYSTEMS; FORTRAN (PROGRAMMING LANGUAGE); MATHEMATICAL OPERATORS; OBJECT ORIENTED PROGRAMMING; SOFTWARE DESIGN;

COMPUTER SOFTWARE;

EID: 76249132080     PISSN: 00983500     EISSN: 15577295     Source Type: Journal    
DOI: 10.1145/1644001.1644004     Document Type: Article

References (49)

1. AKIN, E. 2003. Object-Oriented Programming via Fortran 90/95. Cambridge University Press, Cambridge, U.K.
2. ALEXANDER, C., ISHIKAWA, S., MURRAY, S., JACOBSON, M., FIKSDAHL-KING, I., AND ANGEL S. 1977. A Pattern Language: Towns, Buildings, Construction. Oxford University Press, Oxford, U.K.
3. BALAY, S., BUSCHELMAN, K., EIJKHOUT, V., GROPP, W., KAUSHIK, D., KNEPLEY, M., MCINNES, L. C., SMITH, B., AND ZHANG, H. 2007. PETSc Users Manual, ANL-95/11-Rev. 2.3.3. Argonne National Laboratory, Argonne, IL.
4. BARKER, V. A., BLACKFORD, L. S.,DONGARRA, J., DU CROZ, J., HAMMARLING, S.,MARINOVA, M.,WANIEWSKY, J., AND YALAMOV, P. 2001. LAPACK95 Users' Guide. Society for Industrial and Applied Mathematics, Philadelphia, PA.
5. BERNHOLDT, D. E., ALLAN, B. A., ARMSTRONG, R., BERTRAND, F., CHIU, K., DAHLGREN, T. L., DAMEVSKI, K., ELWASIF, W. R., EPPERLY, T. G. W.,GOVINDARAJU, M., KATZ, D. S., KOHL, J. A., KIRSHNAN, M., KUMFERT, G., LARSON, J.W., LEFANTZI, S., LEWIS,M. J.,MALONY, A. D.,MCINNES, L. C., NIEPLOCHA, J., NORRIS, B., PARKER, S. G. M, RAY, J., SHENDE, S., WINDUS, T. L. AND ZHOU, S. 2006. A component architecture for high-performance scientific computing. Int. J. High Perform. Comput. Appl. 20, 163-202.
6. BLACKFORD, L. S.,DEMMEL, J., DONGARRA, J., DUFF, I.,HAMMARLING, S.,HENRY, G.,HEROUX, M., KAUFMAN, L., LUMSDAINE, A., PETITET, A., POZO, R., REMINGTON, K., WHALEY, R. C. 2002. An updated set of basic linear algebra subprograms (BLAS). ACM Trans. Math. Soft., 28, 2, 135-151. (Pubitemid 135701673)
7. BLACKFORD, L. S., CHOI, J., CLEARY, A., D'AZEVEDO, E., DEMMEL, J., DHILLON, I., DONGARRA, J., HAMMARLING, S., HENRY, G., PETITET, A., STANLEY, K., WALKER, D., AND WHALEY, R. C. 1997. ScaLAPACK Users' Guide. Society for Industrial and Applied Mathematics, Philadelphia, PA.
8. BLILIE, C. 2002. Patterns in scientific software: An introduction. Comput. Sci. Eng., 4, 3, 48-52.
9. BOOCH, G., RUMBAUGH, J., AND JACOBSON, I. 1999. The Unified Modeling Language User Guide, Addison-Wesley, Reading, MA.
10. BRUCKER, K. A., ISAZA, J. C., VAITHIANATHAN, T., AND COLLINS, L. R. 2007. Efficient algorithm for simulating homogeneous turbulent shear flow without remeshing. J. Comput. Phys. 225, 20-32.
11. COLLINS-SUSSMAN, B., FITZPATRICK, B. W., AND PILATO, C.M. 2004. Version Control with Subversion, O'Reilly & Associates, Sebastopol, CA.
12. DECYK, V. K., NORTON, C. D., AND SZYMANSKI, B. K. 1997a. Expressing object-oriented concepts in Fortran 90. ACM Fortran For. 15, 13-18.
13. DECYK, V. K., NORTON, C. D., AND SZYMANSKI, B. K. 1997b. How to express C++ concepts in Fortran 90. Sci. Program. 6, 363-390.
14. DECYK, V. K., NORTON, C. D., AND SZYMANSKI, B. K. 1998. How to support inheritance and run-time polymorphism in Fortran 90. Comput. Phys. Commun. 115, 9-17.
15. DECYK, V. K. AND GARDNER, H. J. 2007. A factory pattern in Fortran 95. In Lecture Notes in Computer Science, 4487/2007, 583-590, Springer Berlin/Heidelberg.
16. DECYK, V. K. AND GARDNER, H. J. 2008. Design patterns in Fortran 90/95. Comput. Phys. Commun. In press.
17. FREE SOFTWARE FOUNDATION. 2004a. Gnu concurrent version system home page. http://www.gnu.org/software/cvs.
18. FREE SOFTWARE FOUNDATION. 2004b. Gnu mailman home page. http://www.gnu.org/software/mailman/mailman.html.
19. GAMMA, E., HELM, R., JOHNSON, R., AND VLISSIDES, J. 1995. Design Patterns: Elements of Reusable Object-Oriented Software, Addison-Wesley, Reading, MA.
20. GARDNER, H. AND MANDUCHI, G. 2007. Design Patterns for e-Science. Springer, Berlin, Germany.
21. GRANT, P. W., HAVERAAEN, M., AND WEBSTER, M. F. 2000. Coordinate free programming of computational fluid dynamics problems. Sci. Program. 8, 211-230.
22. HEROUX, M. A., BARTLETT, R. A., HOWLE, V. E., HOEKSTRA, R. J., HU, J. J., KOLDA, T. G., LEHOUCQ, R. B., LONG, K. R., PAWLOWSKI, R. P., PHIPPS, E. T., SALINGER, A. G., THORNQUIST, H. K., TUMINARO, R. S., WILLENBRING, J. M., WILLIAMS, A., STANLEY, K. S. 2005. An overview of the Trilinos project. ACM Trans. Math. Soft. 31, 3, 397-423.
23. HILL, C., DELUCA, C., BALAJI, V., SUAREZ, M., AND DA SILVA, A. 2004. The architecture of the Earth Systems Modeling Framework. Comput. Sci. Eng. 6, 1, 18-28.
24. JOY, W. AND KENNEDY, K. CHAIRS. 1999. Information technology research: Investing in our future. President's Information Technology Advisory Committee Report. Cited in Oden [2006]. www.nited.gov/pitae/report/pitae report.pdf.
25. KIM, J. R., MOSER, D., AND MOIN, P. 1987. Turbulence statistics in fully developed channel flow at low Reynolds number. J. Fluid Mech. 177, 133.
26. KIRK, S. R. AND JENKINS, S. 2004. Information theory-based software metrics and obfuscation. J. Syst. Softw. 72, 179-186.
27. KNAEPEN, B., KASSINOS, S. C., AND CARATI, D. 2004. Magnetohydrodynamic turbulence at moderate magnetic Reynolds number. J. Fluid Mech. 513, 199-220. (Pubitemid 39142834)
28. LORENZ, E. N. 1963. Deterministic nonperiodic flow. J. Atmos. Sci. 20, 2, 130-141.
29. MARKUS, A. 2006. Design patterns and Fortran 90/95. ACM Fort. For. 26, 1, April.
30. MARTIN, R. C. 2002. Agile Software Development, Principles, Patterns and Practices. Prentice-Hall, Englewood Cliffs, NJ. Cited in Kirk and Jenkins [2004].
31. MAWLAWSKI, M., DAWID, K. AND SUNDARAM, V. 2005. MOCCA-towards a distributed CCA framework for metacomputing. In Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE Computer Society, Los Alamitos, CA.
32. MATTSON, T. G., SANDERS, B. A., AND MASSINGILL, B. L. 2004. Patterns for Parallel Programming. Addison-Wesley, Reading, MA. 25, 1, 13-29.
33. MCGRATTAN, K., BRYAN, K., HOSTIKKA, S. AND FLOYD, J. 2008. Fire dynamics simulator (version 5) user's guide. NIST Special Publication 1019-1025 National Institute of Standards and Technology, Gaithersburg, MD.
34. METCALF, M., REID, J., AND COHEN,M. 2004. Fortran 95/2003 Explained. Oxford University Press, Oxford, U.K.
35. MORRIS, K., KOPLIK, J., AND ROUSON, D. W. I. 2008. Vortex locking in direct numerical simulations of quantum turbulence. Phys. Rev. Lett. 101, 015301.
36. ODEN, J. T. (CHAIR). 2006. Revolutionizing engineering science through simulation. Report of the National Science Foundation Blue Ribbon Panel on Simulation-Based Engineering Science. National Science Foundation, Arlington, VA.
37. ORSZAG, S. A. AND PATTERSON,G. S. 1972. Numerical simulation of three-dimensional homogeneous isotropic turbulence. Phys. Rev. Lett. 28, 2.
38. ROUSON, D. W. I. 2008. Toward analysis-driven scientific software architecture: The case for abstract data type calculus, Sci. Program. 16, 4.
39. ROUSON, D. W. I. AND HANDLER, R. 2007. Towards a variational multiscale large-eddy simulation of the atmospheric boundary layer. In Environmental Sciences and Environmental Computing Vol. III, Envirocomp Institute, Inc., Fremont, CA.
40. ROUSON, D. W. I.,MORRIS, K. AND XU, X. 2005. Dynamic memory de-allocation in Fortran 95/2003 derived type calculus. Sci. Program. 13, 3, 189-203.
41. ROUSON, D. W. I., ROSENBERG, R., XU, X., MOULITSAS, I., AND KASSINOS, S. C. 2008a. A grid-free abstraction of the Navier-Stokes equations in Fortran 95/2003. ACM Trans. Math Soft. 34, 1, Article 2 (Jan.)
42. ROUSON, D.W. I., KASSINOS, S. C.,MOULITSAS, I., SARRIS, I. AND XU, X. 2008b. Dispersed-phase structural anisotropy in homogeneous magnetohydrodynamic turbulence at low magnetic Reynolds number. Phys. Fluids 20, 025101 (Feb.)
43. ROUSON, D. W. I. AND XIONG, Y. 2004. Design metrics in quantum turbulance simulations: How physics influences software architecture. Sci. Program. 12, 3, 185-186.
44. ROUSON, D. W. I., XU, X., AND MORRIS, K. 2006. Formal constraints on memory management for composite overloaded operations. Sci. Program. 14, 1, 27-40.
45. STEVENS, W. P., MYERS, G. J., AND CONSTANTINE, L. L. 1974. Structured design. IBM Syst. J. 13, 2, 115.
46. STROUSTRUP, B. 1997. The C++ Programming Language, 3rd ed. Addison-Wesley, Reading, MA.
47. THE MOZILLA ORGANIZATION. 2004a. Mozilla Bonsai home page. http://ww.mozilla.org/bonsai.html.
48. THE MOZILLA ORGANIZATION. 2004b. Mozilla Bugzilla home page. http://ww.mozilla.org /projects/bonsai.
49. ZHANG, K., DAMEVSKI, K., VENKATACHALAPATHY, V., AND PARKER, S. G. 2004. SCIRun2: A CCA framework for high-performance computing. In Proceedings of the 9th InternationalWorkshop on High-Level Parallel Programming Models and Supportive Environments (HIPS '04). C. Rasmussen, Workshop Chair. 72-79.