Skip to main content
Log in

A parallel multigrid accelerated Poisson solver for ab initio molecular dynamics applications

  • Regular article
  • Published:
Computing and Visualization in Science

Abstract

In this paper we present an application for a parallel multigrid solver in 3D to solve the Coulomb problem for the charge self interaction in a quantum-chemical program used to perform ab initio molecular dynamics. Techniques such as Mehrstellendiscretization and τ-extrapolation are used to improve the discretization error. The results show that the expected convergence rates and parallel performance of the multigrid solver are achieved. Within the applied Carr–Parrinello Molecular Dynamics scheme the quality of the solution also determines the accuracy in energy conservation. All forms of discretization employed lead to energy conserving dynamics. In order to test the applicability of our code to larger systems in a massively parallel environment, we investigated a 256 atom periodic supercell of bulk gallium nitride.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Dacapo: http://www.fysik.dtu.dk/CAMP/dacapo.html

  2. Hpc-cluster: http://www10.informatik.uni-erlangen.de/Cluster/hpc.shtml

  3. The MPI forum: The MPI message-passing interface standard. http://www.mcs.anl.gov/mpi/standard.html

  4. Numerical python: http://www.pfdubois.com/numpy/

  5. Python: http://www.python.org

  6. Rsdft: http://www.rsdft.org

  7. Ancilotto, F., Blandin, P., Toigo, F.: Real-space full multigrid study of the fragmentation of \(_{11}^+\) clusters. Phys. Rev. B 59, 7868 (1999)

    Google Scholar 

  8. Beck T.L. (2000). Real-space mesh techniques in density-functional theory. Rev. Mod. Phys. 72: 1041–1080

    Article  Google Scholar 

  9. Bernert K. (1997). τ-extrapolation—theoretical foundation, numerical experiment and application to Navier–Stokes equations. SIAM J. Sci. Comp. 18: 460–478

    Article  MathSciNet  MATH  Google Scholar 

  10. Bernholc J. (1999). Computational materials science: the era of apllied quantum mechanics. Phys. Today 52(9): 30–35

    Article  Google Scholar 

  11. Brandt, A.: Multigrid methods: 1984 guide with applications to fluid dynamics. The Weizmann Institute of Science, Rehovot, Israel (1984)

  12. Castro A., Marques M.A.L., Alonso J.A., Bertsch G.F., Yabana K. and Rubio A. (2002). Can optical spectroscopy directly elucidate the ground state of c20?. J. Chem. Phys. 116: 1930–1933

    Article  Google Scholar 

  13. Ceperley D.M. and Alder B.J. (1980). Ground state of the electron gas by a stochastic method. Phys. Rev. Lett. 45: 566–569

    Article  Google Scholar 

  14. Chelikowsky J.R., Saad Y., Ögüt S., Vasiliev I. and Stathopoulos A. (2000). Electronic structure methods for predicting the properties of materials: grids in space. Phys. Stat. Sol. B 217: 173–195

    Article  Google Scholar 

  15. Douglas, C., Haase, G., Langer, U.: A Tutorial on Elliptic PDE Solvers and their Parallelization, SIAM (2003)

  16. Gropp W., Lusk E. and Skjellum A. (1999). Using MPI, Portable Parallel Programming with the Mesage-Passing Interface , 2nd edn. MIT Press, Cambridge

    Google Scholar 

  17. Hackbusch W. (1985). Multi-Grid Methods and Applications. Springer, Heidelberg

    MATH  Google Scholar 

  18. Hinsen K. (2000). The molecular modeling toolkit: a new approach to molecular simulations. J. Comput. Chem. 21: 79–85

    Article  Google Scholar 

  19. Hohenberg P. and Kohn W. (1964). Inhomogeneous electron gas. Phys. Rev. 136: B864–B871

    Article  MathSciNet  Google Scholar 

  20. Hülsemann, F., Kowarschik, M., Mohr, M., Rüde, U.: Parallel geometric multigrid. In: Bruaset, A., Tveito, A. (eds.) Numerical Solution of Partial Differential Equations on Parallel Computers, chap. 5, vol. 51 of LNCSE. Springer, Heidelberg, pp. 165–208 (2005). ISBN 3-540-29076-1

  21. Jin Y.G. and Chang K.J. (2002). Efficient real-space multigrid method and applications to clusters and defects in SiO2. J. Korean Phys. Soc. 40: 406–415

    Google Scholar 

  22. Kendall R.A., Apra E., Bernholdt D.E., Bylaska E.J., Dupuis M., Fann G.I., Harrison R.J., Ju J., Nichols J.A., Nieplocha J., Straatsma T.P., Windus T.L. and Wong, A.T. (2000). High performance computational chemistry: an overview of nwchem a distributed parallel application. Comput. Phys. Commun. 128: 260–283

    Article  MATH  Google Scholar 

  23. Kohn W. and Sham L.J. (1965). Self-consistent equations including exchange and correlation effects. Phys. Rev. 140: A1133–A1138

    Article  MathSciNet  Google Scholar 

  24. Martín I. and Tirado F. (1997). Relationships between efficiency and execution time of full multigrid methods on parallel computers. IEEE Trans. Parallel Distrib. Syst. 8: 562–573

    Article  Google Scholar 

  25. Marx, D., Hutter, J.: Ab Inition Molecular Dynamics: Theory and Implementation, vol. 1 of NIC Series. John von Neumann Institute for Computing, Julich, pp. 301–449 (2000)

  26. Mortensen J.J., Hansen L.B. and Jacobsen K.W. (2005). Real-space grid implementation of the projector augmented wave method. Phys. Rev. B 71: 035109–103510911

    Article  Google Scholar 

  27. Ono T. and Hirose K. (1999). Timesaving double-grid method for real-space electronic-structure calculations. Phys. Rev. Lett. 81: 5016–5019

    Article  Google Scholar 

  28. Parrinello M. and Car R. (1985). Unified approach for molecular dynamics and density-functional theory. Phys. Rev. Lett. 55: 2471–2474

    Article  Google Scholar 

  29. Perdew J.P. and Zunger A. (1981). Self-interaction correction to density-functional approximations for many-electron systems. Phys. Rev. B 23: 5048–5079

    Article  Google Scholar 

  30. Richardson L. (1927). The deferred approach to the limit. I. Single lattice. Philos. Trans. R. Soc. Lond. A 226: 229–349

    Article  Google Scholar 

  31. Rüde, U.: Multiple τ-extrapolation for multigrid methods. Tech. Rep. I-8701, Technische Universität München (1987)

  32. Schmid R. (2004). Car–Parrinello molecular-dynamics simulations with real space methods. J. Comput. Chem. 25: 799–812

    Article  Google Scholar 

  33. Schmid R., Tafipolsky M., König P.H. and Köstler H. (2006). Car–Parrinello molecular dynamics using real space wavefunctions. Phys. Status solidi b 243: 1001–1015

    Article  Google Scholar 

  34. Shimojo F., Kalia R.K., Nakano A. and Vashishta P. (2001). Linear-scaling density-functional-theory calculations of electronic structure based on real-space grids: design, analysis, and scalability test of parallel algorithms. Comput. Phys. Commun. 140: 303–314

    Article  MATH  Google Scholar 

  35. Sterk M. and Trobec R. (2003). Parallel performances of a multigrid poisson solver. ISPDC 00: 238

    Google Scholar 

  36. Tafipolsky, M., Schmid, R.: A general and efficient pseudopotential fourier filtering scheme for real space methods using mask functions. J. Chem. Phys. 243(5) (2005)

  37. Torsti T., Heiskanen M., Puska M.J. and Nieminen R.M. (2003). Mika: multigrid-based program package for electronic structure calculations. Int. J. Quantum Chem. 91: 171–176

    Article  Google Scholar 

  38. Trottenberg U., Oosterlee C. and Schüller A. (2001). Multigrid. Academic, New York

    MATH  Google Scholar 

  39. Waghmare U.V., Kim H., Park I.J., Modine N., Maragakis P. and Kaxiras E. (2001). Hares: an efficient method for first-principles electronic structure calculations of complex systems. Comput. Phys. Commun. 137: 341–360

    Article  MATH  Google Scholar 

  40. Wang J. and Beck T.L. (2000). Efficient real-space solution of the Kohn-Sham equations with multiscale techniques. J. Chem. Phys. 112: 9223–9228

    Article  Google Scholar 

  41. Wang J., Wang Y., Yu S. and Kolb D. (2005). Nonlinear algorithm for the solution of the Kohn-Sham equations in solids. J. Phys. Cond. Mat. 17: 3701–3715

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to H. Köstler.

Additional information

Communicated by P. Wesseling.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Köstler, H., Schmid, R., Rüde, U. et al. A parallel multigrid accelerated Poisson solver for ab initio molecular dynamics applications. Comput. Visual Sci. 11, 115–122 (2008). https://doi.org/10.1007/s00791-007-0062-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00791-007-0062-0

Keywords

Navigation