New advances in chemistry and materials science with CPMD and parallel computing

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Abstract

A short overview is presented of the density functional theory and molecular dynamics (DFT–MD) method and of a code (CPMD) based on a plane wave scheme. Its power is shown through the survey of specific applications to diverse frontier areas of chemistry and materials science that make use of parallel computing.

Introduction

The method of choice for computational studies of the chemistry of extended systems is density functional theory (DFT) [28], [32], [33]. The unification of DFT and molecular dynamics (DFT–MD), as achieved in the seminal paper of Car and Parrinello [12], has greatly enhanced the flexibility of DFT by enlarging the range of possible applications, e.g. from solids to liquids, from statics to dynamics, and from solid-state physics to physical chemistry. By providing the ability to treat larger systems and longer time scales, parallel computing makes the applicability of DFT to real systems progressively more feasible.

In this paper, after briefly recalling the basics of the DFT–MD method and of its implementation in the CPMD parallel code by Jürg Hutter [20], we give a survey of applications that we have made over the past few years in diverse frontier areas of chemistry and materials science.

Section snippets

DFT–MD and the CPMD parallel code

In this section, we shall briefly describe the DFT–MD method and the CPMD code [20] and emphasize some details of its parallelization [35]. We point the reader to the relevant literature as well.

The CPMD code is an implementation of DFT in the Kohn–Sham (KS) formulation [32], [33], [28] and of the Car–Parrinello MD scheme [12]. Plane waves are used as the basis set for the valence electron wave functions and pseudo-potentials to describe the interaction between the valence electrons and the

Applications

With the method explained above, one can handle diverse atomic aggregation phases, i.e. molecules and clusters (“isolated” [7]) as well as solids and liquids (with periodic boundary conditions), one can simulate the dynamics of a given system at either constant energy, temperature [43] or pressure [44], and also impose geometrical constraints.

Table 1 contains a summary of applications of the method discussed in Section 2 that have been made over the past decade on IBM machines of various

Conclusion

Here, a brief discussion has been presented of the DFT–MD method, of the computational features of the CPMD code and its advantages when tuned with parallel machines, as well as of the progress made with it in the study of several problems in chemistry and materials science. This constitues only the beginning of a new, direct approach to real materials issues from first principles. In fact, the largest systems one can currently treat accurately on a machine of common access (32 nodes SP2) are a

References (58)

  • M. Bühl et al.

    Chem. Phys. Lett.

    (1997)
  • E.A. Carter et al.

    Chem. Phys. Lett.

    (1989)
  • A. Curioni et al.

    Chem. Phys. Lett.

    (1998)
  • P. Liu et al.

    Surf. Sci.

    (1998)
  • D.S. Maddison et al.

    Synth. Metals

    (1988)
  • J. Wiggs et al.

    Comp. Phys. Commun.

    (1994)
  • M.S.A. Abdou et al.

    J. Am. Chem. Soc.

    (1997)
  • W. Andreoni

    Ann. Rev. Phys. Chem.

    (1998)
  • W. Andreoni et al.

    Phys. Rev. Lett.

    (1996)
  • W. Andreoni et al.

    Appl. Phys. A

    (1998)
  • W. Andreoni, P. Giannozzi, in: W. Andreoni (Ed.), The Physics of Fullerene-Based and Fullerence-Related Materials,...
  • W. Andreoni et al.

    J. Am. Chem. Soc.

    (1996)
  • R.N. Barnett et al.

    Phys. Rev. B

    (1993)
  • A.D. Becke

    Phys. Rev. A

    (1988)
  • C.M. Brown et al.

    Chem. Mat.

    (1996)
  • G.E. Brown

    Chem. Rev.

    (1999)
  • R. Car et al.

    Phys. Rev. Lett.

    (1985)
  • P. Carloni, M. Sprik, W. Andreoni, J. Phys. Chem. 104 (2000)...
  • D.M. Ceperley et al.

    Phys. Rev. Lett.

    (1980)
  • J. Perdew et al.

    Phys. Rev. B

    (1981)
  • L.J. Clarke et al.

    Comp. Phys. Commun.

    (1993)
  • R. Colle et al.

    J. Am. Chem. Soc.

    (1998)
  • See e.g. Conjugated Polymers and Related Materials: The Interconnection of Chemical and Electronic Structure, Oxford...
  • CPMD 3.0 Copyright IBM Corporation (1990–1997) and MPI Festkörperforschung Stuttgart,...
  • A. Curioni, W. Andreoni, Synth. Metals, in...
  • A. Curioni et al.

    J. Am. Chem. Soc.

    (1999)
  • A. Curioni et al.

    J. Am. Chem. Soc.

    (1994)
  • A. Curioni et al.

    J. Am. Chem. Soc.

    (1997)
  • A. Curioni et al.

    Appl. Phys. Lett.

    (1998)
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