Large-scale normal coordinate analysis for molecular structures

Chao Yang, Barry W. Peyton, Donald W. Noid, Bobby G. Sumpter, Robert E. Tuzun

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

Abstract

We apply truncated RQ-iteration (TRQ) and the Jacobi-Davidson (JD) method to perform vibrational (eigenvalue) analysis for large-scale molecular systems. Both algorithms employ a preconditioned iterative solver to construct a low-dimensional subspace that contains desired vibrational modes. We discuss several strategies for speeding up the eigenvalue calculation. In particular, we illustrate how to construct effective preconditioners and analyze the quality of these preconditioners. We show that convergence can be improved by choosing appropriate shifts and deflating the translational and rotational modes. Numerical examples are provided to demonstrate the efficiency of our computation.

Original languageEnglish
Pages (from-to)563-582
Number of pages20
JournalSIAM Journal on Scientific Computing
Volume23
Issue number2
DOIs
StatePublished - 2002
Externally publishedYes

Keywords

  • Eigenvalue computation
  • Normal coordinate analysis
  • Preconditioner

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