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Ab Initio Molecular Dynamics

Book Description

Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques in order that readers can understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely-used Car-Parrinello approach, correcting various misconceptions currently found in research literature. The book also contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly-used program packages, and enabling developers to improve and add new features in their code.

Table of Contents

  1. Cover
  2. Half Title
  3. Title Page
  4. Copyright
  5. Contents
  6. Preface
  7. 1. Setting the stage: why ab initio molecular dynamics?
  8. Part I: Basic techniques
    1. 2. Getting started: unifying MD and electronic structure
      1. 2.1 Deriving classical molecular dynamics
      2. 2.2 Ehrenfest molecular dynamics
      3. 2.3 Born–Oppenheimer molecular dynamics
      4. 2.4 Car–Parrinello molecular dynamics
      5. 2.5 What about Hellmann–Feynman forces?
      6. 2.6 Which method to choose?
      7. 2.7 Electronic structure methods
      8. 2.8 Basis sets
    2. 3. Implementation: using the plane wave basis set
      1. 3.1 Introduction and basic definitions
      2. 3.2 Electrostatic energy
      3. 3.3 Exchange and correlation energy
      4. 3.4 Total energy, gradients, and stress tensor
      5. 3.5 Energy and force calculations in practice
      6. 3.6 Optimizing the Kohn–Sham orbitals
      7. 3.7 Molecular dynamics
      8. 3.8 Program organization and layout
    3. 4. Atoms with plane waves: accurate pseudopotentials
      1. 4.1 Why pseudopotentials?
      2. 4.2 Norm-conserving pseudopotentials
      3. 4.3 Pseudopotentials in the plane wave basis
      4. 4.4 Dual-space Gaussian pseudopotentials
      5. 4.5 Nonlinear core correction
      6. 4.6 Pseudopotential transferability
      7. 4.7 Example: pseudopotentials for carbon
  9. Part II: Advanced techniques
    1. 5. Beyond standard ab initio molecular dynamics
      1. 5.1 Introduction
      2. 5.2 Beyond microcanonics: thermostats, barostats, metadynamics
      3. 5.3 Beyond ground states: ROKS, surface hopping, FEMD, TDDFT
      4. 5.4 Beyond classical nuclei: path integrals and quantum corrections
      5. 5.5 Hybrid QM/MM molecular dynamics
    2. 6. Beyond norm-conserving pseudopotentials
      1. 6.1 Introduction
      2. 6.2 The PAW transformation
      3. 6.3 Expectation values
      4. 6.4 Ultrasoft pseudopotentials
      5. 6.5 PAW energy expression
      6. 6.6 Integrating the Car–Parrinello equations
    3. 7. Computing properties
      1. 7.1 Perturbation theory: Hessian, polarizability, NMR
      2. 7.2 Wannier functions: dipole moments, IR spectra, atomic charges
    4. 8. Parallel computing
      1. 8.1 Introduction
      2. 8.2 Data structures
      3. 8.3 Computational kernels
      4. 8.4 Massively parallel processing
  10. Part III: Applications
    1. 9. From materials to biomolecules
      1. 9.1 Introduction
      2. 9.2 Solids, minerals, materials, and polymers
      3. 9.3 Interfaces
      4. 9.4 Mechanochemistry and molecular electronics
      5. 9.5 Water and aqueous solutions
      6. 9.6 Non-aqueous liquids and solutions
      7. 9.7 Glasses and amorphous systems
      8. 9.8 Matter at extreme conditions
      9. 9.9 Clusters, fullerenes, and nanotubes
      10. 9.10 Complex and fluxional molecules
      11. 9.11 Chemical reactions and transformations
      12. 9.12 Homogeneous catalysis and zeolites
      13. 9.13 Photophysics and photochemistry
      14. 9.14 Biophysics and biochemistry
    2. 10. Properties from ab initio simulations
      1. 10.1 Introduction
      2. 10.2 Electronic structure analyses
      3. 10.3 Infrared spectroscopy
      4. 10.4 Magnetism, NMR and EPR spectroscopy
      5. 10.5 Electronic spectroscopy and redox properties
      6. 10.6 X-ray diffraction and Compton scattering
      7. 10.7 External electric fields
    3. 11. Outlook
  11. Bibliography
  12. Index