In a way the MOTECC-89 project started in the early sixties at the IBM Research Laboratory in San Jose, California. The six years of post-doctoral research, first with Giulio Natta on conductive polymers, with Michael Kasha on spin-orbit effects, with Kenneth S. Pitzer on high temperature molecules and thermo dynamics and with R. S. Mulliken in the quantum chemistry of small molecules had demonstrated pragmatically the importance of a broad-based research and also let me taste some of the excitement to be derived from interdisciplinarity. Thus when I started to gather a department in the newly opened IBM Research Laboratory in San Jose, California, I purposely named it "Large Scale Scientific Computation Department," avoiding reference to chemistry, physics, statistical mechanics or fluid dynamics, which were our main tasks. In the sixties interdisciplinarity was more and more recognized as a most important if not nec essary avenue to cope with the technical needs of our society. However, at that time interdisciplinarity was synonymous with "team work," and true interdisciplinarity was a formidably difficult objective. Although I headed an excellent group of scientists with different backgrounds and there was much progress and creativity, still each one of us was more or less conducting his own research in his own field with occasional cross-field partnerships and with some of the computational techniques as our common base. Later, in 1974, I made a second attempt, this time starting a new department at the Donegani Institute, Montedison, in Novara, Italy.
Sprache
Verlagsort
Verlagsgruppe
Zielgruppe
Für Beruf und Forschung
Research
Illustrationen
Maße
Gewicht
ISBN-13
978-90-72199-05-8 (9789072199058)
DOI
10.1007/978-94-010-9057-5
Schweitzer Klassifikation
1. Introduction to MOTECC-89.- Productivity, Global Simulations and Evolution.- An Overview of MOTECC-89.- An Example of Global Simulation.- 1CAP 3090: Parallel Processing.- The 1CAP 3090 Experimental System.- Parallel Processing Performance Issues.- Early 1CAP Systems.- Conclusions.- 2. A Few Reminders of Basic Mechanics.- to Classical Mechanics.- From Newton to Liouville.- The Evolution to Statistical Mechanics.- Langevin Dynamics.- Fluid Mechanics, The Navier Stokes Equations.- to Quantum Mechanics.- Physical Examples of the Equations of Mechanics.- From d'Alembert to Lagrangian Equations.- The Lagrange Equations.- Hamilton's Equations.- Vibrational Motion and the Harmonic Oscillator.- Classical Anharmonic Oscillation.- Lagrangian Multipliers.- Statistical Mechanics, Boltzmann and Kramers Equations.- Equations of Motion of a Compressible Viscous Fluid.- The Deborah Number.- The Reynolds Number.- The Mach Number.- 3. Independent Electron Models: Hartree-Fock for Many-Electron Atoms.- The Analytic Hartree-Fock Method.- Open Shell Methods and Roothaan Vector Coupling Coefficients.- Basis Sets for Atomic Computations.- Optimization of Orbital Exponents.- Contraction Coefficients.- Geometrical Basis Sets.- Matrix Elements, Spherical Symmetry and Integrals.- The Correlation and Pair Correlation Energies.- Configuration and Momentum Expectation Values.- The Finite Element Method (FEM).- 4. Kinetically Balanced Geometric Gaussian Basis Set Calculations for Relativistic Many Electron Atoms.- Preliminary.- Matrix Elements of the Hamiltonian.- Choice of Basis Sets.- Relativistic Hartree-Fock-Roothaan Equation.- Angular Coefficients.- Evaluation of Matrix Elements.- Finite Nucleus Approximation.- Open-Shell Calculations.- Vector Coupling Coefficients 191Numerical Results.- Conclusions.- 5. Hylleraas Configuration Interaction Method Using Gaussian Functions.- Theory.- Applications and Specific Examples.- Two-Electron Integral Formulas.- The S Integral.- The K Integral.- The N Integral.- The R(ij) Operator.- Three-Electron Integral Formulas.- The S Integral.- The T Integral.- The K Integral.- The N Integral.- Four-Electron Integral Formulas.- The S Integral.- The T Integral.- The U Integral.- 6. KGNMOL: A Program for Molecular Interactions.- Gaussian Type Functions.- The Hydrogen Molecule.- One-Electron Integral Formulae.- Two-Electron Integral Formulae.- General Analytical Formulae.- Special Formulas for Integrals Involving s- and p-Type Functions.- Two-Electron Integrals with Explicit Factorization of the One-Electron Terms.- Geometrical Basis Sets and Their Use.- Special Options for Adding Fragments or Molecules.- Basis Set Superposition Error.- Ab Initio Computation of Large Molecules.- MP2 Option and Parallelization.- Normalization of Gaussian Type Functions.- The Gaussian Product Theorem.- Integrals Related to the Gamma Function.- Incomplete Gamma Function.- The Complete Gamma Function.- 7. HONDO: A General Atomic and Molecular Electronic Structure System.- Wavefunctions and Energies.- Closed Shell Hartree-Fock (SCF).- Spin Unrestricted Open Shell Hartree-Fock (UHF).- High Spin Restricted Open Shell Hartree-Fock (ROHF).- General Restricted Open Shell Hartree-Fock and Generalized Valence Bond (ROHF-GVB).- Configuration Interaction (CI).- Multiconfiguration Hartree-Fock (MCSCF).- Moller-Plesset Perturbation (MP2, MP3, MP4).- Electronic Properties.- Dipole Polarizability and Hyperpolarizabilities.- Molecular Structure Options.- Equilibrium Structure Determination.- Transition State Determination.- Force Constant Calculation.- Infrared and Raman Intensities Calculation.- Reaction Pathway Determination.- Potential Surface Scan.- Non-Gradient Optimization.- Miscellaneous Features.- Integrals and Derivatives.- Point Group Symmetry.- Other Features.- Illustrative Examples.- 8. Monte Carlo and Molecular Dynamics Simulations.- Interaction Potentials.- The Monte Carlo Method.- The Molecular Dynamics Method.- Numerical Integration for the Equations of Motion.- Calculation of Properties.- Periodic Boundary Conditions and Long Range Forces.- Applications and Examples.- Preliminary Study for a New Water-Water Potential.- MD Simulation with a Flexible Water-Water Potential.- Water Simulation in a Crystal of Myoglobin.- BPTI Simulations in Vacuo and in Solution: Preliminary Results.- MD Simulation of Liquid Water with the Expanded Polarization Model.- Free Energy Calculations.- 9. Brownian Dynamics Simulation.- Classical Brownian Theory for Translational Diffusion.- Algorithm.- Implementation for Flexible Protein Dynamics.- Rotational Brownian Motion of Non-Spherical Particles.- Description of Results.- Results for a Finite Peclet Number.- 10. Micro-Hydrodynamics.- Molecular Dynamics Simulations.- Cellular Automata.- Applications and Discussion of Results.- 11. The Equations of Fluid Flow and Their Solution by Finite Element Methods.- The Equations of Fluid Flow.- Derivation of the Navier Stokes Equations.- Reduction to Various Specific Forms.- The Finite Element Method.- The Method of Weighted Residuals.- The H-Version of the Finite Element Method.- The P-Version of the Finite Element Method.- Solution Techniques.- Direct Solution Methods.- Iterative Methods.- Overview of Preconditioning Techniques.- Multilevel Solution Method.- Computational Solution of the Navier Stokes Equations.- Parallel Implementation of the Solution Scheme.- Turbulent Flow.- Reynolds Equations.- Empirical Relations for the Reynolds Stress Tensor.- Direct Numerical Simulation of Isotropic Turbulent Flows.- Dealiasing.- Time Stepping Scheme.- Parallel Implementation of the Numerical Scheme.- Results.- 12. Visualization Techniques for Science and Engineering.- The graPHIGS Application Programming Interface.- Requirements for Molecular Graphics Applications.- The User Interface.- Display of Molecular Models.- Display of Electron Densities and Molecular Orbitals.- Creation and Manipulation of Molecules.- Molecule Building from Templates.- Inquiry of Geometrical Parameters.- Display of Molecular Vibrations.- Animations.- Files Manipulation.- Towards More Realistic Images.- Definition of the Image.- Geometry.- Optical Characteristics.- Viewing and Illumination.- Calculation of Ray Trajectories.- Evaluation of Picture Elements.- Direct Illumination.- Indirect Illumination.- Ambient Illumination.- Adaptive Anti-Aliasing.- Animations of Realistic Images.- Animation Hardware.- Selection of the Recording Medium.- A Video Cassette Recorder Animation System.- The Configuration of the IBM PC-AT.- The Animation Recording Hardware.- An Animation Control Program for the PC-AT.- Windows Oriented Interfaces for Input Specification.- 13. Parallel Algorithms.- General Principles.- Basic Matrix Operators.- Gram Schmidt Projection.- The Gauss Transform.- The Givens Rotation.- The Householder Transform.- Linear System Solvers.- LU Factorization.- Preconditioned Conjugate Gradient Methods.- Real Symmetric Eigenvalue Solvers.- Jacobi Diagonalization.- The Symmetric QR Algorithm.- Orthogonal Basis Set Generation.- Conclusions.- 14. SIRIUS: A General Purpose Direct Second Order MCSCF Program.- 15. Electron Correlation Energy from Hartree-Fock-Type Densities.- The Colle-Salvetti Functional.- The Lie-Clementi Functional.- Expressions for GL-SPP, VWN-SPP and PZ Functional.- Discussion.
