Riassunto
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.
Contenuti
to MOTECC-90.- Global Simulations.- MOTECC: A First “Assembly Line” to Produce Chemical Information.- An Example of Global Simulation: From 3 Nuclei and 10 Electrons to a Million Molecules.- 1CAP 3090: Parallel Processing for Large Scale Scientific and Engineering Problems.- The 1CAP 3090 Experimental System.- Parallel Processing Performance Issues.- Early 1CAP Systems.- Conclusions.- References.- 2. 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.- Density Functionals for Atomic Computations.- Configuration and Momentum Expectation Values.- The Finite Element Method (FEM).- Appendix 2A: Two-Electron Integrals.- Appendix 2B: Pseudopotentials.- References.- 3. 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.- Numerical Results.- Conclusions.- References.- 4. Non-Relativistic Configuration Interaction Calculations for Many-Electron Atoms: ATOMCI.- Tensor Operator.- Recoupling Transformation.- Complete Set of Shell States.- Shell Creation Tensor Operators in LS Scheme.- Complete Shell States in LSQ Scheme.- Generation of Shell States in ATOMCI.- Matrix Elements.- Orthonormal Tensors for Many Shells.- Hamiltonian Operator.- Reduction Formulas for Matrix Elements.- Appendix 4A: Simply Reducible Group.- Integer Representation and Half Integer Representation.- Even and Odd Representation.- Three-j Symbols.- Six-j Symbols and Nine-j Symbols.- Appendix 4B: Rotation Group.- References.- 5. HYCOIN: Hylleraas Configuration Interaction Method Using Gaussian Functions.- Theory.- Applications and Specific Examples.- Appendix 5A: Two-Electron Integral Formulas.- The S Integral.- The K Integral.- The N Integral.- Appendix 5B: The R(ij) Operator.- Appendix 5C: Three-Electron Integral Formulas.- The S Integral.- The T Integral.- The K Integral.- The N Integral.- Appendix 5D: Four-Electron Integral Formulas.- The S Integral.- The T Integral.- The U Integral.- Appendix 5E: Exponential Integral Formulas.- The SE Integral.- The EE Integral.- The KE Integral.- The NE Integral.- References.- 6. HONDO: A General Atomic and Molecular Electronic Structure System.- Wavefunctions and Energies.- Closed Shell Hartree-Fock (SCF) Wavefunction.- Spin Unrestricted Open Shell Hartree-Fock (UHF) Wavefunction.- High Spin Restricted Open Shell Hartree-Fock (ROHF) Wavefunction.- General Restricted Open Shell Hartree-Fock and Generalized Valence Bond (ROHF-GVB) Wavefunctions.- Configuration Interaction (CI) Wavefunction.- Multiconfiguration Hartree-Fock (MCSCF) Wavefunction.- 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.- Crossing Seam Minimum Energy Point Determination.- Non-Gradient Optimization.- Other Options.- Electron Transfer Reactions.- Effective Core Potentials.- Representation of An External Field.- Miscellaneous Features.- Integrals and Derivatives.- Point Group Symmetry.- Illustrative Examples.- References.- 7. KGNMOL: A Program for Large Molecules and Molecular Interactions.- Ab Initio Computation of Large Molecules.- Basis Sets: Gaussian Type Functions.- The Hydrogen Molecule and the Water Dimer.- Basis Set Superposition Error (BSSE).- Special Options for Adding Fragments or Molecules: ADD Option.- Parallelization of KGNMOL and the MP2 Option.- Density Functional for Molecules.- Clementi-Chakravorty Electron-Pair Functional.- Program Organization and Routes.- One-Electron Integral Fonnulae.- 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 Dependent Terms.- Geometrical Basis Sets and Their Use.- A New Loop Structure for Uncontracted Geometrical Basis Sets.- Appendix 7A: Normalization of Gaussian Type Functions.- Appendix 7B: The Gaussian Product Theorem.- Appendix 7C: Integrals Related to the Gamma Function.- Appendix 7D: Incomplete Gamma Function.- Definition of the Incomplete Gamma Function.- Use of Taylor Series Expansions.- Asymptotic Series for the Incomplete Gamma Function.- Use of Tabular Interpolation.- Appendix 7E: The Complete Gamma Function.- References.- 8. SIRIUS: A General Purpose Direct Second Order MCSCF Program.- Why MCSCF?.- Summary of Program Features.- Theory.- Orbital Based Quantum Chemistry: The Hamiltonian.- Parameterization and Orbital Classes.- Restricted Active Space Wavefunctions.- Design of the MCSCF Wavefunction.- Restricted-step, Second-order MCSCF Optimization.- The Direct Iterative NEO Algorithm.- Implementation.- Orbital Classes, Gradient and NEO Transformation.- The Macro Iterations, Step Calculation, and Step Control.- The Micro Iterations, The Dynamical Updating of the Damping Factor, and the Direct MCSCF Step.- Integral Transformations.- Step-Control Algorithm.- Direct Configuration Interaction Theory.- RAS-CI Expansions in a CSF Basis.- Slater Determinants and Strings.- Direct CI for RAS Expansions.- Construction of Density Matrices.- Counter Rotations of CI Coefficients.- Auxiliary Optimization Algorithms.- Split Configuration and Orbital Trial Vectors.- Optimal Orbital Trial Vectors.- Convergence of Solution Vectors in Direct NEO and NR Algorithms.- Transformation to Natural and Fock Type Orbitals.- Intermediate Optimization of Orbitals for Fixed Configuration Coefficients.- Initial Guess of Orbitals and Configuration Coefficients.- Optimization of Core Hole States.- Survey of Applications.- List of General Applications.- Applications on Core Electron Spectra.- Appendix 8A: Calculation of the Orbital Part of Gradient Vectors and Sigma Vectors.- Appendix 8B: Calculation of Generalized Fock Matrices from Regular and One-Index Transformed Integrals.- Appendix 8C: The Diagonal of the Orbital Hessian Matrix.- Appendix 8D: Iterative Solution of CI Eigenvalue Problem.- References.- 9. MOLCAS: A General Purpose Quantum Chemistry Program System for Correlated Wavefunctions.- Program Descriptions.- Integral Evaluation and Handling.- The Two-Electron Transformation Program MOTRA.- The Self Consistent Field (SCF) Program.- The Restricted Active Space (RAS) SCF Program.- The RAS State Interaction (RASSI) Program.- The Configuration Interaction Programs.- Many Body Perturbation Theory (MBPT) Programs.- The Molecular Properties Program.- A Timing Example, The Pyrimidine Molecule.- Concluding Remarks.- References.- 10. MELD: A Many Electron Description.- Integrals.- One-Electron Integrals, Closed Form.- Other One-Electron Integrals.- Two-Electron Integrals.- Auxiliary Functions.- Charge Distributions.- Pseudo Potentials.- Symmetrized Integrals.- Self Consistent Field.- Integral Transformation.- Configuration Interaction.- Eigenvalue Program.- Molecular Properties.- References.- 11. ALCHEMY II: A Research Tool for Molecular Electronic Structure and Interactions.- ALCHEMY II Program Modules.- Weak Molecular Interactions.- The He ― H2O Interaction.- Approximate ICF Configuration Spaces.- Appendix 11A: The MOLECULE Integral Generator.- Appendix 11B: Algorithm for Large Scale Second.- Order MCSCF Calculations.- Overview of the MCSCF Method.- Second Order MCSCF Equation.- Orbital Gradient.- CI Gradient.- Orbital Hessian.- CI-Orbital Coupling.- CI Hessian.- Large CI Expansions.- Matrix Formulation of Orbital Hessians.- Orbital Hessian.- Integral Transformation.- Iterative Solution of MCSCF Equations.- Iterative Solution of a System of Linear Equations.- Convergence Threshold.- The CI Portion of VX.- The Prototype CI Method.- Overview.- Prototype Configurations.- Prototype Matrices.- Prototype Diagonal Matrices.- Prototype Singles Matrices.- Prototype Doubles Matrices.- Discussion.- References.- 12. Continuum by L2 Methods: Molecular Photoionization Cross Section.- Molecular States in the Electronic Continuum.- The K-Matrix Technique.- The Partial Wave Channels.- The L2 Basis Set Approximation.- RPA Matrix Elements in the Continuum.- One- and Two-Photons Transition Matrix Elements.- One-Photon Transitions.- Two-Photon Transitions.- Integral Cross Section by L2 Methods.- Stieltjes Imaging.- Generalization of the Stieltjes Imaging.- Computational Aspects.- The Basis Set.- One-Photon Ionization.- Two-Photon Ionization.- Appendix 12A: Rotationally Averaged Differential Cross Sections.- References.- 13. Dirac-Fock Self-Consistent Field Calculations for Closed Shell Molecules with Kinetic Balance and Finite Nuclear Size.- Preliminary.- Choice of Basis Spinors.- Evaluation of One-Electron and Two-Electron Matrix Elements.- Evaluation of Small-Component Matrix Elements.- Evaluation of Primitive Integrals in Cartesian Form.- Concluding Remarks.- Appendix 13A: Finite Nuclear Size Corrections.- Appendix 13B: Eulerian Angles and Rotation Matrix Elements.- References.- 14. First Principles Molecular Dynamics.- The Interatomic Potential Within DF Theory.- A Dynamical Approach to Energy Functional Minimization.- Molecular Dynamics in the Coupled Electron-Ion Parameter Space.- Conclusions.- References.- 15. LCAO Ab Initio Band Structure Calculations for Polymers.- The Periodic Model of a Polymer Chain.- Principles of LCAO Band Structure Calculations on Polymers.- The Electrostatic Balance Between the Nucleus- and Electron-Electron Interactions.- Multipole Expansion for Long-Range Coulomb Interactions.- The Short- or Long-Rangeness Character of the Exchange Contribution.- Use of Screw Symmetry in Polymer Calculations.- A Simulated Ab Initio Technique: The Valence Effective Hamiltonian (VEH).- Particular Aspects of Computer Implementation.- Band Structure Calculations.- Summation Over Polymeric States and Integrations Over First Brillouin Zones.- Basis Set Linear Dependence.- Band Indexing Difficulty.- Density of States Calculations.- Graphics Interface: BandDos.- Applications.- Appendix 15 A: Tables of VEH Parameters.- Single-Zeta Potentials.- Double-Zeta Potentials.- References.- 16. BNDPKG2: A Linear Combination of Gaussian Orbitals (LCGO) Band Structure Program for Cubic Crystals With One Atom Per Unit Cell.- The LCGO Method for Energy Band Calculations.- BNDPKG 2.- Sample BNDPKG 2 Calculations.- References.- 17. Monte Carlo and Molecular Dynamics Simulations.- Interaction Potentials.- Ab Initio Pair Potentials for DNA-Protein Interactions.- Model Molecules.- Ab Initio Calculations.- Classification of Atoms.- Analytical Form of the Pair Potentials.- Fitting Procedure.- Discussion.- The Monte Carlo Method.- The Molecular Dynamics Method.- Numerical Integration for the Equations of MotionCalculation of Properties.- Calculation of Properties.- Properties Related to Neutron Scattering Experiments.- Periodic Boundary Conditions and Long Range Forces.- Applications and Examples.- Simulation of Liquid Water with the NCC Potential.- MD Simulation With a Flexible Water-Water Potential.- BPTI Simulations in Vacuo and in Solution.- Neutron Scattering Properties.- Water Simulation in a Crystal of Myoglobin.- Local Structural and Dynamical Properties.- Appendix 17A: Free Energy Calculations.- References.- 18. Molecular Dynamics Simulations of Fluid Flows.- Computational Algorithm for a Large Scale Molecular Dynamic Simulation.- Applications and a Discussion of Results.- References.- 19. Brownian Dynamics Simulations of a Complex Fluid System.- Brownian Dynamic Simulation: Basic Concepts.- Fokker-Planck Description.- Langevin Description.- The Simulation Program “BROWNIAN”: An Overview.- The Nonlinear Rheology of the Colloidal Suspension.- Discussion.- Shear Induced Phase Transition in the Colloidal Suspension.- Generalized Brownian Dynamics Techniques.- References.- 20. Cellular Automata.- Cellular Automata.- Two-Dimensional Lattice-Gas Automata.- Simulation of 2D Fluid Flows.- Three-Dimensional Lattice-Gas Automata.- References.- 21. 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.- References.- 22. The Equations of Elasticity and Their Solution by Finite Element Methods.- The Equations of Elasticity.- Computational Techniques for Linear Static Analysis.- Solution of Large 3-D Problems with Finite Elements.- Iterative Solution with the Congugate Gradient Method.- Rapid Operator Application.- Utility of Rapid Operator Application.- Parallel Implementation of Iterative Schemes.- References.- 23. Modeling of Atmospheric Pollutant Transport in Shorelines.- Model Development and Governing Equations.- Equations for the Mesoscale Variables.- Equations for the Synoptic Scale Variables.- Boundary Layer Parameterization.- Diffusivities in the Surface Layer.- Diffusivities in the Planetary Boundary Layer.- Numerical Methods.- Initial and Boundary Conditions.- Summertime Flow Over a Lake.- Summary and Conclusions.- References.- 24. Visualization Techniques and Windowing Interfaces: KGNGRAF, XWIB and REMOTE.- The graPHIGS Application Programming Interface.- to KGNGRAF.- The User Interface.- Display of Molecular Models.- Display of Electron Densities and Molecular Orbitals.- Creation and Manipulation of Molecules.- Superposition of Molecular Structures.- Molecule Building from Templates.- Protein Building from Templates.- Inquiry of Geometrical Parameters.- Display of Molecular Vibrations and Molecular Spectra.- Display of Molecular Energy Diagrams.- Interactive Animations.- Files Manipulation.- Towards More Realistic Images.- Ray Tracing for Molecules.- 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.- XWIB: An X Window Interface Builder.- Format Checking.- Dependency Handling Mechanisms.- Help Messages.- On-Line Documentation.- Other Utility Functions.- REMOTE: Remote File Transfer and Execution.- References.- 25. LCAP: Loosely Coupled Array of Processors Parallel Processing Software.- The Rationale for Parallelism.- Application Characteristics.- Configuration Characteristics.- How LCAP Simplifies Parallel Programming.- LCAP Design Philosophy.- Adapting to a Production Parallel Environment.- LCAP 3090 Design Principles.- LCAP Features for Effective Parallelism.- Features in the Precompiler.- Features with Parallel Calls.- Features with Shared Commons.- Performance Results Attained.- Conclusions.- 26. Parallel Algorithms.- General ...
Le informazioni nella sezione "Su questo libro" possono far riferimento a edizioni diverse di questo titolo.
