Details

Autor(en) / Beteiligte

• Sadus, Richard J.,

Titel

Molecular simulation of fluids : theory, algorithms, object-orientation, and parallel computing

Auflage

Second edition

Ort / Verlag

Cambridge, Mass. : Elsevier B.V.,

Erscheinungsjahr

[2024]

Beschreibungen/Notizen

• Includes bibliographical references and index.
• Intro -- Title page -- Table of Contents -- Copyright -- Dedication -- Preface to the second edition -- Preface to the first edition -- Chapter 1. Introduction -- Abstract -- 1.1 What is molecular simulation? -- 1.2 Progress in molecular simulation -- References -- Chapter 2. Ensembles, thermodynamic averages, and particle dynamics -- Abstract -- 2.1 Statistical mechanics, ensembles, and averaging -- 2.2 Properties from fluctuations -- 2.3 Alternative methods for thermodynamic properties -- 2.4 Particle dynamics -- 2.5 Summary -- References -- Chapter 3. Intermolecular pair potentials and force fields -- Abstract -- 3.1 Calculation of the potential energy -- 3.2 Intermolecular forces -- 3.3 Potentials with a hard sphere contribution -- 3.4 Soft sphere potentials -- 3.5 Fully interpenetrable potentials -- 3.6 Effective pairwise potentials for atoms and simple molecules -- 3.7 Contributions to molecular interactions -- 3.8 Simple atom-based pairwise potentials for molecules -- 3.9 Extension to molecules -- 3.10 Pairwise force fields from molecular mechanics -- 3.11 Case study: Models for water -- 3.12 Application to mixtures -- 3.13 Summary -- References -- Chapter 4. Ab initio, two-body and three-body intermolecular potentials -- Abstract -- 4.1 Ab initio calculations -- 4.2 Two-body atomic potentials -- 4.3 Three-body atomic potentials -- 4.4 Four- and higher-body atomic interactions -- 4.5 Potentials for molecules -- 4.6 Case study: Augmenting ab initio potentials for fluid properties -- 4.7 Summary -- References -- Chapter 5. Calculating molecular interactions -- Abstract -- 5.1 Calculation of short-range interactions -- 5.2 Calculation of long-range interactions -- 5.3 Summary -- References -- Chapter 6. Monte Carlo simulation -- Abstract -- 6.1 Basic concepts -- 6.2 Application to molecules -- 6.3 Advanced techniques.
• 6.4 Path integral Monte Carlo -- 6.5 Summary -- References -- Chapter 7. Integrators for molecular dynamics -- Abstract -- 7.1 Integrating the equations of motion -- 7.2 Gear predictor-corrector methods -- 7.3 Verlet predictor methods -- 7.4 Runge-Kutta integration -- 7.5 Comparison of integrators -- 7.6 Integrators for molecules -- 7.7 Summary -- References -- Chapter 8. Nonequilibrium molecular dynamics -- Abstract -- 8.1 An example NEMD algorithm -- 8.2 Synthetic NEMD algorithms -- 8.3 Application of NEMD algorithms to molecules -- 8.4 Application of NEMD algorithms to mixtures -- 8.5 Comparison with EMD -- 8.6 Summary -- References -- Chapter 9. Molecular simulation of ensembles -- Abstract -- 9.1 Monte Carlo -- 9.2 Molecular dynamics -- 9.3 Summary -- References -- Chapter 10. Molecular simulation of phase equilibria -- Abstract -- 10.1 Calculating the chemical potential -- 10.2 Gibbs ensemble Monte Carlo -- 10.3 MD Gibbs ensemble -- 10.4 NpT + test particle -- 10.5 Gibbs-Duhem integration -- 10.6 Thermodynamic scaling -- 10.7 Pseudo-ensemble methods -- 10.8 Histogram reweighting algorithms -- 10.9 Finite-size scaling -- 10.10 Empirically based simulation algorithms -- 10.11 Accurate determination of SLE -- 10.12 Summary -- References -- Chapter 11. Molecular simulation and object-orientation -- Abstract -- 11.1 Fundamental concepts of OO -- 11.2 Case study: application of OO to the microcanonical MD simulation of Lennard-Jones atoms -- 11.3 Case study: application of object orientation to the microcanonical MC simulation of Lennard-Jones atoms -- 11.4 Case study: combined MD and MC program for Lennard-Jones atoms in the microcanonical ensemble -- 11.5 Case study: extensions -- 11.6 Summary -- References -- Chapter 12. GPU and CPU parallel molecular simulation with CUDA and MPI -- Abstract -- 12.1 Basic GPU implementations with CUDA.
• 12.2 Case study: CUDA implementation of MD code (/mdCU_Ver2.0) -- 12.3 Case study: CUDA implementation of MC code (/mcCU_Ver2.0) -- 12.4 Parallel programming with MPI -- 12.5 Case study: MPI implementation of MD code (/mdMPI_Ver2.0) -- 12.6 Case study: MPI implementation of MC code (/mcMPI_Ver2.0) -- 12.7 Case study: relative performance of MD and MC MPI and GPU codes -- 12.8 Summary -- References -- Appendix 1. Software user's guide -- A.1 C++ code for the molecular dynamics simulation of -- A.2 C++ code for the Monte Carlo simulation of Lennard-Jones -- A.3 C++ code for the combined Monte Carlo and molecular -- A.4 CUDA code for the molecular dynamics simulation of -- A.5 CUDA code for the Monte Carlo simulation of -- A.6 MPI code for the molecular dynamics simulation of -- A.7 MPI code for the molecular dynamics simulation of -- A.8 Compilation -- Appendix 2. List of algorithms -- Appendix 3. Notation -- Acronyms and abbreviations -- Latin alphabet -- Greek alphabet -- Subscripts and superscripts -- Index.
• Description based on print version record.