Numerical simulation in molecular dynamics : numerics, algorithms, parallelization, applications

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Numerical simulation in molecular dynamics : numerics, algorithms, parallelization, applications / Michael Griebel, Stephan Knapek, Gerhard Zumbusch

資料種別:

図書

出版情報:

Berlin : Springer, c2007

形態:

xi, 470 p. ; 24 cm

シリーズ名:

Texts in computational science and engineering ; 5 <BA60746435>

著者名:

ISBN:

9783540680949 [3540680942]
9783642087769 [3642087760] (: pbk)

書誌ID:

BA82869042

子書誌情報

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書誌詳細

注記:

"With 180 Figures, 43 in Color, and 63 Tables"
Includes bibliographical references (p. [431]-466) and index

主題:

化学構造．分子構造

言語:

英語

目次情報:

Computer Simulation - a Key Technology / 1：

From the Schrodinger Equation to Molecular Dynamics / 2：

The Schrodinger Equation / 2.1：

A Derivation of Classical Molecular Dynamics / 2.2：

TDSCF Approach and Ehrenfest Molecular Dynamics / 2.2.1：

Expansion in the Adiabatic Basis / 2.2.2：

Restriction to the Ground State / 2.2.3：

Approximation of the Potential Energy Hypersurface / 2.2.4：

An Outlook on Methods of Ab Initio Molecular Dynamics / 2.3：

The Linked Cell Method for Short-Range Potentials / 3：

Time Discretization - the Stormer-Verlet Method / 3.1：

Implementation of the Basic Algorithm / 3.2：

The Cutoff Radius / 3.3：

The Linked Cell Method / 3.4：

Implementation of the Linked Cell Method / 3.5：

First Application Examples and Extensions / 3.6：

Collision of Two Bodies I / 3.6.1：

Collision of Two Bodies II / 3.6.2：

Density Gradient / 3.6.3：

Rayleigh-Taylor Instability / 3.6.4：

Rayleigh-Benard Convection / 3.6.5：

Surface Waves in Granular Materials / 3.6.6：

Thermostats, Ensembles, and Applications / 3.7：

Thermostats and Equilibration / 3.7.1：

Statistical Mechanics and Thermodynamic Quantities / 3.7.2：

Phase Transition of Argon in the NVT Ensemble / 3.7.3：

The Parrinello-Rahman Method / 3.7.4：

Phase Transition of Argon in the NPT Ensemble / 3.7.5：

Parallelization / 4：

Parallel Computers and Parallelization Strategies / 4.1：

Domain Decomposition for the Linked Cell Method / 4.2：

Implementation / 4.3：

Performance Measurements and Benchmarks / 4.4：

Application Examples / 4.5：

Collision of Two Bodies / 4.5.1：

Extensions to More Complex Potentials and Molecules / 4.5.2：

Many-Body Potentials / 5.1：

Cracks in Metals - Finnis-Sinclair Potential / 5.1.1：

Phase Transition in Metals - EAM Potential / 5.1.2：

Fullerenes and Nanotubes - Brenner Potential / 5.1.3：

Potentials with Fixed Bond Structures / 5.2：

Membranes and Minimal Surfaces / 5.2.1：

Systems of Linear Molecules / 5.2.2：

Outlook to More Complex Molecules / 5.2.3：

Time Integration Methods / 6：

Errors of the Time Integration / 6.1：

Symplectic Methods / 6.2：

Multiple Time Step Methods - the Impulse Method / 6.3：

Constraints - the RATTLE Algorithm / 6.4：

Mesh-Based Methods for Long-Range Potentials / 7：

Solution of the Potential Equation / 7.1：

Boundary Conditions / 7.1.1：

Potential Equation and Potential Decomposition / 7.1.2：

Decomposition of the Potential Energy and of the Forces / 7.1.3：

Short-Range and Long-Range Energy and Force Terms / 7.2：

Short-Range Terms - Linked Cell Method / 7.2.1：

Long-Range Terms - Fast Poisson Solvers / 7.2.2：

Some Variants / 7.2.3：

Smooth Particle-Mesh Ewald Method (SPME) / 7.3：

Short-Range Terms / 7.3.1：

Long-Range Terms / 7.3.2：

Implementation of the SPME method / 7.3.3：

Application Examples and Extensions / 7.4：

Rayleigh-Taylor Instability with Coulomb Potential / 7.4.1：

Phase Transition in Ionic Microcrystals / 7.4.2：

Water as a Molecular System / 7.4.3：

Parallelization of the SPME Method / 7.5：

Example Application: Structure of the Universe / 7.5.2：

Tree Algorithms for Long-Range Potentials / 8：

Series Expansion of the Potential / 8.1：

Tree Structures for the Decomposition of the Far Field / 8.2：

Particle-Cluster Interactions and the Barnes-Hut Method / 8.3：

Method / 8.3.1：

Applications from Astrophysics / 8.3.2：

Parallel Tree Methods / 8.4：

An Implementation with Keys / 8.4.1：

Dynamical Load Balancing / 8.4.2：

Data Distribution with Space-Filling Curves / 8.4.3：

Applications / 8.4.4：

Methods of Higher Order / 8.5：

Cluster-Cluster Interactions and the Fast Multipole Method / 8.5.1：

Error Estimate / 8.6.1：

Comparisons and Outlook / 8.6.4：

Applications from Biochemistry and Biophysics / 9：

Bovine Pancreatic Trypsin Inhibitor / 9.1：

Membranes / 9.2：

Peptides and Proteins / 9.3：

Protein-Ligand Complex and Bonding / 9.4：

Prospects / 10：

Appendix / A：

Newton's, Hamilton's, and Euler-Lagrange's Equations / A.1：

Suggestions for Coding and Visualization / A.2：

Parallelization by MPI / A.3：

Maxwell-Boltzmann Distribution / A.4：

Parameters / A.5：

References

Index

Computer Simulation - a Key Technology / 1：

From the Schrodinger Equation to Molecular Dynamics / 2：

The Schrodinger Equation / 2.1：

A Derivation of Classical Molecular Dynamics / 2.2：

TDSCF Approach and Ehrenfest Molecular Dynamics / 2.2.1：

Expansion in the Adiabatic Basis / 2.2.2：

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