Jinghong Fan
Multiscale Analysis of Deformation and Failure of Materials
Jinghong Fan
Multiscale Analysis of Deformation and Failure of Materials
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Multiscale Analysis of Deformation and Failure of Materials systematically describes the background, principles, and methods within the exciting new field of multiscale analysis. It provides a digestible introduction to the complexities of the interdisciplinary field of multiscale modeling of deformation and failure analysis of materials, respecting the reader's need to critically think and absorb both information and perspective. This type of multiscale analysis has a broad scope of applications, encompassing different disciplines and practices and is an essential extension of…mehr
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Multiscale Analysis of Deformation and Failure of Materials systematically describes the background, principles, and methods within the exciting new field of multiscale analysis. It provides a digestible introduction to the complexities of the interdisciplinary field of multiscale modeling of deformation and failure analysis of materials, respecting the reader's need to critically think and absorb both information and perspective. This type of multiscale analysis has a broad scope of applications, encompassing different disciplines and practices and is an essential extension of mesomechanics.
Presenting cutting-edge research and development within multiscale modeling techniques and frameworks, Multiscale Analysis of Deformation and Failure of Materials systematically describes the background, principles and methods within this exciting new & interdisciplinary field. The author's approach emphasizes the principles and methods of atomistic simulation and its transition to the nano and sub-micron scale of a continuum, which is technically important for nanotechnology and biotechnology. He also pays close attention to multiscale analysis across the micro/meso/macroscopy of a continuum, which has a broad scope of applications encompassing different disciplines and practices, and is an essential extension of mesomechanics. Of equal interest to engineers, scientists, academics and students, Multiscale Analysis of Deformation and Failure of Materials is a multidisciplinary text relevant to those working in the areas of materials science, solid and computational mechanics, bioengineering and biomaterials, and aerospace, automotive, civil, and environmental engineering. * Provides a deep understanding of multiscale analysis and its implementation * Shows in detail how multiscale models can be developed from practical problems and how to use the multiscale methods and software to carry out simulations * Discusses two interlinked categories of multiscale analysis; analysis spanning from the atomistic to the micro-continuum scales, and analysis across the micro/meso/macro scale of continuum.
Presenting cutting-edge research and development within multiscale modeling techniques and frameworks, Multiscale Analysis of Deformation and Failure of Materials systematically describes the background, principles and methods within this exciting new & interdisciplinary field. The author's approach emphasizes the principles and methods of atomistic simulation and its transition to the nano and sub-micron scale of a continuum, which is technically important for nanotechnology and biotechnology. He also pays close attention to multiscale analysis across the micro/meso/macroscopy of a continuum, which has a broad scope of applications encompassing different disciplines and practices, and is an essential extension of mesomechanics. Of equal interest to engineers, scientists, academics and students, Multiscale Analysis of Deformation and Failure of Materials is a multidisciplinary text relevant to those working in the areas of materials science, solid and computational mechanics, bioengineering and biomaterials, and aerospace, automotive, civil, and environmental engineering. * Provides a deep understanding of multiscale analysis and its implementation * Shows in detail how multiscale models can be developed from practical problems and how to use the multiscale methods and software to carry out simulations * Discusses two interlinked categories of multiscale analysis; analysis spanning from the atomistic to the micro-continuum scales, and analysis across the micro/meso/macro scale of continuum.
Produktdetails
- Produktdetails
- Verlag: John Wiley & Sons / Wiley
- Seitenzahl: 512
- Erscheinungstermin: 4. Januar 2011
- Englisch
- Abmessung: 249mm x 175mm x 28mm
- Gewicht: 839g
- ISBN-13: 9780470744291
- ISBN-10: 0470744294
- Artikelnr.: 31187277
- Verlag: John Wiley & Sons / Wiley
- Seitenzahl: 512
- Erscheinungstermin: 4. Januar 2011
- Englisch
- Abmessung: 249mm x 175mm x 28mm
- Gewicht: 839g
- ISBN-13: 9780470744291
- ISBN-10: 0470744294
- Artikelnr.: 31187277
Jinghong Fan, Kazuo Inamori School of Engineering, Alfred University, Alfred, New York Dr. Jinghong Fan is a Professor of Mechanical Engineering at the Kazuo Inamori School of Engineering at Alfred University, Alfred, New York, USA. Dr. Fan serves as the Chairman of the Scientific Committee of the Research Center on Materials Mechanics at Chongqing University. He co-chaired the First and Second International Conference on Heterogeneous Materials Mechanics in 2004 and 2008. He has received several awards in his field, including the National Prize for Natural Science in China in 1987. Publications include books such as Foundation of Nonlinear Continuum Mechanics, 1988, and circa140 papers conference and journal papers. Dr. Fan has served as a guest editor of a number of journal special issues.
About the Author. Series Preface. Preface. Abbreviations. 1 Introduction.
1.1 Material Properties Based on Hierarchy of Material Structure. 1.2
Overview of Multiscale Analysis. 1.3 Framework of Multiscale Analysis
Covering a Large Range of Spatial Scales. 1.4 Examples in Formulating
Multiscale Models from Practice. 1.5 Concluding Remarks. References. 2
Basics of Atomistic Simulation. 2.1 The Role of Atomistic Simulation. 2.2
Interatomic Force and Potential Function. 2.3 Pair Potential. 2.4 Numerical
Algorithms for Integration and Error Estimation. 2.5 Geometric Model
Development of Atomistic System. 2.6 Boundary Conditions. 2.7 Statistical
Ensembles. 2.8 Energy Minimization for Preprocessing and Statistical
Mechanics Data Analyses. 2.9 Statistical Simulation Using Monte Carlo
Methods. 2.10 Concluding Remarks. References. 3 Applications of Atomistic
Simulation in Ceramics and Metals. Part 3.1 Applications in Ceramics and
Materials with Ionic and Covalent Bonds. 3.1 Covalent and Ionic Potentials
and Atomistic Simulation for Ceramics. 3.2 Born Solid Model for
Ionic-bonding Materials. 3.3 Shell Model. 3.4 Determination of Parameters
of Short-distance Potential for Oxides. 3.5 Applications in Ceramics:
Defect Structure in Scandium Doped Ceria Using Static Lattice Calculation.
3.6 Applications in Ceramics: Combined Study of Atomistic Simulation with
XRD for Nonstoichiometry Mechanisms in Y3Al5O12 (YAG) Garnets. 3.7
Applications in Ceramics: Conductivity of the YSZ Oxide Fuel Electrolyte
and Domain Switching of Ferroelectric Ceramics Using MD. 3.8 Tersoff and
Brenner Potentials for Covalent Materials. 3.9 The Atomistic Stress and
Atomistic-based Stress Measure. Part 3.2 Applications in Metallic Materials
and Alloys. 3.10 Metallic Potentials and Atomistic Simulation for Metals.
3.11 Embedded Atom Methods EAM and MEAM. 3.12 Constructing Binary and High
Order Potentials from Monoatomic Potentials. 3.13 Application Examples of
Metals: MD Simulation Reveals Yield Mechanism of Metallic Nanowires. 3.14
Collecting Data of Atomistic Potentials from the Internet Based on a
Specific Technical Requirement. Appendix 3.A Potential Tables for Oxides
and Thin-Film Coating Layers. References. 4 Quantum Mechanics and Its
Energy Linkage with Atomistic Analysis. 4.1 Determination of Uranium
Dioxide Atomistic Potential and the Significance of QM. 4.2 Some Basic
Concepts of QM. 4.3 Postulates of QM. 4.4 The Steady State SchrEURodinger
Equation of a Single Particle. 4.5 Example Solution: Square Potential Well
with Infinite Depth. 4.6 SchrEURodinger Equation of Multi-body Systems and
Characteristics of its Eigenvalues and Ground State Energy. 4.7 Three Basic
Solution Methods for Multi-body Problems in QM. 4.8 Tight Binding Method.
4.9 Hartree-Fock (HF) Methods. 4.10 Electronic Density Functional Theory
(DFT). 4.11 Brief Introduction on Developing Interatomic Potentials by DFT
Calculations. 4.12 Concluding Remarks. Appendix 4.A Solution to Isolated
Hydrogen Atom. References. 5 Concurrent Multiscale Analysis by Generalized
Particle Dynamics Methods. 5.1 Introduction. 5.2 The Geometric Model of the
GP Method. 5.3 Developing Natural Boundaries Between Domains of Different
Scales. 5.4 Verification of Seamless Transition via 1D Model. 5.5 An
Inverse Mapping Method for Dynamics Analysis of Generalized Particles. 5.6
Applications of GP Method. 5.7 Validation by Comparison of Dislocation
Initiation and Evolution Predicted by MD and GP. 5.8 Validation by
Comparison of Slip Patterns Predicted by MD and GP. 5.9 Summary and
Discussions. 5.10 States of Art of Concurrent Multiscale Analysis. 5.11
Concluding Remarks. References. 6 Quasicontinuum Concurrent and
Semi-analytical Hierarchical Multiscale Methods Across Atoms/Continuum. 6.1
Introduction. Part 6.1 Basic Energy Principle and Numerical Solution
Techniques in Solid Mechanics. 6.2 Principle of Minimum Potential Energy of
Solids and Structures. 6.3 Essential Points of Finite Element Methods. Part
6.2 Quasicontinuum (QC) Concurrent Method of Multiscale Analysis. 6.4 The
Idea and Features of the QC Method. 6.5 Fully Non-localized QC Method. 6.6
Applications of the QC Method. 6.7 Short Discussion about the QC Method.
Part 6.3 Analytical and Semi-analytical Multiscale Methods Across
Atomic/Continuum Scales. 6.8 More Discussions about Deformation Gradient
and the Cauchy-Born Rule. 6.9 Analytical/Semi-analytical Methods Across
Atom/Continuum Scales Based on the Cauchy-Born Rule. 6.10 Atomistic-based
Continuum Model of Hydrogen Storage with Carbon Nanotubes. 6.11
Atomistic-based Model for Mechanical, Electrical and Thermal Properties of
Nanotubes. 6.12 A Proof of 3D Inverse Mapping Rule of the GP Method. 6.13
Concluding Remarks. References. 7 Further Introduction to Concurrent
Multiscale Methods. 7.1 General Feature in Geometry of Concurrent
Multiscale Modeling. 7.2 Physical Features of Concurrent Multiscale Models.
7.3 MAAD Method for Analysis Across ab initio, Atomic and Macroscopic
Scales. 7.4 Force-based Formulation of Concurrent Multiscale Modeling. 7.5
Coupled Atom Discrete Dislocation Dynamics (CADD) Multiscale Method. 7.6 1D
Model for a Multiscale Dynamic Analysis. 7.7 Bridging Domains Method. 7.8
1D Benchmark Tests of Interface Compatibility for DC Methods. 7.9
Systematic Performance Benchmark of Most DC Atomistic/Continuum Coupling
Methods. 7.10 The Embedded Statistical Coupling Method (ESCM). References.
8 Hierarchical Multiscale Methods for Plasticity. 8.1 A Methodology of
Hierarchical Multiscale Analysis Across Micro/meso/macroscopic Scales and
Information Transformation Between These Scales. 8.2 Quantitative
Meso-macro Bridging Based on Self-consistent Schemes. 8.3 Basics of
Continuum Plasticity Theory. 8.4 Internal Variable Theory, Back Stress and
Elastoplastic Constitutive Equations. 8.5 Quantitative Micro-meso Bridging
by Developing Meso-cell Constitutive Equations Based on Microscopic
Analysis. 8.6 Determining Size Effect on Yield Stress and Kinematic
Hardening Through Dislocation Analysis. 8.7 Numerical Methods to Link
Plastic Strains at the Mesoscopic and Macroscopic Scales. 8.8 Experimental
Study on Layer-thickness Effects on Cyclic Creep (Ratcheting). 8.9
Numerical Results and Comparison Between Experiments and Multiscale
Simulation. 8.10 Findings in Microscopic Scale by Multiscale Analysis. 8.11
Summary and Conclusions. Appendix 8.A Constitutive Equations and
Expressions of Parameters. Appendix 8.B Derivation of Equation (8.12e) and
Matrix Elements. References. 9 Topics in Materials Design, Temporal
Multiscale Problems and Bio-materials. Part 9.1 Materials Design. 9.1
Multiscale Modeling in Materials Design. Part 9.2 Temporal Multiscale
Problems. 9.2 Introduction to Temporal Multiscale Problems. 9.3 Concepts of
Infrequent Events. 9.4 Minimum Energy Path (MEP) and Transition State
Theory in Atomistic Simulation. 9.5 Applications and Impacts of NEB
Methods. Part 9.3 Multiscale Analysis of Protein Materials and Medical
Implant Problems. 9.6 Multiscale Analysis of Protein Materials. 9.7
Multiscale Analysis of Medical Implants. 9.8 Concluding Remarks. Appendix
9A Derivation of Governing Equation (9.11) for Implicit Relationship of
Stress, Strain Rate, Temperature in Terms of Activation Energy and
Activation Volume. References. 10 Simulation Schemes, Softwares, Lab
Practice and Applications. Part 10.1 Basics of Computer Simulations. 10.1
Basic Knowledge of UNIX System and Shell Commands. 10.2 A Simple MD
Program. 10.3 Static Lattice Calculations Using GULP. 10.4 Introduction of
Visualization Tools and Gnuplot. 10.5 Running an Atomistic Simulation Using
a Public MD Software DL_POLY. 10.6 Nve and npt Ensemble in MD Simulation.
Part 10.2: Simulation Applications in Metals and Ceramics by MD. 10.7
Non-equilibrium MD Simulation of One-phase Model Under External Shearing
(1). 10.8 Non-equilibrium MD Simulation of a One-phase Model Under External
Shearing (2). 10.9 Non-equilibrium MD Simulation of a Two-phase Model Under
External Shearing. Part 10.3: Atomistic Simulation for Protein-Water System
and Brief Introduction of Large-scale Atomic/Molecular System (LAMMPS) and
the GP Simulation. 10.10 Using NAMD Software for Biological Atomistic
Simulation. 10.11 Stretching of a Protein Module (1): System Building and
Equilibration with VMD/NAMD. 10.12 Stretching of a Protein Module (2):
Non-equilibrium MD Simulation with NAMD. 10.13 Brief Introduction to
LAMMPS. 10.14 Multiscale Simulation by Generalized Particle (GP) Dynamics
Method. Appendix 10.A Code Installation Guide. Prerequisites. 10.A.1
Introduction. 10.A.2 Using the KNOPPIX CD to Install the GNU/Linux System.
10.A.3 ssh and scp. 10.A.4 Fortran and C Compiler. 10.A.5 Visual Molecular
Dynamics (VMD). 10.A.6 Installation of AtomEye. Appendix 10.B Brief
Introduction to Fortran 90. 10.B.1 Program Structure, Write to Terminal and
Write to File. 10.B.2 Do Cycle, Formatted Output. 10.B.3 Arrays and
Allocation. 10.B.4 IF THEN ELSE. Appendix 10.C Brief Introduction to VIM.
10.C.1 Introduction. 10.C.2 Simple Commands. Appendix 10.D Basic Knowledge
of Numerical Algorithm for Force Calculation. 10.D.1 Force Calculation in
Atomistic Simulation. Appendix 10.E Basic Knowledge of Parallel Numerical
Algorithm. 10.E.1 General Information. 10.E.2 Atom Decomposition. 10.E.3
Force Decomposition. 10.E.4 Domain Decomposition. Appendix 10.F
Supplemental Materials and Software for Geometric Model Development in
Atomistic Simulation. 10.F.1 Model Development for Model Coordinates
Coincident with Main Crystal Axes. 10.F.2 Model Development for Model
Coordinates not Coincident with Crystal Axes. References. Postface. Index.
1.1 Material Properties Based on Hierarchy of Material Structure. 1.2
Overview of Multiscale Analysis. 1.3 Framework of Multiscale Analysis
Covering a Large Range of Spatial Scales. 1.4 Examples in Formulating
Multiscale Models from Practice. 1.5 Concluding Remarks. References. 2
Basics of Atomistic Simulation. 2.1 The Role of Atomistic Simulation. 2.2
Interatomic Force and Potential Function. 2.3 Pair Potential. 2.4 Numerical
Algorithms for Integration and Error Estimation. 2.5 Geometric Model
Development of Atomistic System. 2.6 Boundary Conditions. 2.7 Statistical
Ensembles. 2.8 Energy Minimization for Preprocessing and Statistical
Mechanics Data Analyses. 2.9 Statistical Simulation Using Monte Carlo
Methods. 2.10 Concluding Remarks. References. 3 Applications of Atomistic
Simulation in Ceramics and Metals. Part 3.1 Applications in Ceramics and
Materials with Ionic and Covalent Bonds. 3.1 Covalent and Ionic Potentials
and Atomistic Simulation for Ceramics. 3.2 Born Solid Model for
Ionic-bonding Materials. 3.3 Shell Model. 3.4 Determination of Parameters
of Short-distance Potential for Oxides. 3.5 Applications in Ceramics:
Defect Structure in Scandium Doped Ceria Using Static Lattice Calculation.
3.6 Applications in Ceramics: Combined Study of Atomistic Simulation with
XRD for Nonstoichiometry Mechanisms in Y3Al5O12 (YAG) Garnets. 3.7
Applications in Ceramics: Conductivity of the YSZ Oxide Fuel Electrolyte
and Domain Switching of Ferroelectric Ceramics Using MD. 3.8 Tersoff and
Brenner Potentials for Covalent Materials. 3.9 The Atomistic Stress and
Atomistic-based Stress Measure. Part 3.2 Applications in Metallic Materials
and Alloys. 3.10 Metallic Potentials and Atomistic Simulation for Metals.
3.11 Embedded Atom Methods EAM and MEAM. 3.12 Constructing Binary and High
Order Potentials from Monoatomic Potentials. 3.13 Application Examples of
Metals: MD Simulation Reveals Yield Mechanism of Metallic Nanowires. 3.14
Collecting Data of Atomistic Potentials from the Internet Based on a
Specific Technical Requirement. Appendix 3.A Potential Tables for Oxides
and Thin-Film Coating Layers. References. 4 Quantum Mechanics and Its
Energy Linkage with Atomistic Analysis. 4.1 Determination of Uranium
Dioxide Atomistic Potential and the Significance of QM. 4.2 Some Basic
Concepts of QM. 4.3 Postulates of QM. 4.4 The Steady State SchrEURodinger
Equation of a Single Particle. 4.5 Example Solution: Square Potential Well
with Infinite Depth. 4.6 SchrEURodinger Equation of Multi-body Systems and
Characteristics of its Eigenvalues and Ground State Energy. 4.7 Three Basic
Solution Methods for Multi-body Problems in QM. 4.8 Tight Binding Method.
4.9 Hartree-Fock (HF) Methods. 4.10 Electronic Density Functional Theory
(DFT). 4.11 Brief Introduction on Developing Interatomic Potentials by DFT
Calculations. 4.12 Concluding Remarks. Appendix 4.A Solution to Isolated
Hydrogen Atom. References. 5 Concurrent Multiscale Analysis by Generalized
Particle Dynamics Methods. 5.1 Introduction. 5.2 The Geometric Model of the
GP Method. 5.3 Developing Natural Boundaries Between Domains of Different
Scales. 5.4 Verification of Seamless Transition via 1D Model. 5.5 An
Inverse Mapping Method for Dynamics Analysis of Generalized Particles. 5.6
Applications of GP Method. 5.7 Validation by Comparison of Dislocation
Initiation and Evolution Predicted by MD and GP. 5.8 Validation by
Comparison of Slip Patterns Predicted by MD and GP. 5.9 Summary and
Discussions. 5.10 States of Art of Concurrent Multiscale Analysis. 5.11
Concluding Remarks. References. 6 Quasicontinuum Concurrent and
Semi-analytical Hierarchical Multiscale Methods Across Atoms/Continuum. 6.1
Introduction. Part 6.1 Basic Energy Principle and Numerical Solution
Techniques in Solid Mechanics. 6.2 Principle of Minimum Potential Energy of
Solids and Structures. 6.3 Essential Points of Finite Element Methods. Part
6.2 Quasicontinuum (QC) Concurrent Method of Multiscale Analysis. 6.4 The
Idea and Features of the QC Method. 6.5 Fully Non-localized QC Method. 6.6
Applications of the QC Method. 6.7 Short Discussion about the QC Method.
Part 6.3 Analytical and Semi-analytical Multiscale Methods Across
Atomic/Continuum Scales. 6.8 More Discussions about Deformation Gradient
and the Cauchy-Born Rule. 6.9 Analytical/Semi-analytical Methods Across
Atom/Continuum Scales Based on the Cauchy-Born Rule. 6.10 Atomistic-based
Continuum Model of Hydrogen Storage with Carbon Nanotubes. 6.11
Atomistic-based Model for Mechanical, Electrical and Thermal Properties of
Nanotubes. 6.12 A Proof of 3D Inverse Mapping Rule of the GP Method. 6.13
Concluding Remarks. References. 7 Further Introduction to Concurrent
Multiscale Methods. 7.1 General Feature in Geometry of Concurrent
Multiscale Modeling. 7.2 Physical Features of Concurrent Multiscale Models.
7.3 MAAD Method for Analysis Across ab initio, Atomic and Macroscopic
Scales. 7.4 Force-based Formulation of Concurrent Multiscale Modeling. 7.5
Coupled Atom Discrete Dislocation Dynamics (CADD) Multiscale Method. 7.6 1D
Model for a Multiscale Dynamic Analysis. 7.7 Bridging Domains Method. 7.8
1D Benchmark Tests of Interface Compatibility for DC Methods. 7.9
Systematic Performance Benchmark of Most DC Atomistic/Continuum Coupling
Methods. 7.10 The Embedded Statistical Coupling Method (ESCM). References.
8 Hierarchical Multiscale Methods for Plasticity. 8.1 A Methodology of
Hierarchical Multiscale Analysis Across Micro/meso/macroscopic Scales and
Information Transformation Between These Scales. 8.2 Quantitative
Meso-macro Bridging Based on Self-consistent Schemes. 8.3 Basics of
Continuum Plasticity Theory. 8.4 Internal Variable Theory, Back Stress and
Elastoplastic Constitutive Equations. 8.5 Quantitative Micro-meso Bridging
by Developing Meso-cell Constitutive Equations Based on Microscopic
Analysis. 8.6 Determining Size Effect on Yield Stress and Kinematic
Hardening Through Dislocation Analysis. 8.7 Numerical Methods to Link
Plastic Strains at the Mesoscopic and Macroscopic Scales. 8.8 Experimental
Study on Layer-thickness Effects on Cyclic Creep (Ratcheting). 8.9
Numerical Results and Comparison Between Experiments and Multiscale
Simulation. 8.10 Findings in Microscopic Scale by Multiscale Analysis. 8.11
Summary and Conclusions. Appendix 8.A Constitutive Equations and
Expressions of Parameters. Appendix 8.B Derivation of Equation (8.12e) and
Matrix Elements. References. 9 Topics in Materials Design, Temporal
Multiscale Problems and Bio-materials. Part 9.1 Materials Design. 9.1
Multiscale Modeling in Materials Design. Part 9.2 Temporal Multiscale
Problems. 9.2 Introduction to Temporal Multiscale Problems. 9.3 Concepts of
Infrequent Events. 9.4 Minimum Energy Path (MEP) and Transition State
Theory in Atomistic Simulation. 9.5 Applications and Impacts of NEB
Methods. Part 9.3 Multiscale Analysis of Protein Materials and Medical
Implant Problems. 9.6 Multiscale Analysis of Protein Materials. 9.7
Multiscale Analysis of Medical Implants. 9.8 Concluding Remarks. Appendix
9A Derivation of Governing Equation (9.11) for Implicit Relationship of
Stress, Strain Rate, Temperature in Terms of Activation Energy and
Activation Volume. References. 10 Simulation Schemes, Softwares, Lab
Practice and Applications. Part 10.1 Basics of Computer Simulations. 10.1
Basic Knowledge of UNIX System and Shell Commands. 10.2 A Simple MD
Program. 10.3 Static Lattice Calculations Using GULP. 10.4 Introduction of
Visualization Tools and Gnuplot. 10.5 Running an Atomistic Simulation Using
a Public MD Software DL_POLY. 10.6 Nve and npt Ensemble in MD Simulation.
Part 10.2: Simulation Applications in Metals and Ceramics by MD. 10.7
Non-equilibrium MD Simulation of One-phase Model Under External Shearing
(1). 10.8 Non-equilibrium MD Simulation of a One-phase Model Under External
Shearing (2). 10.9 Non-equilibrium MD Simulation of a Two-phase Model Under
External Shearing. Part 10.3: Atomistic Simulation for Protein-Water System
and Brief Introduction of Large-scale Atomic/Molecular System (LAMMPS) and
the GP Simulation. 10.10 Using NAMD Software for Biological Atomistic
Simulation. 10.11 Stretching of a Protein Module (1): System Building and
Equilibration with VMD/NAMD. 10.12 Stretching of a Protein Module (2):
Non-equilibrium MD Simulation with NAMD. 10.13 Brief Introduction to
LAMMPS. 10.14 Multiscale Simulation by Generalized Particle (GP) Dynamics
Method. Appendix 10.A Code Installation Guide. Prerequisites. 10.A.1
Introduction. 10.A.2 Using the KNOPPIX CD to Install the GNU/Linux System.
10.A.3 ssh and scp. 10.A.4 Fortran and C Compiler. 10.A.5 Visual Molecular
Dynamics (VMD). 10.A.6 Installation of AtomEye. Appendix 10.B Brief
Introduction to Fortran 90. 10.B.1 Program Structure, Write to Terminal and
Write to File. 10.B.2 Do Cycle, Formatted Output. 10.B.3 Arrays and
Allocation. 10.B.4 IF THEN ELSE. Appendix 10.C Brief Introduction to VIM.
10.C.1 Introduction. 10.C.2 Simple Commands. Appendix 10.D Basic Knowledge
of Numerical Algorithm for Force Calculation. 10.D.1 Force Calculation in
Atomistic Simulation. Appendix 10.E Basic Knowledge of Parallel Numerical
Algorithm. 10.E.1 General Information. 10.E.2 Atom Decomposition. 10.E.3
Force Decomposition. 10.E.4 Domain Decomposition. Appendix 10.F
Supplemental Materials and Software for Geometric Model Development in
Atomistic Simulation. 10.F.1 Model Development for Model Coordinates
Coincident with Main Crystal Axes. 10.F.2 Model Development for Model
Coordinates not Coincident with Crystal Axes. References. Postface. Index.
About the Author. Series Preface. Preface. Abbreviations. 1 Introduction.
1.1 Material Properties Based on Hierarchy of Material Structure. 1.2
Overview of Multiscale Analysis. 1.3 Framework of Multiscale Analysis
Covering a Large Range of Spatial Scales. 1.4 Examples in Formulating
Multiscale Models from Practice. 1.5 Concluding Remarks. References. 2
Basics of Atomistic Simulation. 2.1 The Role of Atomistic Simulation. 2.2
Interatomic Force and Potential Function. 2.3 Pair Potential. 2.4 Numerical
Algorithms for Integration and Error Estimation. 2.5 Geometric Model
Development of Atomistic System. 2.6 Boundary Conditions. 2.7 Statistical
Ensembles. 2.8 Energy Minimization for Preprocessing and Statistical
Mechanics Data Analyses. 2.9 Statistical Simulation Using Monte Carlo
Methods. 2.10 Concluding Remarks. References. 3 Applications of Atomistic
Simulation in Ceramics and Metals. Part 3.1 Applications in Ceramics and
Materials with Ionic and Covalent Bonds. 3.1 Covalent and Ionic Potentials
and Atomistic Simulation for Ceramics. 3.2 Born Solid Model for
Ionic-bonding Materials. 3.3 Shell Model. 3.4 Determination of Parameters
of Short-distance Potential for Oxides. 3.5 Applications in Ceramics:
Defect Structure in Scandium Doped Ceria Using Static Lattice Calculation.
3.6 Applications in Ceramics: Combined Study of Atomistic Simulation with
XRD for Nonstoichiometry Mechanisms in Y3Al5O12 (YAG) Garnets. 3.7
Applications in Ceramics: Conductivity of the YSZ Oxide Fuel Electrolyte
and Domain Switching of Ferroelectric Ceramics Using MD. 3.8 Tersoff and
Brenner Potentials for Covalent Materials. 3.9 The Atomistic Stress and
Atomistic-based Stress Measure. Part 3.2 Applications in Metallic Materials
and Alloys. 3.10 Metallic Potentials and Atomistic Simulation for Metals.
3.11 Embedded Atom Methods EAM and MEAM. 3.12 Constructing Binary and High
Order Potentials from Monoatomic Potentials. 3.13 Application Examples of
Metals: MD Simulation Reveals Yield Mechanism of Metallic Nanowires. 3.14
Collecting Data of Atomistic Potentials from the Internet Based on a
Specific Technical Requirement. Appendix 3.A Potential Tables for Oxides
and Thin-Film Coating Layers. References. 4 Quantum Mechanics and Its
Energy Linkage with Atomistic Analysis. 4.1 Determination of Uranium
Dioxide Atomistic Potential and the Significance of QM. 4.2 Some Basic
Concepts of QM. 4.3 Postulates of QM. 4.4 The Steady State SchrEURodinger
Equation of a Single Particle. 4.5 Example Solution: Square Potential Well
with Infinite Depth. 4.6 SchrEURodinger Equation of Multi-body Systems and
Characteristics of its Eigenvalues and Ground State Energy. 4.7 Three Basic
Solution Methods for Multi-body Problems in QM. 4.8 Tight Binding Method.
4.9 Hartree-Fock (HF) Methods. 4.10 Electronic Density Functional Theory
(DFT). 4.11 Brief Introduction on Developing Interatomic Potentials by DFT
Calculations. 4.12 Concluding Remarks. Appendix 4.A Solution to Isolated
Hydrogen Atom. References. 5 Concurrent Multiscale Analysis by Generalized
Particle Dynamics Methods. 5.1 Introduction. 5.2 The Geometric Model of the
GP Method. 5.3 Developing Natural Boundaries Between Domains of Different
Scales. 5.4 Verification of Seamless Transition via 1D Model. 5.5 An
Inverse Mapping Method for Dynamics Analysis of Generalized Particles. 5.6
Applications of GP Method. 5.7 Validation by Comparison of Dislocation
Initiation and Evolution Predicted by MD and GP. 5.8 Validation by
Comparison of Slip Patterns Predicted by MD and GP. 5.9 Summary and
Discussions. 5.10 States of Art of Concurrent Multiscale Analysis. 5.11
Concluding Remarks. References. 6 Quasicontinuum Concurrent and
Semi-analytical Hierarchical Multiscale Methods Across Atoms/Continuum. 6.1
Introduction. Part 6.1 Basic Energy Principle and Numerical Solution
Techniques in Solid Mechanics. 6.2 Principle of Minimum Potential Energy of
Solids and Structures. 6.3 Essential Points of Finite Element Methods. Part
6.2 Quasicontinuum (QC) Concurrent Method of Multiscale Analysis. 6.4 The
Idea and Features of the QC Method. 6.5 Fully Non-localized QC Method. 6.6
Applications of the QC Method. 6.7 Short Discussion about the QC Method.
Part 6.3 Analytical and Semi-analytical Multiscale Methods Across
Atomic/Continuum Scales. 6.8 More Discussions about Deformation Gradient
and the Cauchy-Born Rule. 6.9 Analytical/Semi-analytical Methods Across
Atom/Continuum Scales Based on the Cauchy-Born Rule. 6.10 Atomistic-based
Continuum Model of Hydrogen Storage with Carbon Nanotubes. 6.11
Atomistic-based Model for Mechanical, Electrical and Thermal Properties of
Nanotubes. 6.12 A Proof of 3D Inverse Mapping Rule of the GP Method. 6.13
Concluding Remarks. References. 7 Further Introduction to Concurrent
Multiscale Methods. 7.1 General Feature in Geometry of Concurrent
Multiscale Modeling. 7.2 Physical Features of Concurrent Multiscale Models.
7.3 MAAD Method for Analysis Across ab initio, Atomic and Macroscopic
Scales. 7.4 Force-based Formulation of Concurrent Multiscale Modeling. 7.5
Coupled Atom Discrete Dislocation Dynamics (CADD) Multiscale Method. 7.6 1D
Model for a Multiscale Dynamic Analysis. 7.7 Bridging Domains Method. 7.8
1D Benchmark Tests of Interface Compatibility for DC Methods. 7.9
Systematic Performance Benchmark of Most DC Atomistic/Continuum Coupling
Methods. 7.10 The Embedded Statistical Coupling Method (ESCM). References.
8 Hierarchical Multiscale Methods for Plasticity. 8.1 A Methodology of
Hierarchical Multiscale Analysis Across Micro/meso/macroscopic Scales and
Information Transformation Between These Scales. 8.2 Quantitative
Meso-macro Bridging Based on Self-consistent Schemes. 8.3 Basics of
Continuum Plasticity Theory. 8.4 Internal Variable Theory, Back Stress and
Elastoplastic Constitutive Equations. 8.5 Quantitative Micro-meso Bridging
by Developing Meso-cell Constitutive Equations Based on Microscopic
Analysis. 8.6 Determining Size Effect on Yield Stress and Kinematic
Hardening Through Dislocation Analysis. 8.7 Numerical Methods to Link
Plastic Strains at the Mesoscopic and Macroscopic Scales. 8.8 Experimental
Study on Layer-thickness Effects on Cyclic Creep (Ratcheting). 8.9
Numerical Results and Comparison Between Experiments and Multiscale
Simulation. 8.10 Findings in Microscopic Scale by Multiscale Analysis. 8.11
Summary and Conclusions. Appendix 8.A Constitutive Equations and
Expressions of Parameters. Appendix 8.B Derivation of Equation (8.12e) and
Matrix Elements. References. 9 Topics in Materials Design, Temporal
Multiscale Problems and Bio-materials. Part 9.1 Materials Design. 9.1
Multiscale Modeling in Materials Design. Part 9.2 Temporal Multiscale
Problems. 9.2 Introduction to Temporal Multiscale Problems. 9.3 Concepts of
Infrequent Events. 9.4 Minimum Energy Path (MEP) and Transition State
Theory in Atomistic Simulation. 9.5 Applications and Impacts of NEB
Methods. Part 9.3 Multiscale Analysis of Protein Materials and Medical
Implant Problems. 9.6 Multiscale Analysis of Protein Materials. 9.7
Multiscale Analysis of Medical Implants. 9.8 Concluding Remarks. Appendix
9A Derivation of Governing Equation (9.11) for Implicit Relationship of
Stress, Strain Rate, Temperature in Terms of Activation Energy and
Activation Volume. References. 10 Simulation Schemes, Softwares, Lab
Practice and Applications. Part 10.1 Basics of Computer Simulations. 10.1
Basic Knowledge of UNIX System and Shell Commands. 10.2 A Simple MD
Program. 10.3 Static Lattice Calculations Using GULP. 10.4 Introduction of
Visualization Tools and Gnuplot. 10.5 Running an Atomistic Simulation Using
a Public MD Software DL_POLY. 10.6 Nve and npt Ensemble in MD Simulation.
Part 10.2: Simulation Applications in Metals and Ceramics by MD. 10.7
Non-equilibrium MD Simulation of One-phase Model Under External Shearing
(1). 10.8 Non-equilibrium MD Simulation of a One-phase Model Under External
Shearing (2). 10.9 Non-equilibrium MD Simulation of a Two-phase Model Under
External Shearing. Part 10.3: Atomistic Simulation for Protein-Water System
and Brief Introduction of Large-scale Atomic/Molecular System (LAMMPS) and
the GP Simulation. 10.10 Using NAMD Software for Biological Atomistic
Simulation. 10.11 Stretching of a Protein Module (1): System Building and
Equilibration with VMD/NAMD. 10.12 Stretching of a Protein Module (2):
Non-equilibrium MD Simulation with NAMD. 10.13 Brief Introduction to
LAMMPS. 10.14 Multiscale Simulation by Generalized Particle (GP) Dynamics
Method. Appendix 10.A Code Installation Guide. Prerequisites. 10.A.1
Introduction. 10.A.2 Using the KNOPPIX CD to Install the GNU/Linux System.
10.A.3 ssh and scp. 10.A.4 Fortran and C Compiler. 10.A.5 Visual Molecular
Dynamics (VMD). 10.A.6 Installation of AtomEye. Appendix 10.B Brief
Introduction to Fortran 90. 10.B.1 Program Structure, Write to Terminal and
Write to File. 10.B.2 Do Cycle, Formatted Output. 10.B.3 Arrays and
Allocation. 10.B.4 IF THEN ELSE. Appendix 10.C Brief Introduction to VIM.
10.C.1 Introduction. 10.C.2 Simple Commands. Appendix 10.D Basic Knowledge
of Numerical Algorithm for Force Calculation. 10.D.1 Force Calculation in
Atomistic Simulation. Appendix 10.E Basic Knowledge of Parallel Numerical
Algorithm. 10.E.1 General Information. 10.E.2 Atom Decomposition. 10.E.3
Force Decomposition. 10.E.4 Domain Decomposition. Appendix 10.F
Supplemental Materials and Software for Geometric Model Development in
Atomistic Simulation. 10.F.1 Model Development for Model Coordinates
Coincident with Main Crystal Axes. 10.F.2 Model Development for Model
Coordinates not Coincident with Crystal Axes. References. Postface. Index.
1.1 Material Properties Based on Hierarchy of Material Structure. 1.2
Overview of Multiscale Analysis. 1.3 Framework of Multiscale Analysis
Covering a Large Range of Spatial Scales. 1.4 Examples in Formulating
Multiscale Models from Practice. 1.5 Concluding Remarks. References. 2
Basics of Atomistic Simulation. 2.1 The Role of Atomistic Simulation. 2.2
Interatomic Force and Potential Function. 2.3 Pair Potential. 2.4 Numerical
Algorithms for Integration and Error Estimation. 2.5 Geometric Model
Development of Atomistic System. 2.6 Boundary Conditions. 2.7 Statistical
Ensembles. 2.8 Energy Minimization for Preprocessing and Statistical
Mechanics Data Analyses. 2.9 Statistical Simulation Using Monte Carlo
Methods. 2.10 Concluding Remarks. References. 3 Applications of Atomistic
Simulation in Ceramics and Metals. Part 3.1 Applications in Ceramics and
Materials with Ionic and Covalent Bonds. 3.1 Covalent and Ionic Potentials
and Atomistic Simulation for Ceramics. 3.2 Born Solid Model for
Ionic-bonding Materials. 3.3 Shell Model. 3.4 Determination of Parameters
of Short-distance Potential for Oxides. 3.5 Applications in Ceramics:
Defect Structure in Scandium Doped Ceria Using Static Lattice Calculation.
3.6 Applications in Ceramics: Combined Study of Atomistic Simulation with
XRD for Nonstoichiometry Mechanisms in Y3Al5O12 (YAG) Garnets. 3.7
Applications in Ceramics: Conductivity of the YSZ Oxide Fuel Electrolyte
and Domain Switching of Ferroelectric Ceramics Using MD. 3.8 Tersoff and
Brenner Potentials for Covalent Materials. 3.9 The Atomistic Stress and
Atomistic-based Stress Measure. Part 3.2 Applications in Metallic Materials
and Alloys. 3.10 Metallic Potentials and Atomistic Simulation for Metals.
3.11 Embedded Atom Methods EAM and MEAM. 3.12 Constructing Binary and High
Order Potentials from Monoatomic Potentials. 3.13 Application Examples of
Metals: MD Simulation Reveals Yield Mechanism of Metallic Nanowires. 3.14
Collecting Data of Atomistic Potentials from the Internet Based on a
Specific Technical Requirement. Appendix 3.A Potential Tables for Oxides
and Thin-Film Coating Layers. References. 4 Quantum Mechanics and Its
Energy Linkage with Atomistic Analysis. 4.1 Determination of Uranium
Dioxide Atomistic Potential and the Significance of QM. 4.2 Some Basic
Concepts of QM. 4.3 Postulates of QM. 4.4 The Steady State SchrEURodinger
Equation of a Single Particle. 4.5 Example Solution: Square Potential Well
with Infinite Depth. 4.6 SchrEURodinger Equation of Multi-body Systems and
Characteristics of its Eigenvalues and Ground State Energy. 4.7 Three Basic
Solution Methods for Multi-body Problems in QM. 4.8 Tight Binding Method.
4.9 Hartree-Fock (HF) Methods. 4.10 Electronic Density Functional Theory
(DFT). 4.11 Brief Introduction on Developing Interatomic Potentials by DFT
Calculations. 4.12 Concluding Remarks. Appendix 4.A Solution to Isolated
Hydrogen Atom. References. 5 Concurrent Multiscale Analysis by Generalized
Particle Dynamics Methods. 5.1 Introduction. 5.2 The Geometric Model of the
GP Method. 5.3 Developing Natural Boundaries Between Domains of Different
Scales. 5.4 Verification of Seamless Transition via 1D Model. 5.5 An
Inverse Mapping Method for Dynamics Analysis of Generalized Particles. 5.6
Applications of GP Method. 5.7 Validation by Comparison of Dislocation
Initiation and Evolution Predicted by MD and GP. 5.8 Validation by
Comparison of Slip Patterns Predicted by MD and GP. 5.9 Summary and
Discussions. 5.10 States of Art of Concurrent Multiscale Analysis. 5.11
Concluding Remarks. References. 6 Quasicontinuum Concurrent and
Semi-analytical Hierarchical Multiscale Methods Across Atoms/Continuum. 6.1
Introduction. Part 6.1 Basic Energy Principle and Numerical Solution
Techniques in Solid Mechanics. 6.2 Principle of Minimum Potential Energy of
Solids and Structures. 6.3 Essential Points of Finite Element Methods. Part
6.2 Quasicontinuum (QC) Concurrent Method of Multiscale Analysis. 6.4 The
Idea and Features of the QC Method. 6.5 Fully Non-localized QC Method. 6.6
Applications of the QC Method. 6.7 Short Discussion about the QC Method.
Part 6.3 Analytical and Semi-analytical Multiscale Methods Across
Atomic/Continuum Scales. 6.8 More Discussions about Deformation Gradient
and the Cauchy-Born Rule. 6.9 Analytical/Semi-analytical Methods Across
Atom/Continuum Scales Based on the Cauchy-Born Rule. 6.10 Atomistic-based
Continuum Model of Hydrogen Storage with Carbon Nanotubes. 6.11
Atomistic-based Model for Mechanical, Electrical and Thermal Properties of
Nanotubes. 6.12 A Proof of 3D Inverse Mapping Rule of the GP Method. 6.13
Concluding Remarks. References. 7 Further Introduction to Concurrent
Multiscale Methods. 7.1 General Feature in Geometry of Concurrent
Multiscale Modeling. 7.2 Physical Features of Concurrent Multiscale Models.
7.3 MAAD Method for Analysis Across ab initio, Atomic and Macroscopic
Scales. 7.4 Force-based Formulation of Concurrent Multiscale Modeling. 7.5
Coupled Atom Discrete Dislocation Dynamics (CADD) Multiscale Method. 7.6 1D
Model for a Multiscale Dynamic Analysis. 7.7 Bridging Domains Method. 7.8
1D Benchmark Tests of Interface Compatibility for DC Methods. 7.9
Systematic Performance Benchmark of Most DC Atomistic/Continuum Coupling
Methods. 7.10 The Embedded Statistical Coupling Method (ESCM). References.
8 Hierarchical Multiscale Methods for Plasticity. 8.1 A Methodology of
Hierarchical Multiscale Analysis Across Micro/meso/macroscopic Scales and
Information Transformation Between These Scales. 8.2 Quantitative
Meso-macro Bridging Based on Self-consistent Schemes. 8.3 Basics of
Continuum Plasticity Theory. 8.4 Internal Variable Theory, Back Stress and
Elastoplastic Constitutive Equations. 8.5 Quantitative Micro-meso Bridging
by Developing Meso-cell Constitutive Equations Based on Microscopic
Analysis. 8.6 Determining Size Effect on Yield Stress and Kinematic
Hardening Through Dislocation Analysis. 8.7 Numerical Methods to Link
Plastic Strains at the Mesoscopic and Macroscopic Scales. 8.8 Experimental
Study on Layer-thickness Effects on Cyclic Creep (Ratcheting). 8.9
Numerical Results and Comparison Between Experiments and Multiscale
Simulation. 8.10 Findings in Microscopic Scale by Multiscale Analysis. 8.11
Summary and Conclusions. Appendix 8.A Constitutive Equations and
Expressions of Parameters. Appendix 8.B Derivation of Equation (8.12e) and
Matrix Elements. References. 9 Topics in Materials Design, Temporal
Multiscale Problems and Bio-materials. Part 9.1 Materials Design. 9.1
Multiscale Modeling in Materials Design. Part 9.2 Temporal Multiscale
Problems. 9.2 Introduction to Temporal Multiscale Problems. 9.3 Concepts of
Infrequent Events. 9.4 Minimum Energy Path (MEP) and Transition State
Theory in Atomistic Simulation. 9.5 Applications and Impacts of NEB
Methods. Part 9.3 Multiscale Analysis of Protein Materials and Medical
Implant Problems. 9.6 Multiscale Analysis of Protein Materials. 9.7
Multiscale Analysis of Medical Implants. 9.8 Concluding Remarks. Appendix
9A Derivation of Governing Equation (9.11) for Implicit Relationship of
Stress, Strain Rate, Temperature in Terms of Activation Energy and
Activation Volume. References. 10 Simulation Schemes, Softwares, Lab
Practice and Applications. Part 10.1 Basics of Computer Simulations. 10.1
Basic Knowledge of UNIX System and Shell Commands. 10.2 A Simple MD
Program. 10.3 Static Lattice Calculations Using GULP. 10.4 Introduction of
Visualization Tools and Gnuplot. 10.5 Running an Atomistic Simulation Using
a Public MD Software DL_POLY. 10.6 Nve and npt Ensemble in MD Simulation.
Part 10.2: Simulation Applications in Metals and Ceramics by MD. 10.7
Non-equilibrium MD Simulation of One-phase Model Under External Shearing
(1). 10.8 Non-equilibrium MD Simulation of a One-phase Model Under External
Shearing (2). 10.9 Non-equilibrium MD Simulation of a Two-phase Model Under
External Shearing. Part 10.3: Atomistic Simulation for Protein-Water System
and Brief Introduction of Large-scale Atomic/Molecular System (LAMMPS) and
the GP Simulation. 10.10 Using NAMD Software for Biological Atomistic
Simulation. 10.11 Stretching of a Protein Module (1): System Building and
Equilibration with VMD/NAMD. 10.12 Stretching of a Protein Module (2):
Non-equilibrium MD Simulation with NAMD. 10.13 Brief Introduction to
LAMMPS. 10.14 Multiscale Simulation by Generalized Particle (GP) Dynamics
Method. Appendix 10.A Code Installation Guide. Prerequisites. 10.A.1
Introduction. 10.A.2 Using the KNOPPIX CD to Install the GNU/Linux System.
10.A.3 ssh and scp. 10.A.4 Fortran and C Compiler. 10.A.5 Visual Molecular
Dynamics (VMD). 10.A.6 Installation of AtomEye. Appendix 10.B Brief
Introduction to Fortran 90. 10.B.1 Program Structure, Write to Terminal and
Write to File. 10.B.2 Do Cycle, Formatted Output. 10.B.3 Arrays and
Allocation. 10.B.4 IF THEN ELSE. Appendix 10.C Brief Introduction to VIM.
10.C.1 Introduction. 10.C.2 Simple Commands. Appendix 10.D Basic Knowledge
of Numerical Algorithm for Force Calculation. 10.D.1 Force Calculation in
Atomistic Simulation. Appendix 10.E Basic Knowledge of Parallel Numerical
Algorithm. 10.E.1 General Information. 10.E.2 Atom Decomposition. 10.E.3
Force Decomposition. 10.E.4 Domain Decomposition. Appendix 10.F
Supplemental Materials and Software for Geometric Model Development in
Atomistic Simulation. 10.F.1 Model Development for Model Coordinates
Coincident with Main Crystal Axes. 10.F.2 Model Development for Model
Coordinates not Coincident with Crystal Axes. References. Postface. Index.