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E-grāmata: Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs

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Edited by (Assistant Professor, Dr. B R Ambedkar National Institute of Technology Jalandhar, India)
  • Formāts: PDF+DRM
  • Sērija : Micro & Nano Technologies
  • Izdošanas datums: 09-Aug-2019
  • Izdevniecība: Elsevier Science Publishing Co Inc
  • Valoda: eng
  • ISBN-13: 9780128169551
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Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and GromacsPalielināt
  • Formāts: PDF+DRM
  • Sērija : Micro & Nano Technologies
  • Izdošanas datums: 09-Aug-2019
  • Izdevniecība: Elsevier Science Publishing Co Inc
  • Valoda: eng
  • ISBN-13: 9780128169551
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Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs presents the three major software packages used for the molecular dynamics simulation of nanocomposites. The book explains, in detail, how to use each of these packages, also providing real-world examples that show when each should be used. The latter two of these are open-source codes which can be used for modeling at no cost. Several case studies how each software package is used to predict various properties of nanocomposites, including metal-matrix, polymer-matrix and ceramic-matrix based nanocomposites. Properties explored include mechanical, thermal, optical and electrical properties.

This is the first book that explores methodologies for using Materials Studio, Lammps and Gromacs in the same place. It will be beneficial for students, researchers and scientists working in the field of molecular dynamics simulation.

  • Gives a detailed explanation of basic commands and modules of Materials Studio, Lammps and Gromacs
  • Shows how Materials Studio, Lammps and Gromacs predict mechanical, thermal, electrical and optical properties of nanocomposites
  • Uses case studies to show which software should be used to solve a variety of nanoscale modeling problems
Contributors xiii
Preface xv
Chapter 1 Introduction to Molecular Dynamics
1(38)
Sumit Sharma
Pramod Kumar
Rakesh Chandra
1.1 Molecular Dynamics
1(1)
1.2 Monte Carlo Simulation
2(1)
1.3 Brownian Dynamics
3(1)
1.4 Dissipative Particle Dynamics
3(1)
1.5 Lattice Boltzmann Method
4(1)
1.6 Basic Concepts
4(21)
1.6.1 Force Field
4(7)
1.6.2 Potentials
11(5)
1.6.3 Ensemble
16(2)
1.6.4 Thermostat
18(4)
1.6.5 Boundary Conditions
22(3)
1.7 Molecular Dynamics Methodology
25(10)
1.7.1 Initial Positions
27(6)
1.7.2 Initial Velocities
33(2)
1.8 Molecular Potential Energy Surface
35(4)
References
37(2)
Chapter 2 Overview of BIOVIA Materials Studio, LAMMPS, and CROMACS
39(1)
Chapter 2.1 Overview of BIOVIA Materials Studio
39(17)
Sumit Sharma
Pramod Kumar
Rakesh Chandra
2.1.1 Modules
40(3)
2.1.2 Simulation Strategy
43(5)
2.1.3 Case Studies
48(7)
References
55(1)
Chapter 2.2 Overview of LAMMPS
56(14)
S.P. Singh
Apurba Mandal
2.2.1 Introduction to LAMMPS
56(1)
2.2.2 Anatomy of a Nanomechanical System
56(1)
2.2.3 Internal Working of LAMMPS Calculations
56(1)
2.2.4 Methodology of MD Simulation Using LAMMPS
57(1)
2.2.5 Development of the Unit Cell Model of Polymeric Nanocomposite
57(3)
2.2.6 Setting the Conditions of Simulation
60(1)
2.2.7 Structural Properties
61(1)
2.2.8 Stress-Strain Behavior
61(2)
2.2.9 Stress Relaxation
63(1)
2.2.10 LAMMPS Input File
64(3)
2.2.11 LAMMPS Output File
67(2)
References
69(1)
Chapter 2.3 Overview of GROMACS
70(31)
Raja Sekhar Dondapati
2.3.1 Introduction
70(2)
2.3.2 Working Principle of GROMACS
72(1)
2.3.3 Computational Chemistry and Molecular Modeling
73(1)
2.3.3.1 Molecular Dynamics Simulations
73(1)
2.3.3.2 Molecular Dynamics Approximation
74(2)
2.3.3.3 Energy Minimization
76(1)
2.3.4 Algorithms
76(1)
2.3.4.1 Periodic Boundary Conditions
77(1)
2.3.4.2 The Group Concept
77(2)
2.3.5 Molecular Dynamics
79(1)
2.3.5.1 Initial Conditions
79(2)
2.3.5.2 Neighbour Searching
81(1)
2.3.5.3 Pair Lists Generation
81(1)
2.3.5.4 Cut-Off Schemes: Group Versus Verlet
81(1)
2.3.5.5 Energy Drift and Pair-List Buffering
82(1)
2.3.5.6 Cut-Off Artifacts and Switched Interactions
83(1)
2.3.5.7 Grid Search
84(1)
2.3.5.8 Charge Groups
84(1)
2.3.6 Compute Forces
84(1)
2.3.6.1 Potential Energy
84(1)
2.3.6.2 Kinetic Energy and Temperature
85(1)
2.3.6.3 Pressure and Virial
85(1)
2.3.7 The Leap-Frog Integrator
86(1)
2.3.8 The Velocity Verlet Integrator
86(1)
2.3.9 Reversible Integrators: The Trotter Decomposition
87(1)
2.3.10 Temperature Coupling
88(1)
2.3.10.1 Berendsen Temperature Coupling
88(1)
2.3.10.2 Velocity-Rescaling Temperature Coupling
89(1)
2.3.10.3 Andersen Thermostat
89(1)
2.3.10.4 Nose-Hoover Temperature Coupling
89(3)
2.3.10.5 Group Temperature Coupling
92(1)
2.3.11 Pressure Coupling
92(1)
2.3.11.1 Berendsen Pressure Coupling
92(1)
2.3.11.2 Parrinello-Rahman Pressure Coupling
93(1)
2.3.11.3 Surface-Tension Coupling
94(1)
2.3.12 The Complete Update Algorithm
95(1)
2.3.13 Output Step
95(1)
2.3.14 Advantage and Functional Characteristics
96(1)
2.3.15 Application of GROMACS
97(1)
2.3.15.1 Biochip Devices
97(1)
2.3.15.2 Molecular Modeling of Biomolecules
98(1)
References
98(3)
Chapter 3 Molecular Dynamics Simulation of Metal Matrix Composites Using BIOVIA Materials Studio, LAMMPS, and GROMACS
101(1)
Chapter 3.1 Prediction of Mechanical Properties of Graphene/Silicon Carbide-Reinforced Aluminum Composites Using BIOVIA Materials Studio
101(13)
Sumit Sharma
Pramod Kumar
Rakesh Chandra
Gaurav Sharma
3.1.1 MD Methodology
104(4)
3.1.2 Results and Discussion
108(4)
3.1.3 Conclusion
112(1)
References
113(1)
Chapter 3.2 Prediction of Mechanical Properties of Graphene/Copper Nanolayered Composites Using LAMMPS
114(11)
Amit Bansal
Prince Setia
Raj Chawla
3.2.1 MD Simulation
116(2)
3.2.2 Results and Discussion
118(5)
3.2.3 Conclusion
123(1)
References
124(1)
Further Reading
124(1)
Chapter 3.3 Molecular Dynamics Simulation of Lithium Metal/Polymer Electrolyte Interracial Properties Using GROMACS
125(16)
Amit Bansal
Prince Setia
Raj Chawla
3.3.1 MD Simulation
127(2)
3.3.2 Results and Discussion
129(9)
3.3.3 Conclusions
138(1)
References
138(3)
Chapter 4 Molecular Dynamics Simulation of Polymer-Matrix Composites Using BIOVIA Materials Studio, LAMMPS, and GROMACS
141(1)
Chapter 4.1 Molecular Dynamics Simulation of Carbon Nanotubes and Polymer/Carbon Nanotube Composites
141(47)
Sumit Sharma
Pramod Kumar
Rakesh Chandra
4.1.1 Introduction
141(1)
4.1.2 Layout
142(1)
4.1.3 Total Potential Energies and Interatomic Forces
142(2)
4.1.4 Stiffness of SWCNTs
144(1)
4.1.4.1 Modeling of SWCNTs
144(1)
4.1.4.2 Geometry Optimization
145(1)
4.1.4.3 Dynamics
146(1)
4.1.4.4 Mechanical Properties
147(1)
4.1.5 Damping of SWCNTs
148(3)
4.1.6 Thermal Conductivity of SWCNTs
151(3)
4.1.7 Results and Discussion
154(1)
4.1.7.1 Elastic Moduli
154(13)
4.1.7.2 Damping in SWCNTs
167(2)
4.1.7.3 Thermal Conductivity of SWCNTs
169(1)
4.1.8 MD Simulation of Polymer/CNT Composites
170(1)
4.1.8.1 Molecular Model of Polymer Matrix
171(1)
4.1.8.2 Elastic Moduli of Polymers
171(1)
4.1.8.3 PmPV/CNT Composite System
172(3)
4.1.8.4 PMMA/CNT Composite System
175(4)
4.1.8.5 Damping in Polymer Composites
179(2)
4.1.8.6 Thermal Conductivity
181(4)
4.1.9 Conclusions
185(2)
References
187(1)
Chapter 4.2 Molecular Dynamics Simulation of Functionalized SWCNT/Polymer Composites Using LAMMPS
188(26)
Sumit Sharma
Amit Bansal
Prince Setia
4.2.1 Introduction
188(3)
4.2.2 Molecular Dynamics Simulation
191(1)
4.2.2.1 Molecular Structures
191(1)
4.2.2.2 Geometry Optimization
192(2)
4.2.2.3 Dynamics
194(1)
4.2.2.4 Mechanical Properties
194(2)
4.2.2.5 SWCNT/PP Composites
196(1)
4.2.3 Results and Discussion
196(15)
4.2.4 Conclusion
211(2)
References
213(1)
Chapter 4.3 Prediction of Tribological Properties of Carbon Nanotube-Reinforced Natural Rubber Composites Using GROMACS
214(13)
Raj Chawla
Sumit Sharma
Manish Dhawan
4.3.1 Introduction
214(2)
4.3.2 Materials and Methods
216(2)
4.3.3 Results and Discussion
218(1)
4.3.3.1 Shear Modulus
218(1)
4.3.3.2 Tribological Properties
219(2)
4.3.3.3 Cohesive Energy
221(1)
4.3.3.4 Friction Stresses
222(1)
4.3.4 Conclusion
223(1)
References
224(3)
Chapter 5 Molecular Dynamics Simulation of Ceramic Matrix Composites Using BIOVIA Materials Studio, LAMMPS, and GROMACS
227(1)
Chapter 5.1 Molecular Dynamics Simulation of Carbon Nanotube-Reinforced Silicon Carbide Composites Using BIOVIA Materials Studio
227(14)
Sumit Sharma
Pramod Kumar
Rakesh Chandra
5.1.1 Introduction
227(5)
5.1.2 MD Methodology
232(1)
5.1.2.1 Geometry Optimization
233(2)
5.1.2.2 Dynamics
235(1)
5.1.2.3 Mechanical Properties
236(1)
5.1.3 Results and Discussion
237(2)
5.1.4 Conclusion
239(1)
References
240(1)
Chapter 5.2 Molecular Dynamics Simulation of Al/Al203 Metal-Ceramic Composite Using LAMMPS
241(8)
Amit Bansal
Prince Setia
Sumit Sharma
5.2.1 MD Simulation
245(1)
5.2.1.1 Interatomic Potential
245(1)
5.2.1.2 Al and A1203 Models
245(2)
5.2.2 Results and Discussion
247(1)
5.2.3 Conclusion
247(1)
References
248(1)
Chapter 5.3 Molecular Dynamics Simulation of Coaxial Boron Nitride/Carbon Nanotubes Using GROMACS
249(10)
Sumit Sharma
Pramod Rakt Patel
5.3.1 MD Simulation
251(1)
5.3.1.1 Interatomic Potential
251(1)
5.3.1.2 CNT-BNNT Composite
252(1)
5.3.2 Results and Discussion
252(5)
5.3.3 Conclusion
257(1)
References
258(1)
Chapter 6 Scripting in Molecular Dynamics
259(70)
Sumit Sharma
Pramod Kumar
Rakesh Chandra
6.1 Working With Scripts in Materials Visualizer
259(3)
6.1.1 Writing Scripts
259(1)
6.1.2 Generating Scripts
260(1)
6.1.3 Checking Script Syntax
260(1)
6.1.4 Debugging Scripts
261(1)
6.2 Running Scripts on Server
262(1)
6.3 Sample Scripts
262(61)
6.3.1 Stress-Strain Script
262(12)
6.3.2 Script for Thermal Conductivity
274(23)
6.3.3 Script for Glass-Transition Temperature
297(26)
6.4 Scripting in LAMMPS
323(5)
6.4.1 Script for Vacancy Formation Energy
323(2)
6.4.2 Script for Deformation of a Nanowire
325(3)
6.5 Scripting in GROMACS
328(1)
References
328(1)
Chapter 7 Applications of BIOVIA Materials Studio, LAMMPS, and GROMACS in Various Fields of Science and Engineering
329(14)
Sumit Sharma
Pramod Kumar
Rakesh Chandra
7.1 Applications of BIOVIA Materials Studio
329(4)
7.1.1 Quantum Tools
330(1)
7.1.2 Classical Simulation Tools
331(1)
7.1.3 Mesoscale Simulation Tools
332(1)
7.1.4 Statistical Tools
332(1)
7.1.5 Analytical and Crystallization Tools
333(1)
7.2 Applications of LAMMPS
333(5)
7.3 Applications of GROMACS
338(5)
References
340(3)
Index 343
Dr Sumit Sharma is Assistant Professor in the Department of Mechanical Engineering at Dr BR Ambedkar National Institute of Technology Jalandhar, India. Before joining this institute, he worked as an Assistant Professor in the School of Mechanical Engineering in Lovely Professional University, India. Dr Sharmas interests are related to both theoretical and experimental aspects of mechanics and dynamics of nanomaterials and structures.
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