Molecular Dynamics for Amorphous Materials: Methodology and applications

316 Pages·2022·65.995 MB·English

by  Carlo Massobrio

The Structure of Amorphous
Materials using
Molecular Dynamics
Online at: https://doi.org/10.1088/978-0-7503-2436-6

The Structure of Amorphous
Materials using
Molecular Dynamics
Carlo Massobrio
Université de Strasbourg, CNRS, Institut de Physique et Chimie des
Matériaux de Strasbourg, UMR 7504, Strasbourg F-67034, France
IOP Publishing, Bristol, UK
ªIOPPublishingLtd2022
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ISBN 978-0-7503-2436-6(ebook)
ISBN 978-0-7503-2434-2(print)
ISBN 978-0-7503-2437-3(myPrint)
ISBN 978-0-7503-2435-9(mobi)
DOI 10.1088/978-0-7503-2436-6
Version:20221101
IOPebooks
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Contents
Preface xi
Acknowledgement xiii
Author biography xv
1 Introduction 1-1
1.1 Why this book? 1-1
1.1.1 The guideline: relying on direct experience 1-4
1.1.2 Inside each chapter 1-5
References 1-8
2 Amorphous materials via atomic-scale modeling 2-1
2.1 The inspiring role of Glass Science 2-1
2.2 From experiments to modelling: toward a connection with 2-3
atomic-scale tools
2.3 Accessing properties: direct and reciprocal space 2-4
2.4 Describing the network topology 2-11
2.4.1 Coordination numbers and units 2-11
2.4.2 Bond-angle distributions and local order parameter 2-13
2.4.3 Making sense out of diffusion in glasses via MD 2-15
2.5 Correlating structural and electronic properties 2-16
2.5.1 Electronic density of states 2-16
2.5.2 Maximally localized Wannier functions 2-17
2.6 Neutron scattering as experimental counterpart to MD 2-22
References 2-26
3 Molecular dynamics to describe (amorphous) materials 3-1
3.1 Molecular dynamics: what for? 3-2
3.2 Beyond two-body potentials 3-4
3.3 Potentials for iono-covalent systems 3-6
3.4 Thermostats for molecular dynamics 3-9
3.4.1 The breakthrough of S Nosé 3-10
3.5 First-principles molecular dynamics via the Car–Parrinello method 3-12
3.5.1 Basic ideas 3-12
3.5.2 The Car–Parrinello method step by step 3-14
3.5.3 Two families of degrees of freedom in non-equilibrium 3-15
v
TheStructureofAmorphousMaterialsusingMolecularDynamics
3.5.4 A first summary and some practical considerations 3-18
3.5.5 The role of thermostats within FPMD 3-20
3.6 Getting acquainted with the total energy 3-25
3.6.1 Electronic kinetic energy: better avoiding confusions! 3-25
3.6.2 The most convenient basis set: plane waves 3-26
3.6.3 Introducing the notion of pseudopotentials 3-27
3.6.4 Exchange and correlation to increase predictive power 3-29
3.6.5 On the impact of the XC functional: the revealing case of 3-30
liquid GeSe
2
3.7 Glassy materials and FPMD: criteria and challenges 3-32
3.7.1 The issue of size limitations 3-33
3.7.2 The issue of the length of the time trajectories 3-35
References 3-37
4 A practical roadmap for FPMD on amorphous materials 4-1
4.1 Choice of the description: classical potentials vs first-principles 4-1
4.1.1 Digging out some failures of classical potentials 4-3
4.2 Methodology: the unavoidable choices to be made 4-4
4.2.1 More on the exchange–correlation functionals 4-6
4.2.2 On the selection and use of pseudopotentials 4-8
4.2.3 The quest of the best fictitious electronic mass 4-9
and timestep
4.2.4 The beauty of the Verlet algorithm 4-10
4.3 Creating a computer glass via MD: the initial conditions 4-11
4.4 Production of trajectories and the setup of a thermal cycle 4-17
4.4.1 An essential summary before hitting the road 4-17
4.4.2 Starting to run carefully and cautiously: a mini guide 4-18
4.4.3 Handling adiabaticity: the gap issue 4-19
4.4.4 Some instructions to be effective when moving to high 4-23
temperatures
4.4.5 Quenching down to the glassy state 4-25
4.5 Dealing with FPMD odds and ends (including non-adiabaticity): 4-29
the case of SiN
4.5.1 State of the art and calculations 4-29
4.5.2 Methodology and the appropriate FPMD schemes 4-30
4.5.3 Focus on the coordination units 4-34
4.5.4 What to learn from the case of SiN? 4-36
vi
TheStructureofAmorphousMaterialsusingMolecularDynamics
4.6 The CPMD code and some thoughts on how to approach the 4-37
‘code issue’: an autobiographical perspective
4.6.1 Inside CPMD: the essentials 4-38
References 4-41
5 Cases treated via classical molecular dynamics 5-1
5.1 Learning about glasses from a Lennard-Jones monoatomic system 5-1
5.1.1 Simple and instructive: a monoatomic glass model 5-1
5.1.2 Assessing the stability aroundT 5-2
gl
5.1.3 Some considerations about qualitative glass models 5-6
5.2 Amorphization by solid-state reaction in a metallic alloy 5-7
References 5-11
6 The atomic structure of disordered networks 6-1
6.1 General consideration: where do we start from? 6-1
6.2 The structure of liquid and glassy GeSe 6-4
2
6.2.1 Methodology 6-4
6.2.2 Liquid GeSe 6-5
2
6.2.3 Glassy GeSe 6-9
2
6.2.4 Modeling these two systems: some thoughts 6-12
6.3 The origin of the first-sharp diffraction peak 6-13
6.3.1 FSDP in the total structure factor 6-13
6.3.2 FSDP in the concentration–concentration partial 6-17
structure factor
6.4 FSDP in disordered network: some considerations before 6-23
to go on
6.5 Evidence of FSDP inS (k): examples 6-24
CC
6.6 What to learn fromS (k) vsS (k) 6-27
CC zz
6.6.1 CalculatingS (k) 6-28
zz
6.6.2 ComparingS (k) andS (k) for the three classes 6-29
zz CC
of networks
6.7 Improving the description of chemical bonding 6-32
6.7.1 Contours of the GGA issue for chalcogenides 6-32
6.7.2 Why BLYP? 6-32
6.7.3 Liquid GeSe : BLYP vs PW, direct space and short-range 6-34
2
properties
6.7.4 Liquid GeSe : BLYP vs PW, reciprocal space and 6-36
2
intermediate range properties
vii
TheStructureofAmorphousMaterialsusingMolecularDynamics
6.7.5 Liquid GeSe : BLYP vs PW, dynamical properties 6-38
2
6.7.6 Glassy GeSe : BLYP vs PW and further thoughts 6-39
2
References 6-40
7 The effect of pressure on the structure of glassy GeSe 7-1
2
and GeSe
4
7.1 Is there any pressure left? 7-1
7.2 GeSe under pressure: a density-driven transition 7-5
2
7.2.1 Introduction: combining experiments and theory 7-5
7.2.2 Neutron diffraction experiments at finite pressure: 7-6
the essential
7.2.3 Understanding the structural transition: results 7-7
7.2.4 Understanding the structural transition: rationale 7-10
7.3 GeSe under pressure: when theory and experiments agree 7-12
4
7.3.1 Behavior under pressure 7-13
7.3.2 Behavior under pressure: rationale 7-16
References 7-19
8 Structural changes with composition in GexSe1−x glassy 8-1
chalcogenides
8.1 Composition makes the difference: early calculations on liquid GeSe 8-1
4
8.2 Glassy GeSe and glassy SiSe and the ‘structural variability’ 8-4
4 4
8.2.1 Structural properties 8-5
8.2.2 Structural variability 8-9
8.3 Altering stoichiometry by adding Ge: glassy Ge Se 8-11
2 3
8.3.1 A glimpse on the correlation between atomic and electronic 8-19
structure
8.3.2 What to learn from glassy Ge Se 8-22
2 3
References 8-23
9 Moving ahead, better and bigger: GeS , GeSe and 9-1
2 9
GeSe vs GeS
4 4
9.1 Introduction 9-1
9.2 Glassy GeS 9-2
2
9.2.1 Real space properties 9-3
9.2.2 Reciprocal space properties 9-7
9.2.3 Bonding properties 9-9
viii
TheStructureofAmorphousMaterialsusingMolecularDynamics
9.3 Glassy GeSe 9-11
9
9.3.1 Comparing the structural models 9-12
9.3.2 Sensitivity to size and production protocols 9-15
9.4 Glassy GeS as compared to glassy GeSe 9-19
4 4
9.4.1 Structure factors and pair correlation functions 9-20
9.4.2 Coordination numbers, structural units and rings analysis: 9-24
a rationale for intermediate range order
9.4.3 Insight into electronic properties and correlation with structure 9-28
References 9-30
10 Accounting for dispersion forces: glassy GeTe and related 10-1
4
examples
10.1 Introduction 10-1
10.2 Functional and dispersion forces: four models to understand their 10-4
impact on glassy GeTe
4
10.2.1 Total structure factors and pair correlation functions: 10-5
a first insight
10.2.2 Partial pair correlation functions, bond angles distributions 10-7
and analysis of local environment
10.2.3 Electronic properties and link with the structure 10-12
10.2.4 What to learn about impact of dispersion forces and 10-13
total energy schemes
10.3 Dispersion forces and disordered GeSe : can we make any progress? 10-14
2
10.4 How to select the best dispersion prescription for glassy GeTe ? 10-18
4
Part I
10.5 How to select the best dispersion prescription for glassy GeTe ? 10-20
4
Part II
References 10-25
11 Ternary systems for applications: meeting the challenge 11-1
11.1 Introduction 11-1
11.2 Ge Sb Te 11-2
2 2 5
11.2.1 Total structure factors and pair correlation functions 11-3
11.2.2 Partial pair correlation functions and analysis of local 11-5
environment
11.3 Ga Ge Te 11-8
10 15 75
11.3.1 Structural properties 11-9
11.3.2 Network topology 11-11
References 11-14
ix