Molecular Dynamics for Amorphous Materials: Methodology and applications

PRELIMS.pdf
	Preface
	Acknowledgement
	Author biography
		Carlo Massobrio
CH001.pdf
	Chapter 1 Introduction
		1.1 Why this book?
			1.1.1 The guideline: relying on direct experience
			1.1.2 Inside each chapter
		References
CH002.pdf
	Chapter 2 Amorphous materials via atomic-scale modeling
		2.1 The inspiring role of Glass Science
		2.2 From experiments to modelling: toward a connection with atomic-scale tools
		2.3 Accessing properties: direct and reciprocal space
		2.4 Describing the network topology
			2.4.1 Coordination numbers and units
			2.4.2 Bond-angle distributions and local order parameter
			2.4.3 Making sense out of diffusion in glasses via MD
		2.5 Correlating structural and electronic properties
			2.5.1 Electronic density of states
			2.5.2 Maximally localized Wannier functions
		2.6 Neutron scattering as experimental counterpart to MD
		References
CH003.pdf
	Chapter 3 Molecular dynamics to describe (amorphous) materials
		3.1 Molecular dynamics: what for?
		3.2 Beyond two-body potentials
		3.3 Potentials for iono-covalent systems
		3.4 Thermostats for molecular dynamics
			3.4.1 The breakthrough of S Nosé
		3.5 First-principles molecular dynamics via the Car–Parrinello method
			3.5.1 Basic ideas
			3.5.2 The Car–Parrinello method step by step
			3.5.3 Two families of degrees of freedom in non-equilibrium
			3.5.4 A first summary and some practical considerations
			3.5.5 The role of thermostats within FPMD
		3.6 Getting acquainted with the total energy
			3.6.1 Electronic kinetic energy: better avoiding confusions!
			3.6.2 The most convenient basis set: plane waves
			3.6.3 Introducing the notion of pseudopotentials
			3.6.4 Exchange and correlation to increase predictive power
			3.6.5 On the impact of the XC functional: the revealing case of liquid GeSe2
		3.7 Glassy materials and FPMD: criteria and challenges
			3.7.1 The issue of size limitations
			3.7.2 The issue of the length of the time trajectories
		References
CH004.pdf
	Chapter 4 A practical roadmap for FPMD on amorphous materials
		4.1 Choice of the description: classical potentials vs first-principles
			4.1.1 Digging out some failures of classical potentials
		4.2 Methodology: the unavoidable choices to be made
			4.2.1 More on the exchange–correlation functionals
			4.2.2 On the selection and use of pseudopotentials
			4.2.3 The quest of the best fictitious electronic mass and timestep
			4.2.4 The beauty of the Verlet algorithm
		4.3 Creating a computer glass via MD: the initial conditions
		4.4 Production of trajectories and the setup of a thermal cycle
			4.4.1 An essential summary before hitting the road
			4.4.2 Starting to run carefully and cautiously: a mini guide
			4.4.3 Handling adiabaticity: the gap issue
			4.4.4 Some instructions to be effective when moving to high temperatures
			4.4.5 Quenching down to the glassy state
		4.5 Dealing with FPMD odds and ends (including non-adiabaticity): the case of SiN
			4.5.1 State of the art and calculations
			4.5.2 Methodology and the appropriate FPMD schemes
			4.5.3 Focus on the coordination units
			4.5.4 What to learn from the case of SiN?
		4.6 The CPMD code and some thoughts on how to approach the ‘code issue’: an autobiographical perspective
			4.6.1 Inside CPMD: the essentials
		References
CH005.pdf
	Chapter 5 Cases treated via classical molecular dynamics
		5.1 Learning about glasses from a Lennard-Jones monoatomic system
			5.1.1 Simple and instructive: a monoatomic glass model
			5.1.2 Assessing the stability around Tgl
			5.1.3 Some considerations about qualitative glass models
		5.2 Amorphization by solid-state reaction in a metallic alloy
		References
CH006.pdf
	Chapter 6 The atomic structure of disordered networks
		6.1 General consideration: where do we start from?
		6.2 The structure of liquid and glassy GeSe2
			6.2.1 Methodology
			6.2.2 Liquid GeSe2
			6.2.3 Glassy GeSe2
			6.2.4 Modeling these two systems: some thoughts
		6.3 The origin of the first-sharp diffraction peak
			6.3.1 FSDP in the total structure factor
			6.3.2 FSDP in the concentration–concentration partial structure factor
		6.4 FSDP in disordered network: some considerations before to go on
		6.5 Evidence of FSDP in SCC(k): examples
		6.6 What to learn from SCC(k) vs Szz(k)
			6.6.1 Calculating Szz(k)
			6.6.2 Comparing Szz(k) and SCC(k) for the three classes of networks
		6.7 Improving the description of chemical bonding
			6.7.1 Contours of the GGA issue for chalcogenides
			6.7.2 Why BLYP?
			6.7.3 Liquid GeSe2: BLYP vs PW, direct space and short-range properties
			6.7.4 Liquid GeSe2: BLYP vs PW, reciprocal space and intermediate range properties
			6.7.5 Liquid GeSe2: BLYP vs PW, dynamical properties
			6.7.6 Glassy GeSe2: BLYP vs PW and further thoughts
		References
CH007.pdf
	Chapter 7 The effect of pressure on the structure of glassy GeSe2 and GeSe4
		7.1 Is there any pressure left?
		7.2 GeSe2 under pressure: a density-driven transition
			7.2.1 Introduction: combining experiments and theory
			7.2.2 Neutron diffraction experiments at finite pressure: the essential
			7.2.3 Understanding the structural transition: results
			7.2.4 Understanding the structural transition: rationale
		7.3 GeSe4 under pressure: when theory and experiments agree
			7.3.1 Behavior under pressure
			7.3.2 Behavior under pressure: rationale
		References
CH008.pdf
	Chapter 8 Structural changes with composition in GexSe1−x glassy chalcogenides
		8.1 Composition makes the difference: early calculations on liquid GeSe4
		8.2 Glassy GeSe4 and glassy SiSe4 and the ‘structural variability’
			8.2.1 Structural properties
			8.2.2 Structural variability
		8.3 Altering stoichiometry by adding Ge: glassy Ge2Se3
			8.3.1 A glimpse on the correlation between atomic and electronic structure
			8.3.2 What to learn from glassy Ge2Se3
		References
CH009.pdf
	Chapter 9 Moving ahead, better and bigger: GeS2, GeSe9 and GeSe4 vs GeS4
		9.1 Introduction
		9.2 Glassy GeS2
			9.2.1 Real space properties
			9.2.2 Reciprocal space properties
			9.2.3 Bonding properties
		9.3 Glassy GeSe9
			9.3.1 Comparing the structural models
			9.3.2 Sensitivity to size and production protocols
		9.4 Glassy GeS4 as compared to glassy GeSe4
			9.4.1 Structure factors and pair correlation functions
			9.4.2 Coordination numbers, structural units and rings analysis: a rationale for intermediate range order
			9.4.3 Insight into electronic properties and correlation with structure
		References
CH010.pdf
	Chapter 10 Accounting for dispersion forces: glassy GeTe4 and related examples
		10.1 Introduction
		10.2 Functional and dispersion forces: four models to understand their impact on glassy GeTe4
			10.2.1 Total structure factors and pair correlation functions: a first insight
			10.2.2 Partial pair correlation functions, bond angles distributions and analysis of local environment
			10.2.3 Electronic properties and link with the structure
			10.2.4 What to learn about impact of dispersion forces and total energy schemes
		10.3 Dispersion forces and disordered GeSe2: can we make any progress?
		10.4 How to select the best dispersion prescription for glassy GeTe4? Part I
		10.5 How to select the best dispersion prescription for glassy GeTe4? Part II
		References
CH011.pdf
	Chapter 11 Ternary systems for applications: meeting the challenge
		11.1 Introduction
		11.2 Ge2Sb2Te5
			11.2.1 Total structure factors and pair correlation functions
			11.2.2 Partial pair correlation functions and analysis of local environment
		11.3 Ga10Ge15Te75
			11.3.1 Structural properties
			11.3.2 Network topology
		References
CH012.pdf
	Chapter 12 Past, present and future
		12.1 Past: what else beyond structure?
		12.2 From past to present, from structural to thermal properties: thermal conductivity
		12.3 Future: the quest of quantitative predictions goes on, thoughts, recommendations and some very recent results
		References