Atomic Structure Prediction of Nanostructures, Clusters and Surfaces -- Contents -- Preface -- 1 The Challenge of Predicting Atomic Structure -- 1.1 Evolution: Reality and Algorithms -- 1.2 Brief Historical Perspective -- 1.3 Scope and Organization of This Book -- References -- 2 The Genetic Algorithm in Real-Space Representation -- 2.1 Structure Determination Problems -- 2.1.1 Cluster Structure -- 2.1.2 Crystal Structure Prediction -- 2.1.3 Surface Reconstructions -- 2.1.4 Range of Applications -- 2.2 General Procedure -- 2.3 Selection of Parent Structures -- 2.4 Crossover Operations -- 2.4.1 Cut-and-Splice Crossover in Real Space -- 2.4.2 Crossovers and Periodic Boundary Conditions -- 2.5 Mutations -- 2.5.1 Zero-Penalty Mutations -- 2.5.2 Regular Mutations -- 2.6 Updating the Genetic Pool: Survival of the Fittest -- 2.7 Stopping Criteria and Subsequent Analysis -- References -- 3 Crystal Structure Prediction -- 3.1 Complexity of the Energy Landscape -- 3.2 Improving the Efficiency of GA -- 3.3 Interaction Models -- 3.3.1 Classical Potentials -- 3.3.2 Ab Initio Methods -- 3.3.3 Adaptive Classical Potentials -- 3.4 Creating the Generation-Zero Structures -- 3.5 Assessing Structural Diversity of the Pool -- 3.5.1 Fingerprint Functions -- 3.5.2 General Features of the PES -- 3.6 Variable Composition -- 3.7 Examples -- 3.7.1 Identification of Post-Pyrite Phase Transitions -- 3.7.1.1 Computational Details -- 3.7.1.2 Results and Discussion -- 3.7.2 Ultrahigh-Pressure Phases of Ice -- 3.7.2.1 Computational Details -- 3.7.2.2 Results and Discussion -- 3.7.3 Structure and Magnetic Properties of Fe-Co Alloys -- 3.7.3.1 Computational Details -- 3.7.3.2 Results and Discussion -- References -- 4 Optimization of Atomic Clusters -- 4.1 Alloys, Oxides, and Other Cluster Materials -- 4.2 Optimization of Substrate-Supported Clusters via GA.

4.3 GA Solution to the Thomson Problem -- References -- 5 Atomic Structure of Surfaces, Interfaces, and Nanowires -- 5.1 Reconstruction of Semiconductor Surfaces as a Problem of Global Optimization -- 5.1.1 The Genetic Algorithm for Surface Reconstructions: the Case of Si(105) -- 5.1.1.1 Computational Details for Si(105) -- 5.1.1.2 Results for Si(105) -- 5.1.2 New Reconstructions for a Related Surface, Si(103) -- 5.1.3 Model Reconstructions for Si(337), an Unstable Surface: GA Followed by DFT Relaxations -- 5.1.3.1 Results for Si(337) Models -- 5.1.3.2 Discussion -- 5.1.4 Atomic Structure of Steps on High-Index Surfaces -- 5.1.4.1 Supercell Geometry and Algorithm Details -- 5.1.4.2 Results for Step Structures on Si(114) -- 5.2 Genetic Algorithm for Interface Structures -- 5.2.1 GA for Grain Boundary Structure Optimization -- 5.2.2 Structures Generated by GA -- 5.2.3 Grain Boundary Energy Calculations -- 5.3 Nanowire and Nanotube Structures via GA Optimization -- 5.3.1 Passivated Silicon Nanowires -- 5.3.2 One-Dimensional Nanostructures under Radial Confinement -- 5.3.2.1 Introduction -- 5.3.2.2 Description of the Algorithm -- 5.3.2.3 Results for Prototype Nanotubes -- 5.3.2.4 Discussion -- 5.3.2.5 Concluding Remarks -- References -- 6 Other Methodologies for Investigating Atomic Structure -- 6.1 Parallel Tempering Monte Carlo Annealing -- 6.1.1 General Considerations -- 6.1.2 Advantages of the Parallel Tempering Algorithm as a Global Optimizer -- 6.1.3 Description of the Algorithm -- 6.2 Basin Hopping Monte Carlo -- 6.3 Optimization via Minima Hopping -- 6.4 The Metadynamics Approach -- 6.5 Comparative Studies between GA and Other Structural Optimization Techniques -- 6.5.1 Reconstructions of Si(114): Comparison between GA and PTMC -- 6.5.1.1 PTMC Results -- 6.5.1.2 GA Results -- 6.5.1.3 DFT Calculations -- 6.5.1.4 Structural Models for Si(114).

6.5.1.5 Discussion -- 6.5.1.6 Concluding Remarks -- 6.5.2 Crystal Structure Prediction: Comparison between GA and MH -- 6.5.2.1 GA Applied to AlxSc1-x Alloys -- 6.5.2.2 Boron -- 6.5.2.3 Minima Hopping -- References -- 7 Perspectives and Outlook -- 7.1 Expansion through the Community -- 7.2 Future Algorithm Developments -- 7.3 Problems to Tackle - Discovery versus Design -- Index.