# Subject description - BE0M35EAS

Summary of Study |
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List of Roles |
Explanatory Notes
Instructions

Charles Kittel, Introduction to Solid State Physics, 8th edition, Wiley IPL, ISBN-13: 9788126535187
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Peter Atkins, Julio de Paula, Physical Chemistry, 9th Edition, Oxford University Press, ISBN-13: 9780199543373
Daan Frenkel, Berend Smit, Understanding Molecular Simulation, 2nd Edition, Academic Press, ISBN-13: 9780122673511

BE0M35EAS | Elements of Atomistic Simulations | ||
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Roles: | Extent of teaching: | 2P+2L | |

Department: | 13135 | Language of teaching: | EN |

Guarantors: | Cammarata A. | Completion: | Z,ZK |

Lecturers: | Cammarata A. | Credits: | 4 |

Tutors: | Cammarata A. | Semester: | Z,L |

**Anotation:**

**Content:**

**Course outlines:**

1. | Introduction to the course: lessons outline, introduction to the computational environment (e.g. bash shell, code compilation) and to the use of High Performance Computing facilities (ssh, rsync, SLURM, parallelism) | |

2. | Fundaments of thermodynamics and statistical mechanics (state variables, laws of thermodynamics, phase space, partition functions, ensembles, ...) | |

3. | Units & dimensions, periodic boundaries conditions, integrators (e.g. Verlet, Leapfrog) | |

4. | Classical force fields, potential energy surfaces, types of interaction, calculation techniques | |

5. | Non-Hamiltonian dynamics, thermostats & barostats (e.g. Berendsen, Nose-Hoover/Rahman-Parrinello) | |

6. | Non-equilibrium MD simulations, external forces, constraints | |

7. | Introduction to quantum mechanics: the postulates of quantum mechanics, the uncertainty principle, time dependent and time independent Schrödinger equation, Hamiltonian, observable quantities and expectation values | |

8. | The hydrogen atom and the hydrogen-like orbitals; Molecular Orbitals, Roothan-Hall Self Consistent Field procedure, Density Functional Theory | |

9. | Crystal structures and reciprocal lattice, the Born-Oppenheimer approximation, the Hellmann-Feynman theorem | |

10. | Free electron model, the Bloch's theorem, energy bands | |

11. | Phonon description of atomic motions | |

12. | Phonon description of thermal properties, anharmonic interactions | |

13. | The Franck-Condon principle, the Jablonski Diagram, Electron-Phonon coupling | |

14. | Atomic-scale design of new materials |

**Exercises outline:**

1. | Introduction to LAMMPS, preparing an input script for energy minimization, introduction to VMD | |

2. | NVE molecular dynamics simulations, case study | |

3. | NpT molecular dynamics simulations, case study | |

4. | Steered MD simulations, case study: sliding of a MoS2 flake on a substrate | |

5. | Introduction to parallel environment in MD simulations | |

6. | Individual student projects on MD simulations and remarks | |

7. | Introduction to ABINIT, preparing an input script for electronic energy minimization, introduction to visualization software for solid state physics (e.g. VESTA) | |

8. | Visualization of hydrogen orbitals and relative energies, analysis of electronic charge density of molecular systems (e.g. electronic charge differences, Electron Localization Function, Bader analysis, Orbital Population) | |

9. | Construction of crystal unit cells, application of the Hellmann-Feynmann theorem: optimization of atomic geometries | |

10. | Electron Density of States, bond covalency analysis | |

11. | Calculation and visualization of phonon modes, phonon Density of States | |

12. | Calculation and analysis of thermal properties from phonon modes | |

13. | Simple example of electron-phonon coupling | |

14. | Materials design, case study: layer shift in MX2 transition metal dichalcogenides |

**Literature:**

P. | W. Atkins and R. S. Friedman, Molecular Quantum Mechanics, 3rd edition, Oxford University Press, ISBN 0-19-855947-X |

H. | Goldstein, C. P. Poole and John Safko, Classical Mechanics, 3rd edition, Pearson Education, ISBN-13: 9788131758915 | |

C. | Cohen-Tannoudji, B. Diu and Frank Laloe, Quantum Mechanics Vol.1, 1st edition, Wiley, ISBN-13: 9780471164333 |

**Requirements:**

**Subject is included into these academic programs:**

Program | Branch | Role | Recommended semester |

Page updated 14.10.2024 17:51:34, semester: Z/2025-6, Z,L/2024-5, L/2023-4, Send comments about the content to the Administrators of the Academic Programs | Proposal and Realization: I. Halaška (K336), J. Novák (K336) |