# Molecular and Materials Modelling This is the directory for notes of the courses [227-0161-00L Molecular and Materials Modelling FS2023](https://moodle-app2.let.ethz.ch/course/view.php?id=19729). The content can be roughly separated into several parts: classical molecular dynamics, quantum-related computation, and energy surface exploration. However, these topics also have overlaps and relations (after all, the quantum description evolved from the classical one). These notes, with handwritten form being the original version, are prepared during the reviewing session before the exam. Therefore, these contents can only be considered as summaries or reviewing materials. On this page, all main topics will be listed. 1. [[Hamilton's principle]] 2. [[Lagrange's equation]] 3. [[Potential, force, momentum, velocity]] 4. [[Intro to molecular dynamics]] 5. [[Verlet algorithm]] 6. [[Shifted potential]] 7. [[Periodic boundary condition]] 8. [[Initialization of simulation]] 9. [[Control of simulation]] 10. [[Statistical quantities]] 11. [[Real space correlations, radial distribution function]] 12. [[Retrospect on statistical mechanics]] 13. [[Ensemble]] 14. [[Thermostats and constant temperature MD]] 15. [[Velocity rescaling]] 16. [[Thermostats by stochastic collision]] 17. [[Quick review on Monte Carlo]] 18. [[Kinetic Monte Carlo]] 19. [[Fundamental on potential term]] 20. [[Expression for potential terms]] 21. [[AMBER force field]] 22. [[Details on LJ]] 23. [[Potential energy surface]] 24. [[Steinhardt order parameter]] 25. [[General algorithm for locating minima and optimization]] 26. [[Locating transit state]] 27. [[Lattice and periodic system]] 28. [[Reciprocal lattice and Bragg's law]] 29. [[Orbital, Fermi-Dirac distribution, DOS]] 30. [[Bloch's theorem and Born-von Karman boundary condition]] 31. [[Crystal momentum, effective mass, group velocity]] 32. [[Tight binding model & LCAO]] 33. [[Secular equation]] 34. [[Hartree method, from Hartree product to HF]] 35. [[Hartree-Fork method]] 36. [[Hartree-Fock-Roothaan method]] 37. [[Basis sets]] 38. [[Begin of DFT, Hohenberg-Kohn theorems]] 39. [[Kohn-Sham approach]] 40. [[Evaluating exchange-correlation energy]] 41. [[Basis-set superposition energy]] 42. [[Solving SCF]] 43. [[Pseudopotential]] 44. [[Projected density of state]] 45. [[Data representation]] 46. [[Landmarks]] 47. [[Reweighting and enhanced sampling techniques]] 48. [[Dimensionality reduction]] 49. [[Smooth overlap of atomic positions]] 50. [[Two pair potential vs many body potential]] 51. [[Embedded atom method and the Glue potential]] 52. [[Machine learning potential]] 53. [[Free energy surface]] 54. [[Evaluating FES]] 55. [[Free energy related method]] Other practical information: - [[Git command summary]] - [[Bash operation summary]] - [[Linux command summary]] **Optics and photonics: modelling structures with FDTD** This side project aims to gain practical insights into photonic structures. Some exercises may be conducted using MEEP, a free and open-source software package. The official manual can be found at [https://meep.readthedocs.io/en/master/](https://meep.readthedocs.io/en/master/). The Python interface will be used, and the package has been installed in WSL2. Exercises are selected from the tutorials in [the MEEP documentation](https://meep.readthedocs.io/en/master/Python_Tutorials/Basics/) and subsequent sections, as well as from some more complex and computationally intensive examples on [Simpetus Projects](http://www.simpetus.com/projects.html). As for the simulations for the photodetector project, [Lumerical FDTD](https://www.ansys.com/products/optics/fdtd) will be used. The design consideration and script will also be included here. Theoretical topics beyond modeling (e.g., waveguide theory) will be included in the [[Index (Optics)]] section. 1. [[FDTD simulation for GeSn photodetector with high absorption coefficient]]