Computer Simulation of Condensed Matter
Code  Completion  Credits  Range 

D11SIKL  ZK 
 Garant předmětu:
 Jaroslav Hamrle, Štefan Zajac
 Lecturer:
 Jaroslav Hamrle, Petr Sedlák, Štefan Zajac
 Tutor:
 Jaroslav Hamrle, Petr Sedlák, Štefan Zajac
 Supervisor:
 Department of Solid State Engineering
 Synopsis:

Computer simulation in condensedmatter physics is becoming an important tool used by both experimentalist and theorists to develop new materials and technologies. Thus, solution of many practical problems can be transferred from the real to a „virtual“ laboratory. During the course, students will be introduced to the theoretical background of basic computation methods and let to test the acquired knowledge in practical exercises. Each lesson is organized as a tutorial where typical problems are solved with detailed explication of the computation methods used. The course is taking place in Computer classroom of the Department of Solid State Physics. Practical demonstration and exercises are using Material Studio simulation environment (Accelrys Software Inc.).
 Requirements:

Knowledge of quantum physics and numerical mathematics (lectures 02KVAN, 01NUMB at FNSPE)
 Syllabus of lectures:

1. Setting up models of molecules, macromolecules, crystals, surfaces, slabs and nanostructures. Rules applied to get realistic starting structures. Work with fragment libraries. Creation of projects. Exercise: MS Materials Visualizer.
2. Construction of extended amorphous assemblies with periodic boundary conditions under various selected thermodynamic conditions. Exercise: Amorphous Cell.
3. Classical simulation theory: Concept of force fields, bond deformations, nonbond interactions, special types of force fields, application of molecular mechanics approaches in Materials Studio, Exercise: MS Discover, MS Forcite, MS Forcite Plus.
4. Classical simulation theory: Minimization tasks (geometry optimization of molecule, energy minimization, mathematical methods for finding energy minima, energy pathways and transition structures). Exercise: MS Discover
5. Classical simulations theory: Computer simulations of dynamic system evolution (thermodynamic ensembles, phase space, treatment of longrange interactions, dissipative particle dynamics and other approximate methods). Exercise: MS Amorphous Cell, MS Mesodyne.
6. Geometrical and statistical analysis of the calculated results. Exercise: analytical tools embedded in MS Materials Visulizer, MS Amorphous Cell, MS Discover, and MS Forcite.
7. Scattering theory and crystalline structure determination: Powder diffraction, Rietveld refinement with energies. Exercise: MS Reflex Plus
8. Quantum mechanical concepts: Schroedinger equation, Selfconsistent field theory, DFT, HohenbergKohn theorems, KohnSham ansatz, pseudopotentials, Exercise: MS CASTEP, MS DMol3.
9. Quantum mechanical concepts: Semiempirical approach. Exercise: MS VAMP.
10. Quantum mechanical concepts: Firstprinciples molecular dynamics  CarParrinello method, Exercise: MS CASTEP, MS DMol3.
11. Quantum mechanical concepts: phonons and dielectric response calculation. Exercise: MS CASTEP.
12. Quantum mechanical concepts: Evaluation of optical absorption and emission spectra. Exercise: MS VAMP.
13. Quantum mechanical concepts: Stability of molecular structures. Exercise: MS DMOL3.
 Syllabus of tutorials:

A practical exercise will follow each of the treated theoretical topics.
 Study Objective:

Knowledge:
Basics of the theory and structure of bulk solid states.
Skills:
Mastering basics of the theory and practical realization of computer simulations for most common condensedstate systems.
 Study materials:

Key references:
[1]. A.R. Leach: Molecular Modeling: Principles and Applications, 2nd edition, Prentice Hall, ISBN 0582382106, Harlow 2001.
Recommended references:
[2]. R. M. Martin: Electronic Structure: Basic Theory and Practical Methods (Vol 1), Cambridge University Press, ISBN 0521782856, Cambridge 2004.
Special aids:
Computer classroom of DSSE equipped with MS software.
 Note:
 Timetable for winter semester 2023/2024:
 Timetable is not available yet
 Timetable for summer semester 2023/2024:
 Timetable is not available yet
 The course is a part of the following study plans: