Code: 11SIKL Computer Simulation of Condensed Matter
Lecturer: doc. Ing. Ladislav Kalvoda CSc. Weekly load: 2+2 Completion: EX
Department: 14111 Credits: 4 Semester: W
Description:
Computer simulation in condensed-matter 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.).
Contents:
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, non-bond 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 long-range 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, Self-consistent field theory, DFT, Hohenberg-Kohn theorems, Kohn-Sham ansatz, pseudopotentials, Exercise: MS CASTEP, MS DMol3.
9. Quantum mechanical concepts: Semi-empirical approach. Exercise: MS VAMP.
10. Quantum mechanical concepts: First-principles molecular dynamics - Car-Parrinello 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.
Seminar contents:
A practical exercise will follow each of the treated theoretical topics.
Recommended literature:
Key references:
[1]. A.R. Leach: Molecular Modeling: Principles and Applications, 2nd edition, Prentice Hall, ISBN 0-582-38210-6, Harlow 2001.

Recommended references:
[2]. R. M. Martin: Electronic Structure: Basic Theory and Practical Methods (Vol 1), Cambridge University Press, ISBN 0-521-78285-6, Cambridge 2004.

Special aids:
Computer classroom of DSSE equipped with MS software.
Keywords:
Condensed mater; computer simulations of; molecular dynamics; ab-initio simulations; semi-empirical methods; density functional theory; scattering theory; properties calculations; practical exercises.

Abbreviations used:

Semester:

Mode of completion of the course:

Weekly load (hours per week):