Introduction to Condensed Matter Simulations
Code  Completion  Credits  Range 

11ZSKL  KZ  2  1P+1C 
 Course guarantor:
 Ladislav Kalvoda
 Lecturer:
 Jan Drahokoupil, Ladislav Kalvoda
 Tutor:
 Supervisor:
 Department of Solid State Engineering
 Synopsis:

Computer simulation in condensed matter becomes an important tool in developing new materials and technologies used by both experimenters and theorists. The solution of many practical problems is thus transferred from real to 'virtual' computer lab. During the course, students will be introduced to basic computational methods and procedures based on classical nonquantum physics models , and will test their knowledge on practical examples.
 Requirements:
 Syllabus of lectures:

1Introduction to approaches of condensed matter computer simulations: MM, MD, MC, DFT, CALPHAD, FEM
2Design of a computer atomistic model (molecules, macromolecules, crystal, amorphous substances, liquids, surfaces, layers, nanostructures, homo and heterosystems); Working with libraries of structural fragments; Create and save a project
3Initial model optimization, geometric boundary conditions of the model, thermodynamic ensemble, phase space, partition function
4Molecular mechanics: concept of force fields, deformations of bonds, nonbonding interactions, special types of force fields, algorithms of molecular mechanics implementation
5 Longrange interactions, types, methods of their quantification
6Geometric optimization of ensembles, minimization of energy, mathematical methods of finding minimum energy
7Molecular dynamics, equations of motion and their integration
8Monte Carlo method, model construction, static and dynamic systems simulation
9Statistical trajectory analysis, temporal and ensemble averages, ergodic hypothesis, energy trajectories and transition structures
10Transition processes, transition states, analysis of geometric and energetic properties
11Mesoscale modeling: reasons for using mesoscale models, dissipative particle dynamics, mean field models, transition from atomistic to mesoscale models
12Scattering theory, prediction and determination of crystal structure, simulation of powder diffraction diagrams
13Rietveld's refinement of the atomistic model, application of energy constraines to the model.
 Syllabus of tutorials:

1Introduction to approaches of condensed matter computer simulations: MM, MD, MC, DFT, CALPHAD, FEM
2Design of a computer atomistic model (molecules, macromolecules, crystal, amorphous substances, liquids, surfaces, layers, nanostructures, homo and heterosystems); Working with libraries of structural fragments; Create and save a project
3Initial model optimization, geometric boundary conditions of the model, thermodynamic ensemble, phase space, partition function
4Molecular mechanics: concept of force fields, deformations of bonds, nonbonding interactions, special types of force fields, algorithms of molecular mechanics implementation
5 Longrange interactions, types, methods of their quantification
6Geometric optimization of ensembles, minimization of energy, mathematical methods of finding minimum energy
7Molecular dynamics, equations of motion and their integration
8Monte Carlo method, model construction, static and dynamic systems simulation
9Statistical trajectory analysis, temporal and ensemble averages, ergodic hypothesis, energy trajectories and transition structures
10Transition processes, transition states, analysis of geometric and energetic properties
11Mesoscale modeling: reasons for using mesoscale models, dissipative particle dynamics, mean field models, transition from atomistic to mesoscale models
12Scattering theory, prediction and determination of crystal structure, simulation of powder diffraction diagrams
13Rietveld's refinement of the atomistic model, application of energy constraines to the model.
 Study Objective:
 Study materials:

Key references:
[1] T.A.Beu: Introduction to Molecular Dynamics Simulations. CRC Press LLC, 2019.
[2] V. Brázdová, D.R. Bowler: Atomistic Computer Simulations: A Practical Guide. Wiley VCH 2013. ISBN: 9783527410699
Other references:
[3] A.R. Leach: Molecular Modeling: Principles and Applications, 2nd edition, Prentice Hall, ISBN 0582382106, Harlow 2001.
 Note:
 Timetable for winter semester 2024/2025:
 Timetable is not available yet
 Timetable for summer semester 2024/2025:
 Timetable is not available yet
 The course is a part of the following study plans: