Course: Computer simulations in many body physics

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Course title Computer simulations in many body physics
Course code UFY/SIM1
Organizational form of instruction Lecture + Lesson
Level of course Doctoral
Year of study not specified
Frequency of the course In each academic year, in the winter semester.
Semester Winter
Number of ECTS credits 5
Language of instruction Czech, English
Status of course Compulsory-optional
Form of instruction unspecified
Work placements unspecified
Recommended optional programme components None
Course availability The course is available to visiting students
Lecturer(s)
  • Předota Milan, doc. RNDr. Ph.D.
Course content
Content of lectures: Introduction Laboratory and computer experiment, methods molecular dynamics (MD) and Monte Carlo (MC). Description of many particle system, intermolecular forces, correlation functions. Basics of MC Mathematical formulation of the problem, naive and preferential sampling, lattice systems, simulations in NPT and NVT ensembles, boundary conditions and technical details, optimization. Applications: hard sphere and Lennard-Jones liquids Basics of MD Equations of motion, Verlet and Gear integrators, simple thermostats. Applications: particles in homogeneous and radial gravitation fields, Lennard-Jones liquid. Content of practicals: Solving of simulation tasks in accord with the content of the lectures.

Learning activities and teaching methods
Monologic (reading, lecture, briefing), Demonstration, Activating (simulations, games, drama)
  • Class attendance - 39 hours per semester
  • Preparation for classes - 39 hours per semester
  • Preparation for exam - 40 hours per semester
Learning outcomes
Introduction to classical computer simulations. Methods Monte Carlo, molecular dynamics. Solution of realistic tasks in programs GROMACS, LAMMPS.
Student will understand simulations as a computer (pseudo)experiment, will be able to prepare, run, and analyze molecular simulations in programs Gromacs a LAMMPS.
Prerequisites
Basics of work in linux (can be quickly gained).

Assessment methods and criteria
Oral examination, Student performance assessment, Analysis of student's work activities (technical works)

To acquaint students with the fundamentals of Monte Carlo method, molecular dynamics and modeling of continuous systems. To model simple model systems using available software. Uderstand the style of work in computer modeling usin computer pseudoexperiments.
Recommended literature
  • D. Frenkel, B. Smit, Understanding Molecular Simulation, Academic Press, 2002..
  • I. Nezbeda, J. Kolafa, M. Kotrla, Úvod do počítačových simulací: Metody Monte Carlo a molekuární dynamiky, Karolinum 2003..
  • Uživatelský manuál a návody (tutorials) k programu GROMACS: http://www.gromacs.org.


Study plans that include the course
Faculty Study plan (Version) Category of Branch/Specialization Recommended year of study Recommended semester
Faculty: Faculty of Science Study plan (Version): Biophysics (1) Category: Physics courses - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Biophysics (1) Category: Physics courses - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Biophysics (1) Category: Physics courses - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Biophysics (1) Category: Physics courses - Recommended year of study:-, Recommended semester: Winter