Simulation Methods in Many-Particle Systems

PhD course in Simulation Methods in Many-Particle Systems
Autumn 2016

Book: Frenkel and Smit: Understanding Molecular Simulations, available electronically from the library website.

Lecturer and course responsible: Astrid de Wijn.

The examination consists of a theory part (hand-in exercises and oral exam) and a practical part, programming assignments. You must pass everything to pass the course. Some addition notes:

Hand-in exercises. Do not hesitate to ask for help from me or eachother, via email or by dropping by.
Programming assignments. The MC and MD projects are related. Read both descriptions all the way through before you start writing your code. Think about the structure of your programs and functions before you start writing them. You can send in your reports by email. Include your code electronically.
Here is a list of common bugs and other things you might want to think about if you run into trouble with the programming.
This course is based on a course I used to teach at Stockholm University. Spring 2015 edition. It was taken over by Lars Pettersson, who seems to be following more or less the same course plan, but has written much nicer lecture notes. The current course at Stockholm University
I am providing scans of my lecture notes, but they are not very clear if you haven't been to the lectures. The purpose of my lecture notes is to remind me of what to say to you. So you can probably use them to remember what I said. If you have any comments or find any mistakes, please let me know.

Schedule and preliminary plan for lectures. This may change as we go along.

Lecture	date/time/location	topic(s)	reading material	assignments to be handed in
1	Tue. 13 Sept. 16:00 - 18:00, Astrid's office	What and why. Introduction into MD and MC. Structure of a simulation. Practical issues with programming.	Chapter 1, sections 4.1, 4.2.1, 4.2.2.	none
2	Fri. 23 Sept. 14:00 - 16:00, Astrid's office	Lennard-Jones potential. Integration algorithms: Verlet and Runge-Kutta.	4.2.3, 4.3	none
3	Mon. 26 Sept. 14:00 - 16:00, Astrid's office	Symplectic integration.	A.3.2	programming 1.1
4	Tue. 4 Oct. 14:00 - 16:00, Astrid's office	Resource scaling, Lyapunov instability, cutoffs.	4.3, 12.1	programming 1.2, hand-in 1
5	Thu. 13 Oct. 14:00 - 16:00 , Astrid's office	Ewald summation. Statistical physics! Ensembles.	A.3.3, D.3	programming 1.3
6	Tue. 18 Oct. 14:00 - 16:00, Astrid's office	Averages. Thermostats, Langevin and Nosé-Hoover.	6.1, 6.2	programming 1.4, hand-in 2 and 3
7	Fri. 28 Oct. 14:00 - 16:00, Astrid's office	Radial distribution function. Langevin and Nosé-Hoover. Introduction into MC, MC integration.	3.1	programming 1.5, 1.6, hand-in 4
8	Tue. 1 Nov. 14:00 - 16:00, Astrid's office	Importance sampling, Ising model as an example, Markov chains. Detailed balance.	3.1, 3.2, 5.1, 5.2	programming 1.7
extra	Thu. 3 Nov. 14:00 - 16:00, Astrid's office	Crash course in Statistical Mechanics.	Schroeder sections 6.1, 6.2, 6.4, 6.5
9	Tue. 8 Nov. 10:00 - 12:00, Astrid's office	Metropolis. Trial moves, early rejection. Cluster moves. Ensembles in MC.	3.3, 5.3, 5.4, 14.3	programming 1.8, hand-in 5
10	Tue. 15 Nov. 14:00 - 16:00, Astrid's office	Free-energy calculations. Computer lab.	7.1, 7.2, (7.3, 7.4)	programming 1.9, hand-in 6
11	Tue. 29 Nov. 14:00 - 16:00, Astrid's office	Effective force fields, internal degrees of freedom of molecules, constraints, SHAKE.	15.1	programming 1.10, 1.11
12	Tue. 6 Dec. 14:00 - 16:00, Astrid's office	Quantum MD, Car-Parrinello, diffusion quantum MC, if there is time.	15.2	programming 2.1, hand-in 7 and 8
	approximately Tue. 13 Dec., Astrid's office	Everything! Oral exam.	Everything!	programming 2.2

PhD course in Simulation Methods in Many-Particle SystemsAutumn 2016

PhD course in Simulation Methods in Many-Particle Systems
Autumn 2016