Computer simulation of physical systems I
PHYS-403
Media
Media
This file is part of the content downloaded from Computer simulation of physical systems I.
Computer Simulation of Physical Systems I
General
Master semester 1
Professor:
Alfredo Pasquarello
Sécrétariat:
Juliana Velasquez
Assistants:
Yongbin Zhuang
Giorgio Palermo
Stefan Riemelmoser
Report of Fall Semester 2024-25
Fall Semester 2024-25
- InformationHere, information about the course... (Text and media area)
- Information 10.09.2024 (Page)
- Information 15.10.2024 (Page)
- Information 23.10.2024 (Page)
- Information 19.11.2024 (Page)
- Information 19.11.2024 (2nd) (Page)
- Information 19.12.2024: Provisional exam schedule (File)
Programme
- Ordinary differential equationsmethods for numeric... (Text and media area)
- Classical molecular dynamicsVerlet algorithm, dete... (Text and media area)
- Random variablesdefinitions and properties, genera... (Text and media area)
- Random walksbinomial and Gaussian distributions, p... (Text and media area)
- Monte Carlo integrationdirect sampling, importance... (Text and media area)
- Classical molecular dynamics: advanced topicsEwald... (Text and media area)
Life sessions
Week 01
- C01/1 Presentation of the course (Text and media area)
- Course 01/1 - pdf (File)
- Report: Requirements (19.11.2024) (File)
- C01/2 Ordinary differential equations (1/2) (Text and media area)
- Course 01/2, 21.09.2021 (29:21) (URL)
- Course 01/2, 2020 (33:59) (URL)
- Course 01/2 - pdf (File)
- C02/1 Ordinary differential equations (2/2) (Text and media area)
- Course 02/1, 21.09.2021 (43:17) (URL)
- Course 02/1, 2020 (38:59) (URL)
- Course 02/1 - pdf (File)
- C02/2 Classical molecular dynamics (Text and media area)
- Course 02/2, 21.09.2021 (49:45) (URL)
- Course 02/2, 2020 (46:55) (URL)
- Course 02/2 - pdf (File)
- References for classical molecular dynamics (Page)
Week 02
- C03/1 Integration algorithms for MD - Verlet algor... (Text and media area)
- Course 03/1, 28.09.2021 (25:24) (URL)
- Course 03/1, 2020 (19:54) (URL)
- Course 03/1 - pdf (File)
- C03/2 Issues about accuracy and stability (Text and media area)
- Course 03/2, 28.09.2021 (34:37) (URL)
- Course 03/2, 2020 (31:24) (URL)
- Course 03/2 - pdf (File)
- C04/1 Molecular dynamics of Lennard-Jones liquid (Text and media area)
- Course 04/1, 28.09.2021 (34:37) (URL)
- Course 04/1, 2020 (34:48) (URL)
- Course 04/1 - pdf (File)
- Original reference of Rahman (Page)
- E01 Task I: Testing integration algorithms for the... (Text and media area)
Week 03
- C04/2 Static property: pair correlation function (Text and media area)
- Course 04/2, 05.10.2021 (51:32) (URL)
- Course 04/2, 2020 (53:05) (URL)
- Course 04/2 - pdf (File)
- C05/1 Dynamic property: diffusion coefficient - Ei... (Text and media area)
- Course 05/1, 05.10.2021 (36:33) (URL)
- Course 05, 2020 (1:04:02) (URL)
- Course 05/1 - pdf (File)
- E02 Task II: Molecular dynamics of Lennard-Jones l... (Text and media area)
Week 04
- C05/2 Velocity-velocity autocorrelation (Text and media area)
- Course C05/2, 12.10.2021 (24:23) (URL)
- Course 05/2 - pdf (File)
- C06/1 Sampling the canonical ensemble (Text and media area)
- Course C06/1, 12.10.2021 (1:06:22) (URL)
- Course 06/1, 2020 (56:01) (URL)
- Course 06/1 - pdf (File)
- E03 Task II: Molecular dynamics of Lennard-Jones l... (Text and media area)
Week 05
- C06/2 Nosé-Hoover thermostats (Text and media area)
- Course C06/2, 19.10.2021 (58:06) (URL)
- Course 06/2, 2020 (49:53) (URL)
- Course 06/2 - pdf (File)
- Original references of Nosé and Hoover (Page)
- C07/1 Notions of probability - Central limit theor... (Text and media area)
- Course 07/1, 19.10.2021 (30:56) (URL)
- Course 07/1, 2020 (35:26) (URL)
- Course 07/1 - pdf (File)
- E04 Task II: Molecular dynamics of Lennard-Jones l... (Text and media area)
Week 06
Exercises 05 (15 October, 10:15, room: CO023) - Exercises 06 (15 October, 15:15, exceptionally in room: SG0217)
- E05 Task III: Nosé-Hoover thermostats (1/2) (Text and media area)
- E06 Task III: Nosé-Hoover thermostats (2/2) (Text and media area)
Week 07
- C07/2 Random number generators (1/2) (Text and media area)
- Course 07/2, 02.11.2021 (44:32) (URL)
- Course 07/2, 2020 (44:01) (URL)
- Course 07/2 - pdf (File)
- C08/1 Random number generators (2/2) (Text and media area)
- Course 08/1, 02.11.2021 (39:04) (URL)
- Course 08/1, 2020 (25:17) (URL)
- Course 08/1 - pdf (File)
- E07 Finalization of Task II & III (report) (Text and media area)
Week 08
- C08/2 Nonuniform random number distributions (Text and media area)
- Course 08/2, 09.11.2021 (42:45) (URL)
- Course 08/2, 2020 (44:46) (URL)
- Course 08/2 - pdf (File)
- C09/1 Random walk and diffusion (Text and media area)
- Course 09/1, 09.11.2021 (41:01) (URL)
- Course 09/1, 2020 (37:25) (URL)
- Course 09/1 - pdf (File)
- E08 Task IV: Testing random number generators (1/1... (Text and media area)
Week 09
- C09/2 Monte Carlo integration through uncorrelated... (Text and media area)
- Course 09/2, 16.11.2021 (43:56) (URL)
- Course 09/2, 2020 (56:05) (URL)
- Course 09/2 - pdf (File)
- C10/1 Importance sampling (Text and media area)
- Course 10/1, 16.11.2021 (45:48) (URL)
- Course 10/1, 2020 (53:12) (URL)
- Course 10/1 - pdf (File)
- E09 Task Va: Basic Monte Carlo integration (1/2) (Text and media area)
Week 10
- C10/2 Correlated sampling (Text and media area)
- Course 10/2, 23.11.2021 (47:15) (URL)
- Course 10/2, 2020 (37:25) (URL)
- Course 10/2 - pdf (File)
- C11/1 Metropolis algorithm (Text and media area)
- Course 11/1, 23.11.2021 (37:36) (URL)
- Course 11/1, 2020 (32:22) (URL)
- Course 11/1 - pdf (File)
- Original reference for Metropolis algorithm (Page)
- E10 Task Va: Basic Monte Carlo integration (2/2) (Text and media area)
Week 11
- C12/2 Errors in correlated sampling (Text and media area)
- Course 12/2, 30.11.2021 (48:30) (URL)
- Course 12/2, 2020 (48:28) (URL)
- Course 12/2 - pdf (File)
- Documentation: errors in correlated sampling (File)
- Original reference for blocking analysis (Page)
- C11/2 Monte Carlo simulation of Lennard-Jones liqu... (Text and media area)
- Course 11/2, 30.11.2021 (38:37) (URL)
- Course 11/2, 2020 (27:38) (URL)
- Course 11/2 - pdf (File)
- E11 Task Vb: Blocking analysis (1/1) (Text and media area)
Week 12
- C12/1 Monte Carlo simulation of 2D spin syste... (Text and media area)
- Course 12/1, 07.12.2021 (47:42) (URL)
- Course 12/1, 2020 (49:08) (URL)
- Course 12/1 - pdf (File)
- C13/1 Ewald summation (1/2) (Text and media area)
- Course 13/1, 07.12.2021 (35:21) (URL)
- Course 13/1, 2020 (29:39) (URL)
- Course 13/1 - pdf (File)
- E12 Task VI: Monte-Carlo simulation of Lennard-Jon... (Text and media area)
Week 13
- C13/2 Ewald summation (2/2) (Text and media area)
- Course 13/2, 14.12.2021 (53:06) (URL)
- Course 13/2, 2020 (42:53) (URL)
- Course 13/2 - pdf (File)
- C14/1 Constraints in MD (1/2): introduction (Text and media area)
- Course 14/1, 14.12.2021 (32:43) (URL)
- Course 14, 2020 (54:52) (URL)
- Course 14/1 - pdf (File)
- E13 Task VI: Monte-Carlo simulation of Lennard-Jon... (Text and media area)
Week 14
- C14/2 Constraints in MD (2/2): general method... (Text and media area)
- Course 14/2, 21.12.2021 (43:09) (URL)
- Course 14/2 - pdf (File)
- E14 Finalization of Task VI (report) (Text and media area)
- Deadline for handing in the report for all student... (Text and media area)
Tasks for exercise sessions
- Task I: numerical integration algorithms (Page)
- Task II: NVE molecular dynamics simulation (Page)
- Task III: NVT molecular dynamics with Nosé-Hoover thermostat (Page)
- Task IV: random number generators and 1D random walks (Page)
- Task Va: Basic Monte-Carlo integration (Page)
- Task Vb: Blocking analysis (Page)
- Task VI: Monte-Carlo simulation of Lennard-Jones liquid (Page)
Bibliography and Links
Recommended reading:
- F. J. Vesely, Computational physics: An introduction
- J. M. Thijssen, Computational physics.
- S. E. Koonin, Computational physics.
- T. Pany, An introduction to computational physics.
- M. P. Allen and D. J. Tildesley, Computer simulation of liquids.
- D. Frenkel and B. Smit, Understanding molecular simulation: from algorithms to applications.
Code of ethics concerning the citing of information sources english french
Useful links for programming:
Numerical recipes
ATLAS from sourgeforge.net.org
LAPACK from netlib.org
BLAS from netlib.org
RPM packages for ATLAS, LAPACK and BLAS from Axel Kohlmeyers CPMD home page.
FFTW from fftw.org
FFTPACK from netlib.org
Fortran95 Self-study guide by Rachael Padman Michaelmas
Introduction to programming in Fortran 90 by Pradeep P. Bhat, Michail Stamatakis
Manuals and guides for working under the Linux/Unix environment:
Unix quick-reference card (list of commonly used commands)
Bash Guide for Beginners (more recent versions available online)
Gnuplot reference card (list of commands)
The not-so-FAQ on Gnuplot (a must-see for gnuplot users)
Project of Spring Semester
Spring Semester
Course room: CE5
Exercise room: CHB2392