Introduction to atomistic simulations 2003

53363-0 Introduction to atomistic simulations 2003 / Johdatus atomistisiin simulointeihin 2003

Summary in English
Prerequisites: Knowledge of the basics of programming and the Unix environment, the structure of matter and thermodynamics. The course is also suited to chemists.
Contents: Visualization and animation of atomic data. Molecular dynamics simulations, which enable following the motion of a set of pointlike objects (typically but not necessarily atoms). During the course, the students get to write in a supervised manner their own molecular dynamics code, capable of simulating atom motion in simple metals. Genetic algorithm and conjugate gradient energy minimization of atomic systems. Overview of quantum mechanical and classical models of atomic interaction, and a detailed description of modern classical force models for metals, semiconductors, ionic and organic materials. Literature: Lecture notes.
Yhteenveto suomeksi
Kurssin tarkoituksena on johdattaa opiskelija atomitasolla toimiviin fysikaalisiin simulointimenetelmiin ja antaa valmiudet kirjoittaa simulointikoodeja käytännössä. Kurssin aikana osallistujat kirjoittavat ohjatusti yksinkertaisen simulointikoodin. Opittuja koodausmenetelmiä voi käyttää hyväksi useissa muissakin yleisissä fysiikalisissa simuloinneissa. Lisäksi kurssilla esitellään viimeaikaista kehitystä simulointimenetelmissä ja atomistisissa vuorovaikutusmalleissa tarkoituksena antaa yleiskuva siitä millaista mallia kannattaa soveltaa mihinkin ongelmaan.
Kurssin sisältö: Tietokonesimuloinnit fysiikassa, atomidatan visualisointi ja animointi, molekyylidynaamiset simulointimenetelmät, atomistisistä vuorovaikutusmalleista: kvanttimekaanisten, tight-binding- ja semiempiiristen mallien käyttöalueet, "breathing sphere"- polymeerimalli, geneettiset algoritmit rakenne-optimoinnissa sekä atomistisen simulointidatan vertaaminen kokeisiin.

Lecturer 2003: Prof. Kai Nordlund
Lectures Tue 12-14 room D114
Exercises Thus 12-14 Accelerator laboratory seminar room! (note change)
First lecture Tue 14.1 at 12.15

The course is given in English in anyone who does not know Finnish turns up.
Literature: lecture notes. As background material e.g. the books

Allen, Tildesley: "Computer simulation of Liquids" (Oxford University Press, Oxford, England, 1989)
J. von Boehm: "Molekyylidynamiikka-menetelmä" (Otatieto, Espoo, 2000)
may be used.
Requisite background information: The basics of programming and the Unix environment. Basic knowledge of the structure of matter and thermodynamics.

Lecture notes in postscript

Package 1: Introduction, contents and visualization methods

Package 2: Basics of MD, initialization, time step choice, speedup methods

Package 3 a: Neighbour lists

Package 3 b: mdmorse program description

Package 3 c: mdmorse F90 code prettyprinted

Package 3 b: mdmorse C code prettyprinted

Package 4: Solving the equations of motion

Package 5: Force calculation, pair potentials, potential fitting

Package 6: Theory, ensembles, P and T control

Package 7: Quantum mechanical interaction models

Package 8: Interaction models for metals

Package 9: Interatomic potentials for semiconductors

Package 10 a: Molecular interaction models 1. Reactive models

Package 10 b: Molecular interaction models 2. Molecular mechanics

Package 11: Ionic interactions

Package 11 b: Breathing sphere polymer model

Package 12: Conjugate gradients, genetic algorithms

Package 13: Metropolis MC simulation

Package 14: Comparison with atom-resolution experiments

Lecture 15: Summary and end

Exercises in postscript

1: lattice generation, deadline Tue Jan 21, session Thu Jan 23.

Note: no exercise session on Thu Jan 30!

2: Gaussian random numbers, deadline Tue Feb 4, session Thu Feb 6.

3: mdmorse init, neighbourlist, deadline Tue Feb 11, session Thu Feb 13.

4: Solution of equations of motion, deadline Tue Feb 18, session Thu Feb 20.

5: Force calculation, deadline Tue Feb 25, session Thu Feb 27.

6: Cutoff effects, energy conservation, deadline Tue Mar 4, session Thu Mar 6.

7: Maxwell-Boltzmann distribution, T control, deadline Mar 11, session Thu Mar 13.

8: Pressure control, melting I, deadline Tue Mar 25, session Thu Mar 27.

9: Sintering of nanoclusters, deadline Tue Apr 1, session Thu Apr 3.

10: Melting 2, surface melting, deadline Tue Apr 8, session Thu Apr 10.

11: Ion impact, deadline Tue Apr 15, session Thu Apr 17.

12 (BONUS): Metropolis MC for NPT, deadline Mon Apr 28, session Tue Apr 29.

mdmorse code

Now (Mar 27) complete, also contains Berendsen T and P control!

F90 version	C version
Makefile	Makefile
atoms.in	(same as for Fortran)
mdmorse.in	(same of for Fortran)
main.f90	main.c
modules.f90	global.h
inout.f90	inout.c
forces.f90	forces.c
neighbourlist.f90	neighbourlist.c
physical.f90	physical.c
solve.f90	solve.c
-	-
Original, incomplete version in tar package	Original incomplete version in tar package

metropolismc code

metropolismc.f90

Exercise points

Opiskelija		Bonus	Laskari				
			bugit	1	2	3	4	5	6	7	8	9	10	11	12X	SUM	% of total
----------		-----	---	---	---	---	---	---	---	---	---	--	--	---	---	------
Max Piste		0	12	18	24	21	30	18	18	24	18	25	21	-	229	50.000

Kalle Heinola   F       -       -       12      17      21      25      10      17      6       -       -       -       -       108     23.581
Mika Jahma      C       -       11      15      24      21      -       -       -       -       -       -       -       -       71      15.502
Niklas Juslin   C       -       8       -       -       21      -       -       -       -       -       -       -       -       29       6.332
Tommi Järvi     C       -       12      18      24      21      20      18      18      24      18      25      19      45      262     57.205
Antti Lauri     F       -       6       18      24      21      20      16      18      6       18      -       15      -       162     35.371
Olli Lehtonen   F       15      12      18      24      21      30      15      18      24      18      25      21      50      291     63.537
Kenichiro Mizohata F    -       11      18      24      21      30      14      14      24      -       -       -       -       156     34.061
Mikael Nizovsky C       -       5       18      23      21      20      12      17      12      6       20      19      -       173     37.773
Olli Pakarinen  F       -       5       12      3       21      20      8       -       12      6       5       13      40      145     31.659
Jens Pomoell    F/C     -       -       -       24      21      30      18      18      6       18      25      19      45      224     48.908
Mika Tantarimäki C      -       6       10      24      21      20      14      16      15      15      20      25      20      206     44.978
Stefan Taubert  F       -       8       6       0       18      20      -       12      3       -       25      8       -       100     21.834

To sum these use:
expand | awk '{ scores=substr($0,24); n=split(scores,a); s=0; for(i=1;i<=n;i++) s+=a[i]; printf "%s\t%d\t%-.3f%%\n",$0,s,s/229*50; }'

The final grades on the course are given as follows:

% of total
----------
<25.0	i
<45.0	+
<50.0	1-
<56.0	1	
<62.0	1+
<68.0	2-
<76.0	2
<82.0	2+
<88.0	3-
>=88.0	3

Exercise solutions

Only such solutions are provided here which are needed for future execises. All solutions are of course given at the exercise sessions.

Exercise 1, part 1: sample code

Exercise 2, part 1: Gaussian numbers code

Exercise 3: physical.f90 , neighbourlist.f90 ; physical.c , neighbourlist.c

Exercise 4: solve.f90 , solve.c ,

Exercise 5: forces.f90 , forces.c ,

Exercise 6: Solutions

Exercise 7: solve.f90 , solve.c with Berendsen T control

Exercise 8: forces.f90 , main.f90 , forces.c , main.c with Berendsen P control

Exercise 9: solution.txt

Lecture notes in postscript from 2001

These will be updated for 2003. The old notes are provided if the reader wants to take a preview of the contents, but it is not worth printing these as at least a few of them will be revised rather extensively.

Luento 1: Johdanto ja visualisointimenetelmät

Lecture 2: Basics of MD, initialization

Lecture 3: Neighbour lists, mdmorse code

Lecture 4: Algorithms to solve equations of motion

Lecture 5: Force calculation, basics of potentials

Lecture 6: Theory, P and T control

Lecture 7: Quantum mechanical methods

Lecture 8: Metal interaction models

Lecture 9: Semiconductor interaction models

Lecture 10: Molecular interaction models

Lecture 11 a: Ionic interactions

Lecture 11 b: Breathing sphere polymer model