Course syllabus

Course-PM

FFR120 / FYM119 Simulation of complex systems lp2 HT25 (7.5 hp)

This course is offered by the department of Physics.

Contact details

Examiner

Giovanni Volpe giovanni.volpe@physics.gu.se

Lecturers

Giovanni Volpe giovanni.volpe@physics.gu.se
Agnese Callegari agnese.callegari@physics.gu.se 

TAs (Homework Assessment and Project Tutoring)

Aarón Domenzain aaron.domenzain@physics.gu.se 
Agnese Callegari agnese.callegari@physics.gu.se 
Alex Lech alex.lech@physics.gu.se 
Daniel Midtvedt daniel.midtvedt@physics.gu.se 
Hang Zhao hang.zhao@physics.gu.se 
John Tember john.tember@physics.gu.se 
Mirja Granfors mirja.granfors@physics.gu.se 
Norma Palmero Cruz norma.palmero.cruz@physics.gu.se 
Vide Ramsten vide.ramsten@physics.gu.se 
Yu-Wei Chang yu-wei.chang@physics.gu.se 

Course purpose

This course introduces simulation techniques frequently used in complex systems to handle models with many heterogeneous parts. For example, you will work with agent-based modelling, evolutionary game theory, cellular automata, and networks, exploring applications to physics, biology and social sciences. You will also learn how to critically examine the outcomes of simulations to reach sound conclusions.

Schedule

TimeEdit, until +2 weeks from now (graphic).

TimeEdit, complete schedule: graphic and text.

Course literature

Textbook: Aykut Argun, Agnese Callegari & Giovanni Volpe. Simulation of Complex Systems. IOP Publishing, 2022. Link to the IOP book webpage: https://iopscience.iop.org/book/mono/978-0-7503-3843-1 (you can download different formats: PDF, ePub3, Kindle). Errata: http://softmatterlab.org/books/simulation-of-complex-systems/errata-book-simulation-of-complex-systems/ Notes and comments: https://softmatterlab.org/books/simulation-of-complex-systems/notes-book-simulation-of-complex-systems/ GitHub page:  https://github.com/softmatterlab/SOCS jupyter notebook of the lectures: see Files

 

Course Design

 

Week	Date Time	Place	Content	Chapter	To Do
45	04/11 8-10	SB-H8	Introductory Lecture - G. Volpe
45	04/11 10-12	SB-H8	Lecture - G. Volpe	1 and 2	Read Chapters 1 and 2
45	04/11		HW1 announced
45	05/11 8-12	F-T7203, F-T7204, FT4011	Help session - TAs
45	06/11 8-12	F-T7203, F-T7204, FT4011	Help session - TAs
45	07/11 10-12	SB-H8	Lecture - A. Callegari	3 and 4	Read Chapters 3 and 4

 

Week	Date Time	Place	Content	Chapter	To do
46	10/11 07:00		DEADLINE: Register for HW1		Register on Canvas before the deadline
46	10/11 07:00		Project Registration Opens		Register on Canvas
46	10/11 8-12	F-T7203, F-T7204, FT4011	Help session - TAs   [Help HW1]
46	10/11 13-15	HC4	Lecture - A. Callegari    [Info about projects]		Read Syllabus (Project)
46	11/11 8-10	SB-H8	Lecture - A. Callegari	5 and 6	Read Chapters 5 and 6
46	11/11 10-12	SB-H8	Lecture - A. Callegari	7 and 8	Read Chapters 7 and 8
46	11/11		HW2 announced
46	12/11 07:00		DEADLINE: Submit HW1		Submit PDF on Canvas before the deadline
46	12/11 8-12	F-T7203, F-T7204	HW1 assessment		Only for student who have registered to the assessment
46	12/11 13-17	E-Studion	HW1 assessment		Only for student who have registered to the assessment
46	13/11 8-12	TP-L10	Projects Pitch Session - all TAs		Read the 20 project topics
46	15/11 07:00		DEADLINE: Project Registration Closes		Register for Project on Canvas before the deadline

 

Week	Date Time	Place	Content	Chapter	To do
47	17/11 07:00		DEADLINE: Register for HW2		Register on Canvas before the deadline
47	17/11 8-12	F-T7203, F-T7204, FT4011	Help session - TAs   [Help HW2]
47	18/11 8-10	SB-H8	Lecture - G. Volpe	9 and 10	Read Chapters 9 and 10
47	18/11 10-12	SB-H8	Lecture - G. Volpe	11 and 12	Read Chapters 11 and 12
47	18/11		HW3 announced
47	19/11 07:00		DEADLINE: Submit HW2		Submit PDF on Canvas before the deadline
47	19/11 8-12	F-T7203, F-T7204	HW2 assessment		Only for student who have registered to the assessment
47	19/11 13-17	ED3354, ED3358	HW2 assessment		Only for student who have registered to the assessment
47	21/11 8-12	ES62, ES63, ED3358	Help session - TAs
47	22/11 07:00		DEADLINE: Communicate project typology (if choosing 2-, 3-people project)		No communication must be done if a student chooses to do an individual project

 

Week	Date Time	Place	Content	Chapter	To do
48	24/11 07:00		DEADLINE: Register for HW3		Register on Canvas before the deadline
48	24/11 8-12	F-T7203, F-T7204, FT4011	Help session - TAs   [Help HW3]
48	25/11 07:00		DEADLINE: Submit Project Abstract + Methods		Submit PDF on Canvas before the deadline
48	25/11 8-10	SB-H8	Lecture - G. Volpe	13 and 14	Read Chapters 13 and 14
48	25/11 10-12	SB-H8	Lecture - G. Volpe	15 and 16	Read Chapters 15 and 16
48	25/11		HW4 announced
48	26/11 07:00		DEADLINE: Submit HW3		Submit PDF on Canvas before the deadline
48	26/11 8-12	F-T7203, F-T7204	HW3 assessment		Only for student who have registered to the assessment
48	26/11 13-17	ED3354, ED3358	HW3 assessment		Only for student who have registered to the assessment
48	27/11 8-12	F-T7203, F-T7204, FT4011	Project Help Session 1 - TAs [Feedback Project Abstract and Methods]		Check the time slot for your project topic

 

Week	Date Time	Place	Content	Chapter	To do
49	1/12 07:00		DEADLINE: Register for HW4		Register on Canvas before the deadline
49	1/12 8-12	E-Studion	Help session - TAs   [Help HW4]
49	2/12 8-12	SB-H8	Lecture - A. Callegari [Poster And Report Info]		Read Syllabus - Poster and Report
49	2/12		HW5 announced
49	3/12 07:00		DEADLINE: Submit HW4		Submit PDF on Canvas before the deadline
49	3/12 8-12	F-T7203, F-T7204	HW4 assessment		Only for student who have registered to the assessment
49	3/12 13-17	E-Studion	HW4 assessment		Only for student who have registered to the assessment

 

Week	Date Time	Place	Content	Chapter	To do
50	8/12 07:00		DEADLINE: Register for HW5		Register on Canvas before the deadline
50	8/12 07:00		DEADLINE: Submit Project References		Submit PDF on Canvas before the deadline
50	9/12 07:00		DEADLINE: Submit Poster Draft		Submit PDF on Canvas before the deadline
50	9/12 8-12	F-T7203, F-T7204, FT4011	Project Help Session 2 - TAs [Feedback Project References]		Check the time slot for your project topic
50	10/12 07:00		DEADLINE: Submit HW5		Submit PDF on Canvas before the deadline
50	10/12 8-12	F-T7203, F-T7204	HW5 assessment		Only for student who have registered to the assessment
50	10/12 13-17	E-Studion	HW5 assessment		Only for student who have registered to the assessment
50	11/12 8-12	F-T7203, F-T7204, FT4011	Project Help Session 3 - TAs [Feedback Poster Draft]		Check the time slot for your project topic
50	12/12 07:00		DEADLINE: Submit Peer Review Poster Draft [GRADED]		On Canvas

 

Week	Date Time	Place	Content	Chapter	To do
51	15/12 07:00		DEADLINE: Submit Report Draft		Submit PDF on Canvas before the deadline
51	16/12 07:00		DEADLINE: Submit Poster [GRADED]		Submit PDF to Canvas before the deadline
51	17/12 8-12	F-T7203, F-T7204, FT4011	Project Help Session 4 - TAs [Feedback Report Draft]		Check the time slot for your project topic
51	19/12 8-12	KA, KB	Poster Presentation [GRADED]		Submit PDF on Canvas before the deadline
51	19/12 13-17	SB-Multisal	Poster Presentation [GRADED]		Submit PDF on Canvas before the deadline

 

Week	Date Time	Place	Content	Chapter	To do
52	22/12 07:00		DEADLINE: Submit Peer Review Report Draft [GRADED]		On Canvas

 

Week	Date Time	Place	Content	Chapter	To do
2	8/01 07:00		DEADLINE: Submit Project Report [GRADED]		Submit PDF to Canvas before the deadline

 

Learning Objectives

• Understand and describe simulation methods covered in the course.
• Develop simulation codes for various models.
• Plan and execute a small-scale simulation project.
• Discuss ethical implications of modeling choices and simulations.

 

Examination Form

The course has no written final exam. Grading is based on:

• Homework: 40% of the final grade.
• Project: 60% of the final grade, with deliverables including a poster and a written report.

For homework and project guidance, you can reach out to the TAs during the simulation lab sessions, the homework help sessions, and the project meeting sessions.

 

Homeworks (40% course grade)

The homework problem sets provide you with hands-on experience of simulation of complex systems techniques. You are strongly encouraged to team up and collaborate on the homework assignements, to ask your classmates if you are stuck at some point, and to assist classmates in need of advice. But you must write and run your own code, and have your own work assessed.

Grading: Out of the five homeworks, you need to solve and get assessed on three homeworks.
If you get assessed on more than three homeworks, only the best three scores will be considered. [Please note that there is no requirement about the minimum number of HWs assignments that you get assessed on and no minimum threshold to "pass" the HW part of the course. For example: if you decide not to do the HWs at all, you will have a 0 score for the HW part. Still, it is possible to pass the course if you do well with the project and get an overall grade of at least 50.]
Each homework accounts for max 10 points. Each homework is made of 4 different questions. Solving correctly: 
        1 question out of four will give 5 points of 10
        2 questions out of four will give 7.5 points of 10
        3 questions out of four will give 9 points of 10
        4 questions out of four will give 10 points of 10

Note that it does not matter which question(s) of the homework you solve correctly, just the number. For example: 

• Student A solves correctly question 1 of HW1: student A gets 5 points.
• Student B solves correctly question 3 of HW1: student B gets 5 points. 
• Student C solves correctly question 1 and 3 of HW1: student C gets 7.5 points.
• Student D solves correctly question 2, 3, and 4 of HW1: student D gets 9 points.

Assessment:
Book a time slot for the assessment. Beware of the deadline! After the deadline is passed, you won't be able to book a time slot and you won't get assessed for that HW. No exceptions will be made. The deadlines for the HW assessment registration is indicated in the table below. The registration for a given HW assignment opens the day the HW is announced.
Be prepared for the assessment: Generate all your figures and/or videos up front. There will be no time for running code during the assessment. Check that you have answered all questions carefully. You should be able to give reasoned answers regarding your programming choices as well as being able to discuss the implications of your results. Don't forget to submit your HW solution in Canvas before 07:00 of the assessment day! Format: single PDF containing figures and codes.

Deadlines (Homeworks)

• 10 November, 07:00: Registration for HW1 closes.
• 12 November 07:00: Deadline to upload your HW1 solution in Canvas.
• 17 November, 07:00: Registration for HW2 closes.
• 19 November 07:00: Deadline to upload your HW2 solution in Canvas.
• 24 November, 07:00: Registration for HW3 closes. 
• 26 November 07:00: Deadline to upload your HW3 solution in Canvas.
• 1 December, 07:00: Registration for HW4 closes.
• 3 December 07:00: Deadline to upload your HW4 solution in Canvas.
• 8 December, 07:00: Registration for HW5 closes.
• 10 December 07:00: Deadline to upload your HW5 solution in Canvas.

 

How to calculate the Homework Contribution (HC) to the Course Score (CS)

The Homework Score (HS) is a number between 0 and 30, because it is the sum of the best three scores received in the individual HW assignments.
To calculate the homework contribution  to the course score you apply the formula: HC = 4 * HS / 3

Examples:

• You have solved HW1, HW3, HW4 and HW5 with respectively 10, 5, 0, 5 points.  Your HS is 20. Your HC is 26.67 .
• You have solved HW1, HW2 with respectively 7.5 and 7.5 points.  Your HS is 15. Your HC is 20.
• You have solved HW1, HW2, HW3, HW4, HW5  with respectively 0, 5, 5, 5, 5 points. Your HS is 15. Your HC is 20.

 

Project (60% course grade)

The purpose of the project work is to provide you with training in

• Developing your own small research-style project, choosing one among the proposed topics.
• Presenting your independent work in writing and as a poster.

The deliverables are a poster presentation (0-20 points) and a written report (0-50 points).

The project presentation will be on December 19, 2025. Attendance is mandatory.

The final written report is due by January 8, 2025. No late reports will be accepted.

General information

The project topics (see: Files > Project Topics: [Project Topics])  are proposed to the students by the TAs.
Each student must register to one (and only one) of the topics. Registration happens through Canvas, on a "first come-first served" basis.
The registration opens on 10 November and the deadline to register to a project topic is 15 November 07:00 (Saturday).

Each student must then choose whether to conduct their project individually (1 person team) or in a team of 2, 3 students in total.  The teams are self-organized by the students and must be formed among the students signing up for the same topic. If you are going to do a 2-, 3-, students project, you must agree this with the other students and communicate your group to the course examiner (Giovanni Volpe) by email before 22 November at 07:00. If you have signed up for a project topic but you have not communicated you are in a team, then we consider that you are working individually.

These are the possible configuration for the project:

• 1-person project -> Final report: 5 pages (exact number of pages, including 5-10 references)
• 2-people project -> Final report: 9 pages (exact number of pages, including 10-20 references)
• 3-people project -> Final report: 13 pages (exact number of pages, including 15-30 references)

Please note that, after communicating the arrangement, no change to the report size will be made even if some students drop out of a group. For example: three students agree to work together, but one drops out — the two remaining students will have to submit a 3-people project report, as they have committed to do.

Formats and Templates

• The format for the poster is: A3, PDF, portrait. There is no compulsory template.
• The template for the final report is found here: [Project Template]. It is compulsory to use the provided template with no further style customization. The points for the different parts of the project are provided in the template.

Deadlines (Project)

• 10 November, 07:00: Project Registration opens
• 15 November, 07:00: Project Registration closes
• 22 November, 07:00: Communicate before this deadline if choosing a 2-people or a 3-people project (no communication due if you choose to work individually).
• 25 November, 07:00: Project Abstract and Methods Overview due
• 8 December, 07:00: Project Relevant References due
• 9 December 07:00: Poster Draft due
• 12 December 07:00: Peer-review of Posters Draft of assigned students due
• 15 December 07:00: Project Report Draft due
• 16 December 07:00: Poster (final, for presentation) due
• 19 December 8-12 and 13-17: Project presentation (compulsory for all students)
• 22 December 07:00: Peer-review of Project Report Draft of assigned students due
• 8 January 07:00: Project Report (final) due

Project Help Sessions

After committing to a project topic, you will have to develop your own project question and direction. As a support in carrying out your project, you have:

• Possibility to discuss with the other peers choosing the same project topic [consider those peers as a discussion group].
• Possibility to ask project-related questions to a TA during four Q&A sessions (27 November, 9 December, 11 December, 17 December)
• A dedicated Lecture on Poster and Report Report Info on 2 December.

Meetings with reference tutor are on

• 27 November (Project Help Session 1: feedback on Project Abstract + Methods)
• 9 December (Project Help Session 2: feedback on Project References)
• 11 December (Project Help Session 3: feedback on Poster Draft)
• 17 December (Project Help Session 4: feedback on Report Draft)

 

Poster presentation (0-20 points)

The presentation of the project should clearly show what you have done.
Put the emphasis on what your problem formulation is, a general discussion about how you tackled it, what problems you had, and what your conclusions are.

Checklist for poster presentation

When preparing your poster, consider the following guidelines:

• Structure: Is the poster well structured?
• Clarity: Is it clear from the presentation what is being investigated?
• Format: Does the presentation fit the requested format? (i.e.: PDF, portrait, well readable when printed in A3 format.)
• Motivation: Is it explained well why the project is important? 
• Conclusion: Are conclusions and implications clear? 
• Methods: Are the methods explained sufficiently but not excessively?
• Presentation quality: Is the poster engaging and visually appealing?

 

Criteria for evaluation of Poster presentation

• Interactive Engagement in Poster presentation [0-4 points]: During the poster presentation: you need to visit the various posters and ask questions. You need to write down on the Q&A sheet (provided during the poster session) the questions you ask and the relative answer you receive. You need to annotate at most 1 question+answer per poster visited. You will get 0.5 points for each question+answer, with a maximum of 4 points.
• Peer-Review Engagement [0-4 points]: You will be assigned two other projects to Peer-Review (poster draft). During the peer-review, you should submit a substantial comment to each poster draft, showing that you have read it. You should give 5 suggestions for improvement. If your comments are substantial, you will receive 2 points for each comment submitted. Maximum 4 points in this part.
• Poster evaluation [0-12 points]: You will receive max 2 points for each the following criteria:

               * Structure: Does the poster have a title, list of authors, affiliation?
               * Clarity: Is it the take-home message clearly identifiable in the poster?
               * Format: Does the presentation fit the requested format? (i.e.: PDF, portrait. When printed in A3 format, should be readable, i.e., minimum fontsize 11pt.)
               * Motivation: Is it explained why the project is important? 
               * Conclusion: Is there a clearly identifiable conclusions statement? 
               * Methods: Are the methods explained sufficiently but not excessively?

 

Report (0-50 points)

The report should be written according to the template provided. Link to the directory with the template files: [Project Template] .

Structure your report like a scientific article, with an abstract summarising the rationale and results of the project; an introduction shortly explaining its background and motivating why the question is interesting; methods and/or results section(s) describing an overview of the available models for the task, your model and what you do with it; a result and discussion section; and ending with a conclusion. Put some work into the discussion and conclusion sections. This is where you demonstrate that you truly understand the implications of your work, including shortcomings and uncertainties. It is important that the discussion does not fall out as a simple summary of what the figures show.

Write in plain language and write enough to say what you need to say. Don't think "the report feels short, better throw in some extra figures." If you can say the same thing in fewer words, do so.

Be sure to reference any source you use. The report should be readable and understandable on its own, but there is no need to reproduce for example derivations of equations from your sources; a citation is enough.

Figures are an important part of the report, but only those that substantially contribute to your analysis should be included. Make sure that each figure is well designed with informative captions (not just "Fig. X shows how quantity A depends on quantity B"). If you find it hard to do this, you probably are not clear on why you include an figure, so cut it out.

Most importantly, use your own judgement and try to write a report you would like to read.

Checklist for project report

When preparing your project report according to the provided template, consider the following guidelines:

• Structure: Is the project report well structured, i.e., conformal to the project template?
• Motivation: Does the project have a clear research question?
• Background: Is the background of the research question well explained, including references to the literature?
• Overview: Does the overview consider possible methods, explain their use case scenario, discuss their features with advantages and disadvantages, with references to the literature?
• Methods: Are the methods explained adequately? Is the analysis appropriate for convincingly answering the research question?
• Execution: Does the project answer the initial or iterated research question?
• Figures: Are the figures included informative with descriptive captions? Are the figures referenced in the text?
• Format: Have you used the provided template?
• Outlook: Are the implications of the results clearly stated?
• Contributions, Conflict of Interest, Data and Code availability : Are such statements included in the report? 

Note that the report template contains the maximum points that can be obtained for each part.

Note also that the research question does not have to be answered in the affirmative. A negative result is equally valid as long as an analysis is carried out that properly explains the negative result and what eventually would work better. 

 

Criteria for evaluation of Project Report

• Peer-Review Engagement [0-6 points]: You will be assigned three other projects to Peer-Review (project report draft). During the peer-review, you should submit a substantial comment to each report draft, showing that you have read it. You should give 5 suggestions for improvement. If your comments are substantial, you will receive 2 points for each comment submitted. Maximum 6 points in this part.
• Project evaluation [0-44 points]: Check the project report template to see the maximum points assigned to the different parts of the report. Also, you will find there all the information about the requirements on number of pages, figures, references, and other important details of the grading.

 

How to calculate the Project Contribution (PC) to the Course Score (CS)

The Project Score (PS) is a number between 0 and 70, because it is the sum of the Poster points (0-20) and the Report points (0-50).
To calculate the project contribution  to the course score you apply the formula: PC = 6 * PS / 7 

Examples:

• You have 15 Poster points and 27 Report points.  Your PS is 42. Your PC is 36 .
• You have 20 Poster points and 40 Report points.  Your PS is 60. Your PC is 51.43.
• You have 0 Poster points and 38 Report points.  Your PS is 38. Your PC is 32.57.

 

 

Calculation of final grade

You can get at most 40 points from the homework contribution (HC) and 60 points from the project contribution (PC). The maximum combined score (or Course Score, CS) is 100.

The grade limits will be:

• Chalmers students: 50 points for grade 3, 70 points for grade 4, and 90 points for grade 5.
• GU students: 50 points for G and 80 for VG.