PHYS 338 - Computer Simulations in Physics
Instructor: Katharina Vollmayr-Lee, kvollmay@bucknell.edu, Olin 152, x7-3109 Classes: TR 10:20-11:40, zoom: (link), Zoom ID 97645789035 Passcode 808111Office Hours: (tentative) M 2-3:30, T 4:30-5:30, and F 10:30-12:00,
zoom: (link)
Mtg.ID: 972 7054 5774
Office Hours during Finals: Fr,05/14 10:30-12am; Mo,05/17 9:30-11 am;
and please let me know in case you need some additional meeting
Texts:
- (Online Chs:) M. Newman, Computational Physics
- (Online:) H. Gould, J. Tobochnik, W. Christian, An Introduction to Computer Simulation Methods
Computer Simulation Symposium
- Zoom: (link), Zoom ID 97645789035 Passcode 808111
- Poster with Schedule (May 6/10/12)
Course Information
Announcements:
- Office Hours during Finals: Fr,05/14 10:30-12am; Mo,05/17 9:30-11 am;
and please let me know in case you need some additional meeting
- Kalman Symposium: April 17, 2021, Info & Zoom Link (Comuter Simul. Talk 12:15 E.C. & M.B.)
- PA Young Women in Physics Conference: April 24, 2021, Information & Registration (free)
Assignments
Please submit Homework via gradescope. For Python scripts: please copy them also into your ~/share.dir/ and give read-permission (see Linux Exercise).
| Due | Topic | Homework |
| Feb.4 | Python: Jupyter & In/Out & Variables | HW 1 (Linux Excercise, Sign-Up ) |
| Feb.9 | Python: Arithmetic & Decisions | HW2: Bibliography/Model |
| Feb.16 | Python: Lists, Arrays & Functions | HW3 (final version bibliography/model) |
| Feb.18 | Random Walks | HW 4 (python 19a-c and Paper Description) |
| Feb.25 | Talk-Tools | HW 5 (1st Version of Introduction/Background) |
| March 4 | Fractal Growth | HW 6 (First Main Project Paper 1st Version) |
| March 11 | Fractal Growth & Talk Tools | HW 7 due 03/13/ 8am (Final Verson of 1st Main Project Paper) |
| March 16 | Mini-Project I Talks | HW 8: Mini-Project I |
| March 18 | Main Project Talks | HW 9: Talks (3/18) & Flow Chart (3/20) |
| March 23 | Main Project Talks | HW 10: Flow Chart (3/20) & Talks (3/23) & 1st Vs Program (3/27) |
| March 30 | Molecular Dynamics Simulations | HW 11: 1st Vs Program (3/27) & Final Vs of Flow Chart |
| April 1 | Molecular Dynamics Simulations | HW 12: 2nd Vs Program (4/3) |
| April 6 | Molecular Dynamics Simulations | HW 13: 3rd Vs Program (4/6) |
| April 8 | Molecular Dynamics Simulations | HW 14: 1st Vs Results & Interpretation (4/13, 10 am) |
| April 13 | Scientific Figures & Your Project | HW 15: 2nd Vs Results & Interpretation (gradescope) (4/15, 10 am) |
| April 20 | Traffic Flow | HW 16: Final Vs of Main Project Program (4/21, 8 am) |
| April 27 | Traffic Flow | HW 17: Final Vs Program (4/24, 8 am) & Results Sec. (4/29 8am) |
| April 29 | Traffic Flow | HW 18: Abstract (5/1, 8 am) |
| May 4 | Traffic Flow | HW 18: Abstract (5/1, 8 am) Future: 1st Vs 2nd Paper (5/6) |
| May 6 | Symposium Talks | HW 19: 1st Vs 2nd Paper (5/9) |
| May 10 & 11 | Symposium Talks | HW 20: Final Vs 2nd Paper (5/18, 6:30pm) |
In-Class Work
- Feb. 2: Course Info & Literature Search
- Linux Exercise
- Feb. 4: HW2: Bibliography/Model, Python (jupyter,script,in/out)
- Feb. 9: Python: Arithmetic & Decisions
- Feb. 11: Python: Arithmetic, Decisions, Repetitions, and Lists, and Arrays
- Feb. 16:
Paper,
Traffic Flow Paper by D. Chowdhury et al.preprint and pdf and annotated
Python: Decisions, Repetitions, and Lists, and Arrays, and Functions - Solutions for Python Intro Section Tasks 11-20 are for example in ~kvollmay/share.dir/inclass2021.dir/classpython12.py
- In-Class Work: Random Walks 1 dim. (Feb. 18) , msd for SiO2
- Solutions for one dimensional random walk are for example in ~kvollmay/share.dir/inclass2021.dir/classrndwalk2d.py
- Feb. 25: In-Class Work: Random Walks 1 dim. (Feb. 25) ,
msd for KALJ [AJP 88, 401 (2020)],
msd for SiO2,
In-Class Work: latex & xfig
for uploading on overleaf: templateWithBibAll.zip ,
for latex in linux environment: templateWithBib.tex , myRefs.bib , cubic.pdf , samplefig.pdf - March 2: (Xfig & 2d random walk & fractal growth intro) March 2 ,
- March 4: (Intro to Fractal Growth, DLA model): March 4 , (Cellular Automata Intro) , Pictures Fractals in Nature, Mandelbrot Set, Picture of window with ice fractals fractal pictures (from books) , DLA Rules , DLA Flow Chart ,
- March 9:
The Physics/Astronomy alumni panel is Tuesday March 9 at 8:00 p.m. at This Zoom link. To see flyer with information about the panelists, Click here.
see below for more information on writing scientific papers
Fractal Growth (continued): March 9 , DLA Rules , DLA Flow Chart , - March 11:
- Scientific Talks: How to Give Talks (KVL) , further resource: Great Talks (by Prof. A. Graves)
- Talk Examples: SiO2 (BU 2009) , Granular Gas / Hydrodynamics (APS 2011) and Ohio, April 2017 (SiO2 Jumps & Scaling)
- Latex Beamer: March 11 , for uploading on overleaf: beamer_example_All.zip , for latex in linux environment: beamer_example.tex, fig1.eps, fig2.eps, fig3.eps
- Fractal Dimension: March 11 , Mini-Project I
- March 30: In-Class Work: MD Simulation Molecular Dynamics Simulation: Intro & Surprise ,
- April 1: In-Class Work: MD Simulation Molecular Dynamics Simulation: SHO and Driven Damped Pendulum , Simple Harmonic Oscillator Euler Step Divergence & MD intro
- April 6: In-Class Work: MD Simulation Molecular Dynamics Simulation of Driven Damped Pendulum
- April 8 & 13: In-Class Work: MD Simulation Miniproject II , DDP Summary Table
- April 15: Scientific Figures
- Figures Intro: Graphical Representation (Prof. I. Sulai, Phys310 talk) (therein figures and summary of [Edward R. Tufte, "The Visual Display of Quantitative Information," 2nd ed. (Graphics Press, Cheshire, Connecticut, 2018)]), further examples: Research by Prof. B. Marsh (Maps of Institutionalized Racial Inequaility)
- in class-work: xmgrace
- April 20: Traffic Flow
- April 27: Traffic Flow
- April 29: Traffic Flow
- Traffic Flow Paper by D. Chowdhury et al.preprint and pdf and annotated
- Paper: Model Section,
- Paper: Annotated Model Section,
- Update-Rules ,
- Flow Chart ,
- April 29
- May 4: Traffic Flow Miniproject III (May 4)
Guidelines For Main Project
- Previous Simul. Projects: Spring 2019, Spring 2017, Spring 2015, Spring 2012, Spring 2011, Spring 2010, Spring 2009, Spring 2008, Spring 2005, Spring 2003
- Traffic Flow Paper by D. Chowdhury et al.preprint and pdf and annotated
- Computational Physics Section of AJP (eds.Gould & Tobochnik)
- Bibliography/Model
- Paper
- Further information about scientific papers: The Art of Scientific Report Writing (Oxford), Ten Steps to Writing an Effective Abstract, Preparing a Manuscript for Publication; (Journal of Undergraduate Research In Physics)
- in-class: latex & xfig
for uploading on overleaf: templateWithBibAll.zip ,
for latex in linux environment: templateWithBib.tex , myRefs.bib , cubic.pdf , samplefig.eps - Scientific Talk Tools:
- Scientific Talks: How to Give Talks (KVL) , further resource: Great Talks (by Prof. A. Graves)
- Talk Examples: SiO2 (BU 2009) , Granular Gas / Hydrodynamics (APS 2011) and Ohio, April 2017 (SiO2 Jumps & Scaling)
- Latex Beamer: March 11 , for uploading on overleaf: beamer_example_All.zip , for latex in linux environment: beamer_example.tex, fig1.eps, fig2.eps, fig3.eps
- Scientific Figures:
- Figures Intro: Graphical Representation (Prof. I. Sulai, Phys310 talk) (therein figures and summary of [Edward R. Tufte, "The Visual Display of Quantitative Information," 2nd ed. (Graphics Press, Cheshire, Connecticut, 2018)]), further examples: Research by Prof. B. Marsh (Maps of Institutionalized Racial Inequaility)
- in class-work: xmgrace
Literature Search Tools
- Scientific Papers: Web of Science (accessible from FastX session or Databases next line) and Google Scholar
- BU pages: Library & IT (includes ILL and Journals A-Z), Databases (use to get to Web of Science when off campus; includes social science paper data bases)
- Books: BU Library Catalog (World Cat)
- Physics Sources: APS Journals (PRL,PRE, etc.), IOP Journals, ADS Labs (NASA) search, arXiv.org (preprints)
Computer Tools
- FastX (linuxremote server via web browser)Links & Info
- In past: Xmanager Power Suite Installation (for windows):Info 2020
and
vpn info
- In past: Linux on Mac:X11 (E.Wessler) or XQuartz and see CSCI203 Info.
- Linux Summary and Linux Exercise
- Computer Tools (PHYS310 Junior Lab)