Physics 210: Introduction to Computational Physics
Contents
1. Term Projects The term project component of PHYS 210 is extremely important and for most of you will present the most significant challenge in the course Either individually or in consultation with the instructor each student must choose a topic for a term project in some area of computational physics or a related area carry out the project produce a write up on it in the basic style of a scientific technical paper and make two short presentations to the class on their work You are encouraged to develop your own project ideas but all project topics must be approved by the instructor Some possibilities for term projects are posted on the Term Project Ideas page which may be updated as the course progresses expect that many of you will complete a project from one on the suggestions and there will not restrictions on the number of students tackling any given subject Topics for term projects must be chosen no later than October 11 During the classes and lab periods on October 16 and 18 each student will give a brief presentation on their proposed project speaking order will be alphabetical by last name The amount of time available for each presentation will be a very short 6 minutes so talks will need to be carefully prepared and efficiently executed Some form of presentation software including Powerpoint must be used to prepare your talk and you must generate a PDF version that you will need to e mail to one of the TAs in a timel2. Tuesday Thursday September 6 Course Overview amp Unix Introduction to Computer Lab account configuration September 11 September 13 Unix Unix September 18 September 20 Maple Maple HW1 due September 25 September 27 Maple Maple October 2 Discussion of term project proposals wig ciabad i Finite Difference Approximation HW2 due MATLAB October 11 October 9 Finite Difference Approximation Finite Difference Approximation Term project topics must be chosen October 16 October 18 Project Proposal Presentations Project Proposal Presentations II Project Proposal Presentations Project Proposal Presentations II October 23 October 25 Finite Difference Approximation Finite Difference Approximation October 30 November 1 Finite Difference Approximation Finite Difference Approximation HW3 due November 6 November 8 Newton s Method Newton s Method November 13 November 15 Cellular Automata Cellular Automata HW4 due November 20 November 22 Free time to work on projects L1A Free time to work on projects Free time to work on projects Free time to work on projects November 27 12 30 13 30 Project Presentations 1 L1A 13 30 15 30 Project Presentations 2 L1A 15 30 17 30 Project Presentations 1 L1B Note All presentations in Computer Lab November 29 12 30 13 30 Project Presentations 2 L1B 13 30 15 30 Project Presentations 3 L1A 15 30 17 30 Project Presentations 3 L1B Projects due No
3. physics ubc ca 3 of 3 08 27 2012 10 25 AM Physics 210 Intro Computational Physics UBC Fall 2 file Public Members matt Teaching 12Fall PHYS210 Physics 210 Intro Computational Physics Homework Assignments This document will be updated throughout the course Note Please refer to the Syllabus Schedule section of the main Course Page for due dates of assignments To ensure that you download the most recent version of homework assignments it is safest to first clear the disk and memory caches of your browser or ensure that the Preferences Advanced Cache setting of your browser is set so that cached documents are compared to on line versions every time Problem Set Handout PDF September 20 Unix Linux Web page authoring HTML amp shell scripts nore for Prob 2 October 4 Maple Worksheets programming Handout PDF IMPORTANT HOMEWORK amp TERM PAPER POLICY ACADEMIC MISCONDUCT First please refer to the section of the UBC Calendar on Policies and Regulations especially the sections Student Declaration amp Responsibility Academic Honesty amp Standards Academic Misconduct Disciplinary Measures BW NA and ensure that you fully understand them In addition in the context of this specific course all students must understand and abide by the following policies Consultation and discussion with classmates is permitted and in fact encouraged HOWEVER ALL H
4. you do not already have an account you can self register for one during the first lab or otherwise as early as possible in Hennings 203 For information concerning the services provided by the IT section of the dept please refer to the IT catalogue You may also be able to use your laptop home machine to do some of the class work especially if you are able and willing to install a Linux distribution Ubuntu recommended on it them Dependent on class interest in this possibility we may hold one or more sessions in which the TAs and will help you with the installation Note however that you will be doing the installation at your own risk we can not be responsible for the loss of the original operating systems or of any data on your machine 08 27 2012 10 23 AM Physics 210 Introduction to Computational Physics U file d bh0 home matt teaching 1 2Fall PHYS210 admin 3 of 8 Grades Tests Homework amp Labs Term Projects and Late Work Policy EXTREMELY IMPORTANT Please refer to the Homework Page for the course policy on Homework Term Projects and Academic Dishonesty Your final grade in this course will be determined on the basis of your performance on four 4 homework assignments a term project and a presentation on your term project with the following weighting e Homework Assignments 60 e Term Projects including writeup 35 due Dec 4 11 59 PM e Term Project Presentation 5 Final marks may be s
5. Maple 4 lectures 4 labs e Use of a modern symbolic manipulation language for routine computations e Basic Maple programming MATLAB 1 lecture 9 labs Introduction to MATLAB as an interactive tool for numerical calculations Introduction to MATLAB plotting facilities MATLAB programming writing scripts and functions Specific MATLAB scripts programs mostly motivated by topics covered in lectures praia Proposal Presentations 2 lectures and labs 08 27 2012 10 25 AM Physics 210 Intro Computational Physics UBC Fall 200 _file d bh0 home matt teaching 12Fall PHYS210 admin Finite Difference Approximations for ODEs 3 lectures e Definition of finite difference approximation FDAs e Use of FDAs to approximate simple ordinary differential equations such as are encountered in particle dynamics Finite Difference Approximations for PDEs 3 lectures e Mathematical formulation and solution of wave equation in one spatial dimension e Use of FDAs to approximate simple wave equations Newton s Method 2 lectures 2 labs e Newton s method for solution of nonlinear equations single and systems e Examples of use of Newton s method and implementation using MATLAB Cellular Automata 2 lectures e Definition of cellular automata CA some examples applications to physics and other areas and related models e Implementation of CA s using MATLAB m Project Presentations 2 lectures and labs Maintained by choptuik
6. OMEWORK amp TERM PROJECTS SUBMITTED MUST BE YOUR OWN WORK To be more specific the following occurrences not an exhaustive list WILL be treated as possible cases of academic misconduct I assume in the following that cheating is fundamentally a two person interaction let X and Y be two students 1 Work where student X s work is byte wise identical to Y s work for no good reason and there seldom is a good reason 2 Work where X s source code is the same or very nearly the same as Y s with primarily comments and or names of variables changed ADDITIONAL REMARKS CONCERNING TERM PROJECTS Again although you are free to consult and discuss with your classmates and others concerning 1 of 2 08 27 2012 10 34 AM Physics 210 Intro Computational Physics UBC Fall 2 file Public Members matt Teaching 12Fall PHYS210 your term projects the work that you do for your project as well as writeup and presentation must be your own work Additionally you must NOT use materials particularly source code that you locate on the Web or elsewhere in your term project all programming and analysis that you do for your project must be original to you although the ideas and or algorithms underlying your programming need not be as long as they are properly cited Bear in mind that if you copy something from the Web it is now quite easy for an instructor to find the same location that you did The University takes all forms of academic mi
7. Physics 210 Introduction to Computational Physics U file d bh0 home matt teaching 1 2Fall PHYS210 admin Physics 210 Introduction to Computational Physics Fall 2012 COURSE HOME PAGE this page http laplace physics ubc ca 210 Instructor Matthew Matt W Office Hours Mon amp Wed 1 00 2 00 PM amp Drop in e mail Choptuik appt preferred Office Hennings 403 Web page http laplace physics ubc ca matt Office Phone 604 822 2412 E mail choptuik physics ubc ca TAs Arman Akbarian and Daoyan Wang Hennings 408 SCHEDULE e LECTURES TUESDAY amp THURSDAY 12 30 13 30 HENNINGS 201 e LABS o L1A TUESDAY amp THURSDAY 13 30 15 30 HENNINGS 205 o L1B TUESDAY amp THURSDAY 15 30 17 30 HENNINGS 205 COURSE LINKS COURSE NOTES SYLLABUS SCHEDULE Contains links to lab activities HOMEWORK NEWS last update August 24 10 00 AM Online Course Resources Course Software Availability for Personal Machines Learning Goals amp Course Topics Suggested Hard Copy References Term Project Ideas Student Pages PHAS IT Catalogue Course Summary This course will provide an introduction to techniques and applications in computational physics Topics to be covered include Unix Linux fundamentals an introduction to symbolic amp numeric computation and programming with Maple MATLAB octave and MATLAB programming and specific topics and applications in physics and numer
8. cific applications from physics and mathematics including 1 The use of finite difference techniques to approximately solve simple ordinary differential equations equations of motion of the type encountered in particle dynamics 2 Dynamics of one or more particles in interaction with one another or with an external potential using finite difference techniques 3 The use of finite difference techniques to approximately solve simple partial differential equations wave equations 4 Solution of nonlinear equations 5 Simulation of simple cellular automata 6 A moderately challenging problem of your own choosing i e your term project Note that in the above as well as the course outline below references to MATLAB also refer to the open source clone octave which does not have all of the features of MATLAB and we use will octave exclusively in the computer labs However will do my best not to use any octave specific elements in the course so that anything that you learn about octave should apply to MATLAB in particular any octave code presented should also work in MATLAB COURSE TOPICS amp OUTLINE again note the above caveat I cannot guarantee that this schedule is exact Note There will often be overlap in the topics covered in lectures and especially labs e g finite difference approximation MATLAB programming Unix 3 lectures 3 labs e Unix Linux fundamentals with a focus on use of the command line
9. e Manual o An A Z Index of the Linux Bash command line o An Introduction to the Unix Shell by S R Bourne creator of the the original sh from which bash derives e bash scripting o Bash Scripting Tutorial o Linux Shell Scripting Tutorial A Beginner s handbook o Advanced Bash Scripting Guide o Google bash scripting tutorial or bash scripting guide or bash programming etc yourself for many more sites _ Editors 1 of 6 08 27 2012 10 24 AM Physics 210 Intro Computational Physics UBC Fall 2 file d bh0 home matt teaching 12Fall PHYS210 admin e gedit o Online Gedit Manual e emacs xemacs o www gnu org software emacs The home page for GNU Emacs containing links to a wealth of information about emacs a Online GNU Emacs Manual o XEmacs org The home page for the XEmacs project containing links to a wealth of information about XEmacs Online XEmacs User s Manual Local copy of XEmacs User s Manual PDF Note This manual is nearly 400 pages in length so you may want to think carefully before you print it e vim gvim o www vim org The home page for the Vim project also containing links to a wealth of information about vim o Linux vi and vim editor Tutorial and advanced features This was the first document returned on Aug 12 2010 by the google search vim editor tutorial o Google vim editor tutorial yourself for many other tutorials Searching the Web e Google Ar
10. effort devoted to the project originality and completeness and quality of the written report Your written report and the source code for your project are due by November 30 11 59 PM except under very extenuating circumstances In addition during the classes and lab periods on November 27 and 29 each student will again give a brief presentation this time on their completed project and in reverse alphabetical order The basic instructions concerning preparation etc are the same as for the proposal talks above further details will be supplied later and the final presentation is worth 5 of your final grade IMPORTANT You should note that completing a good term project is much different than finishing a homework or even a few homeworks in particular it is virtually impossible to do a decent job on a term project in the space of a few days It is the nature of computational physics as in experimental physics and in many other pursuits that things will go wrong unexpectedly and it can often take much more time than anticipated to get programs to work Moreover coding a functional program is typically just the first stage in completion of the project you also will need time to generate and analyze results as well as to write things up In addition you can expect that the projects will be graded reasonably rigorously and that doing well in the homeworks will not automatically guarantee that you do similarly well with your project Nonet
11. evelopment o GLU headers and libraries runtime and development o GLUT headers and libraries runtime and development o XForms headers and libraries runtime and development o JPEG headers and libraries o X11 Miscellaneous extensions library libxext o X11 libxi development files libxi devel o mpeg encode if you want to be able to geenerate MPEG animations e Installation instructions Login as root or become superuser on your machine then execute the following mkdir p root install 2 of 3 08 27 2012 10 25 AM Physics 210 Intro Computational Physics UBC Fall 2 file d bh0 home matt teaching 12Fall PHYS210 admin cd root install wget ftp laplace phas ubc ca pub xfpp3d xfpp3d tar gz tar zxf xfpp3d tar gz cd xfpp3d configure make install Assuming that all of the prerequisites are installed on your system this should build xfpp3d and install it in usr local bin xflat2d xflat2d_rgb e Download xflat2d tar gz xflat2d_rgb tar gz e Software prerequisites As for xfpp3d above e Installation instructions As for xfpp3d above but replace all occurrences of xfpp3d with xflat2d or xflat2d_rgb XVS e Download xvs tar gz e Installation instructions DV e Download DV tar gz e Installation instructions Maintained by choptuik physics ubc ca Supported by CIFAR NSERC CFI BCKDF and UBC 3 of 3 08 27 2012 10 25 AM
12. finition of the input format Sample input file inputlife from Game of Life simulation Use xflat2d lt inputlife to view Documentation describing the creation of mpeg animations using this program is available HERE xflat2d_rgb Identical to xflat2d except that sites are colored with an aribitrary color specified as an 0 0 1 0 normalized RGB triple e g 0 0 1 0 0 0 is green 1 0 1 0 1 0 is white etc that can change at each time step Basic help is available via xflat2d_rgb h Refer to the above link for the help message which includes a definition of the input format Sample usage xflat2d_rgb lt input Documentation describing the creation of mpeg animations using this program is available HERE xvs xvs is a visualization tool for analyzing among other things the output of time dependent PDEs in one spatial dimension or time dependent cuts of higher d solutions Some documentation for xvs is availabe HERE Contact the instructor or one of the TAs should you need help DV DV is a visualization server similar in spirit to xvs but capable of visualizing 2 D and even 3 D data Basic online documentation is available HERE Information on using DV to make mpeg animations is available HERE Contact the instructor of one of the TAs should you need help 08 27 2012 10 24 AM Physics 210 Intro Computational Physics UBC Fall 2 file d bh0 home matt teaching 12Fall PHYS210 admin 6 of 6 Nume
13. g Linux In particular your will then be able to ssh into hyper phas ubc ca and start up graphical applications such as gedit xmaple etc and the applications will appear on your Windows screen Performance won t be as good as it would be if you had Linux installed and were running applications locally but provided that your network connection is sufficiently fast it should suffice for you to do at least some of your homework and term project work outside of the computer lab The software can be downloaded from HERE and there is additional documentation about installing and using it HERE 1of3 08 27 2012 10 25 AM Physics 210 Intro Computational Physics UBC Fall 2 file d bh0 home matt teaching 12Fall PHYS210 admin IMPORTANT Before you install XMing you should install the PuTTY ssh client see above which you will use to establish connections between your Windows machine and hyper During the process of installing Xming you will be presented with a Select Components dialog choose the Normal PuTYY Link SSH client option Once you have installed Xming and assuming you have placed an Xming icon on your desktop you start the server simply by clicking on the icon alternately you can start Xming from the All Programs menu Once the server starts you won t see any specific windows etc associated with Xming but an X icon should appear on the panel indicating that it is running Right clikcing on the icon will give you a
14. guably still the premier Web search engine e Bing The relatively new kid on the block from the corporation that needs not be named e WolframAlpha Wolfram s new Computational Knowledge Engine Worth checking out if you haven t yet done so Web Authoring Creating Web Pages HTML documents 1 Use a web authoring tool e The seamonkey browser installed on the lab machines includes composer that allows you to easily create and modify basic web pages such as those used for this course To use it start seamonkey then either choose Composer from the Window pull down menu at the top of the browser or click the Composer icon looks like a pen and piece of paper at the bottom left Usage of composer should be largely self explanatory and there is a built in help facility for the seamonkey package see the section Creating New Web Pages e In addition to composer the following dedicated web authoring applications are also installed o bluegriffon o bluefish o kompozer 2 Doing it by hand i e using a text editor and learning HTML e HTML Tutorials o HTML Dog Tutorials o W3schools Tutorials o HTML Code Tutorial o Google html tutorial for many more e HTML References o HTML 4 Reference 2of6 08 27 2012 10 24 AM Physics 210 Intro Computational Physics UBC Fall 2 file d bh0 home matt teaching 12Fall PHYS210 admin o W3schools Reference o The definitive specification for HTML 4 01 from the W3C organ
15. heless expect that provided you have choose a good topic for you and allocate a reasonable amount of time for your work you will all be able to do well with this part of the course In summary then please take your term projects very seriously and do your best to begin work on them as soon as is feasible 5 of 8 08 27 2012 10 23 AM Physics 210 Introduction to Computational Physics U file d bh0 home matt teaching 1 2Fall PHYS210 admin Finally be sure that you understand and abide by the University and course policies concerning Academic Honesty as they pertain to your term projects and as are laid out in the Homework page Other Help You should also feel free to contact me via e mail preferred or phone if you have quick questions or if you are having difficulty getting something to work Perhaps most importantly you should strive to develop the ability to make effective use of the available documentation for the software you are using on line help man pages Web resources etc AS you are no doubt aware the amount of information online combined with the power of search engines such as Google provides a powerful resource for self educations on a broad range of topics This is particularly true for computer related subjects 6 of 8 08 27 2012 10 23 AM Physics 210 Introduction to Computational Physics U file d bh0 home matt teaching 1 2Fall PHYS210 admin SYLLABUS SCHEDULE
16. hly magazine published by the IEEE which has articles on many topical aspects of computational science Generally accessible to undergrads Journal of Computational Physics JCP This is an advanced research journal in computational physics but in doing research for your term project you may find references to articles published in it General Physics Resources American Physical Society APS American Institute of Physics AIP Canadian Association of Physicists CAP Canadian Undergraduate Physics Journal American Astronomical Society AAS The Institute of Physics IOP Currently maintains Physics Web arXiv org e Print Archive Maintained by choptuik physics ubc ca 08 27 2012 10 24 AM Physics 210 Computational Physics UBC Fall 2012 file d bhO home matt teaching 12Fall PHYS210 admin Physics 210 Intro Computational Physics Term Project Ideas NOTES e All term project topics must be approved by the instructor talk to me or send e mail for approval even if the term project appears in the Specific Suggestions for Term Projects below e Topics must be chosen by October 11 and term project proposals will be presented on October 16 and 18 e Final project presentations will be held November 27 and 29 e Project writeups are due Nov 30 11 59 PM SPECIFIC SUGGESTIONS FOR TERM PROJECTS e Non linear dynamical systems o Simple models for chaos using continuous equations ordinary differentia
17. ical analysis There will be a significant programming component in virtually all stages of the course See the Syllabus below for a provisional lecture lab schedule as well as the Learning Goals amp Course Topics page for a more detailed overview 1 of 8 08 27 2012 10 23 AM Physics 210 Introduction to Computational Physics U file d bh0 home matt teaching 1 2Fall PHYS210 admin 2 of 8 Text Reference Material and Notes Due in large part to the diversity of topics to be covered there is no required text for the course However because much of the course will be MATLAB based have adopted the following as an optional text e MATLAB An Introduction With Applications 4th edition Amos Gilat John Wiley amp Sons 2010 feel that this book is written at a suitable level for an introductory course has generally been well received by students in reviews that have seen and should be especially useful if you have little or no experience in MATLAB and importantly little or no experience in computer programming The UBC bookstore currently has copies in stock 105 79 58 for new old rental However earlier versions of the text including the 2nd and 3rd edition should suffice for the course and you may be able to get these from Amazon etc for less than the bookstore is charging for the 4th edition Note that in the labs we will actually be using an open source version of MATLAB called octave and refe
18. ilities o xfpp3d o xflat2d xflat2d_rgb o XVS o DV LINUX Should you wish you can install Ubuntu on your laptop and or home machine The TAs will be available to help you with this but although there are ways of performing the installation in a highly safe manner we cannot guarantee that you might encounter some problems that could lead to a loss of data or very infrequently to a loss of your prior operating system presumably Windows or Mac OS See HERE for instructions on how to prepare your Windows machine for a Linux installation chkdsk disk clean up and defragmentation but note that these still need to be updated for Windows Vista and 7 PuTTY ssh client for Windows If you don t have a ssh client installed on your Windows machine s you can download and install the free package PuTTY HERE recommend that you click the A Windows installer for everything except PuTTYtel link in the latest release version beta 0 60 section save the file to disk then double click on the file icon to inititate the installation Once installed you will be able to use PuTTY to open terminal windows to remote machines such as hyper This in turn will allow you to do basic command line work on hyper and other machines that accept ssh connections from within Windows XMing X Server for Windows Installation of this free software on your PC laptop running Windows will allow you to run an X server on your system without installin
19. inks to other sites and resources Mathtools net Another exchange site for MATLAB users contains physics section A collection of Matlab Resources including tuorials compiled by lan Mitchell UBC CS Octave e octave Home Page o octave documentation HTML o info documentation for help with octave s doc command HTML Scilab e scilab Home Page Visualization Utilities xfpp3d OpenGL xforms based program for animating 2 and 3 D particle motion Basic help is available via xfpp3d h Refer to the above link for the help message which includes a definition of the input format Sample 20 body input file input20 Use xfpp3d lt input20 to view Sample 20 body input file input20c that uses different colors for different particles Use xfpp3d c lt input20c to view Documentation describing the creation of mpeg animations using this program is available HERE MATLAB octave function file nbodyout m Function nbodyout writes typical N body output to file in the format expected by xfpp3d Note that this function file is installed in phys210 octave on hyper 08 27 2012 10 24 AM Physics 210 Intro Computational Physics UBC Fall 2 file d bh0 home matt teaching 12Fall PHYS210 admin 5 of 6 xflat2d Open GL xforms based program for visualization of two dimensional binary valued lattices Basic help is available via xflat2d h Refer to the above link for the help message which includes a de
20. ization advanced o Google html reference for many more Graphing XY plots e gnuplot o Gnuplot 4 2 A brief Manual and Tutorial o Gnuplot site collection o Google gnuplot tutorial for many more e sm Supermongo User s Manual PDF 226 pages o Reference Manual o Tutorial e xmgrace also known as xmgr or ACE gr o User Guide Maple Symbolic Manipulation e Maple Maplesoft Home Page including links to various Maple Web sites NOTE The current version of maple is Maple 16 In the course however we will be referring to documentation from earlier versions o Maplesoft Application Center a Applications from Astrophysics Chemistry Dynamical Systems Physics Quantum Mechanics Maple Documentation from Past Versions Maple 9 Learning Guide PDF 332 pages Maple 5 by Example HTML Maple 10 Introductory Programming Guide PDF 398 pages Maple 10 Advanced Programming Guide PDF 452 pages 3 of 6 08 27 2012 10 24 AM Physics 210 Intro Computational Physics UBC Fall 2 file d bh0 home matt teaching 12Fall PHYS210 admin 4 of 6 MATLAB Numerical Computing with MATLAB by Cleve Moller Individual chapters in PDF Experiments with MATLAB by Cleve Moller Individual chapters in PDF Resources from Mathworks the distributors of MATLAB o MATLAB Central Contains searchable contributions from the MATLAB user community o MATLAB Tutorial Contains Mathworks tutorials as well as l
21. l equations ODEs o Simple models for chaos using discrete equations o Predator prey models and other biologically motivated systems e Simulation of the motion of N interacting particles in two dimensions using finite difference approximations FDAs o Gravitational interactions positive mass only o Electrostatic interactions postive and negative charges o General potentials and types of charge o Simple molecular dynamics calculations e Simulation of the motion of N interacting particles in three dimensions using finite difference approximations FDAs o Toomre model of galaxy collisions o Equilibrium configuration of N identical charges on the surface of a sphere e Simulation of simple time dependent partial differential equations PDEs using FDAs o One or two dimensional wave equations possibly non linear o One or two dimensional diffusion equations possible non linear o One dimensional time dependent Schrodinger equation e Solution of time independent partial differential equations PDEs using FDAs o Two dimensional Laplace Poisson equations e Cellular automata o Traffic simulations e Neural Networks o Simulation of simple neural network including training for specific task e Genetic Algorithms o Implementation of a basic genetic algorithm and application to a test problem e Particle Physics o Simulation of basic features of a particle detector including event generation and event reconstruction e Optics o Ray tracing through
22. lly amp Associates 31 50 from Chapters ca Comprehensive quick reference style tome Linux in a Nutshell A Desktop Quick Reference Siever et al O Reilly amp Associates 41 95 from Chapters ca Comprehensive quick reference style tome with Linux emphasis Unix for the Impatient 2nd ed Abrahams and Larson Addison Wesley 824 pages 39 95 from Chapters ca Quite comprehensive covers both vi and emacs and will provide more than enough information for this course The Unix Programming Environment Kernighan and Pike Prentice Hall 350 pages 62 95 from Chapters ca A classic Unix reference which although old is still well worth studying for those of you interested in becoming Unix experts Maple Symbolic Manipulation The following sources are available online we will be using portions of some of them in our study of Maple Maple Documentation from Past Versions Maple 9 Learning Guide PDF 332 pages Maple 10 Introductory Programming Guide PDF 398 pages Maple 10 Advanced Programming Guide PDF 452 pages Maple 5 by Example HTML MATLAB e MATLAB An Introduction with Applications Amos Gilat 4th Ed John Wiley amp Sons 2010 1 of 2 08 27 2012 10 24 AM Physics 210 Intro Computational Physics UBC Fall 2 file d bh0 home matt teaching 12Fall PHYS210 admin Optional text for the course 418 pages 98 95 from Chapters ca The UBC bookstore should also have this book in s
23. ntage of the lab time to discuss possible term project ideas with us Finally at any time you should feel free to use lab time to ask any of us about aspects of the computer work that are giving you trouble Lab work will not be graded 08 27 2012 10 23 AM Physics 210 Introduction to Computational Physics U file d bh0 home matt teaching 1 2Fall PHYS210 admin Late Work Policy Strictly Enforced You are strongly urged to submit your homework by the due date However from time to time and provided that the circumstances are sufficiently extenuating work may be submitted late subject to the following conditions 1 If an extension is required the extendee must submit a request for an extension via e mail to the instructor before the assignment is due 2 Submitted homework which absolutely must be submitted before the homework key is distributed must similarly be accompanied by an e mail indicating completion of the work Note that all messages are to be sent to the instructor not the TA and that if you finish the homework on time no additional action on your part is required Finally note that if you are unable to complete an assignment or term project on time due to illness or an equivalent circumstance e g severe illness and or death of a family member please inform me as soon as possible and will ensure that you are given sufficient time to complete your work once your situation has been resolved
24. ntro Computational Physics UBC Fall 200 _file d bh0 home matt teaching 12Fall PHYS210 admin 1 of 3 Physics 210 Intro Computational Physics Learning Goals amp Course Topics Outline Caveat Depending on how things progress we may not have time to achieve all of the following goals or to cover all of the material in the outline but we will try LEARNING GOALS 1 THEMATIC GOALS 1 To become acquainted with the use of modern computer technology to formulate and solve problems from physics and related fields computationally This will generally involve a Identifying or isolating a specific problem that requires solution Formulating the problem in mathematical terms as precisely as possible a Identifying appropriate approximations algorithms existing software etc that will allow you to solve the problem a Implementing the solution process on the computer using programming scripting etc in one or more computer languages as necessary Performing the calculations on the computer using your implementation a Analyzing and interpreting the results of the calculations a Possible iteration of one or more of the above steps in view of the results and analysis 2 To become familiar with basic to intermediate techniques in computer programming that will be of use in solving problems from physics and related fields 3 To be exposed to selected topics in physics and mathematics that are representati
25. o solve the problem including discussion of overall flow of the program e Discussion of computations numerical experiments that were performed e Analysis of results e Conclusions may include suggestions for future work e References Bibliography e Appendix including program listing if desired Note that for some projects not all of the above sections will be relevant but as always feel free to check with me should you have any questions about your writeup will also ask you to make any programs that you write for your term project available to me through your homework directories on your PHAS accounts and except in special cases which need to be cleared by me and the TAs should be able to run your programs on my own PHAS account the appropriate software environment Maple MATLAB Java etc In particular your term project code cannot be MS Windows specific The suggested paper length is about 10 20 pages double spaced please including title page figures and graphs and references If you include program listings they should be listed single spaced You are encouraged to use the LaTeX typesetting system to write your paper but this is not mandatory As noted above the term project is worth 35 of your grade Factors that will be taken into account in my grading of your projects will include but are not necessarily limited to scope and difficulty of the problem degree to which project was completed successfully
26. pull down menu that includes an option to exit the server Also when using PuTTY in conjunction with Xming you should ensure that any connections that you establish to hyper or other machines on which you wish to run graphical applications have X forwarding enabled otherwise those applications like kate will not be able to display on your Windows system Note that PuTTY has a facility for saving and loading sessions with the configuration settings saved as well that you should learn how to use You way notice in some of the on line information about Xming that you are supposed to be able to download Xming s own ssh client XMing portablePuTTY for free but at least at this time that does not seem to be the case As always you can contact myself Ben or Jason should you have any questions problems with the installation or use of Xming OCTAVE In principle you can install octave on a Windows machine but it isn t straightforward and may not be worth the effort Note that assuming that you have putty and xming installed you should be able to ssh to the main PHAS server hyper and use octave from there NOTE These programs can only be installed on Linux systems and you should only attempt installation should you think you really need one or more of them xfpp3d e Download xfpp3d tar gz e Software prerequisites depending on your flavour of Linux Unix not all will be required o OpenGL headers and libraries runtime and d
27. rences to MATLAB here and in the rest of the course material are to be understood to be references to octave as well You should also observe that there is a wealth of online material available about MATLAB I ve accumulated a few links to some key sites in the Online Course Resources page including a link to a site that provides for individual use only a complete text by the author of the first version of MATLAB The Course Resources page also contains links to sites relevant to other topics that we will cover in the course Some of these topics such as Unix Linux and basic MATLAB programming will be directly discussed in lectures or covered in labs Others such as the use of a text editor of your choosing will be self study topics since a key goal of this course is to enhance your ability to use help facilities online resources and the like to master new algorithms and software applications Finally at times will distribute notes to the class or at least make them available on line via the Course Notes page However at other times will lecture using the blackboard and then you will be responsible for taking your own notes Computer Access To participate in this course you must have a Physics and Astronomy PHAS computer account which will provide you with access to the computers in the PHAS computer lab Hennings 205 and and use of the machines in that lab should suffice for completion of your homework and projects If
28. rical Algorithms e Numerical Recipes Home Page and online books including Fortran 77 PDF Fortran 90 PDF and C PDF Complete text of all three obsolete but still useful editions of Numerical Recipes in PDF format e Netlib Repository Large collections of mathematical software papers and databases Browse or Search the Netlib libraries e LAPACK User s Guide html e LAPACK Source Code browse directory General Computational Physics Resources NOTE Entries marked with denote online journals to which UBC subscribes To access the articles in these journals typically in PDF format you will either have to be using a computer connected to the UBC network including UBC wireless or have your computer configured for remote access See HERE for the various options you have to enable remote access e Open Source Physics OSP e American Journal of Physics AJP The articles in this journal are generally accessible to undergrads and some are devoted to aspects of computational physics click HERE for a list of 200 papers with the keyword computational in the full bibliographic record You may find this to be a good resource for ideas for term projects o A Recent Resource Letter by Rubin Landau published in AJP and providing a guide to print and electronic literature relevant to a computational physics course PDF Computing in Science amp Engineering also see its predecessor Computers in Physics Bi mont
29. sconduct very seriously and so do I All strong evidence of cheating will therefore be reported to and dealt with through the Head of the Department of Physics amp Astronomy Maintained by choptuik physics ubc ca 2 of 2 08 27 2012 10 34 AM Physics 210 Intro Computational Physics UBC Fall 2 file d bh0 home matt teaching 12Fall PHYS210 admin Physics 210 Intro Computational Physics Suggested Hard Copy References Index e Unix and Linux e Maple e MATLAB UNIX and Linux There are many available Unix books representing a wide range in levels of presentation With the rapid increase in popularity of Linux many of the available references now focus on that particular flavour of Unix If this is your first experience with Linux and you would like a hard copy reference suggest that you first browse the Operating Systems section of a bookstore with a decent computers section the UBC Bookstore has deteriorated over the years in this respect to try to find something which appears suited to you The following books are fairly representative and if not available in town can be ordered online e Learning the Unix Operating System A Concise Guide for the New User Peek at al O Reilly amp Associates 15 92 from Chapters ca An earlier version of this guide provided a good quick introduction to Unix but didn t cover any of the popular editors Unix in a Nutshell System V Edition 3rd Edition Robbins O Rei
30. series of lenses prisms mirrors etc e Pedagogy 1 of 2 08 27 2012 10 25 AM Physics 210 Computational Physics UBC Fall 2012 file d bhO home matt teaching 12Fall PHYS210 admin o Interactive demonstration of some physical process phenomena that allows user to experiment with parameters initial conditions etc e Stochastic random processes o Generalizations of diffusion limited aggregation o Monte Carlo integration with application to some physical problem o Simulated annealing with application to some physical problem Projects from a previous offering of PHYS 210 are available HERE and may provide you with some ideas for your own projects Note however that my expectations for your project are somewhat different from the previous instructor s In particular as described in the main course page there should be a significant programming aspect to all projects i e something that goes beyond the use of built in facilities to perform the bulk of your calculations and a full writeup must be included in all cases Maintained by choptuik physics ubc ca 2 of 2 08 27 2012 10 25 AM Physics 210 Intro Computational Physics UBC Fall 2 file d bh0 home matt teaching 12Fall PHYS210 admin Physics 210 Computational Physics Course Software Availability for Personal Machines INDEX e Linux Ubuntu e Octave e PuTTY ssh client for Windows e XMing X server for Windows e Visuali zation Ut
31. tock by late September The 3rd Ed is also available from Chapters ca and will suffice for this course as will earlier versions e Introduction to MATLAB for Engineers amp Scientists Dolores M Etter Prentice Hall 1995 Older shorter but much cheaper text 145 pages 53 30 from Chapters ca Maintained by choptuik physics ubc ca Supported by CIAR NSERC CFI BCKDF and UBC 2 of 2 08 27 2012 10 24 AM Physics 210 Intro Computational Physics UBC Fall 2 file d bh0 home matt teaching 12Fall PHYS210 admin Physics 210 Intro Computational Physics Online Course Resources Please e mail suggestions or corrections to choptuik physics ubc ca This page subject to update throughout the course Last updated September 6 2009 Note PDF denotes Adobe Portable Document Format Index Text Editors Searching the Web Graphing XY plots Maple Symbolic Manipulation MATLAB Octave amp Qtoctave Scilab Visualization Utilities xfpp3d xflat2d xflat2d_rgb XVS o DV e Numerical Algorithms e General Computational Physics Resources e General Physics Resources General Information Unix Linux bash e Unix Linux General information Unix Linux bash amp tcsh Web Authoring Creating Web Pages HTML documents o Unix Tutorial for Beginners U Surrey UK o The Linux Documentation Project TLDP e bash o Bash Guide for Beginners Includes sections on writing scripts o Bash Referenc
32. ubject to small adjustments based on overall class performance Tests There will be NO tests or exams in this course Homework and Labs Homework See the syllabus below for provisional scheduled homework due dates Homework will be assigned about 2 weeks before it is due late homework may be accepted at the instructor s discretion and as per the Late Homework Policy described below As the course progresses the Homework Schedule web page will be updated with information concerning the assignments including the homework handouts themselves Each homework will contribute equal weight to your final mark but again the homework component of your mark may be subject to adjustments based on overall class performance Assignments will tend to become more challenging as the course progresses but I view this as a feature that favours you Labs A chief purpose of the labs is to provide you with time to acquire the extremely important hands on skills needed to master the course material and which by nature is difficult to teach learn in a traditional lecture setting Some of the lab sessions will be concerned with specific topics in which case will generally provide a set of online notes that we will work through together For others you will be have free time to work on your assignments and term projects assisted as necessary by the TAs myself and your classmates In the early stages of the course you should also take adva
33. v 30 11 59 PM 7 of 8 08 27 2012 10 23 AM Physics 210 Introduction to Computational Physics U file d bh0 home matt teaching 1 2Fall PHYS210 admin Syllabus Notes e Lecture topics are listed in regular font Lab activities other than working on the current homework and or term projects and which will be updated throughout the course are listed in italics and will link to a description of the lab activity when appropriate e Homework assignments are denoted H1 through H4 and have due dates as indicated above e See Learning Goals amp Course Topics page for a more detailed outline of course material e Term projects are due FRIDAY NOVEMBER 30 last day of classes not last class day Other Important Dates e Tuesday September 18 Last day for withdrawal from this course without withdrawal standing of W recorded on your academic record e Monday October 8 Thanksgiving Day University closed e Friday October 12 Last date for withdrawal from this course with withdrawal standing of W recorded on your academic record Monday November 12 Holiday in lieu of Remembrance Day University closed Friday November 30 Last day of classes Wednesday December 5 Examinations begin Wednesday December 19 Examinations end See the UBC 2012 2013 Calendar and Academic Year all year pages for more information Maintained by choptuik physics ubc ca 8 of 8 08 27 2012 10 23 AM Physics 210 I
34. ve of some typical application areas in real world computational physics some of this material may already be familiar to you 4 To gain experience in searching for and finding information on specific topics areas in understanding that information and then applying it i e research and self instruction 5 To gain experience in presenting the results of scientific work and in writing up the results of that work in the form of a scientific paper 2 SPECIFIC GOALS Successful completion of this course which includes understanding the lecture material completing the homeworks with a reasonable degree of proficiency and presenting and submitting a good term project should provide you with the ability to do the following ata minimum 1 Work comfortably within a Unix Linux environment with an emphasis on the use of the command line 2 Use Maple to interactively perform basic symbolic manipulation and numerical computations 3 Write simple Maple procedures programming as part of an introduction to the use of Maple as a powerful computing environment 4 Perform basic to intermediate level numerical computations using MATLAB 08 27 2012 10 25 AM Physics 210 Intro Computational Physics UBC Fall 200 _file d bh0 home matt teaching 12Fall PHYS210 admin 2 of 3 interactively 5 Write basic to intermediate level MATLAB scripts and functions programming 6 Use your MATLAB programming skills to address spe
35. y manner so that all of the talks can be assembled into a single set of slides Details concerning this will be provided later There will be no grading of this aspect of your term projects the purpose of this exercise is to ensure that you have chosen an appropriate topic and that you have a good though perhaps not complete understanding of what will be required to complete it In keeping with the spirit of the course all term projects should involve programming to a significant extent and students are encouraged to use MATLAB octave or possibly Maple to implement their projects assuming that you do so you are expected to do more than use some built in MATLAB Maple facility to perform the bulk of your computations You are also free to use other programming languages of your own choice if you wish to do so only ask that you check with me before you start work on your proposal so that can ensure that the overall project appears appropriate 4 of 8 08 27 2012 10 23 AM Physics 210 Introduction to Computational Physics U file d bh0 home matt teaching 1 2Fall PHYS210 admin All term projects must be written up in the style of a scientific technical paper a typical structure will be e Title and Abstract e Introduction including basic description of problem to be solved simulated analyzed etc e Mathematical formulation of the problem as relevant e Description of techniques algorithms analysis tools etc used t
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