Syllabus

Vitals

• Course Number and Title: PHYS 1510: Mathematical Methods of Physics.
• Catalog Description: "This course is an introduction to mathematical methods in physics. Topics covered include using spreadsheets (Excel), algebraic languages (Mathematical[sic]), and interpreted languages (Python) to solve basic physics problems. Elementary numerical methods and scientific visualization is also covered. Topics of coverage may include: approximation techniques, numerical differentiation and integration, matrices, complex variables, and solution of transcendental equations." (North Park University 2009)
• General Education: This course does not satisfy any General Education area requirements.
• Meeting Time/Place: MW 1 pm–2:05 pm (Carlson Tower, Room C-21).
• Credit: 2 sh.

Instructor

• Name: Johnny Lin.
• Email: johnny at johnny-lin.com (Replace "at" by "@". This is the best way to reach me).
• Twitter: jwblin (I'm not on the public timeline, however).
• Work Phone: (773) 244-6266.
• Office Location: Carlson Tower, Room C-26.
• Office Hours: See my schedule for my regular office hours, make an appointment to see me, or just drop in if my door's open.
• Personal Link: http://www.johnny-lin.com.
• My RateMyProfessors.com Rating.

Texts & Supplies

Required texts:

• De Jong, Marvin L., Mathematica for Calculus-Based Physics, Addison-Wesley, 1999, ISBN 020160339X.
• Martelli, Alex, Python in a Nutshell, 2nd Edition, O'Reilly Media, 2006, ISBN 0596100469.
• Siever, Ellen, et al., Linux in a Nutshell, 6th Edition, O'Reilly Media, 2009, ISBN 0596154488.

All texts are required and are available at the bookstore.

Computer requirements: All students are expected to have unfettered access to a personal computer (Windows, Mac, Linux, etc.) or netbook with broadband-speed Internet access. Student access to University computing labs fulfills this requirement. All students are assumed to be proficient with a word processing program and a presentation program (e.g., Microsoft Word and Powerpoint), and willing to learn a spreadsheet program (e.g., Microsoft Excel). All students must have a valid email account that they check on a daily basis.

See the list of External Links for additional resources on the subjects of the course.

Goals & Topics

Goals: First and foremost, I hope you will discover a new dimension of worshiping God through both the process and content in learning about using computational tools.

At the end of this course, you should also have developed the rudimentary tools needed to use computational tools to do research in science. This course is not a programming course per se but rather focuses on using computer programming skills to solve scientific problems. My hope is also that during this course you will grow in learning how to learn (see the External Links page for some tips on learning).

Our class motto is: "The right tool for the job."

Topics: Course topics include:

• Tasks in scientific computing.
• Basic numerical methods (implemented on a spreadsheet).
• Basic exploratory statistical data analysis (implemented on a spreadsheet).
• Simple problem solving and dynamics modeling (implemented in Mathematica).
• Basic operating system theory and structure.
• Everyday use of the GNU/Linux operating system (filesystem, permissions, search, piping, redirection, etc.).
• Text editors (vi).
• Shells and shell commands and scripts (bash).
• Scripting and interpreted languages for calculations and analysis (implemented in Python).

Requirements

Homework: The Assignments List contains details for most homework assignments. The Schedule gives assigned and due dates, as well as the details about homework not described in the Assignments List.

Quizzes: Weekly, on Wednesdays. In-class, various formats.

Final exam: Friday, May 7, 10:30 am–12:30 pm. In-class and comprehensive.

Please note that learning programming cannot be crammed in. (In contrast, once you have learned how to program, you can write a program in an all-night frenzy if you want.) You must start the assignments early and see me promptly if you get stuck. Otherwise, you will likely go around in circles wasting time and energy.

Grading

Your course grade is calculated based on the following formula:

• Homework: 50%
• Quizzes: 30%
• Final Exam: 20%

If you have turned in no less than 60% of the Homework and taken no less than 60% of the Quizzes, I will replace your cumulative Quizzes grade with your Final Exam grade if the Final Exam grade is higher.

Scale: The chart below shows the lower-end cutoffs for each possible passing letter grade. The University, as a policy, does not award A+ grades.

Lower Cutoff (inclusive)	Letter Grade
94%	A
90%	A–
87%	B+
84%	B
80%	B–
77%	C+
74%	C
70%	C–
67%	D+
64%	D
60%	D–

Makeups & Late Policy

There are no makeups for quizzes, exams, or presentations/demonstrations unless for reasons of physical health, bereavement, or University business.

Work is accepted only in class. Work turned in any other way without prior arrangements being made may have 10% automatically deducted from it. It may be considered late anytime after it is collected in class. Work late:

• 1 class session: 20% is deducted.
• 2 class sessions: 40% is deducted.
• > 2 class sessions: Not accepted.

Late penalties are waived for reasons of physical health, bereavement, or University business. Please see me/send me an email if something like this comes up.

Collaborating

As with any relationship, I expect honesty, respect, and grace to be the foundation of our time together. I expect this for myself, as well as for you. Collaborating in work is a wonderful opportunity to practice all three principles. Cheating, however, is an affront (to the first two) or an abuse (of the last) of these norms, and so will result (at a minimum) in a zero for the Assignment involved. If you are not sure what constitutes cheating, please ask me; here are some guidelines to help you on this issue:

• For problem sets, papers, reports, presentations, and projects: I encourage you to work together and discuss your ideas freely. Each person must, however, write-up the Assignment themselves; do not just re-copy one another's solutions.
• For writing assignments of any form, plagiarism is, of course, cheating. Plagiarism involves representing another's work as your own and/or without proper acknowledgment. The most common form is the use of another's words without quotation or citation.
• For the quizzes and exams: These should be your own work, written without the use of other help or resources, unless explicitly specified.

While I make solutions inaccessible on class websites after the class is over (to decrease temptations to cheat), our department is small, and so you probably know someone who has taken this class before and has copies of exams, problem sets, and/or solutions. I also have a policy of giving students solutions to as much work as I can because I want students to use their old work in studying for the final (or other exams). Thus, I realize that solutions are potentially in circulation. However, I ask that current students limit their consultation of work from previous sections in certain ways. Here are specific scenario categories:

• Consultation of problem set solutions from previous sections while you are working on that same problem: This constitutes cheating.
• Consultation of papers, reports, projects or presentations from previous sections while working on a current section's paper, report, project or presentation: This does not constitute cheating. I encourage you to use other people's work to give you ideas (though, as mentioned above, please do not just copy their work) for these types of Assignments!
• Consultation of any Assignments (including problem set solutions, papers, exams, etc.) from previous sections while studying for a current section's quiz or exam: I do not consider this cheating.

For example, if you have a friend who took this course before and you consult his/her problem set solutions while studying for an exam, that does not constitute cheating. However, if you consult those problem set solutions while working on that problem set, that does constitute cheating.

I believe these are reasonable guidelines that balance a number of competing interests, and that do not constitute an unfair burden on conscientious students. Recall that I do not curve grades, so dishonest students really are hurting themselves and God, but not other students. Please let me know if you have any concerns.

The Internet and Programming: The Internet is one of the greatest programming helps ever invented. Almost any programming problem can be solved using Google. That being said, you still need to take care not to plagarize another's code. Here are some guidelines:

• If you use a few words of someone else's code: If it's obvious, you probably don't need to attribute this use. If it's not obvious, you should put a comment line in saying where you got it from (the URL, at least).
• If you use substantial amounts of someone else's code: You must put a comment line in saying where you got the block of code from.
• If you use ideas from someone else's code: Obvious ideas probably don't need to be attributed. Non-obvious ideas do, and you should put a comment line in saying where you got the ideas for your code from. This will help you track the context of your solution.
• If you copy code from a copyrighted source: Directly copying is probably fine for personal study, but it is not fine for any programs you later distribute. You could get into serious legal trouble if you use someone else's copyrighted code without their permission. This is true even if you attribute your source, or if you give away your program for free. If you do use copyrighted code, make sure you note in your program you have done so, so if you ever do distribute your program you'll know whether you're in potential legal jeopardy. Or better yet, just never use copyrighted code in your programs without their permission!

Disabilities

"Students with disabilities who believe that they may need accommodations in this class are encouraged to contact the Academic Services Learning Specialist by email or by phone at (773) 244-5737, or stop by the office located on the 2nd floor of the Student Services Building. Please do so as soon as possible to better ensure that such accommodations are implemented in a timely manner. If needed, appointments can be relocated" (North Park University 2009). More information is available online at http://www.northpark.edu/disability.

Schedule

This schedule of assignments is sorted forward-chronologically. All work is due the following class session after it was assigned, unless otherwise noted. (Assigned work that says "not collected" is due the next class session, but will not be turned in for credit; those assignments are to help you learn what you need to in order to do the later assignments.) The list on this schedule includes all those on the Assignments List (except Extra Credit, which is described only on the Assignments List) as well as exercises from readings and tutorials that are not included on that list.

As an additional resource, I've compiled a list of external links to supplement the readings and exercises.

Class #	Date	Description
1	Mon. Jan 11	Topics: Course administration, introduction to scientific computing, introduction to spreadsheets (references, names, copy/paste, fill down). Assigned: Basic Excel Tutorial assignment.
2	Wed. Jan 13	Topics: Using spreadsheets to solve equations through iteration and graphing. Assigned: Iterative and Graphical Solutions of Equations assignment.
—	Mon. Jan 18	No class—Martin Luther King, Jr. Day
3	Wed. Jan 20	Topics: Quiz 1. Numerical differentiation and integration using spreadsheets. Assigned: Numerical Differentiation assignment. Numerical Integration assignment.
4	Mon. Jan 25	Topics: Exploratory statistical data analysis using spreadsheets. Assigned: Exploratory Data Analysis assignment.
5	Wed. Jan 27	Topics: Quiz 2. Introduction to Mathematica: Go through the built-in Mathematica tutorials "Your First Mathematica Calculations" (tutorial/YourFirstMathematicaCalculations in the search bar of the Mathematica documentation window) and "The Syntax of the Mathematica Language" (tutorial/TheSyntaxOfTheMathematicaLanguage) and the "Hands-on Start to Mathematica" screencast in class. Assigned: Solving Problems assignment.
6	Mon. Feb 1	Topics: More solving problems in Mathematica. Assigned: More Problems and Functions assignment.
7	Wed. Feb 3	Topics: Quiz 3. Simple dynamics modeling using Mathematica. Assigned: Simple Dynamics Modeling assignment.
8	Mon. Feb 8	Topics: Vector calculations using Mathematica. Assigned: Vector Calculations assignment.
9	Wed. Feb 10	Topics: Quiz 4. Set up GNU/Linux accounts on snow, set-up shell environment (copy .bashrc and .bash_aliases from /home/jlin), introduction to computing, GNU/Linux commands, getting help. Assigned: None of these assignments will be collected. However, you ignore them (and all uncollected assignments) at your own peril! The material that's covered will be crucial for later assignments: Download a copy of Rute User's from here. Note that this is a tarred bzip2 file, so after you download it you have to use bunzip2 to decompress it, then tar to unwrap the archive. The index.html file in the rute folder is the title page of the book. We will be reading a number of selections from Rute User's over the course of the term. When you do the examples in Rute User's, you will need to do them either in a Terminal window on a Mac or a Cygwin window on one of the Windows PCs in C-22. To open a Mac Terminal window, go to Applications –> Utilities and double-click the Terminal icon. To open a Cygwin window, go to Start –> All Programs –> Cygwin and start Cygwin Bash Shell. If you log in to snow, you can also do the Linux examples in a Terminal window there. Read and do the examples in Ch. 1–2 in Rute User's. Read Ch. 1 (Introduction) in Linux in a Nutshell. Read and do the examples in Sections 3, 4.1–4.8, and 4.14–4.15 in Rute User's.
10	Mon. Feb 15	Topics: GNU/Linux commands (cont.), text editors, regular expressions. Assigned: None of these assignments will be collected: Do the "Learning vi — The Cheatsheet Method" web tutorial. Use only vi or vim, not gvim. Read and do the examples in Section 5 in Rute User's (the discussion on pattern matching in Ch. 7 in Linux in a Nutshell might help in understanding what all those symbols mean). Read Appendix D.1–D.3 in Rute User's.
11	Wed. Feb 17	Topics: Quiz 5. Scripting, processes, piping, redirection. Assigned: Assigned: None of these assignments will be collected: Do "A Quick Guide to Writing Scripts Using the bash Shell". Read and do the examples in Sections 8.3, 8.5, and 9.1–9.5 in Rute User's.
12	Mon. Feb 22	Topics: Accounts, remote services, permissions, links. Assigned: Read and do the examples in Sections 11.7 and 12.1–12.5 in Rute User's (not collected). Read and do the examples in Sections 14 and 15 in Rute User's (not collected). Basic GNU/Linux assignment.
13	Wed. Feb 24	Topics: Quiz 6. Introduction to programming, code documentation, Python elements, functions. Assigned: Read "Programming Fundamentals: What Programs Can Do," a set of lecture notes by Dave Rogers. Type in the program examples he gives (not collected). Read and do all exercises from Sections 3.1–3.13 from Handbook of the Physics Computing Course (not collected). Functions, Tests, and Looping assignment.
14	Mon. Mar 1	Topics: Functions and modules. Assigned: Keyword Input Parameters assignment.
15	Wed. Mar 3	Topics: Quiz 7. NumPy arrays and array looping. Assigned: Transposing Arrays assignment.
Sat., Mar 6–Sun., Mar 14: No class—Spring Break
16	Mon. Mar 15	Topics: Array operations. Assigned: A Slope Function assignment.
17	Wed. Mar 17	Topics: Quiz 8. Array operations (cont.). Assigned: A Distance Function assignment.
18	Mon. Mar 22	Topics: Array masking and search functions. Assigned: The Where Function assignment.
19	Wed. Mar 24	Topics: Quiz 9. Array masking and search functions (cont.). Assigned: Array Masks assignment.
20	Mon. Mar 29	Topics: Array masking and search functions (cont.), floating point comparison. Assigned: A "Has-Elements-Close-To" Function assignment.
21	Wed. Mar 31	Topics: Quiz 10. Array masking, search functions, and floating point comparison (cont.). Assigned: A "Where-Is-Close" Function assignment.
—	Mon. Apr 5	No class—Easter Break
22	Wed. Apr 7	Topics: Quiz 11. More complex array operations. Assigned: Curl Function assignment (due Wed. Apr 14). Read the list of non-object Python topics, sent to you via email. Come up with questions on those topics to ask next class (not collected).
23	Mon. Apr 12	Topics: Review of non-object Python, object-oriented programming. Assigned: Read this definition of what is an object (not collected).
24	Wed. Apr 14	Topics: Quiz 12. Object-oriented programming. Assigned: Object Decomposition assignment.
25	Mon. Apr 19	Topics: Object-oriented programming (cont.). Assigned: Bibliography Object assignment.
26	Wed. Apr 21	Topics: Quiz 13. Object-oriented programming (cont.). Assigned: Distance Calculation Object assignment (due Wed. Apr 28).
27	Mon. Apr 26	Topics: Object-oriented programming (cont.). Assigned: Nothing new.
28	Wed. Apr 28	Topics: Quiz 14. Object-oriented programming (cont.). Assigned: Curl Calculation Object assignment.
29	Mon. May 3	Topics: Object-oriented programming (cont.). Any and all extra credit is due today (see the description at the top of the Assignments List for details). Assigned: Nothing new.
—	Fri. May 7	10:30 am–12:30 pm: Final Examination.

Other Course Administration Issues

For details regarding all other course administration issues (e.g., dropping the course, conditions under which Incompletes are awarded, etc.), please see the current University Catalog.