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JCP265H5F LEC0101

Introduction to Scientific Computing

Course Outline - Fall 2022

Course Description

This course is an introduction to computing in the physical sciences. Students will gain experience utilizing numerical software tools used in both academic and industrial settings. A variety of numerical techniques will be covered, with topics to include: curve fitting, numerical approximations of derivatives and integrals, root finding, solutions of differential equations, Fourier series, Monte Carlo methods, and more. Students will also acquire skills in data analysis and visualization. No prior experience in computer programming is required. [24L, 24P]

Prerequisite: (PHY146H5 or PHY136H5 (minimum grade of 80%)) and (PHY147H5 or PHY137H5 (minimum grade of 80%)) and (MAT135H5 and MAT136H5) or (MAT135Y5 or MAT137Y5)

Exclusion: CSC108H5 or CSC108H1 or CSC120H1 or CSC148H1 or CSCA08H3 (SCI)

Distribution Requirement: SCI

Course Learning Outcomes

In this course, we will learn to address scientific problems in both physics and chemistry using computation. On successful completion of the course, students will be able to write programs and be able to document their programs so that they are readable by others. We will be learning to code in Python, which is a widely used programming language. No prior knowledge of Python or another programming language is necessary for this course. By the end of the course, students will be proficient in the following:

1. Writing pseudocode (designing a program in words before starting to program) and translating this pseudocode to a program in Python.

2. Debugging programs (identifying and correcting errors in their own code and code written by others).

3. Critiquing Python programs for correctness, efficiency and good programming style.

4. Documenting Python programs using comments and docstrings.

5. Writing readable programs using good programming style (e.g. readable variable names).

6. Using Python libraries for science and data science (e.g. NumPy, SciPy, Pandas).

7. Visualizing scientific data using Python libraries (e.g. matplotlib, seaborn).

Textbooks and Other Materials

Textbook (Optional): Paul Gries, Jennifer Campbell, Jason Montojo, Practical Programming: An Introduction to Computer Science Using Python 3.6 The Pragmatic Bookshelf, 3rd Edition (2017).

Available for purchase as an ebook (.pdf and Kindle formats): https://pragprog.com/titles/gwpy3/practical-programming-third- edition/

Assessment and Grading

Type

Description

Due Date

Weight

Lab

9 labs (5% x 9 = 45%)

On-going

45%

Term Test

Term Test 1

2022-10-19

15%

Term Test

Term Test 2

2022-12-07

15%

Class Participation

Attendance and participation in lectures and practicals

On-going

5%

Other

Final Project

2022-12-06

20%

Total

100%

Midterm Tests

The midterm tests will be 90 minutes in length and will take place during the regularly scheduled practical time starting preciseyly at 1:10 pm. There may be a switch to online test writing in the event that a switch to online course delivery is mandated. Detailed instructions on how to access and complete online term tests will follow via the course Quercus site should such an event manifest.

Procedures and Rules

Missed Term Work and Tests, Late Penalties and Absence Declarations

Penalties for all term work missed or otherwise submitted late is as described in the text that follows unless valid and documented reasons exist for special consideration. Students may submit a request for special consideration within one week of the due date of the missed item of term work or date of the missed test. Requests for special consideration may be made by e-mail to the Course Instructor, from a valid University of Toronto (UofT) e-mail account. Students must also successfully complete an online absence declaration via ACORN and provide the Course Instructor with a confirmation of this declaration (e.g. a screenshot) in their petition for special consideration, which contains their student name, student number, absence dates and confirmation number. Note that ACORN absence declarations must be recorded for each day that you are absent - as soon as it begins up until the day you return to your classes or other activities. The ACORN absence declaration tool lets you record absences for up to 14 consecutive days, one of which must be the day you access the tool (if you are still absent) or the day prior (if you have returned). If you need to record an absence outside of this range, please contact the Office of the Registrar. More information about Absence Declarations can be found here. The Course Instructor will inform the student by e-mail (as per the communication policy above) whether special consideration is granted following due diligence on the documentation provided.

If a student misses a midterm test, a mark of zero (0%) will be assigned unless a request for special consideration is made and granted by the Course Instructor. In the case that special consideration is granted, the mark value of the missed test will be re- assigned to i) a make-up test, which will be written on the Department of Chemical and Physical Sciences Make-Up Day (date to be determined) or ii) a make-up test that will be scheduled at the earliest mutually convenient time for the Course Instructor and student.

If a student misses a practical session, a mark of zero (0%) will be assigned for that experiment and associated term work unless a request for special consideration is made and granted as described above. There will be no make-up laboratory sessions and the mark value of the laboratory will be re-assigned to the term tests in the case that special consideration is granted.

If a student misses the final presentation of the term project, a mark of zero (0%) will be assigned for that presentation and associated term work unless a request for special consideration is made and granted as described above. Term projects submitted past the deadline will not be accepted without a request for special consideration as described above.

Re-evaluation Requests

Requests for re-evaluation of an article of term work (e.g. test, assignment, laboratory report, etc.) must be made in writingwithin 1 month of the return of the article of term work and include a brief explanation as to why the request is being made. Term work submissions can be written in pencil; however, re-marking of term work written in pencil is not permitted. Similarly, articles of term work on which correction media has been used will be exempt from re-evaluation. Re-evaluation requests must be made to the same person that did the initial grading of the article of term work (normally, this is a Teaching Assistant). Note that the final mark assigned to a re-evaluated article of term-work may go up or down based on the outcomes of re-evaluation (in whole or in part, at the discretion of the marker). Disputes in grading subsequent to re-evaluation by the original marker may be brought forward to the Course Instructor for final adjudication. You, as a UTM student, have the right to appeal a mark beyond the Course Instructor only if the term work in question is worth at least 20% of the course mark.

Laboratory Conduct: Expectations, Roles, and Responsibilities.

Students and all members of the teaching team (i.e. the Teaching Assistant(s) and Instructor) have specific roles and responsibilities in the effective and efficient operation of the laboratory. Students are expected to adhere to all safety rules and to come to the lab prepared. Preparation includes a thorough review of the laboratory manual and associated theory related to the laboratory work to be conducted (notes and flowcharts in your laboratory notebook are highly recommended), review of all required standard operating protocols (SOPs) for use of instrumentation, completing calculations beforehand and completion of all assigned pre-laboratory exercises. Students who fail to come to the laboratory prepared, show a lack of preparedness during the laboratory, and/or violate laboratory safety protocols will be asked to leave the laboratory and a mark of zero (0%) will be assigned for that experiment and associated term work (e.g. the associated laboratory report).

Communications Policy

Students are welcome and encouraged to meet with the Course Instructor during the posted office hour(s). Office hours will be held in person unless online course delivery is mandated. In this event, details for connecting to office hours via Zoom will be posted on the course Quercus site. Note that virtual office hour visits will not be recorded. Visits outside of the regularly scheduled office hour(s) can be made by appointment. Correspondence by e-mail is also acceptable. In all e-mail correspondence regarding this course, please note the following:

1. Please send e-mail only from your @utoronto.ca or @mail.utoronto.ca account.

2. In the Subject line of your message, please include the course code and a brief description of the topic, e.g. "[Course code] - Request for an appointment regarding potentiometry".

3. Please include your full name and student number in all correspondence.

4. Please consult the course syllabus and course website before sending questions by e-mail

I will endeavour to respond to e-mail within two workdays at the latest. Students are responsible for all information posted to the course Quercus site and e-mails sent by the Course Instructor, Laboratory Technicians and Teaching Assistants.

Student Technology Requirements and Connection Tools

During times when a switch from in-person to online course delivery is mandated, Zoom will be used for remote course delivery (i.e. lectures, tutorials, and practicals) and office hours. Students are therefore expected to review and be in compliance with the University of Toronto's requirements for online learning and to register for a UTM Zoom account prior to the first course meeting. Students are also strongly encouraged to familiarize themselves with the resources available on the UTM Library's Learn Anywhere website.

Privacy and Use of Course Materials

All course materials belong to the Course Instructor, the University, and/or other sources (depending on the specific facts of each situation) and are protected by copyright. In this course, you are permitted to download materials for your own academic use, but you should not copy, share, or use them for any other purpose without the explicit permission of the Course Instructor. In the event of a mandated switch to remote course delivery, this course, including your participation, will be recorded on video and will be available to students in the course for viewing remotely and after each session. Course videos and materials belong to your instructor, the University, and/or other sources depending on the specific facts of each situation, and are protected by copyright. Do not download, copy, or share any course or student materials or videos without the explicit permission of the instructor. For questions about recording and use of videos in which you appear please contact your instructor.

Information Security Risks

If you are a citizen of another country, and/or accessing your courses at the University of Toronto from a jurisdiction outside of Canada, please note that you may be subject to the laws of the country in which you are residing, or any country of which you have citizenship. The University of Toronto has a long-established commitment to freedom of expression, with this right enabled by an environment valuing respect, diversity, and inclusion. In your classes, you may be assigned readings, or discuss topics that are against the law in other jurisdictions. I encourage you to become familiar with any local laws that may apply to you and any potential impact on you if course content and information could be considered illegal, controversial, or politically sensitive. If you have any concerns about these issues, please contact your instructor directly to discuss with them

Academic Integrity

UTM wishes to remind students that they are expected to adhere to theCode of Behaviour on Academic Matters regardless of the course delivery method (i.e. in-person or online). Potential academic offences include, but are not limited to:

Using or possessing an unauthorized aid or aids or to obtain unauthorized assistance in any academic examination or term test or in connection with any other form of academic work. Use of unauthorized aid(s) and unauthorized assistance includes working collaboratively, in-person or online, with others on assessments that are expected to be completed individually, in addition to accessing unauthorized resources (search engines, chat rooms, Reddit, etc.) for assessments completed online.

Representing as one's own, any idea or expression of an idea or work of another in any academic examination or term test or in connection with any other form of academic work, i.e. to commit plagiarism.

Submitting, without the knowledge and approval of the instructor to whom it is submitted, any academic work for which credit has previously been obtained or is being sought in another course or program of study in the University or elsewhere; Submitting any academic work containing a purported statement of fact or reference to a source which has been concocted.

All suspected cases of academic dishonesty will be investigated following procedures outlined in the Code of Behaviour on Academic Matters. If you have questions or concerns about what constitutes appropriate academic behaviour or appropriate research and citation methods, you are expected to seek out additional information on academic integrity from your instructor or from other institutional resources.

Normally, students will be required to submit their course essays to the University's plagiarism detection tool for a review of textual similarity and detection of possible plagiarism. In doing so, students will allow their essays to be included as source documents in the tool's reference database, where they will be used solely for the purpose of detecting plagiarism. The terms that apply to the University's use of this tool are described on the Centre for Teaching Support & Innovation web site (https://uoft.me/pdt-faq).

Students are permitted opt-out of using the University's plagiarism detection tool and notice of this decision must be delivered to the Course Instructor no later than the end of day on which the first class meeting occurs. This notice should be provided via email, as per the communication policy specified herein. In such a case, you may be asked to submit all of your rough work for an assignment and you may be required to have a short meeting with the Course Instructor to discuss your research methodology.

Academic Rights

You, as a student at UTM, have the right to:

Receive a syllabus by the first day of class.

Rely upon a syllabus once a course is started. An instructor may only change marks' assignments by following the University Assessment and Grading Practices Policy provision 1.3.

Refuse to use the University's plagiarism detection tool (you must be offered an alternative form of submission).

Have access to your Instructor for consultation during a course or follow up with the Department Chair if the Instructor is unavailable.

Receive at least one significant mark (15% for H courses, 25% for Y courses) before the last day you can drop a course for H courses, and the last day of classes in the first week of January for Y courses taught in the Fall/Winter terms.

Submit handwritten essays so long as they are neatly written. Have no assignment worth 100% of your final grade.

Not have a term test worth 25% or more in the last two weeks of class. Retain intellectual property rights to your research.

Receive all your assignments once graded.

View your final exams. To see a final exam, you must submit an online Exam Reproduction Request within 6 months of the exam. There is a small non-refundable fee.

Privacy of your final grades.

Arrange for representation from Downtown Legal Services (DLS), a representative from the UTM Students' Union (UTMSU), and/or other forms of support if you are charged with an academic offence.

Inclusivity Statement

You belong here. The University of Toronto commits to all students, faculty, and staff that you can learn, work, and create in a welcoming, respectful, and inclusive environment. In this class, we embrace the broadest range of people and encourage their diverse perspectives. This team environment is how we will innovate and improve our collective academic success. You can read the evidence for this approach here.

We expect each of us to take responsibility for the impact that our language, actions and interactions have on others. The Department of Chemical and Physical Sciences (CPS) denounces discrimination, harassment and unwelcoming behaviour in all its forms. You have rights under the Ontario Human Rights Code. If you experience or witness any form of harassment or discrimination, including but not limited to, acts of racism, sexism, Islamophobia, anti- Semitism, homophobia, transphobia, ableism and ageism, please tell someone so that we can intervene. CPS takes these reports extremely seriously. You can talk to anyone you feel comfortable approaching, including your professor, teaching assistant, technician, an academic advisor,

our Chairs, members of our Equity, Diversity and Inclusivity Committee, or any staff member at our Equity, Diversity & Inclusion Office.

You are not alone. Working together, we can all achieve our full potential.

Course Code of Conduct and Expectations

Each member of this course is expected to maintain a:

Professional and respectful attitude during all course activities, including lectures, labs, and online activity. Personal calendar/schedule/organizer to ensure that all course activities are completed and due dates are met.

Collection of class notes recorded independently based on concepts covered in lectures and labs (students registered with Accessibility Services requiring a class note-taker will have access to this accommodation).

Familiarity with the University's policy on Academic Integrity (see: the section entitled Academic Integrity, above, and the Code of Behaviour on Academic Matters).

Familiarity with the University policy on Conflict of Interest and Close Personal Relationships

(see: https://www.provost.utoronto.ca/planning-policy/conflict-of-interest-close-personal-relations/). Note that a conflict of interest arises when your personal interests conflict with your responsibilities as a student of the University. For example, if you have, or have had, a familial, sexual, or otherwise close relationship with a member of the teaching staff, you will almost inevitably be in a conflict-of-interest situation, which may affect your academic performance. Please disclose any potential conflicts-of-interest to the Course Instructor and/or Department Chair as soon as possible.

Familiarity with the University policy on Sexual Violence and Sexual Harassment

(see: http://www.governingcouncil.lamp4.utoronto.ca/wp-content/uploads/2016/12/p1215-poshsv-2016-2017pol.pdf). Note that sexual violence is any sexual act or act targeting a person's sexuality, gender identity or gender expression, whether the act is physical or psychological in nature, that is committed, threatened or attempted against a person without the person's consent. All members of the University community should have the ability to study, work, and live in an environment free from sexual violence and sexual harassment.

Equity Statement

The University of Toronto is committed to equity and respect for diversity. All members of the learning environment in this course should strive to create an atmosphere of mutual respect. As a Course Instructor, I will neither condone nor tolerate behaviour that undermines the dignity or self-esteem of any individual in this course and wish to be alerted to any attempt to create an intimidating or hostile environment. It is our collective responsibility to create a space that is inclusive and welcomes discussion.

Discrimination, harassment and hate speech will not be tolerated. If you have any questions, comments, or concerns, you may contact the UTM Equity and Diversity officer at [email protected]a or the University of Toronto Mississauga Students' Union Vice President Equity at [email protected].

Accommodations for Learning Needs

The University of Toronto Mississauga supports accommodations for students with diverse learning needs, which may be associated with mental health conditions, learning disabilities, autism spectrum, ADHD, mobility impairments, functional/fine motor impairments, concussion or head injury, blindness and low vision, chronic health conditions, addictions, deafness and hearing loss, communication disorders and/or temporary disabilities, such as fractures and severe sprains, or recovery from an operation.

If you have a learning need requiring an accommodation, we recommend that students register as soon as possible with Accessibility Services.

Phone: 905-569-4699

Email: [email protected]a

Accommodations for Religious Observances

Following the University's policies, reasonable accommodations will be made for students who observe religious holy days that coincide with the due date/time of an assignment, lab session, or lecture. Students must inform the instructor before the session/assignment date to arrange accommodations.

Mental Health

As a university student, you may experience a range of health and/or mental health challenges that could result in significant barriers to achieving your personal and academic goals. Please note, the University of Toronto (St. George and Mississauga campuses) offer a wide range of free and confidential services that could assist you during these times.

As a CPS student, you have an Academic Advisor who can support you by advising on personal matters that impact your academics. Other resources include:

Accessibility Services

Health & Wellness (St.  George) Health & Counselling Centre (UTM) My Student Support Program (MySSP) Good2Talk Student Helpline

Navi

If you find yourself feeling distressed and in need of more immediate support resources, consider reaching out to the counsellors at My Student Support Program (MySSP) or visiting the Feeling Distressed webpage.

Acknowledgement of Traditional Lands

We wish to acknowledge this land on which the University of Toronto operates. For thousands of years it has been the traditional land of the Huron-Wendat, the Seneca, and the Mississaugas of the Credit. Today, this meeting place is still the home to many Indigenous people from across Turtle Island and we are grateful to have the opportunity to work on this land.

Other Information

Attendance and Participation

Attendance and participation in lectures and practicals is very important to your success in this course. Lectures will include many practical examples and students will be encouraged to work together on writing and debugging programs. Programming is learned through practice, and this course will offer many opportunities for you to develop your coding skills. Accordingly, attendance and participation will count for 5% of your final grade.