COURSE SYLLABUS
GEOL 4470/5470 – Intro GeoModeling
Semester 2022 Spring
Instructor Information:
Instructor: Neil Humphrey
Phone: 307 314 2332
E-mail: neil@uwyo.edu
Office(s):
rm 320 GEOL (old building) , rm 2042(lab, newbuilding)
Office Hours: T 3-4:30 W 3:00-4
(appointment needed)
Course Information:
Meeting times 1:20-2:35 Tu+Tr,
meeting rm 1006. I am hoping to remain
Face-to-Face, but if Covid gets bad, we may have to go online. In addition, although the class official time
ends at 2:35, I will remain in the computer lab to help students until about
3pm. This extra 20mins or so is a
valuable addition to help students with the homework projects.
Course runs from Jan 18, 2020 - May 08, 2020
The course URL is: http://geofaculty.uwyo.edu/neil/teaching/Numerical_web/default.htm
Homework, notes and supplemental material will be posted to the above site and you will need to reference it regularly.
Prerequisites:
At least one semester of college level calculus and of college level physics are required. A few geology/geophysics courses will greatly help the student appreciate the course and master the material. Any student lacking the above will need permission of the instructor.
Course Description:
Introductory course in numerical modeling in the geosciences, offering coding experience as well as insight into the generalities of modeling. We develop, in class, simple geo-models, which allow experience constructing and testing computer models. As a minimum we will develop one extensive Finite Difference model; other techniques will depend on student interests. The course will use the PYTHON language (which will be taught at the minimal level needed for this course). This is a lab course with lectures, much of the time you will be working on problems, helping each other and I will be trying to help also.
Disability Statement:
If you have a physical, learning, sensory or psychological disability and require accommodations, please let me know as soon as possible. You will need to register with, and provide documentation of your disability to University Disability Support Services (UDSS) in SEO, room 330 Knight Hall.
Objectives/Outcomes/Standards:
The aim of this course is to equip students with both the technical and philosophical basis to judge the plethora of models in our discipline. It is also an introduction to some of the standard modeling techniques used to approach geo-science problems. We will study modeling at both a practical level and at a meta-level. There are universalities to all modeling, and indeed, much of modeling turns out to border on the philosophical, and involves such questions as “should we model” or “can we ever prove or validate our work”. This second aim of the course will be specifically designed to help you judge talks and papers that use models that you don’t really know or understand.
A third objective of this course is to help demystify the process of modeling, and help the students get over the common feeling that modeling is only for the most mathematically or physically prepared students. We will demonstrate that most modelling only requires clear thinking and relatively simple mathematical techniques.
The 3 main outcomes will be:
1. diffuse modeling anxiety in students
2. improve the ability of students to judge the models and modeling that they encounter in their work.
3. develop the skills needed to set up simple models. This includes learning how to abstract real world problems into a computationally manageable form and learning the techniques to solve the model.
Since this is a graduate or senior level course, with the stated intent of diffusing modeling anxiety and improving student ability, there is not a standard to which all students will be compared. Success in the course will be judged on participation and individual improvement during the course (see grading standards below).
Text(s) and Readings:
Recommended texts: (these will be on reserve in the Geology Library)
For python and numpy:
Python for scientists, J. Stewart, Cambridge.
Learning scientific programming with Python, C Hall, Cambridge
Python and matplotlib essentials for scientists and engineers, M Wood, IOP ebooks (cheap)
For course theory:
Intro to Numerical Geodynamic Modeling, T. Gerya, Cambridge
Mathematical Modeling of Earth’s
Dynamical Systems, Slingerland and Kump, Princeton
Geodynamics, Turcotte and Schubert (I have an older edition in PDF if anybody wants)
Course Requirements/Assignments:
The course revolves around modeling exercises. Most of these will be computer based. The preferred language is Python, which is supplied on the computers in the GEOL computer lab, and free to download. We will be using the free ANACONDA distribution of Python3, although you are free to use other languages. The course will include a tutorial in Python sufficient to allow students that have had little exposure with coding to use the language to do the homework. You will be expected to work on these exercises out of class time and you will need to budget several hours per week working on these assignments. The assignments will be marked and graded by myself, during class time. During each class I visit you while you are working both to observe your homework, and to help you on your current assignment. The purpose of my ‘grading’ your work is mainly to give feedback to help the student. Assigned grades will depend more on a reasonable attempt at the assignments, than on achieving the correct result. The assignments will be discussed in class to allow students to learn from theirs and others mistakes. Active participation in these discussions is a required part of the course work. Most of the exercises will be started during class time, to allow feedback and help. In and out of class collaboration is encouraged.
Grading Standards:
This course is graded on an ABCF (no fractions) scale. However, since one of the principles of this course is the diffusion of modeling anxiety, a main principle of the grading is that the attempt to complete an assignment receives the bulk of the marks, only minimal extra points are awarded for the correct results. This course will NOT have exams. Grades will be assigned by the following grading rubric.
[Note, grades B and below are similar for both seniors and graduates (however, note that a grade below B is essentially a failing grade for a graduate student), the main difference is the grade of ‘A’: an undergraduate can receive an ‘A’ on effort, while an ‘A’ can only be obtained by graduate students by correct completion of the exercises.]
Grading Rubric: a grade of B will be assigned if:
1- the student attends all lectures, unless an absence is approved by the instructor: (1 unapproved absence for grad students or 2 for undergraduates will result in a one grade reduction)
2- the student participates in class discussions: students need to understand the exercises sufficiently to join class discussions, even if they have not been able fully complete the assignments. Consistent lack of contribution to class discussions will lead to a grade reduction.
3- the student attempts all the computer/modeling exercises that we develop during the course, although it is recognized that the level of success will vary widely. Lack of a meaningful attempt at the assignments will result in a grade reduction.
Note, absences or failure to participate in discussions, and/or failure to attempt the exercises will lower the grade. A grade of A will only be assigned if the student completes the above, and (if an undergraduate) either shows significant improvement throughout the course, or (if a graduate student) if the student completes the bulk of the exercises correctly. As you can see, the grading is somewhat subjective. If you disagree strongly with this subjectivity, you can discontinue the class.
Attendance/Participation Policy:
University sponsored absences are cleared through the Office of Student Life. Note that absences also need to be cleared with the instructor (see grading policy)
Course Outline:
This course is somewhat freeform and will be determined by student interest. However, we will start with a heat flow problem, since it will introduce many of the basic concepts, including Finite Difference approaches. Subsequent topics will be determined by student input, however I would like to leave time at the end to develop a very simple Finite Element model to demonstrate this powerful technique.
Possible topics: (we will start with heat flow, but everything after #1 is open for student input)
1. Heat flow, the cooling of magmas, the warming of permafrost etc. Introduction to explicit and implicit finite difference models. Introduction of 1D, 2D, spatially heterogeneous, and transient models.
2. Slow viscous flow, a simple multi-variate model of simulated magma flow.
3. One or more of :
Cellular automaton model of fluid flow or of landscape evolution.
Chaos model of a highly non-linear system, such as a slider block model of earthquake recurrence
Monte Carlo techniques of error propagation in non-linear analytic or numerical models
Bayesian Stats Model of a simple geo-problem, mainly to illustrate the Bayesian updating approach.
4. We will look at a very simple 2D finite element problem to introduce the technique.
(We can substitute topic 3 with a topic that the class is interested in pursuing, such as linear geo-chem systems, "pretty picture" and GIS models, geometric, and other areas of student interest)
The instructor may make changes
to the syllabus as the course proceeds. If necessary, these changes will
be announced in class. Substantive changes made to the syllabus shall be
communicated in writing to the students.
Classroom Behavior Policy:
At all times, treat your presence in the classroom and your enrollment in
this course as you would a job. Act professionally,
arrive on time, pay attention, complete your work in a timely and professional
manner, and treat all deadlines seriously.
You will be respectful towards you classmates and instructor. Spirited debate and disagreement are to be
expected in any classroom and all views will be heard fully, but at all times
we will behave civilly and with respect towards one another. Personal attacks,
offensive language, name-calling, and dismissive gestures are not warranted in
a learning atmosphere. As the instructors,
we have the right to dismiss you from the classroom, study sessions, electronic
forums, and other areas where disruptive behavior occurs.
Electronic devices such as mobile phones should be set to silent or turned off. Laptops are, allowed for note-taking purposes. No video or audio recording during class is allowed to protect the privacy of your fellow students.
Classroom Statement on Diversity:
Statement on Diversity: UW Regulation 2-117 contains the following statement: “The University of Wyoming values an educational environment that is diverse, equitable, and inclusive. The diversity that students and faculty bring to class, including age, country of origin, culture, disability, economic class, ethnicity, gender identity, immigration status, linguistic, political affiliation, race, religion, sexual orientation, veteran status, worldview, and other social and cultural diversity is valued, respected, and considered a resource for learning.” This course embraces this statement, both in the way we expect students and instructors to interact and in the material that is covered in the readings, labs, and lectures.
In this class, you have the right to determine your own identity. You have the right to be called by whatever name you wish and to have that name pronounced correctly. You have the right to be referred to by whatever pronouns you wish. You have the right to adjust any of these things at any point in your education. If you find that there are aspects of course instruction, subject matter, or class environment that result in barriers to your inclusion, please contact the instructor privately without fear of reprisal.
Disability Support:
The University of Wyoming is committed to
providing equitable access to learning opportunities for all students. If you have
a disability, including but not limited to physical, learning, sensory or
psychological disabilities, and would like to request accommodations in this course
due to your disability, please register with
and provide documentation of your disability as soon as
possible to Disability Support Services (DSS), Room 128 Knight Hall. You may
also contact DSS at (307) 766-3073 or udss@uwyo.edu. It is in the student’s best interest to
request accommodations within the first week of classes, understanding that
accommodations are not retroactive. Visit the DSS website for more information at: www.uwyo.edu/udss”
Academic Dishonesty
Academic dishonesty will not be tolerated in this
class. Cases of academic dishonesty will be treated
in accordance with UW Regulation 2-114.
The penalties for academic dishonesty can include, at my discretion, an
“F” on an exam, an “F” on the class component exercise, and/or an “F” in the
entire course. Academic dishonesty means
anything that represents someone else’s ideas as your own without
attribution. It is intellectual
theft – stealing - and includes (but is not limited to) unapproved assistance
on examinations, plagiarism (use of any amount of another person’s writings,
blog posts, publications, and other materials without attributing that material
to that person with citations), or fabrication of referenced information. Facilitation of another person’s academic
dishonesty is also considered academic dishonesty and will be treated
identically.
In
other words, no cheating! It will be
hard to carry out in this class, but is an important aspect of scientific
ethics. In this class you will have to quote or otherwise use considerable
material from various other sources. To
avoid ‘academic dishonesty’ in this context, you will have to be careful to clearly
distinguish between ideas that you have obtained from other sources, and ideas
that you have generated yourself. In the
course of class discussions, this will be a challenge that will be part of your
responsibility in passing the course.
Please note we expect you to use lots of outside sources and opinions,
and that is fine as long as you do not say or even imply they are your own and
not somebody else’s ideas.
Duty
to Report:
UW faculty are committed to supporting students and upholding the University’s non-discrimination policy. Under Title IX, discrimination based upon sex and gender is prohibited. If you experience an incident of sex- or gender-based discrimination, we encourage you to report it. While you may talk to a faculty member, understand that as a "Responsible Employee" of the University, the faculty member MUST report information you share about the incident to the university’s Title IX Coordinator (you may choose whether you or anyone involved is identified by name). If you would like to speak with someone who may be able to afford you privacy or confidentiality, there are people who can meet with you. Faculty can help direct you or you may find info about UW policy and resources at http://www.uwyo.edu/reportit
You do not have to go through the experience alone. Assistance and resources are available, and you are not required to make a formal complaint or participate in an investigation to access them.
Student Resources:
CAMPUS RESOURCES
DISABILITY SUPPORT SERVICES: udss@uwyo.edu, 766-3073, 128 Knight Hall, www.uwyo.edu/udss
COUNSELING CENTER: uccstaff@uwyo.edu, 766-2187, 766-8989 (After hours), 341
Knight Hall, www.uwyo.edu/ucc
ACADEMIC AFFAIRS: 766-4286, 312 Old Main, www.uwyo.edu/acadaffairs
DEAN OF STUDENTS OFFICE: dos@uwyo.edu, 766-3296, 128 Knight Hall, www.uwyo.edu/dos
UW POLICE DEPARTMENT: uwpd@uwyo.edu, 766-5179, 1426 E Flint St, www.uwyo.edu/uwpd
STUDENT CODE OF CONDUCT WEBSITE: www.uwyo.edu/dos/conduct
Out of class support opportunities:
New Studying Resource: CircleIn
UW has made CircleIn, a virtual studying
app/website, available to you and your classmates. You can easily hop on a
video call with classmates, create study groups, and share helpful content.
Earn points and rewards, just for helping and collaborating with your
classmates.
To get started on your computer, phone, or other device, Download the App or visit the App’s
Desktop Version. Search University of Wyoming, enter your school
log-in credentials, and select “Authorize” to get started.
Want to learn more? Visit the Student Informational Website.