WaterUnderground

Teaching & Supervision

Research mini-conference in fourth year groundwater class

Research mini-conference in fourth year groundwater class

Fourth year and graduate students led a fun mini-conference during class in Groundwater Hydrology (CIVE 445, Civil Engineering at University of Victoria) yesterday. Local consulting and government hydrogeologists joined, making the students both nervous and excited to be presenting to professionals with up to forty years of groundwater experience. The presentations were the culmination of a term-long independent group research project – they also write a research paper (which is peer-reviewed by their classmates). And the mini-conference culminated in beers at the grad club, unfortunately drinking beer brewed with surface water.

It seemed like a win-win-win for everyone. The students loved meeting and presenting to, and being grilled by, the people who had mapped the aquifer they were modeling or asked if their model is based on any real data. The practitioners loved seeing the new ideas and enthusiasm of the students. And I loved seeing the interaction and learning.

For any prof reading this, here is a description of the Group Research Project and the conference poster:

 

 

 

 

 

What is a hydrogeologist?

What is a hydrogeologist?

Hydrogeologists are a diverse group, in part because we come to this discipline from so many different paths.  We come from different academic programs in engineering, geological sciences and environmental sciences.  These differences in backgrounds create a diversity of perspectives, which enriches hydrogeology and allows for dynamic collaborations.  Engineers and geophysicists are known for bringing quantitative skills to hydrogeology, while geologists shine in problems involving stratigraphy, structural geology and embrace uncertainty.  Geochemists and environmental scientists are often stronger in contaminant hydrogeology.  However, each of these backgrounds also have their deficiencies.  This is underscored by looking at programs in civil engineering and geology, which are two of the most common undergraduate degrees among hydrogeologists. Aside from foundational math and science courses the first years of these programs, they usually only share an elective course in hydrogeology.  A review of hydrogeology courses covered by Gleeson et al. (2012)  showed that aside from a few topics, these courses vary substantially in their content.

 

Hydrogeologists are often found crossing streams wearing ghost-buster backpacks (or so it seems from here)

This is further complicated by how professionals are licensed in many jurisdictions, which is often based on these academic programs rather than whether someone has the capacity to practice hydrogeology.  Engineers are required to have engineering fundamentals in areas such as statics, dynamics, and engineering design, along with competency is areas such as structural and transportation engineering for civil engineering. Geologists receive professional registration based on core competencies in subjects such as mineralogy, sedimentology, paleontology and structural geology.  Registration for fields more closely aligned with hydrogeology, such as environmental geoscience and geological engineering may consider hydrogeology as a core requirement.  In general, this means that somebody registered as a professional engineer or geoscientist might be a hydrogeologist but they also may have very little knowledge of hydrogeology.  Environmental scientists and similar fields might be better prepared to practice hydrogeology in some instances but professional registration is not as common.

Maybe this involves graduate school?  Many practicing hydrogeologists have advanced degrees.  These programs are often designed to give a broad base in hydrogeology and typically deliver material in:

  • physical hydrogeology
  • chemical/contaminant hydrogeology
  • geochemistry
  • numerical modeling
  • field techniques

Additional material on porous media, geotechnical engineering and hydrology are frequently also covered.  Anyone with a background in these areas is probably a hydrogeologist.  However, there are still some grey areas.  Can someone who doesn’t understand numerical models be a hydrogeologist? What about someone who has never done field work?  Where to draw the line is unclear and may differ substantially based on who is asking the question.  However, if the goal is to promote competent practitioners and researchers in hydrogeology, the traditional paths through engineering and geoscience may be less than ideal.  The requirement of knowledge outside hydrogeology at the expense of core knowledge may be holding us back. On the other hand, a great number of us did not enter university with the goal of becoming a hydrogeologist and maybe we need these more traditional programs as gateways.

What most hydrogeologists working really looks like (from here)

Water Underground has a new home on the EGU Network Blogs

Water Underground has a new home on the EGU Network Blogs

The newest addition to the Network Blogs is a groundwater nerd blog written by a global collective of hydrogeologic researchers for water resource professionals, academics and anyone interested in groundwater, research, teaching and supervision.

Water Underground was started, and is currently led, by Tom Gleeson. It is the first blog to be jointly hosted by the EGU Blogs and the AGU blogosphere.

Why not take a look at some the past posts to get a feel for what is to come on the new EGU/AGU blog? You can read about what stalagmites can teach us about past and present climate and what scientists mean by crustal permeability. The advances in groundwater research also feature on the blog. Posts on supervision and teaching will be of interest to Earth scientists at all stages of their career too.

Posts in the blog are contributed by a collective of hydrology experts and reviewed by one of the frequent contributors to help improve style and clarity. Tom, and the contributing authors, want to foster a lively community via the blog, so discussion as well as comments on posts is encouraged. Not only that, if you have something to share, be sure to contact the editorial team as submissions are always welcome! Simply drop them a line at: waterundergroundblog@gmail.com

Here at EGU we are thrilled to have Water Underground join our diverse community of geoscience bloggers. Please join us in welcoming Water Underground to the Network Blogs!

By Laura Roberts,  EGU Communications  Officer

FloPy: A Python interface for MODFLOW that kicks tail!

FloPy: A Python interface for MODFLOW that kicks tail!

Authored by: Kevin Befus – Assistant professor, Department of Civil and Architectural Engineering at the University of Wyoming


Groundwater modeling is getting better. Models are becoming more sophisticated with simpler interfaces to add, extract, and process the data. So, at first appearances, the U.S. Geological Survey’s (USGS) recent release of a Python module named FloPy for preparing, running, and managing MODFLOW groundwater models seems to be a step backwards.

Oh, but it isn’t.

KB1

First, a couple disclaimers. Yes, at the time of writing this I work for the USGS and use this new Python module for my research. Did I have to use FloPy? No. Am I glad I did? YES! Before using FloPy, I dabbled in the various non-commercial MODFLOW interfaces but got bogged down on how many drop down menus, pop-up menus, wizards, and separate plotting programs with their own menus were needed to make a meaningful groundwater model on top of a new lexicon of variable names (IUPWCB must mean “internally unknown parameter with concentrated bacon”, right?).

FloPy made its official debut in February 2016 with a Groundwater methods report 1. Bakker et al. do an excellent job telling us why we should use FloPy. I’ll leave that to you and tell you what I think.

Here’s what is great about FloPy:

  1. FloPy is 100% MODFLOW. No tweaks to anything. You choose the executable file you want it to use or compile it yourself, and you’re off!
  2. You have the near-infinite data management, manipulation, and plotting capabilities of Python at your fingertips. Python has a lot of packages. It can be overwhelming. You can rely commercial packages like ESRI’s arcpy if you want, but there’s a list of free libraries that give you even more freedom to get the input data just right. Since I mentioned freedom, here’s the list of free libraries I find useful but it is in no way an endorsement nor exhaustive: scipy, numpy, gdal, osgeo, fiona, shapely, cartopy, pyshp, pandas, matplotlib, and let’s not forget…flopy!
  3. It’s easy to duplicate and alter an existing model. Once you have your script perfect for running a particular groundwater model, you can take pieces of it to make a slightly altered version, or you can pop it in a loop that runs through your uncertain inputs for sensitivity testing. Change your grid with the flip of a variable, and make sure that mesh converges!
  4. Loading other MODFLOW models works great. Say you want to run someone else’s model with slightly different recharge, but their recharge is variable in space. Since FloPy incorporates numpy’s grid/matrix handling capabilities, you can change individual entries with row-column selections or change the whole recharge grid by multiplying it by either a single number or say a random matrix with a normal distribution and some added noise. If you just want to use their recharge data to run your own model, you can save the position coordinates (they have hopefully provided you with their coordinate system and model transformations) and recharge arrays to your very favorite format (csv, nc, mat, tif) and load it later as a matrix to add to your model, all in a single Python script.
  5. Building off of the ability to load or create MODFLOW models, FloPy has functions for plotting 2D map or cross-section views of the model discretization, boundary conditions, and results. Shapefiles can be included in these plots if they are in the same coordinate system as the model or extracted from the model (ever want a polygon feature of every model cell with attributes for every property of that cell?). I do my own shapefile manipulations in Python, but FloPy has some great plotting tools built in.
  6. You already have the data in Python. See what adding a low permeability layer does to spring discharge. Then, with the model made, you have to make sense of it. Maybe develop some interesting spatial or time series analyses. Enter Python. Plotting with matplotlib also makes beautiful, journal article-worthy figures…with enough sweat and tears from your end (not as many as you may think). Yes, this is a repeat of 2), but, seriously, it’s in PYTHON!
  7. FloPy is totally free. Python is free. Tons of science-oriented libraries in Python are free.

KB2.JPG

Here’s a flashy example.  It is straightforward and only takes one script to create a SEAWAT model from scratch and plot the 2D steady state salinity distribution and flow vectors for a simple Henry 2 problem based on a slightly edited FloPy example script.  There are more than a dozen example scripts available on the FloPy site as well as a very cool capture ratio script provided in the methods report 1.

For the groundwater educators out there, a FloPy groundwater model script can be paired with homework questions that get students testing how changing hydraulic conductivity in certain parts of the model changes the water table configuration. Or maybe a new well needs to be drilled on a plot of land near a spring… The scenarios are endless. Students can develop a fundamental understanding of groundwater flow while getting experience with both groundwater modeling and computer programming. Win, win, and win.

Essentially all of the standard MODFLOW packages are operational in FloPy, and there are varying levels of support for some of the specialized MODFLOW compilations and processing tools (e.g., MODFLOW-USG, MODFLOW-NWT, MT3DMS, SEAWAT, PEST, and MODPATH). PEST and MODPATH are currently not executable with FloPy, but these features will probably be added in a future release (I have made my own klugy modules for running ZoneBudget and MODPATH that interface reasonably well with the rest of FloPy).

Get on your way and give FloPy a try today!


Links

The Python package is available online at https://github.com/modflowpy/flopy.

The documentation is available online at http://modflowpy.github.io/flopydoc/index.html.

The USGS FloPy page is http://water.usgs.gov/ogw/flopy/.


References

Bakker, M., V. Post, C. D. Langevin, J. D. Hughes, J. T. White, J. J. Starn, and M. N. Fienen (2016), Scripting MODFLOW Model Development Using Python and FloPy, Groundwater, doi:10.1111/gwat.12413.

Henry, H.R., 1964. Effects of dispersion on salt encroachment in coastal aquifers. In: Cooper, H.H. (Ed.), Sea Water in Coastal Aquifers: U.S. Geological Survey Water- Supply Paper 1613-C p. C71–C84.


About the author:

Kevin Befus is a groundwater hydrologist with geology and geophysics experience — examining geological, biological, and chemical processes, especially considering their connections to water across scales.

KB3

One hell of a great groundwater textbook now available free

One hell of a great groundwater textbook now available free

‘Groundwater’ the seminar text book from Freeze and Cheery (1979) is free in pdf now…just follow the links here. This text book is almost as old as I am and important parts of modern hydrogeology are rusty or non-existent (like hydroecology amongst other topics) but it is still lucidly written and useful.  I routinely send students to read chapters so I am happy that it is now available free.

Kudos to Pearson Publishing, Alan Freeze and John Cherry and Hydrogeologists without Borders! I look forward to Groundwater2.0 which is in the works!

 

 

The new and exciting face of waterunderground.org

The new and exciting face of waterunderground.org

by Tom Gleeson

I started waterunderground.org a few years ago as my personal groundwater nerd blog with the odd guest post written by others. Since I love working with others, I thought it would be more fun, and more interesting for readers, to expand the number of voices regularly posting. So here is the new face of the blog…

http://www.fragilestates.org/wp-content/uploads/2012/10/collective-action.jpg

a kind of weird image of collective action

What is the new blog all about?

Written by a global collective of hydrogeologic researchers for water resource professionals, academics and anyone interested in groundwater, research, teaching and supervision. We share the following aspirations:

  • approachable groundwater science at the interface of other earth and human systems
  • encourage sustainable use of groundwater that reduces poverty, social injustice and food security while maintaining the highest environmental standards
  • compassionate, effective supervision
  • innovative, effective teaching
  • transparency of scientific methods, assumptions and data

Check out more details and how to be part of the blog on about.

Frequent contributors include:

  • Andy Baker (University of New South Wales, Australia) – caves and karst (I actually visit the water underground!), climate and past climate
  • Kevin Befus (University of Wyoming, United States) – groundwater-surface interactions, coastal groundwater, groundwater age
  • Mark Cuthbert (University of Birmingham, United Kingdom) – groundwater recharge & discharge processes, paleo-hydrogeology, dryland hydro(geo)logy, climate-groundwater interactions
  • Matt Currell (RMIT University, Australia) – isotope hydrology; groundwater quality; transient responses in aquifer systems
  • Inge de Graaf (Colorado School of Mines, United States) – global groundwater withdrawal, flow and sustainability
  • Grant Ferguson (University of Saskatchewan, Canada) – groundwater & energy, regional groundwater flow, sustainability
  • Tom Gleeson (University of Victoria, Canada) – mega-scale groundwater systems and sustainability
  • Scott Jasechko (University of Calgary, Canada) – global isotope hydrology; groundwater, precipitation, evapotranspiration
  • Elco Luijendijk (University of Gottingen, Germany) – paleo-hydrogeology,deep groundwater flow,large scale groundwater systems
  • Sam Zipper (University of Wisconsin – Madison, United States) – ecohydrology, agriculture, urbanization, land use change

Making guidelines for graduate students

Making guidelines for graduate students

I strive for effective, compassionate supervision and I clarify my goals, approach and expectations in my guidelines for graduate students (available here, from McGill’s best practices in supervision). As I wrote, most students enter a relationship with a thesis advisor without a clear idea of what they can expect so I compiled this handout to give you some idea of what I expect of you as student and what you can expect of me as an advisor. So that this never happens, I hope:

supervision

My highest level priority is for both of us to communicate and set mutually-agreed-upon goals (LINK OTHER POST) and then both do our best to make those goals into reality. As one of my students, I plan to treat you as a junior colleague who is maturing into a professional engineer or scientist. This means that you can actively co-create opportunities to meet your goals, and also puts a large responsibility on your shoulders to live up to the expectations of performance that are required of a colleague.

I have found clarifying my goals, approach and expectations in my guidelines for graduate students have helped students and helped me be a more effective and compassionate supervisor.


Thank you to the awesome Cutting Edge Workshop for Early Career Geoscience Faculty where I learned about graduate student guidelines a few years ago. I emphatically encourage all young faculty to attend!

How to peer review: skill-building in a grad classes

How to peer review: skill-building in a grad classes

I teach how to peer-review in graduate class because I think it is a core skill for any professional.  I first demystify peer-reviewing and academic journals, and answer questions that all students have about these topics that they have heard about but rarely learn about using this:

peer review

Nicholos and Gordon EOS, 2011

I describe my personal experience as a manuscript submitter, reviewer and associate editor. And then I outline the structure and types of questions to ask during a peer review (both listed below), and challenge them with three, increasingly difficult steps to learn how to peer review:

  • first, peer review already published papers (which is surprisingly hard since it is already well edited but this is useful as practice and since it is impersonal).
  • Second, peer review an open access manuscript that is currently in review (i.e. HESSD  or other open access journal). These can be actually submitted to the journal or not.
  • Third, they peer-review eachother`s term papers before final submission of paper to me as part of the grade.

At each step myself or a TA gives them feedback and evaluates their peer reviews.

Good structure for a peer-review

  • Short summary (1-2 sentences) and general assessment of novelty/contribution. Give the author(s) a few compliments here….everyone likes to eat the good-bad-good sandwich rather than just the bad sandwich.
  • Discuss major concerns or suggestions for authors. Aim for positive criticism here.
  • Recommend course of action: reject, accept with major revisions or accept with minor revisions.
  • Document minor concerns with explicit page and line numbers.

Good questions to ponder:
Contributions and Audience:
What are the important contributions of this paper?
Does the paper make a significant, new contribution to this research area?
Who is the intended audience?

Technical soundness:
Are the methods fully described?
Is the mathematical/theoretical development (if any) complete and accurate?
Is the approach, experimental design, review or statistical analysis appropriate?

Organization and Style:
Is the paper a description of an experiment or concept or a synthesis of previous work?
Is the paper well written and organized?
What is the hypothesis, objectives or goals put forth?Are all the tables and figures necessary?
Can the paper be shortened?

Evaluation:
Are the interpretations of data and results justified?
What are the major conclusions? Are they significant? Are they interesting? What remains answered?

Your reactions:
Did you gain something from the paper (be specific)?
How does the paper relate to other topics discussed in class?Are such questions and/or methods relevant to your own research?

How I start good supervisory relationships with graduate students

How I start good supervisory relationships with graduate students

Many professors are confused about why a certain graduate student is happy or unhappy, under performing or performing well. I am far from a perfect supervisor, but I try to avoid this confusion by getting to know my graduate students on a relatively deep but professional level as quickly as possible, by doing the following in our first meeting:

  • sharing results of a personality test;
  • discussing our biggest goals, hopes and fears about their graduate work; and
  • planing a very short two-week research project.

Before the meeting, the student and I take a free online personality test and prepare to discuss goals, hopes, fears and a research project. Below I outline the how and why of each part of the first meeting… hopefully I will never be this professor:

phd012609s

1. Share results of a personality test

Sharing the results of a personality test is often the perfect ice breaker since it is talking about emotions, but not about a student’s personal life. I use the Myers-Briggs Type Indicator because it is what i am most familiar and comfortable with but other personality tests such as colour code or FourSight could also work.  Myers-Briggs is a physiological test that highlights how people perceive the world and make decisions; a free online version can be completed very quickly.

I usually start by describing my personality type (INTJ) and that there are 16 different personality types, emphasizing that no type is better or worse than any other for science or any other part of life.  Then I ask them if they are comfortable sharing their personality type and we discuss how the two types fit together. I find this very effectively focuses on how we can work best together and acknowledges that everyone is different.  And for students who are uncomfortable, each Myers-Brigg’s type is linked to a Harry Potter character which can be fun:

Harry Potter Myers Briggs

http://inthefrontseat.blogspot.ca/2013/09/harry-potter-myers-briggs-chart.html

2. Discuss our biggest goals, hopes and fears about their graduate work

The Myers-Briggs sharing often naturally leads to this important discussion where both the student and I share our biggest goals, hopes and fears for their graduate work. I usually start by sharing, and I am usually brutally honest. I usually have a goal of how their project fits into my broader research program, and sometimes specific hopes of how the student and I may grow, learn or interact. In some cases I have been really honest about my fears that I don’t know enough about the topic, I don’t have as much time to devote to supervising them as I would like, or the project may fail, etc. Most students find the honesty refreshing.

Then I ask the student to share and we end up writing down shared goals, hopes and fears so that they can be reviewed at later meetings. This becomes the template of what we hope we will both get out of their graduate work, so we return to these goals, hopes and fears a couple of times per year to check in and re-evaluate.

goals

www.runnersgoal.com

3. Plan a very short two-week research project

Finally, we decide on a mini research project which should actually be doable in two weeks, and is not just be a literature review. The topic can be related to their overall graduate project or not, and can come from the student, professor or both. It could involve analysis, modeling, field work etc. In two weeks time  a 1000-2000 word research paper is due.

This mini-project often accomplishes a lot:

  • focuses on the student on research rather than their new classes, new apartment, new city etc.
  • helps both of us figure out how to best work together (i.e. lots of meetings and guidance or not)
  • Builds the student’s confidence in starting something new in this new environment
  • helps me evaluate their research and writing skills so that we can better tailor their graduate project.

It is a pretty intense first meeting that takes preparation, emotional intelligence and usually two hours but I find the dividends are always well worth the effort.


Thanks to DISCCRS for teaching me the value of the Myers-Briggs test and Mark Jellinek for the short research project idea.

What busy profs would like to read in a blog post about active learning

What busy profs would like to read in a blog post about active learning

During a great workshop today on active learning in engineering at McGill I asked two questions (using Socrative) , of the audience. Here is a summary of 24 answers I received:

1) I would like to read blog posts about:

  • activities for large classes (18% of people)
  • activities for small classes (30% of people)
  • technology in active learning (22% of people)
  • wacky or creative ideas for active learning(30% of people)

2) I might read a blog post about teaching and supervision if…

  • It takes into account the sheer lack of time and resources for preparation; ie quick and easy ideas to engage a bored class!
  • it was linked through twitter
  • It was regularly updated and interesting!
  • It does not take too long
  • it helps me achieve better my teaching objectives compared to my current teaching practice
  • It related to economics / social science a bit
  • Its short and introduce tips and examples
  • It gives concrete practical examples of activities for teaching and making students more active
  • I was interested
  • I knew where to find it
  • It dealt with distance education
  • they talked about encouraging creativity and critical thinking
  • it was about new and creative strategies that I can use in my class
  • it included the occasional evidence-based pieces that demonstrate real impact
  • Give ideas about how to get the students more active
  • It’s concrete, thoughtful and provides ideas
  • it was relevant and to the topic. I also would like to see it promoted within the departments to encourage conversation about teaching and learning
  • It is useful

My summary is that people want to hear about all types of different aspects of active learning and they would be motivated to read posts if it interesting and provided something useful.

Thanks Michael Prince of Bucknell for the great workshop and Milwaukee Mag for the image.

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