November 2019 Research Updates

November Calendar (October/December)
This is an ongoing post of research updates during the month. Updates are provided every few days, and you can easily reach the update by clicking the link in the calendar.
11/4/19 – Another Month

I’ve made a lot of progress in regards to grading of the midterm in Earth Rocks. I spent a good deal of time over the weekend to make sure I was finished today. I have another 8 to grade (maybe a few more after this), but the bulk of it is done. Today, I’m working on creating a code to visualize the results the 2D model is giving. I need to compare the results I am getting for different inputs as I finalize the conditions for HCN. I’m struggling because I don’t know how to use the result data file, .pkl. I think I will reach out to someone who knows Python because I fear there isn’t a simple solution.

I hope to finish this tomorrow if not today. I am in the meantime trying to run a few codes for the melt ponds at 10s of meters at a finer resolution to see if we can have slightly higher resolution for instances of drainage. Right now, I am running at 0.01 m starting depth and at 0.1 cm increments. It seems to be working for ppts at 100, 500, 750, and 1000 at 1 second time steps. That is very slow, but all I’m looking for is low depth results (~10m).

I got the email for my revisions today. They shouldn’t be too drastic, but I only have a month. I noticed when trying to resubmit a revised paper, the Cassini Special Issue is no longer an option. I can only assume that I am too late for that. I didn’t realize I’d be penalized for the review process taking the time it took. I suppose it doesn’t really matter in which edition it gets published, but it is disheartening nonetheless. It would have been nice to see my work in the final review of Cassini work.

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11/8/19 Stagnation

This has not been a great week. It’s so easy to keep pushing off discussing my progress until I feel like I have something substantial to say, but I don’t think that’s productive. I finished grading midterms, but that didn’t take all week. I helped Gavin and Carol with a couple things. Of course, that only took a few hours at best. I reviewed my feedback from the reviewers on my paper, and I spent a bit of time checking and changing the planetary ice MATLAB code. I got some aid from Chase on how to use the results the 2D heat transfer model, but I’ve yet to do anything with it. I can talk about little things I did, but the crux of it is I could have done better.

It was a week of distractions and procrastination. My goal is to shame myself into avoiding letting this happen again by talking about it here. I will say, I’ve gotten better at staying off Facebook. That was a serious problem for a while, but I’ve made a point to simply avoid the most distracting (online games) aspects while working by avoiding it outside of work too. That doesn’t mean there aren’t other distractions too. One thing I’ll try doing moving forward with this blog is start by setting up goals before each day to help me focus.

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11/11/19 – Reviewing Python and Beginning Edits

Goals: Begin reviewing the notes Chase sent me. I need to read through it and set up a template file or framework of troubleshooting. I don’t have to get it working, but I need to at least have something that should be outputting/visualizing results. Lastly, I will spend 2 hours working on my manuscript edits.

Results: Success! Or at least partial success. I still have to create a code to plot the results, but I figured out how to load and save the ‘.pkl’ results as a ‘.mat’ file. Chase provided me with a fantastic walk through of how to deal with the results. I haven’t gone through the entire example he provided; it loads and plots the results in Python. Once I figured out how to load the data, I was able to Google how to convert it a ‘.mat’ file.

Note for self: this is saved as a python code called ‘’

I was mistaken when I read that the paper was due in early December. I think that was when they wanted me to decide on if I wanted to resubmit it. It is due January 3rd now, but I still want to try and deal with it sooner rather than later. I started the edits. My “2-hour” window was a good motivator, but I did get distracted there a few times. Overall, I still think it was a successful approach. I’ve begun by addressing individual comments based on those that seem easiest to address. These are minor changes, and even those that are more significant have room for some pushback.

One said change is a request for a traditional crater size-frequency distribution. I don’t hate the idea of this, but I dread the amount of work it will take because I need to learn how these are formed. I’ve attached an example here. I assume the cumulative frequency is the crater count and the area then is either the area of a crater of that size, the total area covered given the number of craters that size, or the area of the region (planet) being studied.

Other then the work I had planned, I met with the Space Grad Council.

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11/12/19 – Producing plots

Goals: With the data uploaded to MATLAB, the next step with dealing with the 2D heat transfer model results will be using the data in MATLAB. My goal is to finish reviewing the example Chase has provided me with; I expect it to be a fairly quick process since I’ll be doing in MATLAB. This should be done at the latest by the end of Wednesday. On Tuesday and Thursday, I will spend at least 2 hours working on the proposal (each day). I will spend at least 2 hours (total) editing the manuscript over the next two days. I’ve also got lab and will spend a bit of time preparing for that.

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11/13/19 Plots made and limited writing

Results: I figured out how to export the results into a MATLAB compatible ‘.mat’ file, and I easily made a few graphs from it. That leads me to the final step of finalizing the chemistry parameters for Titan now that I have the size and Temperatures working and the results plotted (I’ll work on sharing an example here). Unfortunately, writing was not so successful. I spent a maybe half an hour working on my proposal, not enough, and I didn’t get around to working on the edits. Granted, I had lab Tuesday afternoon and again Wednesday afternoon, but I could have done better.

With lab, I have to change focus to grading for a few days. That’s the goal until its finished. I feel confident I can finish these by Tuesday.

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11/18/19 Grading progress

Goals: My goal is to be done with these by Tuesday. I need to load the Wednesday labs (or some of them) and grade my part of the three Thursday sections. I also realized I still need to catch up on some of the TEPs seminar’s I’ve missed. My goal is to watch them (there are only a few I think) while I grade because it the labs are easy enough to grade without requiring too much thought.

Result: Grading has gone well! I have loaded all the Wednesday sections (that I have), and I’ve graded 2 out of the three Thursday sections. The 3rd one is the smallest of the three, so I feel confident that I will get through it tomorrow (probably with time to spare).

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11/20/19 Grading complete, python needs finishing!

Results: I finished all the grading on Tuesday as I hoped I would. I did not get the TEPS videos yet. I really just need to have the play while I work. It will be the quickest way possible. I didn’t set any hard goals for myself today. However, I spent time working with the 2D code to figure out the final inputs to make. I need a clear plan moving forward.

Goal: I don’t have a hard goal set for the TEP; it still isn’t a priority. I’m at the point where I need to 1) input the 1D concentration model results into the 2D model. This means use the data I have and fit it to the concentration fit curves that Jacob et al. 2018 outlined. Then 2) figure out how to adjust the lens shape to be a cylinder. I need 1) done by the end of the day Friday, and I want to contact Chase about 2) tomorrow; that shouldn’t be a massive change.

This is important because I want to have a 2D model result in my proposal and for my December 5th meeting (at 2PM) with my committee. Which, I don’t know if I mentioned I finalized that meeting as well. Of course, I don’t want to leave my proposal writing unattended, but rather than set a time limit, I’m going to make it a content one. I need each section outlined to have a rough outline of the content I will discuss there beyond the titles I have created, including tables and figures where applicable. Again, this is by the EOB on Friday. This is a clear goal that can be met regardless of if I get distracted.

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11/22/19 Fitting data

Results: I’ve condensed all of my concentration data into a file, but I still need to trim the anomalous data and fit it to the curve. This goal was a disaster and a major let down. I did not make progress on the proposal. I got distracted by having to collect and organize the Astrobiology documents for the new Astro professor. At least that is pretty much done. Then Thursday, I lost a big chunk of time helping someone with a MATLAB problem.

Goals: I am adjusting these goals. I will have these fits finished by EOB on Tuesday. Wednesday, I will try and produce results using these fits. Thursday and Friday will be proposal writing. I am also going to find times to watch these seminars. I need to think about the Manuscript as well. I will reassess my progress on Tuesday and decide where to go from there.

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11/27/19 Fitting taking time

Results: It is taking a lot more time than I would like to fit this data. I have the fit ready, but the filtering takes time. I wasn’t prepared for it (with a code ready). If you recall, the model is freezing 100s of meters of water into ice, and it is doing it on a centimeter scale. This takes a lot of time. To speed it up, I run the model at 10 m segments throughout the water depth. The trick is, it takes time for the model to “calibrate”. Essentially, we can see the concentration changing drastically as it levels into the actual concentration. At deeper depths, where the thermal gradient barely changes, this equates to a sharp increase then a leveling off that we would expect at these low depths.

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11/28/19 Finalizing the fit and expense report

I finished the fit, but now I am faced with a new problem. The fits don’t fit my data appropriately. These fits are the constitutive equation Buffo et al (2019) uses to show the model output is following what we would expect. We are getting higher concentrations than expected, but I think a big part of this is needing more data. The higher concentrations have been difficult to run, and I now recognize where the gaps need to be filled. I am working on running those, but in the mean time, I going to use the data I have to run the code to run the 2D heat transfer model. This process of trimming the data was tedious, but the code is now there to do use with ease in the future.

In other news, I successfully watched all the TEPS seminars I missed, and emailed them to confirm I had done it. Then I spent a big chunk of time finalizing my expense report for the cash advance I got over the summer. I don’t know why, but these reports are some of the most stressful things about grad school. I’m not usually a very anxious person, but this is an area where it happens. The result, I procrastinate it as long as possible. Even now, there are tedious forms and revisions needed; these are the very things I dreaded.

Goals: My committee meeting is fast approaching. I am going to begin working on my presentation for that and use my proposal as a framework to go by (and vice versa). I need to finish the expense report updates and go to research forum. Then I will focus on the python code. I need a result. That means plug in these model parameters, and then change the shape of the lens. The shape may be postponed if it proves too difficult. I have to look at my manuscript revisions next week too; I can’t keep pushing that off. I think I will try and fit work in Saturday or Sunday, but I have a lot to do at home which may prevent me. We’re in the endgame now.

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11/29/19 Updating 2D heat transfer model and fixing expense report

Results: I mad a few updates to the expense report, and it should be good to go now. I logged in the concentration data (as it stands) into Python. These are just constants that are found in the constitutive equations Buffo et al. (2019) discusses) because our results should be following those very equations. As I said, they aren’t, at least not entirely.

Some equations fit for some of the concentrations, and like I said, I am working on getting more data where necessary to improve these results. The other constants needing to be changed are those used to define the eutectic (melting temperature of water by HCN concentration). The model assumed a 2nd order polynomial would work, but I upped it to 9th order for a more precise fit. Here is a figure showing those results; I won’t (and haven’t) posted many figures of these results because it isn’t my code. Therefore, I am trying to limit the amount of results I show.

Then, I realized the shape was already defined as an option in the code (thanks Chase!). I’m letting it run for a 80 km crater over 200 m depth, but with a grid size of 10 m along the depth and 100 m along the radius of the crater. I want to shrink these values, but I need to run the code on a faster computer to do that. I’m happy with this progress, even if it took longer than I’d have liked. Until Monday, I may just let it go, let it go, and watch Frozen.

Return to Calendar. Go to December.

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