Aloooooone

This is my second day without my graduate student. So far, this week is going pretty poorly.

I spent all of Friday and some of Monday analyzing my CaTiO3 results. When I moved on to BaTiO3 and SrTiO3 on Monday, several structures failed much in the same way my CaTiO3 structures were failing before. But I fixed that problem in calcium titanate. Shouldn't the solution be transferable to other compounds? There was no reason I could see that it shouldn't. Titanium is still the dominant cation in each compound. The Ti-O potential parameters should work. (I did try the Ba-O and Sr-O parameters just for kicks. They predictably failed.) It took me an entire day to figure out what the problem might be with my BaTiO3 calculations. Hours of poring over papers I don't understand (and still don't).

Once I had a theory as to why they might be failing, I tried to figure out how I would fix it. The material became highly technical very quickly. I do not have the knowledge or expertise to understand how to derive these potentials--that's the stuff that PhD theses are made of. So I decided to email my professor this morning to ask to meet with him. His response: "Oh, crap I never mentioned to you .... I left for 3 weeks. I won't be back until July 19."

He asked me about the problem, in case there was a grad student or postdoc he could point me to, and I summed it up for him. He said no one in town would know enough about interatomic potentials to help, but gave me the email for one of his former postdocs who is now an assistant professor at University of Texas, Austin.

Here is that email, with the subject, "Hello! I'm Prof. Fennie's REU student." I hope she responds.

Hi! So I think Craig cc'd you on my last email to him, but I started running into some problems the day after he left for a trip, and while my graduate student (Eva Smith) is at a conference for the week. 

My project is that I'm using GULP to optimize structures using buckingham potentials (and spring potentials, for the core-shell model) and comparing the optimized structures from this method to those calculated using DFT methods.

I've been using potentials from Lewis and Catlow (http://iopscience.iop.org/0022-3719/18/6/010) and started with CaTiO3. I originally had some problems with an error message reading "Largest core-shell distance exceeds cutoff of cuts" on the structures P4mm, Amm2, R3m, and Pnma. Once I found out that the spring potential and shell charge of the oxygen ion depend on the cation (from the paper above), I changed the O parameters to those corresponding with Ti instead of Ca and I no longer got that error message. 

Now, I'm trying to apply the same method to BaTiO3 and SrTiO3. I'm still using the O parameters corresponding to Ti, but now P4mm is failing (with the same original "Largest core-shell distance" error message) in STO, and P4mm and R3m are both failing in BTO. (They also fail when I use the O parameters corresponding to Ba.) 

I thought the Ti-O potential parameters would be transferable between compounds, but this is apparently not the case. My hypothesis is that I'm using these potentials incorrectly. They were originally calculated for binary oxides, and I'm using them for ternary oxides. But I don't have enough technical knowledge of the material (I just finished my second year of undergrad) to know if my hypothesis is correct, and if it is, how to derive the ternary potentials from the binary potentials. The literature on this is extremely vague and unclear, especially for an amateur like me. 

If you have the time, and if you have any insight into this situation, I would be incredibly grateful. With Eva, Brian Abett (my other guiding graduate student), AND Craig all gone, and none of the other students in the group familiar with interatomic potentials, I'm feeling a little lost and adrift.

I did a lot of research into the error message itself, but I truly think that it's a symptom of something else being in error. With CaTiO3, it was the potential parameters, which is what makes me think I've been using them incorrectly, possibly by not accounting for the fact that they're ternary oxides. Does this seem likely to you? Do you know anything about potentials in ternary oxides?
Thank you so much. I've heard your name many times; they miss you back here. :)

Best wishes,
Meredith Staub

I want to solve this problem. I want Eva and Craig to come back, and I can show them how I fit all the pieces back together, how hard I worked to use concepts I barely understand to fix a problem I could barely diagnose. I just don't have the technical knowledge to do it by myself. 

NYC and Waterfalls

I had an incredibly busy weekend! I spent 18 hours on Saturday on a trip to New York City, a place I had never been to before. Then on Sunday, we took a trip to a local swimming area in one of the gorge creeks, featuring a gorgeous waterfall!

The weekend's story will be told in pictures.

Oh Deer!

If you think I'm unoriginal....well, you're right. Anyway, look how close the deer is!

I've been having some very frustrating days, and some very rewarding days. It's giving me a very good idea of what grad school is like. In fact, one of the graduate students in my group (a guy I had never talked to) walked into the office today. (He happened to be the same grad student who had let me into the office this morning after finding out I was key-less and the first one to arrive.) He sat down and asked how my research was going, and we talked a little bit about physics, research, physics research, graduate school, and Cape Cod (where he is going next week, and where I will not be going this summer, to my despair). I said that my research was tedious, but that I was learning a lot. He said all research was drudge work to a certain extent. It's just more laborious and repetitive when you're younger and becomes a little more creative when you're older: but you're always doing more work than your professor.

That sounded like an embittered-grad-student thing to say, but he said he loved graduate school, and that I was basically getting a taste for it now. Come in at 10am, leave whenever you like. He said he hoped I wasn't locking myself into 9-5. I said it was more like 10-5:30ish. He nodded in approval, admired Illinois as my choice for undergrad, and said that Cornell would be a good choice for graduate school.

I'm definitely considering it. The atmosphere seems really friendly, very supportive, and the research environment here is thriving. The town is gorgeous (aside from being a little middle-of-nowhere), there's so much natural beauty, and the campus isn't too small. I really like it here. My calves are getting used to the constant hills.

I Made A Thing

Instead of downloading Matlab for oodles of dollars, we decided to try Octave as a computational program. It's one of those free open-source alternatives. It operates right in my terminal (which is interesting), and the exciting part that I wanted to share was that I wrote a script for it and it works and I feel so cool. The script is simple. It's literally three lines. It formats a bunch of numbers I plug in into a matrix (so I don't have to worry about semicolons), puts the eigenvectors and eigenvalues of that matrix into two other matrices (by a built-in function), and returns just the diagonal matrix of eigenvalues.

It's way easier than that sounds. It's seriously extremely simple. But I did it and I'm so proud. I want another excuse to write a script. Just so I can feel cool and programmer-like. Especially since I'm limited in my problem-shooting with this other program by my programming abilities. I'm not sure how to make the program able to find this library of values. I'm sure it has something to do with paths, but I really don't know anything more than that and my ignorance is burning my brain.

Yesterday I saw a thesis defense by one of the students of my professor. I saw him in the kitchen earlier that day, and asked (by way of making conversation), "So are you going to the thesis defense later?"

He looked at me kinda funny and said with an awkward chuckle, "Yeah, yeah....they uh, they make me go to those."

I realized my stupidity later with an appropriate amount of painful embarrassment, but hopefully he thought I was joking. Are you going to your own student's thesis defense? Aha. Ahahaha. Ho ho. So funny.

And my grad student just left for the weekend, so I'm stuck doing a bunch of reading. Yay. I think I'll do it not in this basement office. The lack of windows is really, really bothering me. Even if it's raining every day, which it is. Ithaca is very rainy. I lamely imagine it to be like a greener, fresher London.

Low Key, No Key

So I don't get a key to the office. It took me an entire week and a half to find this out.

First of all, the process is absurd. It required signatures from three different people, AND online safety training. Tracking down three separate people is really hard when they all have work to do and none of it includes signing your silly little form, girl.

Really, the only problem was the last guy. From what I could tell, he was the go-to facilities manager. I visited his office twice a day. Sometimes the lights would be on, sometimes off, sometimes his door would even be open. Not once was he there. My graduate student sent him an email. Two emails. Emailed someone else, who replied with his cell phone number.

Today, on my way to the first floor to get signal to call the number, I decided to stop by his office one more time. Hallelujah!

I walked in with a meek knock on the door. He stared at me. "Are you Mr. Kenyon?" I asked. Without replying, he saw the form I was holding and held out his hand for it. I gave it to him.

In silence, he flipped through the form, opened a program on his computer and entered me into the system in silence (except to ask, "Is that a d?" in my name; it was very clearly a d). He then got up, unlocked a file cabinet full of key hooks, and started rummaging through it.

For twenty minutes. I kid you not. He did not speak to me for this entire time, just mumbled to himself. I couldn't discern any of it, but I think some of it was numbers.

So Much Prettiness!

Today the RAs of the dorms we live in arranged for a picnic down by the gorge. It was nothing fancy: make your own sandwiches, a jug of Arnold Palmer and some plastic cups, and chips. A good number of people showed up, most likely tempted by the prospect of free food.

The place we ate at was somewhere I had visited while I was exploring this week. I never went down by the water because I was alone, and there were plenty of warning signs telling me not to. Of course, people ignored these signs and went down to the water in large groups! So I went as well!

We sat on logs and watched the water rush by. I took my shoes off and walked barefoot through the water on several shelves of rock. Several people, also barefoot, trekked through ankle-deep water downstream. We went upstream, and ended up close enough to a waterfall to stick our hands in it! Everything was beautiful.

Afterwards, several of us decided to go to the Cornell Plantations. We took a rather circuitous route, but got lots of pictures along the way. We saw the botanical gardens of the plantations, took many many flower pictures, and then walked back to West Campus.

Pictures through the link below!

Big Notebooks and Big Textbooks

When I met with my professor yesterday, he mentioned that I should get a lab notebook. It made sense. Something to write things down in, so I would have all of my notes in one place. I'd already been scribbling some things in the margins of my planner. He said to use the account number we had (I apparently have funds!) and to go to the stockroom and "buy" a notebook or whatever else I needed.

So in the stockroom, there were some weird notebook choices. Most of them had graph paper on the inside, which I didn't know if I would like. I just wanted something normal. Several of them were hardcover, which I didn't really like either: felt too much like writing in a book.

But when I finally found the only normal notebooks they had, they were all wide-ruled! And if there's one thing I can't stand, it's wide-ruled paper. Call me crazy. But it makes you write bigger, which makes you write worse, and then you're writing less things in more space and it's ugly and it annoys me to no end.

Starting to feel overwhelmed, I grabbed one of the graph paper notebooks with a flexible cover, and a 30-cent folder for good measure (to store the papers I have to read). But now that I'm writing in this notebook, I realize how big and obnoxious it is. Especially since I don't need to put any diagrams in it or anything. It's SUPER fancy for what little I need to do in it. I guess I didn't realize it at the time because the hardcover notebooks were fancier and they distracted me.

This notebook makes me feel very pretentious. Like look at me I'm a scientist ho ho ho with my big notebook it even has graph paper do you write on graph paper I didn't think so that's for scientists like me

My professor also gave me two textbooks to read. One just says QUANTUM PHYSICS in big letters on the cover and looks very intimidating. The other is a solid state physics book which at least has a colorful cover. Most of work today will be getting through those and some scientific papers. I might even take notes in my notebook! That'll fill its pages and make it look like I actually need it to be large and heavy and expansive for my expansive scientist thoughts. I already copied over all of my margin-notes from my planner, which fill a whole page. I really did need a notebook of some sort.

I should add: I mapped the elevation change from where I live to where I work.

186 feet of elevation. That's approximately 18 stories. I climb 18 stories to get to work, in only four tenths of a mile! And almost half of that (84 feet) occurs in only a quarter of that distance! (That stupid slope. Most miserable part of my morning.) So now I feel justified in complaining.

First Day of Work

....was reading. A lot!

I worked mostly with the graduate student who will be supervising me during my project: Eva. She's extremely nice--very practical, very smart, very clear. I really like working with her so far; she's answered all of my questions and generally been very encouraging. She gave me lots of reading material to go through for this research, so I started going through it today. I actually spent about four and a half hours on it.

It's a little frightening, to be honest. There were a few times where I just had to stop reading, look at the wall, and take a deep breath while muttering in my head I'll be fine I'll be fine This is fine. It's complex stuff. This materials research--specifically looking at the electronic properties of materials--involves a healthy blend of quantum mechanics and chemistry, neither of which I am familiar with or good at. I'm trying to pick up what I can with this reading. It's not impossible, just extremely difficult, and I know I'm only retaining a surface-level layman's knowledge, which bothers me. I want to understand.

I'm probably being impatient, but. My professor is supposed to come in tomorrow and talk to me about the specifics of the project that he wants me to do. I'm hoping for a small mini-lecture on the physics of it, hoping he can clear things up at least a little bit. Enough for me to start getting it on my own.

I felt good about the fact that I figured out how to operate the simulation program I'm going to be using. Now, if I told you I was doing computational materials science, running a simulation program, the first thing that comes to mind I'm sure is some colorful program with a rainbow of molecules in complex, beautiful structures. It actually has a text file as input and a text file as output, in the ugly technical serif font of the terminal. Not very exciting at all. I had to brush up on my Unix commands (which I felt good about, because that was something I KNEW!).

Then we had a large dinner with all of the REU programs here at Cornell. There are a little less than 200 students, from what I gathered. 20 of them are in the CCMR program, like me. There's a bioinformatics program, a botany program, a veterinary program, the particle physics program, and a program for minorities which seemed to have a melange of majors and interests. Everyone I've met here has been extremely nice. There literally isn't a single one of them I don't like. No one is mean, shallow, or even obnoxious (usually the ones you notice right off). They're all friendly, and everyone wants to do fun things as a group. We're not loners and we try not to let anyone be alone if they don't want to be. It's really very cool, and very satisfying.

A little intimidating is the fact that I think I'm the only one here without research experience. Once again, I feel like I got something I wasn't qualified for. There are also people here with amazing experiences, like working for NASA or having their name on a published paper already....I just don't know how Cornell could have picked me with my boring application.

But I'm not despairing. Eva and Professor Fennie are very friendly and seemed very interested in my success. All of the people around me are so kind. I have a while to work this out.

To see pictures and a description of the campus, click the link below!

Sophomore Year Over

I finished the senior slideshow! Lots of pictures, very time-consuming. It seriously took the majority of my time. I barely managed to finish one and a half articles before I had to leave to go home, and had to finish the rest at home. I offered to do more work for Bill if he needed me (transcriptions and small articles and the like), but nothing ever came my way.

So I stayed at home, doing the senior band slideshow for my brother's graduating class in all of my oodles of spare time. It was a smash hit at the senior awards night. I ended it with a baby picture of me and my brother followed by an adult picture of me and my brother, with a text saying "Thanks to my sister for her help" etc, and it made my mom cry when she saw it. I basically did the whole thing myself, but Ben helped pick the music and helped me edit it a little at the end.

Side note: Windows Movie Maker is absolutely worthless for anything but slideshows. It's clunky, inaccurate, difficult to use for the more detail-oriented things. But for slideshows? It's a breeze. Meanwhile, my high-grade video editor at work made it harder for me to do the MechSE slideshow! So for doing slideshows, please stick to Windows Movie Maker. Very convenient and easy. Don't use it for much else.

I went out with Steven a lot, watched a lot of television to make up for all that I had missed (which was a lot), saw two movies in theaters, hung out with my grandmother, watched my brother graduate, and went out to dinner with my family--several times. (I swore it would make me gain 10 pounds, but as much as we always say that, it very rarely does.)

Now I'm at Cornell! It's very exciting. Ithaca is "gorges" as they say here, meaning there are lots of gorges and they're gorgeous (in case you are pun-challenged). I met my roommate (who is extremely nice!) as well as all of my other suitemates (also nice!) and the guys from the suite down the hall (nice nice nice everybody's nice). We all went out to dinner at Moosewood, which was really good food and a lot of fun. It looks like we'll all get along really well--seemed to be a hodgepodge collection of science-oriented pleasant people. :)

It's really refreshing to be around people who aren't JUST from the Chicago suburbs. It's actually really exciting. There's someone from Puerto Rico, someone from Montana, New York, Ohio, Pennsylvania....it's just really exciting. Makes me happy.

Also, I'll be cooking! (Although I have leftovers from dinner tonight, so I will probably just eat those tomorrow haha.) I'll try to find original things to do, but I have a suspicion it'll just be the usual suspects. Grilled cheese, stir fry, pasta, and....eggs. But maybe once in a while I'll throw something special together.

Anyway! Orientation is tomorrow! So excited to finally meet my professor and find out what I'll be doing!