We don't need no education

Dear Diary,

 It's the fall-time right of passage.  Each Burke student must teach the ABCs at some point before they leave the program, just as they must take the program for credit before they leave.  The only question is always:  Who has to teach?  And I'm sure for the incoming students, they ask: What do you think the teacher's gonna look like this year?

Well, diary, I will be teaching at least some of the course this year.  Fun, fun.   Yep, it finally comes to me:  preparing, teaching, grading, answering questions without messing up, reading the text for the first time, being just another brick in the wall, etc.

[Editor's note: Hey, teacher, leave them kids alone]

All used up

Dear Diary,

After many long, hard journeys, my travel grant is all used up.  Ok, well, I spent three more dollars than the allotment, no joke!  Thank you ARCS for the funding.  It really brought me places and physics I wouldn't have gone otherwise.

Your sincerely,
Dr. Who

More puzzles

Dear Diary,

John von Neumann was a mathematician alive when quantum mechanics was getting big.  Allegedly, he was faster and smarter than Bethe.   Somehow I can't quite believe that...Bethe was used to calculate mental math to check the first computers.

But anyway, there's a story about von Neumann and a puzzle:  Given two bikes twenty miles apart and on a course to collide (each bike travels at 10 mph and starts 20 miles apart), a fly travels from one tire's edge to the tire on the other bike repeatedly until is it squashed (always at 15 mph--it turns around instantaneously on reaching the bike).

How far does the fly travel?

There's an easy way to get this answer and it's to recognize that it takes the bikes 1 hour to meet, so the fly travels 15 miles.

But there's a hard way, and apparently von Neumann calculated this instantly on hearing the question.  Once answered, the questioner said, "Oh, you must know the trick." (solution presented above) But von Neumann said, "What trick?  I just summed up the geometric series."

Oh man, diary!  How do you even set up the geometric series for this?  I'd love to know!

And then there were three

Dear Diary,

It was great to hear from Dave about his experience in graduate school and get a reprieve from the blog.  I wish him the best.

It turns out we've had a mass exodus from the group recently.  Raphael is leaving for San Diego, Paul took a job in northern California, and Li is secretly working full time on secret things.  The worst part about all of this is updating the information on the website.  Let's just focus on the alumni section.  Each alternating person has either a white or gray box and these need to be set by hand in our html code.  This is a huge pain if Dave (last name starting with "F") needs to be inserted in the top of the list and all following entries changed.  Sad!

Now we're down to three.  I'll be removed from my one desk Hilton on the ground floor, where the sun never hits that side of the building (keeping it cool in the summer time and refreshingly chill in the "winter"), to the second floor office where air remains unmoved, hot and stuffy.  My beloved white board and I will part, but the Cheshire cat grin of hallway noise will follow.  My only compensation is a larger desk and the ability to retreat to my Fortress of Solitude in another building.  I secretly tried to get two postdocs, my current neighbors, who currently have tiny desks to move into there and prevent this.  They requisitioned another office instead, telling me to try and be happy.

He that commends me to mine own content
Commends me to the thing I cannot get.
 I, to the science, am like a drop of water.
That in the ocean seeks a postdoc, who, failing there to find a fellowship,
Unseen, uninspired, publishes his worth:
So I to find a degree and an escape,
and in that quest, unhappy, lose myself.

I to Spain for a few weeks, as the world turns beneath me.

Saying Goodbye

It's time I come clean about the radio silence that has washed over this blog.

Back in April of this year, I started to realize that things between grad school and I weren't going to work out. I'd found myself failing to really care about my research and, though things were going well in practice (time spent at a national lab, papers, presentations, etc.), I could tell that there was a gap in principals between me and science.

I've spent my entire life labeling myself as a scientist. It's really the only way I know how to describe myself. I have a sleeve of science tattoos adorning my left arm (that now seems a bit shortsighted) and have always been captivated by the quantum world. But in the process of breaking the news to Kieron (who was cooler about the whole thing than I could have ever hoped for), I verbalized that my intrigue is only fascination. It's not the sort of deep passion that makes a theoretician grind through a hard derivation. It's not the sometimes-harmful drive that causes an experimentalist to want to work in lab until 3 in the morning.

It's a sort of grit. And I have plenty, but I don't have that kind of grit. I like the process of problem solving, and using data to tell stories. But science in and of itself doesn't grab me. And it's crazy to admit that, because the last decade of my life has been spent trying to better understand science.

But in some ways, I was really using science as a way to better understand myself. My grad school experience has taught me a variety of things, but most valuably, it taught me who I am. And for that I will always be grateful.

Life beyond my feeble attempt at a PhD will start in NYC with me as a back-end engineer at a data-driven marketing company. I'm excited, nervous, and thrilled to be on the cusp of a new adventure. And I look forward to using the problem solving prowess I've developed trying to understand the strange, strange world of density functional theory.

Cookies

Since the beginning of 2015, I've been the honorary cookie person for the group. My job is to bring tasty treats to the group meetings to compliment the delicious coffee that Kieron makes.

Every so often, we collect money from everyone to pay for the cookies, and our funds are running low. We'll have to get some more cash during the group meeting today. Wanting to make this a smooth process, I dove into the recesses of our old minutes from previous group meetings to find out the rates each person pays ($5 for grad students, $20 for profs etc).

Using my mad UNIX skills, I started grepping around for the word "cookie" and oh me oh my did I find something marvelous. The following is the output I received after typing "grep cookies *.tex" into our minutes subdirectory:

130528.tex:Raphael - group leader - cookies, journal club, toner
130723.tex:Special guest:  Steve White and delicious purple cookies courtesy of Eunji Sim.
130723.tex:Cookie money is to be collected so we can continue to have cookies.  The pricing will remain
130723.tex:Kevin also has to pay but wonders if not eating the cookies means he can get out of it. There is a cookie mandate, however.  The tax collector is Raphael for those who still need to pay. No visitors are charged.
130917.tex:There are no cookies today.  Lucas misses them especially.
130924.tex:Cookies come extra fancy today with only three gourmet cookies per plastic tray.  They disappear quickly.
131015.tex:%Tuesday duties:  calendar, cookies, meetings, emails...
131022.tex:Justin bring cookies!  Stefan joins us!  Everyone has lunch!
131022.tex:I ate a bacon cookie!  It was delicious and it made me delirious!
131112.tex:Many jokes about smart cookies are made.
140121.tex:Li:  Today we have soft cookies.\\
140121.tex:Kieron: it's not a real cookie if it's a soft cookie.
140422.tex:Justin:  Are cookies ever accomplished?\\
140603.tex:The cookies are slightly stale and in low supply.  Raphael was doing so good as temporary group manager.  Was.
140708.tex:Kieron just stole Tony's cookie.  Justin laughed hard -- maybe unreasonably hard. 
140708.tex:Li suggests that in the future Tony licks all his cookies before he sets them down.
140826.tex:with the cookies.  But it was only Peter, Dhonyong, and Attila which was not
140922.tex:Aurora will get cookies.
140923.tex:Aurora will get cookies.
150414.tex:Dave is the new cookie guy because Aurora is set to disappear at some point.
150414.tex:Also, cookies are supplies and he is the supply guy.

Going Thermal

One of the downsides of not writing frequently is that this entry is going to clash in tone quite a bit with my last update.

Research is going awesome! I finally have a version of my derivation that looks (vaguely almost sorta kinda) presentable and my code for the thermal version of the calculation is up and running. I'm getting pretty plots and things are looking pretty good. I might be able to start testing different response functions soon. Which would be super cool.

I was completely and totally overwhelmed by my project up until a few weeks ago. Something suddenly clicked. I finally saw how all the pieces I was working with fit together and my results started to make sense to me. I'm beginning to even understand what comes next, which is a pretty cool feeling. The ABCs of DFT is also going really well, and one of the most exciting effects of the class has been a general increase in my understanding of many parts of my research, as well as what other people in the group are doing.

On the downside, I shaved my beard off because I was curious and now I look like I'm 12.

Winter is coming...

Well okay; "winter" as far as OC is concerned. And actually, come to think of it, that reference doesn't really apply to what I'm writing about, but whatever. I'm committed now (because I miss GoT and really want the next season to come out already).

This quarter was tough. Like, seriously tough. I realized earlier this week that my expectations of theory research were completely and totally incorrect. More to the point, I went about this first project almost entirely the wrong way, taking to the problem like a bull in a china shop. Which, in case you're curious, didn't work too well.

I've recently started getting into lock picking (just as a hobby; no plans to recreate Oceans 11 any time soon) and what I enjoy most about it is how deliberate one has to be to get through a 6 pinner with security pins. You can't just jam two ends of a paperclip into the lock and expect the thing to open. It takes time, finesse, and patience.

Theory is a lot like that. I'm sure that as I learn more, things will go maybe a little smoother, but the fact is, there is always going to be something new in any problem worth researching just by the nature of how research works. I often tell people that theoretical chemistry is neat because it lies at the intersection of chemistry, physics, and mathematics. The past week or so has made me realize that I was regurgitating this lip service without realizing what it actually means.

I wish I'd gotten more done this quarter, but working through this has been really valuable. It's a cliché, but I almost feel like I've learned to crawl over these past few weeks.

Now it's time to try and stand up.

That moment

when you hit "shift+enter" on a mathematica notebook and the fraction you've been waiting to see for over 2 months pops out and you make this face:

All Aboard the Strugglebus!

Sometimes research doesn't go well. Other times, it really doesn't go well. And sometimes, it's a veritable dumpsterfire. I've slid through all three of these stages this quarter and my project doesn't seem to be relenting any time soon.

The most frustrating part of it all is that, just by looking at the integral I'm wrestling with, I know I should be able to compute it. I know the answer, I know the integrand is well behaved (in most places at least), and I know for sure that people have done it before. But calculating this thing is like baking a soufflé: if anything is done even slightly incorrectly, you're gonna have one floppy, deflated pastry. And nobody wants that.

One thing I have learned from all this struggling however is that I have a good support system. I've of course been complaining to my family and friends whenever I've gotten the chance, but I've also received help from various group members, both previous and current. The integral is inadvertently teaching me an enormous amount of many-body physics, UEG stuff, a dash of perturbation theory, and more than I'd care to know about Fourier transforms so even struggles are, I suppose, time well spent (though often it doesn't feel like it). Regardless of the future research I do with this thing, it's been a hell of a teaching tool.

I just hope that the finite-temperature form isn't too much worse...

Dumpster Fire

This week is the coolest week ever.

1. Our DFT midterm was given to us on Sunday. It's due next Monday. It looks like fun.
2. NSF is due Friday.
3. My research project is currently just trying to integrate a stupid two dimensional function. And I can't do it. Oh and I've been doing this for almost a month.
4. I destroyed my leg during a long run on Sunday so I can't relieve stress.

Ohheygradschool.

Writing, writing, and more writing!

First off, I should apologize to my faithful audience for my absence. I know I said I'd write up a little thing about Spain and whatnot, but research, NSFing, and DFT class have been all-consuming and it's felt wrong to take time away from those things for blogging. But! Blogging is important so here I am. Writing a blog post.

Which is fitting in some respects because recently, all I've been doing is writing. The NSF GRFP stuff is due in 11 days (hoooooooly moly) and I've been frantically polishing and rewriting and polishing and fixing and editing and pruning nonstop it seems. It's a lot of fun though. I've always enjoyed writing and I really have to put a different hat on when I'm writing sciency stuff. This stream of consciousness style I write in for this blog is really how I prefer to write, but that doesn't jive when you only have two pages and (presumably) an exhausted reader who probably wants to go home. Conciseness is key and I'm way too flowery in my writing.

Luckily, Kieron is really good at taking long sentences and turning them into a handful of words. Justin has been invaluable as well in fixing my word choice. It's nice having people to help you out! Then again that's been my experience in this group since I first got here.

Research has been progressing more slowly recently, though that's thanks to Apple's new operating system which un-taught my computer how to compile fortran and TeX, and my general lack of knowledge concerning physics-y stuff. DFT class has been a blast though, particularly since a lot of what we're learning is more about how to think about quantum mechanics. Which is weird. Quantum stuff is weird.

Grad School Year 2: The DFT Strikes Back

At some point, I'll write up a little something about the whirlwind tour of Spain that Justin and I enjoyed, but for now, the quarter starts today! It's weird being a second year. Over the next 10 weeks, I will have only one class to worry about, no teaching to distract me, and a whole lot of research to keep me busy.

It's exciting, frankly. I enjoyed my classes last year for sure but, thanks to LANL, I know what it feels like to just do science without other stuff gumming up my time. And I want that back. Being gone for two weeks was cool and all, but mostly I just want to return to "routine" (if there is such a thing in grad school) and dive into DFT.

The class starts today and I look forward to seeing how the class will enhance my understanding of the research I've done and the research I will do. Speaking of which, I should probably finish up the homework that's due in an hour.

Hola, ¿qué tal?

Hooray, Spain! After enduring my first trans-atlantic flight and a french-filled connection in Brussels (a place I will definitely visit in the future), I found myself in a rather alien place full of non-perpendicular roads and buildings that looked older than anything I'd ever seen before. San Sebastian is a very popular holiday location for europeans and I can absolutely understand why. The views are utterly breathtaking and the food is to die for. Since I don't speak spanish, I often just smile confusedly at the waiter or waitress who has been tasked with serving me until they suggest something, to which I always reply, "si, si. Gracias!"

Other than the sheer deliciousness, eating in Spain is a wholly different process because socializing outdoors is way more prevalent here than it is in the states. Lunch is a communal affair, lasting a few hours and a number of courses. Meals always feature alcohol (sometimes whether you order it or not) and coffee or espresso. The waitstaff never comes to ask you how you're doing because you're always busy chatting and, I must say, I'm completely taken with the way they do things here.

I lament that I can't speak the lingo because I feel like I'm missing out on the immersive nature of spending a week+ in a completely foreign place. Luckily, the conference is in english so I'll know just how little DFT I know.

Speaking of the conference, I'm currently at it. I'm sitting in an empty lecture hall trying desperately to digest the delicious food I ate for lunch while running some calculations. It's all fantastic. I like it here.

Whoa

I totally forgot to write last week because I was back in Irvine.

I've returned to UCI and I gotta say, it's nice to be back. As much as I was loving the extracurriculars out in New Mexico, I missed the sort of science we do here. We ask deep, theoretical, fundamental questions about DFT and that was not the sort of thinking/problem solving I was doing out at LANL.

I'm already working on something with Kieron and Aurora, which is really cool. It's nice to be on a project that feels as though it's wandering in uncharted territory. I'm also really engaged with the project because it's a finite-temperature kinda thing; that's the stuff I'm gonna be up to my eyeballs in really soon.

And the finite-temperature stuff looks so cool! The math is really pretty. There's all this groovy stat mech language lying underneath everything and I'm looking forward to seeing how everything ties together.

I'm also finishing up my first-year exam, as well as making a poster for Spain. Both of which are next week.

Hoooooly moly I'm going to be in Europe in like, 11 days.

Week 10: So long, farewell, auf wiedersehen, goodbye!

So that's it then. Dan and I finished our final project, uploaded it to the git repository (which crashed like, 16 times before everything was said and done), and had our final meeting with Charlie and Marc. They were both super cool and thanked us for our work this summer. Charlie also mentioned that either of us were welcome to come back next summer, which was nice to hear.

Saying goodbye was hard. I won't miss New Mexico all that much; I'm looking forward to moving back somewhere a bit more dense. I won't miss Los Alamos much either; it's beautiful for sure, but other than hiking and camping, there is absolutely nothing to do in that town. I will however miss the people. 

Over the course of these 10 weeks, the science has been fun and the green chile has been delicious, but above all else, I will remember the crazy camping hijinks, the late nights spent just talking about the inevitable existential questions one encounters while in grad school, the road trips all across New Mexico, the rock climbing followed by intense renditions of Don't Stop Believin' at karaoke night, and the 22 people I shared that dingy basement with.

It's been real, Computational Physics Workshop.

Week 9: Warning - This Post is Actually About the Program I'm In

On Wednesday, I woke up at 5:30 in the morning. I didn't need to, but my body pulls this stunt every time I know I have a presentation to do. It's a mixture of anxiety caused by the fear of oversleeping and anticipation because my god, do I love giving presentations.

I managed to fall back asleep for a half hour or so until waking up again, this time just 30 seconds before my alarm was going to go off anyway. I rolled out of bed, spruced up the beard, brushed my teeth, showered, picked out a shirt and tie, threw on those socks my dad got me for christmas that are covered in mathy equations, fed my landlady's cat, and began walking to the bus stop.

The bus seemed to travel far slower than usual this morning. The greens and browns of the northern New Mexican high desert smeared past the Park 'n Ride shuttle window while Green Day (Nimrod, in case you're curious; it's a solid album) wafted out of my earbuds. Once we arrived in Los Alamos, I wandered past security up to Research Park. I found the conference room that would be my home for the rest of the day, located the free coffee, and engaged in the nervous but pleasant chatter that always proceeds a "big" speaking engagement.

The day was split into two parts. First, we'd each give a quick, 3 minute presentations that would outline the longer talks we would give later in the day. The higher-ups at LANL would attend these quick-looks and use them to decide which talks they'd like to see in the afternoon. It was made very clear early on that between the short and long talks, the short ones were the important ones. Our coordinator also made sure to explain that the 3 minute time limit was a hard one. We had a schedule, and we were going to stick to it.

After finishing my cup of coffee, I found my partner and complimented his outfit. The dude wore a full on suit and looked sharp as hell. I felt silly but was glad I'd decided to at least wear a tie. As 9 o'clock drew nearer, we were told to grab seats towards the back so that the important people could sit in the front. The clock struck precisely 9:04 and we began. The first few talks flew by pretty quickly and I could feel adrenaline slowly leeching into my bloodstream as group after group inundated the room with their concentrated morsels of science. The first warm dense matter (WDM) group (who ran orbital free stuff) went up and dropped a few of our punchlines but before I knew it, Dan was up.

His presentation went really well. In it, he detailed what WDM is, why it's tricky to model, why we care about it, and how to calculate electrical resistivity using the Ziman-Evans formula. Before I could blink, he was done, the audience was applauding, and my presentation was already up on the wall.

We were mandated to provide an introductory slide before getting into the science so naturally, I dotted it a few jokes, a Star Wars quote (both of which went over well), and self-depricated about being from New Jersey. Then I got down to business. Our most exciting data was on display for the whole room to see. I felt like I did a solid job of explaining what our conclusions were, why they were significant, and why it was worth coming to our longer talk later in the day. We had a story and it felt pretty compelling. It was over before I knew it, but apparently Dan and I made a convincing argument for coming to see our talk.

When the afternoon session rolled around, there were far fewer people in the room. Friends had come by for the earlier talks (probably because they were short and came with the prospect of free coffee) but now, only summer students, mentors, and a few lost lab employees were present. That is until the WDM presentation(s) started. The room noticeably swelled up and I saw some faces I recognized. Obviously, Charlie and Marc were there since they were our mentors, but there were some other DFT-ers in the room, too. The long talk was an utter joy to give. Dan and I were really able to get down to the meat of how our calculations worked. I got to explain how we eliminated a handful of models, how we selected our exchange-correlation functional, and what our future goals with this code might be. We even got some questions, and I was even able to answer them. It was pretty groovy.

Then our presentation was over. And all the WDM people left. And the room was far less full. It was cool. Our science felt important. The rest of the afternoon was... long. The presentations were good, but four hours of constant exposure to 20 minute snipits of science is exhausting. By the end of it though, we were all relieved to be over this penultimate hurdle (I still have to write this paper-thingy). We all felt accomplished. It was a clear demarcation in the program.

The program is almost over.

Week 8: 748 Miles

Sorry for the late post, but this was one heck of a busy weekend.

First, I suppose I should mention something work related. The bug hasn't been fixed, my plot is still kinky, but our results are solid everywhere else and the project is drawing to a close. This week we will be giving our final presentations and I can't wait to do so. I've always enjoyed giving talks and I've been sitting with this data for so long that it will be nice to talk about it with some strangers. It also sounds like we might get a paper out of this summer which is nice.

On to the fun though. On Friday, myself and four other students piled into the back of a Subaru Outback and began traveling towards southern New Mexico. The first destination on our list was White Sands National Monument. If you're ever in New Mexico, you need to make it a point to get down there. The park is completely covered in white gypsum sand and is so large that you can very clearly see it on google maps. We spent the better part of an evening there and camped nearby overnight. Seeing the moonrise over that place was seriously spine tingling.

Then things got even better. We broke down camp and traveled over to Carlsbad Caverns, the largest cave in the US (contiguous maybe? I don't remember). The cave itself is broken down into a few rooms that have paths laid out for you to walk on. Pictures don't do it justice (and also I haven't ripped them off my phone yet). The cave was originally a sea and most of the features down there are either fossilized coral or stalagmites which have formed from drips and drops over the course of millions of years. If you head there and have somewhere nearby to stay at for the night, you can watch the bats fly out around 7 pm. We however needed to find another place to camp, so we left after doing the hike.

We ended up camping at Bottomless Lakes State Park, a place I'd happily camp at again. The views were lovely and we got to watch a series of thunder storms (that were safely far away from us) light up the sky. The clouds recessed and left us with an incredibly clear sky full of stars and another beautiful moon.

Moral of the story: if you like to be outside, you need to head to New Mexico at least once. Possibly twice.

I know I'll certainly be back before too long. Oh also, 748 miles is how far we drove. Over the course of three days. I'm just now starting to get feeling back in my legs.

Week 7: Kinks

That title is totally click-bait. But I swear it's relevant!

I finally hit a massive obstacle in my project earlier this week. One of the plots I generated had a pretty nasty kink in it where it shouldn't have had one. This lead to a number of days spent under the hood of my code debugging, re-writing subroutines, checking types, and making sure I didn't exceed the 132 character/line limit (thanks for nothing, Fortran 90).

Today, I finally had a break through. The plot I was generating featured points whose y-values came from an integrand. The integrand is chock full of... interesting quantities that are computational expensive to calculate. The two most complex are the external potential and the structure factor, both of which come from a program that, for all intents and purposes, is a black box to me.

None of my other plots had any issues, so from the outset I was suspicious that the issue was in my code. Still, I started from the top of my integration routine and worked all the way down until it had to be something in my integrand itself that was misbehaving. I checked the fermi-dirac function I was using, the physical parameters that gave the integral correct units, the fineness of my grid, and even how many digits of pi my code was using. Finally I came to the potential and the structure factor. It had to be one or the other. Removing each separately showed that there was an unusual jump in the potential where my kink was. Victory.

The win is hollow though. I still have no idea why the potential is misbehaving and although it looks like that's the issue, I can't really be sure. I just hope that whatever the issue is, it won't have affected the rest of our results.

I can't believe that it's already the end of week 7. Before I know it, I'll be back at sea level and won't need a cryptocard to check my email.

Week 6: Descent

Today at work, it became really clear to me that the summer is almost over.

I've alluded to our progress in a few of my other entries, but Dan and I are truly at the production stage of our project now. There are a few tweaks and optimizations being done, but most time is being spent crushing the Moonlight data cluster with thousands (literally) of calculations all at once. I sure hope the HPC guys and gals don't completely hate us.

The time one has while jobs are running is a very slippery thing. It's easy to get distracted by an article or a book chapter or (honestly, more commonly), a funny picture of a cat. I'm also not used to having downtime while calculations are running because I haven't needed any HPC for any of my code in grad school up until this point. Sure, I ran stuff in undergraduate, but that was eons ago and I had classes + homework to keep my occupied.

One of the best aspects of having free time at work is that I get to write. Fleshing out the story of our results is far and away the most fun part of doing science in my mind, and goodness me do we have a cool story to tell. I'm not entirely sure which parts of it I'm allowed to talk about and which I'm not, so I'll have to be vague, but the true star of our project will be a set of data that totally and completely surprised us. We predicted that one of our models would behave a certain way and it did the opposite. There's a rationalization we're happy with,  and the result is consistent with our other data, but I love a surprise.

Results that confound and befuddle remind me why I like science in the first place; until you set up an experiment and parse the data, you can't be sure of anything.

Sorry that this entry didn't feature any mortal danger or cattle.