Thesis Countdown (part 3)

34 days to go.

I sit here, waiting for my timer to finish. My break is nearly up, and I know that I’ll soon get back to work. I have been working remarkably consistently over the past few days (even accounting for the relative peace of my home in comparison to the office). Why?

It comes down, I think, to two things. Firstly, the quality of one’s keyboard cannot be underestimated as a productive factor. Mine is excellent, and I highly recommend that you get a new one. Most keyboards are fairly soft on the fingers with little tactile feedback, which actually makes writing on them remarkably difficult. The reason is that cheap keyboards use cheap switches to convert your key presses into electrical impulses – so called “rubber dome” switches.

More expensive mechanical switches use spring action and metallic contacts to do the same job, but tend to be more robust and have a stronger tactile feel to them. It’s difficult to understate the difference that a small change like that makes – typing tends to feel more responsive because you can tell exactly when you’ve hit a key. I love it, and you should all get mechanical switches in your keyboards. Mine is a Corsair K70 with Brown switches, highly recommended. It’s probably the second best birthday or Christmas present I’ve ever had (the best is my coffee maker, which I cannot live without).

Getting back to the original thought, the second reason I’ve been so productive is the timer. A concept recently introduced to me is the “pomodoro” method of time management, where you work for 25 minutes and take a 5 minute break (then repeat). I find that this helps me to concentrate for reasonable periods of time while allowing me just enough time to let my brain reset occasionally. It also means I don’t have to commit to very long periods of work if I can’t manage it – committing myself to an hour or more at a time meant that I was just finding excuses not to work.

After repeatedly Googling “25 minute timer” for the Google timer, I ran across tomato-timer.com, a page specifically dedicated to helping you time out your pomodoro method.

No, I have no idea why the pomodoro method is named after tomatoes.

Last night I was panicking about my Chapter 7, which is about the most recent data that I’ve acquired and has the potential to be really quite interesting. The main problem is that I can’t see certain patterns when I’d expect to. I had a chat with my supervisor today about those data (and showed them to him in detail along with my modelling), and he seemed to be much less critical about the results than I was. In fact, he even persuaded me that missing the tail I was expecting wasn’t such a big surprise. I’m not sure if I’m convinced yet, I need to think it over a bit more. Still, having someone be generally positive towards ones work has the general effect of cheering one up. Bloody marvelous, darling.

To wrap up the day, I spend a couple of hours with the metaphorical scissors. I cut eight pages by taking multiple figures and smooshing them together into more information-dense versions. I find this quite pleasing, and a nice way to end the day.

Maybe I will manage to finish this beast after all.

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Thesis Countdown (part 2)

35 days to go.

I sit here writing a few words at a time while simulations run. They’re producing quite pretty pictures. This pleases me. While I’d love to sit and make pretty pictures all day, though, I have to keep sight of the fact that they serve a specific purpose. They’re designed to demonstrate the mathematics of the Theory section in my thesis, and no more. Perhaps I will come back to them later and see what else I can do with them.

I spent quite some time fretting last night over why my oscillator model wasn’t beating. The panic started to set in and I gave up for the night. First thing this morning, I realised I was just plotting the wrong variable due to a typo in my Matlab script.  ¯\_(ツ)_/¯

Having finished that work, it appears that my second major pass on the Theory chapter is done. I think it’s looking quite nice, and I am pleased enough with it to leave it alone for a while. I turn my attention to tearing more sections out of the results chapters – 25 pages down in the same number of minutes. That sounds bad, but with a little restructuring the chapter in question is reading a lot better. I’m beginning to think that many of these removed parts won’t even make appendices, which is a little disappointing. Still, we don’t need pictures like this:

Not even interesting if I describe it.

Not even interesting if I describe it. Just a sine wave.

That would take up about a page all told, when accompanied by text. It’s just not information dense enough or even particularly important. Having said that, there is something which I dislike about modern science: pictures like this tend to be missing altogether too often. The small details and bits of information which eliminate doubts or questions, those are important to someone trying to repeat your work. The sad fact is that they’re not at all interesting to your reader/examiner in any other case, and therefore aren’t worth the page space.

Today’s main panic is about Chapter 7, which is about only very recent data. With this, I’ve been going back and forth on what it actually means. Originally, I was quite happy that it was the effect I was looking for because I saw a nice little tail in the data on one side. More recently, I did a bit more modelling to try to support my claim about the data’s expected shape – and I reproduced something useful. But then I realised that my data only follow the predicted shape in a few of the cases I’ve measured – many more fail to see a characteristic “tail” towards the left hand side (which is important). No hypothesis I’ve come up with explains this observation, and when that type of thing happens you’re quite open to the accusation that you simply did a bad experiment.

Now, I think that I did a pretty good experiment considering the time I had. But it worries me that I can’t narrow down why I saw what I did. I suppose I could explain it if I thought very hard and came up with a very elaborate reason, but complicated claims require exponentially more complicated proof, which the data do not support.

One of these days I’m going to explain why I feel my PhD has been unusually difficult in this regard. In the mean time, it’s on to writing Chapter 1: The Beginninging.

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Thesis Countdown (part 1)

36 days to go.

I recently filed the paperwork which confirmed to my University that I intend to submit my thesis. This should have been a happy moment. Instead, I panicked.

How on earth am I going to do this?

Thing is, I’ve been trying to write the damn things for months. Arguably, nearly a year. The process has been painful and I have hated every week of it, but I made a lot of progress. I went from having a lot of blank pages to a lot of half-finished chapters. Now, I have to take this mess and craft it into a readable thing and quickly.

… and I don’t think that I can do this in just 36 days. With the timer hanging over my head like some sort of impractically clockwork sword of Damocles, I am panicking. So, as with every time I panic, I come here.

I thought that it would be useful to keep a log of how I do. For me, this is one big experiment in forcing myself to work effectively. Right now, I genuinely don’t think that I’ll finish on time – but so many other people say I will. I consistently doubt myself. It would be nice to show myself that I can work through these things and succeed… and if I can’t, then I will have told you so. I’ll write a short post like this every day to record how well (*badly) I end up doing.

Today, I took all of my separate chapters and combined them into one thing. I’m writing in Word 2010 (go on, scold me for not using LaTeX), so it took a little time to figure out exactly what to do. I’m still struggling a little with the details of numbering captions, but that’ll work out soon.

My thesis has eight chapters right now, and all told it’s somewhat too long. Part of that is because I’m really good at just writing things, so I inevitably have a few too many words. Another part is that I really like putting in figures. If a picture paints a thousand words, by my thesis is mostly RGB encoded right now.

That wouldn’t be so much of a problem if I had made good use of all the pictures, but I think many of them are redundant or not as informative as they should be. A large part of the challenge to overcome between now and submission is just reducing that volume by cutting bits out which don’t help the overall thesis very much. Thankfully, that’s remarkably easy to do at the moment. I have several chapters in my sights right now, specifically Chapters 6-7 and Chapter 3. They have a LOT of figures.

The biggest problem right now is the Theory chapter. I thought I had a pretty reasonable handle on it until I tried actually writing it, now I’m not so confident. I realised I need some more pictures to illustrate how the theory actually comes out (graphs are easier to read than equations). That means I have to run a few simulations, which I hadn’t even written at the start of the day. Doing such things takes time, and it took me a few hours just getting started. Still, I get to make more pretty pictures!

More words tomorrow.❤

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It’s Funny How Motivation Works…

I tweeted recently that a networking meetup focused on careers in the games industry didn’t go my way. I had been very excited to start discussing how I could approach the industry and what people want. It failed to meet almost every one of my hopes, and in the weeks since I’ve realized that I wasn’t blameless in this. Cue a serious bit of self-reflection.

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The “Best” Game Mechanic.

An acquaintance posed a difficult question to me today:

“What is the most interesting game mechanic you have seen?”

2016-02-22_00006

Beep, beep!

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Hydrogen Wavefunction “Holiday Update”

I took some time off this week to visit some family and do some wedding planning. It was fun, and while I was away I took some time to write an update to my Hydrogen Wavefunction project on GitHub. In short, I upgraded the text functionality to be robust against weird inputs (i.e. it’s now more user friendly) and started clearing up code in functions which could be used as good example functions for the main features of the toolbox.

In doing this update, I learned how to use regular expressions – something I had never really worried about before undertaking this project. It was nice to expand my horizons, as I’m aware how useful and ubiquitous regex is as a toolset.

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The “P” in PhD stands for Programmer.

I’ve been looking at future careers recently, and one general piece of advice I had for most of the careers I’m interested in involve showing rather than telling people about my skills. I definitely consider programming one of my best skills (I’m self-taught and I speak 5 languages to different degrees of competence), so how do I show people my coding projects?

I’ve actually written thousands of lines of code for my PhD, most of which is throwaway, but it would be nice to show some of my more generally approachable projects. To that end, I’ve started up my GitHub account and started uploading things which I think are interesting. The first project I’ve picked out is a very recent thing I wrote called Hwavfn.m. It’s a toolbox designed to let a Matlab user visualise the Hydrogen wavefunction. It doesn’t stop there: you can actually use it to look at how superpositions of wavefunctions behave.

This is a representation of the electron orbiting a Hydrogen atom - The "hotter" parts of the image are where it is more likely to be found if you were to observe it. This is the ground state of the Hydrogen atom - it would look like this "normally", until you do something to it. This state is known as the "1s" state for historical reasons.

This is a representation of the electron orbiting a Hydrogen atom – The “hotter” parts of the image are where it is more likely to be found if you were to observe it. This is the ground state of the Hydrogen atom – it would look like this “normally”, until you do something to it. This state is known as the “1s” state for historical reasons.

This type of program is significant to my PhD, which revolves around controlling atoms which behave a lot like Hydrogen (they are known as Rydberg states), and demonstrating that I can control the shape and size of their wavefunctions in quite a sophisticated way. I use the toolbox to visualise the kinds of things I can do to the atoms, as shown in the picture below.

This is a much more complicated state of the Hydrogen atom - I have put it in a superposition of the 1s, 2p+, and 2p- states (which all have different shapes). The cool thing is that I can make real atoms do this, and they are not in *either* of the states, they are in *all the states at once*.

This is a much more complicated state of the Hydrogen atom – I have put it in a superposition of the 1s, 2p+, and 2p- states (which all have different shapes). The cool thing is that I can make real atoms do this, and they are not in *either* of the states, they are in *all the states at once*.

What’s most cool about my usage of this package though, is that I can use it to simulate what the atom looks like over time. When you make a complicated state like the one above, it actually changes its appearance over time. If I leave the state in the picture above for a few picoseconds, you are more likely to find the electron in a completely different location!

The Hydrogen atom in the same mixture of 1s, 2p+, and 2p-, but this time left for a few picoseconds. It's showing something which Physicists refer to as an "interference" behaviour. I'm effectively showing the effects of the electron - a *particle* - behaving like a *wave*. Isn't that cool?

The Hydrogen atom in the same mixture of 1s, 2p+, and 2p-, but this time left for a few picoseconds. It’s showing something which Physicists refer to as an “interference” behaviour. I’m effectively showing the effects of the electron – a *particle* – behaving like a *wave*. Isn’t that cool?

Anyway, I have digressed a bit. I will be developing my toolbox to be a bit more user friendly (as well as refactoring some code and making some of the things you have to edit a bit less dumb). I expect that it can be used as an interesting teaching tool for showing what Hydrogen wavefunctions look like; for showing how superpositions work and what the results of the Time Dependent Schrödinger Equation look like. It’s quite exciting!

I’m expecting to update the package weekly, and hopefully I’ll achieve my goals for it in the next month or two. Currently it’s in the “practical but ugly” state which I had to leave it for work, and I’m looking forward to making a much better job of it over time.

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