Another day at the beamline...

During the down time I've been trying to learn a bit about making computer generated pictures using ray tracing programs.

The reason for this is simple. Often a great deal can be communicated through nice pictures that would be awkward or opaque through spoken word or text alone. At the same time poor quality pictures or representations of what you're attempting to explain can also obfuscate. So I decided that I'd had enough of making simple little pictures in MS-powerpoint. I wanted something more.

I downloaded POV-Ray and set to work. With a modest amount of mathematics and programming already under my belt, this turned out to be rather straight forward to use. Perhaps the simplest thing to make is a sphere, so I set about learning how to render pictures of a few spheres :

So there's my first attempt. A nicely colored row of spheres. It wasn't too hard to make actually. And to be honest, all I really need to know how to make are spheres. lots of them. LOTS AND LOTS OF THEM.

One of the systems near and dear to me is the surface of a particular gold crystal facet (though to be sure, the other facets are interesting too as are plenty of other crystals). It's a square cut through the face-centered-cubic lattice of gold atoms. The top row of atoms the rearranges itself into a hexagonal pattern. The hexagonal pattern can then be one of two possible orientations (rotated 90 degrees from each other). Furthermore because the surface atoms do not line-up perfectly with the atoms underneath, the surface ends up rippled and crumpled in a particular way.... See? I could keep going and going about the positions and so forth, but a simple picture would be sooooo much better.

Ah to be in Paris and in love...


Finally... Finally... we submitted my first paper from my work as a post-doc. It's been a little over a year now (and was a large leap in terms of science), but we've got our first paper sent off. It's far from time to really celebrate though. It will be a month or two before it comes back from the referees and they'll certainly have some things we need to fix. I say "certainly" because we submitted the paper to Physical Review Letters. This essentially assures us of having negative comments from the referees. It's almost a given. The question is how negative and how we respond.

The trade off is that this is (aside from perhaps Nature) about the best place for a physicist to publish research. Because of that, they're pretty selective about what makes it through and the referees are supposed to be tough on the authors. The converse is that we've got (I think) a really good paper with some very interesting results (interesting to a wide variety of people). Nothing is certain, except that it will never get published if it's never submitted.

This is particularly exciting for me as it will be my first paper with Hoydoo and my first in the realm of surface physics. It's been quite a big jump between my thesis project in graduate school and the research I'm doing here. However, I'm glad to have made the transition and be contributing in a second field. I suppose that's part of what I like about being a physicist. Despite some difficulty it's very possible to switch between different interests with some degree of fluidity.

We had some extra time today when one of the facility scientists abruptly (and obscenely) took the beam down. He needed to do some work on a piece of equipment we use and that required us to stop working. The best situation would have been if he'd informed us in the morning that he'd need to do his work in the afternoon. Or... since he didn't warn us at all, to allow us a few minutes to finish our work (ball-park, at most 30 minutes of time). Or... he could have stressed the urgency of what needed to be done and apologized, but taken it away. Instead he got in a fit, stormed off to get a supervisor/coordinator person, and came back to curse and yell at us.

You know... if you're going to curse, you've got to do it well enough that people will be impressed by your ability curse instead of being offended. His... eloquence with 4-letter words was somewhat lacking. Anyhow, he acted quite childish and then took the beam down. sigh... So we used the spare time to finish our paper and send it off!

Today was quite a day and follows on the heels of "quite a day."

This was my first chance to host a visit for a guest scientist, in this case Paul G. Evans from the University of Wisconsin at Madison. I recently joined the colloquium committee for the Materials Science Division. The committee selects and invites speakers to give our weekly colloquium (no self nominations!). I met Paul a couple of months ago at a workshop and wanted to learn more about his work (something I'm a bit unfamiliar with). One of the best ways to do that is have someone come out to give a talk! I enjoyed putting this together and, so long as I'm not in charge of it every week, it's something I'll probably continue to enjoy in the future.

It's been a rather long day because we're also currently running our experiments. Two of mine are actively running in the Materials Science building, while one of the other post-docs has an experiment running at the Advanced Photon Source. Being in so many places at once is difficult. It's not easy to violate causality.

This all comes after the day before which gave me one of the best experimental results we've gotten thus far. It was one of those rare days where everything worked (including the experimenter!). We went to look for something we'd seen indirectly with our other experiments and found it. Having an independent confirmation (in this case, a radically different experimental technique) of a result is very, very reassuring. In particular it's coming at a good time as we're ready to submit a paper on the first set of experiments. Now that we're in "phase 2" and the results are confirmed it goes quite a ways to setting my mind at ease. If you're going to make a rather interesting, potentially controversial claim, then it really helps to have several different pieces of evidence. ie...the bigger the claim, then the better the evidence.

The experiment we're running at the APS is on "free" beamtime. There is a new device (x-ray source) that needs to be tested. The scientists in charge have it set up, and nominally working. However, the real test for them is if people can come in and do science with it. We're that group of people (we hope).

The reality is of course that nothing is free. As the x-ray source is new, it has some issues and problems that must be solved before we have a hope of doing good science. And part of our effort will be spent helping the beamline scientists solve these problems. Ideally everything will work rather quickly and we'll get to take some nice data. But for now there are no promises. We've got some oddities in the photons coming down the pipe and we're not quite sure what to make of it. Conversely, at the moment these oddities don't really have an adverse effect on our measurements. However, it's something that needs to be worked out.

One of the worst things in experimental science is having data that is inconclusive. However, something more insidious is when you equipment fails and conspires against you. I say "conspires" because at times I think we'd all swear there's some evil genius inside the machine purposefully twarting our efforts.

The current manifestation of this "entity" was causing us to lose the motor positions and alignment of our diffractometer (the giant green-aqua thing we use to take x-ray scattering data).

These are the works of man, this is the sum of our ambition : To make this little motor turn (in a known, reliable, repeatable fashion.






I spent much (too much) of the last day getting this little motor to spin properly. In the end we had two different mistakes compounding each other. Having two issues concurrently makes life more difficult because the cause becomes more difficult to identify. A typical problem solving approach to this is to first ask, "is there anything known to commonly fail that we should check first, or does the way it's failing indicate a particular problem?" Assuming that doesn't work (it didn't), the next phase is to proceed methodically through the rest of the parts, removing them from the list of possibilities. The problem here, is that with failure in two different areas, the above method doesn't exactly work.

Eventually we figured things out, but it was painfully long. I'll spare you the details, but we were running our motor at too high of a power, causing occasional jams, and our connection coupling from the motor would occasionally lose contact when one of the other motors was in motion. sigh...

For posterity's sake I should reproduce something here. After checking all over the web I could not find this information for the wiring of a particular model/kind of motor. So, after figuring out how a 4-phase motor should work, plenty of measurements with a multi-meter, and a bit of cursing similar (but different) wiring identification schemes, I finally got it. For a 4-phase (four-phase) Slo Syn synchronous stepping motor, model M061 - CE08 (made by Superior Electric) the connection wiring is as follows.

Label on the Motor : A,B,C,D,E,F,G,H
Matching common female connector : 1,2,3,4,5,6,7,8 (there's only one orientation here)
Using the standard 8 wire bundle (though any will do)
Connecting to a standard stepper-motor plug connector (male).


Motor Letter, Motor Connector (wire color) - stepper male connector plug letter
B,2 (red) - to A
H,8 (red/white) - B
D,4 (green) - C
F,6 (green/white) -D
G,7 (black) - E
A,1 (white) - F
E,5 (orange) - H
C,3 (black/white) - J

W & T short together
U & X short together

We short W&T, U&X because we use software limits on the motors, not hardware limits on the machine.

On the motor itself, the phase pulse out/return pairs are :
A/H - phase 2
B/G - phase 1
C/F - phase 3
D/E - phase 4

Hopefully google will pick that up for the next time someone needs that information.