Why so hard, Mr. Gaussian?

August 31, 2006 at 12:14 am | | everyday science, software

I’ve been doing some electronic structure calculations recently, and this is a job for Gaussian03. Sweet Gaussian. It’s a fine choice for electronic structure calculations, but there are some true oddities.

1. The program is probably the most popular suite for solving quantum mechanical calculations. Thousands of chemists use it and pay through the nose to do so. However, it is almost completely undocumented. For example, see the description of the transition option under the Density keyword (Figure 1). What is the transition density? Ought I know? Basically, do any calculation with any method other than B3LYP/6-31G and you’re screwed.

Transition=N or (N,M)
Use the CIS transition density between state M and state N. M defaults to 0, which corresponds to the ground state.

Figure 1. Out of context? no. See for yourself.

2. Why does it crash? I realize it’s a complicated system and lots can go wrong. But, why doesn’t the output file give any useful information about the system failure. It’s a smart program. It should know why it failed and speak its mind. Figure 2 shows one of my favorite error messages. Of course, there is no content about such errors in the documentation.

Erroneous write during file extend. write 172031 instead of 4096
Write error in NtrExt1

Figure 2. Actually, I know what this error is. The computer ran out of hard disk space. But, it wasn’t easy to figure out. Try googling the error message. You’ll find a bunch of people trying to figure out what NtrExt1 means.

Why isn’t there a wiki-gaussian? I don’t know, but I hope I’m not banned for asking.

Relatively Awful

August 23, 2006 at 1:58 am | | cartoons

Let’s find the most poopy cartoon involving Einstein. Get a wiff of Figure 1 for some truely poopy cartoonin’.

Figure 1. Look at me.

What is wrong with Einstein’s arms? Is he wearing a burlap sack? Is that a chalkboard? I don’t even want to start, baby, with the dialog.

So, the challenge is to find a worse cartoon. My numbers suggest at least 10^3 terrible Einstiens out there. Find them and post them. If you’re not a member, place the link in the comment section, and I’ll make Kendall post it for you. Happy hunting and godspeed.


August 16, 2006 at 11:43 pm | | cool results

I’m just finishing up a class on Fourier transforms, and the discreet transform has me all gooey about sampling. Have you ever noticed that computer screens shown on TV sometimes have a line moving though the picture? It’s a sampling error. The frame rate of the TV camera is similar to the refresh rate of the computer screen. As a result, the refreshing sweep is visible. It’s like strobing a light with exactly the same frequency as a spinning fan. The result to your eye is a stationary fan. Check out the link in Figure 1.

Figure 1. Remember, this movie is shot and shown in real time.

Good Conduct

August 15, 2006 at 5:47 pm | | everyday science, hardware

My lab is involved in several highly sensitive experiments that require complex data acquisition hardware. Much of our hardware is homemade, old, or inevitably unstable. As a result, we have to spend time fixing these systems, and that cuts into actual experiment time. To streamline the repair work and prevent future breakdowns, we have developed the flow chart shown in Figure 1.

Figure 1. Dishearteningly accurate.

I really like this figure. It’s truly a contender for best figure ever.

Wiktionary, I’ve got a word for you

August 11, 2006 at 11:37 am | | wild web

I’m a big fan of wiki. But, I just ran across wiktionary.org, and I don’t like it.

Wikipedia makes sense. A bunch of people compiling ideas and information. But, compiling word definitions sounds silly when you consider the already available resources and the mistakes people will certainly make.

Oh snap, time for the burrito truck.

Stereotypes are Real

August 4, 2006 at 8:39 am | | nerd

My alma mater did well in the National Quiz Bowl Tournament this year with a 6th place finish. We beat Harvard for the win back in ’79, and that was when the game was pure and winning really mattered. Our victorious team is featured in Figure 1.

Figure 1. Winners.

There are no barbers in Davidson, North Carolina.


August 1, 2006 at 4:37 pm | | everyday science, hardware

Our 12 W Ar ion laser needed a tube change.* All it took was three weeks to convince Spectra Physics and two days with the service engineer. In the end, she’s a beaut’, Clark (see Figure 1).


Figure 1. Looking good, Billy Ray. Feeling good, Louis.

*The tube is changed every 6-12 months.

2 Inch Improvements

July 21, 2006 at 11:29 am | | cool results

We use a few parabolic mirrors on our optics table to align and focus a couple of beams to a tight spot. It’s important that these mirrors be well aligned because power density is really important for our (non-linear) purposes.

The mirrors need to be replaced from time to time. Last week the big 2 inch mirror was removed, as shown in Figure 1. Replacing the mirrors can be a little

Figure 1. It’s dirty, also the coating is improper.

worrisome. Of course, there is no signal without the mirror in place, and proper alignment can be difficult because one of the beams is almost invisible. No worries, though. Once the system was working again, we got twice the previous signal, as shown in Figure 2. 2x is mighty fine.

Figure 2. Sort of hard to tell if this is good or bad. It’s OK.

Thermite: A Classic

July 18, 2006 at 11:46 pm | | lab safety, science and the public

There are a handful of reactions used almost exclusively to convince undergrads that chemistry is hip and/or cool. You’ve got your oscillating reactions, exploding hydrogen balloons, and all sorts of pretty colors turning clear. But, the granddaddy of them all is the thermite reaction. (Our friend Dylan at Tenderbutton contributed the melting slot machine).

One of the summer classes just fired off this classic reaction, and I happened to be there to record it. Check it out.


Impressive Caleb, but check out the masters.

Easy on the Eyes

July 11, 2006 at 11:50 am | | cool results

I work with fluorescent proteins. Can you tell which FPLC fraction contains my sample? Not only can you see the purple fraction of victory, but the ones that follow are a little green with an immature form of the protein. See Figure 1.


Figure 1. Sweet jesus, that’s some good ‘tein.

Lab Agriculture

July 6, 2006 at 3:49 pm | | everyday science

I like to have a little life in lab. So, I plant various crops. In particular, cotton it a nice choice for any budding scientist, as shown in Figure 1. A nice pepper plant is also a good idea. The pepper is well suited for indoor growth, as shown in Figures 2 and 3.


Figure 1. God’s Q-tip.

pepper 11.JPG

Figure 2. Great stems.

pepper 21.JPG

Figure 3. Right after this picture was taken, my dog was run over by a tractor and a horse kicked my father.

f=e^(very complicated)

April 12, 2006 at 10:37 pm | | everyday science, software

Dealing with engrained technology can be a little frustrating. Many years ago, a grad student wrote a program in LabView to fit Gaussians and exponentials. This is a simple problem, and there are many fine programs for dealing with numerical analysis. The problem with LabView is that it isn’t one of them. As shown in Figure 1, it gets a little complicated.

Figure 1. This is not even half of the damn thing.

To be fair, it does work. It fits mighty nicely after it is debugged and running, as shown in Figure 2. As my co-worker says, “When it works it works well.”


Figure 2. A good fit.

Raving with Acrylic teef?

March 29, 2006 at 2:28 pm | | cool results, nerd


The consequences of snowboarding continue. As shown in Figure 1, it looks like acrylic behaves more like water than delicious tonic water under UV light. It’s too bad. I prefer homogenous teef.


Figure 1. Inhomogenous teef.

I am practicing several dance moves enriched with head shaking to minimize teef exposure, as shown in Figure 2.


Figure 2. The Cobra: a popular dance routine.

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