For a while now I’ve been dying to share some of the new nanostructures I’ve discovered during ion-assisted vapor deposition of CI(G)S thin films. My paper was published in the Journal of Applied Physics last fall (sorry for the blog outage over the winter-break). The paper is titled: “Nanostructured light-absorbing crystalline CuIn(1–x)GaxSe2 thin films grown through high flux, low energy ion irradiation;” http://dx.doi.org/10.1063/1.4823987. There are a lot of unanswered questions about the work that leaves me dreaming up different solutions to how these films are growing. Read More
I have no idea why this took so long, but I finally have the code to import and output various graphs of the reciprocal space maps (RLM or Q-space) taken using the Xpert Xray diffraction system. One of the difficulties in outputting the older data has been solved by our new line-scan detector system. The data is now taken in the more simple Omega-2Theta space instead of Omega-Omega2Theta space. With the help of Mauro Sardela, the fantastic research scientist who runs the XRD lab at the Materials Research Laboratory (FS-MRL), I’ve properly translated the data into Q-space using the same equations the Xpert Epitaxy software uses.
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For years while Apple had proprietary system software, I was itching to get a Unix system underneath and have the ease of the windowing system. Well, after OsX was released, I was ecstatic. Why? Because of the ease of some tasks in Unix in comparison to other OS’s. This post is only one example of what you can do if you do a bit of research into how to use your Mac. For those who have un*x boxes, this will merely be a place-holder for a few AWK scripts for you.
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After some new scans, it appears the XRDMLread.m function I talked about is doing a pretty good job of getting the 2-axis scans into MATLAB. I was able to alter the code to accept the standard Epitaxy software’s translation to Q-space. (In Epitaxy the default is R = 0.5 I believe.) So, the following image was imported with XRDMLread.m the plotted with the standard 2-d example from the author’s website. The code was altered to output 10000xRLU units the same as Epitaxy (Panalytical). I haven’t checked all the numbers, but it’s looking ok so far. Unfortunately the color-scale looses it’s meaning as far as intensity is concerned, it appears at first glance.
Working a bit with my old q-space map code, I’m able to accomplish the following:
Note the strange love-handles the data gains. I suspect this might be due to the Gridfit function (see MATLAB files repository) I used for regridding the data. Gridfit.m uses an extrapolant method. My suspicion is it is trying to fill out the square of the data matrix and is accomplishing relatively correct values for near-by-data that is outside the scanned range. I’ll try it again with regrid or something similar in the future when I have time.
If anyone knows where the current site for XRDMLread.m is, I’d love to link to it. It appears the site may be down (graduated student I suspect). You can obtain the wonderful XRDMLread.m function and examples on the XRDMLread.m website. For now, I have to wait until I hear from the authors before I can share the file. I also don’t yet trust my icky 3D code, so I prefer not to release that until I have things hashed out. Sorry!
I’m extremely happy that Panalytical has published their XRDML file format and that the makers of XRDML.m have released their .m files for MATLAB. In the past, when Philips had the Xpert systems, the data was stuck for the most part in proprietary data formats. [You could slice the data and output in ascii- but making that work was a pain- which is why I never released that previous code.] I’m much closer to the 3d plotting now, and hope to finish it up before the thesis (my primary work which is not this plotting) is published.
Wishing you luck in you research!
It’s not often that someone goes about deciding to make a film about graduate studies. It just so happens that Thirteen (PBS-NY) has done just that. Their film “Naturally Obsessed: The Making Of A Scientist” is quite an excellent snap-shot of the struggle of graduate students to get their PhD degree and accomplish something very difficult. Of course each of our struggles is unique. We are all dealing with our own situations, with our own fields (some not even in laboratories- the horror- is that real science? hahahah).
Speaking of our own struggles, what most of the public often does not get a feel for is the absolute devotion, almost to insanity, towards finding the solutions we are looking for. Many of the comments by the graduate’s spouses touched home for me. In each of the graduates followed in this film I saw bits of myself. One thing however, that is different, is the struggle for the specific protein structure. Often that struggle is a lot less well-defined. In this situation, you either get the structure of AMPK or you don’t. I guess it’s a lot like their attempts at creating crystals. Sure, you get crystals, but if they don’t have a periodic structure, you’ll never get diffraction. In my situation, the variables in our studies are very difficult to control, and so often one doubts one’s work solely on the question of reproducibility. Many scientists struggle with this same situation. People think that doing things like “measuring temperature” is a very easy thing. In reality, it is a very very difficult thing. Especially in a vacuum. That question just arose the other day in discussing our science with a new undergraduate assistant. As we talked more and more on the difficulties of measuring temperature we all saw his eyes grow larger in wonder. The simplest of problems can often be the most difficult. How accurate do you need to measure it? What standard will you use? Do you believe your thermocouple, your thermometer, or your pyrometer? What if the emissivity of the surface changes?
This is the life of a scientist. And the film below attempts to capture the lives and struggles of a few graduate students who are hoping for a career in science. It’s a struggle. But, you have heard me say that enough. To learn more about it I strongly suggest you watch this film. For the graduate student, I warn you: you’ll see yourself in this. For those who aren’t scientists: this may end up being a comedy, and I kindly refer you to Marg Simpson’s commentary on graduate students posted earlier in this blog.
My congratulations to Thirteen for doing such an excellent job on this one hour film. They didn’t have a lot of time to share with you everything regarding our struggles and achievements, but they distilled it quite well in the time available.
Well, I’m one of those guys who believes a picture is usually worth a ton of words. I’ve got a few images to share here on the matlab code I’ve been working on for reciprocal space mapping in MATLAB. I’m still not 100% on my code right now, so I’m not sharing it for the time-being. In particular, I use an import function for .x00 slices for two-axis scans in the Panalytical/Philips XPert system. If you are using XRDML, skip the files for .x00 import that I have in other posts on this blog. In anycase, without much explanation here are the images…
In the time I’ve been doing my research work at the Univ. of IL, I’ve come across a number of graphs from various past researchers, older papers, stuck on the side of machines (calibration curves), and even hand-drawn or chart-recorder graphs in my numerous projects. The only major problem with those graphs I’ve found is that they aren’t in a digital form for further use with other data (instrument response functions) or to include in your own work as a reference. So, what to do?
Well, there’s an easy solution. It’s not the perfect solution, as it’s a bit slow, I’ll get to that in a second, but it’s a great solution to the problem, and has worked for me a number of times now. To top it off, it’s open-source, donation-ware, and cross-platform: Engauge Digitizer (see post at LifeHacker.com). Don’t let the website and lack of recent updates deter you. Tools that can do what Engauge does are few and far between. So, it is definitely worth a try. Here’s an example of how I’ve used it just the other day (prompting this post- I’ve used it for years now, but the recent use reminded me I should share it with others). [click "More" to see an example use and learn more]
Boston rocked: I’m writing this on a new iPod Touch! Filmetrics was running a drawing for those who brought samples to test! Big thankyou’s go out to Filmetrics and AVS. I will write more about the conference in a series of posts coming soon. I’m hoping everyone had a great week while I was gone.
The society formerly known as the American Vacuum Society (AVS) is holding their international conference in Boston, MA next week! And I’ll be there! [Exciting!] If you are going to be there, drop me a line on the blog and we can snag a coffee or beer together.
The programs and cards sent out may have a familiar image!
My AFM image of the CuInSe2 Bicrystals I grow in our lab won second place in the Art-Zone competition last year! It was great fun! [Thanks goes to AVS for being a fantastic organization!]
Wish me luck with my talk!!
One thing I find extremely helpful in my research, is the ability to download citations for articles my co-workers send. I like to import them into BibDesk and auto-file the journal articles by first-author. Unfortunately, not everyone has Bibtex export abilities. This isn’t too bad, as BibDesk imports most major citation files. One thing that I do abhorr, is when a major company decides not to offer a citation download option! Science Direct is the fellow who gets my wrath this evening. It’s so bad I’ve been looking for other companies who keep track of journals that have downloads for the ones that Science Direct publishes!
I wonder if you pay their absurd journal prices, if you get citation downloads…