Installing RUMP/Genplot in Linux! (finally)

Posted in Linux, School, Science! by Cameron Kopas | No Comments »
My research requires that I use Rutherford Backscattering Spectroscopy to analyze samples at least a few times a week.  I use this amazing technique to characterize multilayer samples, and regularly get information such as: composition by layer, contaminants present, layer thickness/structure, and crystallinity.  There is a powerful (albeit command line) software package available for analyzing these files, called RUMP/Genplot, but it has so far been only available for Windows. (well it was “available” for Linux, DOS, and OS/2, but the professor who wrote it never responded to my emails requesting a Linux copy).
Anyway, I was very pleased to learn recently that the program has gone from a paid license, to being completely free.  Even more recently, they posted the source filename (previously completely hidden) with a note that an experienced user should be able to find the file.   This meant that I could perform data analysis on my own computer, and not have to run down to the iBeam lab every time i wanted to re-check some results!
Well, needless to say, I finally managed to get RUMP/Genplot for RBS analysis compiled on Linux, I suspect it will work the same way on OSX, Solaris, or any of the exotic UNIX variants that the program is compatible with.

first, download the source code tarball at:
http://www.genplot.com/downloads/linux/cgs32j.tar.gz

(the filename might have to be updated with future versions)

if the user is on a mac, they need to install Xcode first (free, form the apple app store https://developer.apple.com/xcode/ ).  any *NIX distribution should already have a c compiler installed.

due to the nature of the makefiles, you have to copy it to the “home” user directory, not any downloads directory, so in the terminal, cd to the downloads directory, then;  (note, the $ preceding each line indicates that this line is to be entered into the terminal, it is not a command itself)

$  mv ./cgs32j.tar.gz ~/cgs32j.tar.gz
move to the main user directory
$  cd ~/
then unzip

$ tar -xzf cgs32j.tar.gz

then move into the new directory
$  cd ./cgs

now you need to choose the correct makefile for your operating system.

$  ls

will output a list of the files in the directory.  makelnx is “Makefile for Linux”  and makeosx is “makefile for OSX”

choosing the makefile for your system,  run it using make -f.  the -f flag allows you to choose a particular file, otherwise “make” will be confused by the multiple files available

$  make -f makelnx

wait for that to finish, then as long as it ends with “leaving directory[…]”  and does not spit out any errors, its done.
The program is all command line, so it must be launched from the terminal each time,  to launch, open a terminal, cd to the ~/cgs/bin directory and start it using:
$  ./rump

then you can use the program as normal.

sweet!  maybe now i’ll write a “getting started with RUMP/GENPLOT” article, since learning basic analysis is horrible.

Morning Science

Posted in Life in General, Science! by Cameron Kopas | No Comments »

two  pictures are below, one of a clear shirt, and another of the same shirt as viewed in a foggy bathroom mirror.

Now, putting on this shirt in the morning, I was very excited to see that there was no purple visible in the mirror’s fogged-up reflection, but the blue lines are fine (this was even more exaggerated a minute or so before I took the picture, look toward the top of the image for the most severe effect).

Even if you know it is there, and wanted to, you can’t really see any purple stripes in the fog.  I think the problem is almost the same as astronomers had seeing into forming stars- dust (or in our case, condensed water vapor) blocks light. The reason for this would be that shorter wavelengths are more easily blocked than longer ones (purple being of shorter wavelength than blue which is shorter than green; yellow; orange; red; and so on).

Astronomers solved this problem by instead of looking at the visible wavelengths, building telescopes which record (higher wavelength) Infrared light data.  They could then see through those bothersome clouds of dust surrounding all of the cool stuff going on at the birth of a star.

Unfortunately, I don’t have infrared-vision yet, so for now I’ll have to settle for just not looking for purple in a foggy mirror.

Engineering!

Posted in Life in General, Science! by Cameron Kopas | No Comments »

Moved into my apartment yesterday morning, and of course, I forgot plenty of things.  One of these happened to be a shower curtain.

duct tape and plastic bags

Well while it doesn’t look very effective, the duct-tape and space bags worked great.  No water escaped the tub.  I’m still going to get a real shower curtain though, and as soon as possible.

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