Take a Peek at Some of the Freshest Projects Around
For this last project, I thought I'd throw in something for the mad scientists out there. According to the home page, GAMGI's goals are to provide the community with a free software package to construct, view and analyze atomic structures, and to make it as powerful and as simple to use as possible. GAMGI's developers also are probably the most hard-core free-software advocates I've seen since Stallman himself. Scattered throughout the installation instructions and user manuals are loads of exhortations to harness the power of source and compile it yourself, as well as many other passionate free-software-related endeavors.
Here are GAMGI's stated aims from these obviously passionate developers:
GAMGI aims to be useful for: 1) the scientific community working in atomistic modeling, which needs a graphic interface to build and analyze atomic structures; 2) the scientific community at large, which needs a graphic interface to study atomic structures and to prepare images for presentations; 3) teaching the atomic structure of matter in schools and universities, even inviting students to run GAMGI at home; 4) science promotion, in exhibitions and science museums.
Installation can be a little tricky for the newbie, but anyone comfortable with things such as make's role or symlinking should be okay. GAMGI is designed to be as standardized as possible in its requirements, and it should work with any standard X11 installation, though it does have one or two esoteric library requirements. Glib and GTK should be fine with most systems, as well as FreeType, but you may have to seek out and install Expat and Gtkglarea.
For those seeking a simple binary, an RPM is usually provided at GAMGI's download page. The RPM is designed to be LSB-compliant and should convert easily with a utility such as alien for Debian-based systems. At the time of this writing, however, the link was taken down, so please check the site again at a later date or bug the developers. For those seeking to compile from source (keeping the developers happy), a few more steps than your run-of-the-mill tarball need to be taken. First, it's easiest if GAMGI is extracted and compiled somewhere public, such as /usr/local/src, as you probably will want to symlink to the compiled binary later. Grab the tarball from the given link and extract it.
Once extracted, simply open a console and make your way to the src directory under the new folder. Now run the command make, and if all goes well, GAMGI should compile successfully. If make returns errors, check that you have all of the needed libraries installed. If they are, your shared libraries may be installed to another path than what GAMGI's make script is expecting. Edit the make_local file in the src directory and continue. Once compilation has completed, you can run the gamgi binary from the src directory, or symlink to it for easier access with the command:
# ln -s /usr/local/src/gamgi-(version)/src/gamgi ↪/usr/bin/gamgi
Once all that nasty stuff is out of the way, the weird science can begin. Some interesting templates and tutorials have been included in GAMGI's dat directory. From the menu, choose File→Import and choose an atomic structure at random. Ever wondered what adrenaline looks like? Try molecule/drugs/adrenaline.xml. Presto! An adrenaline molecule appears in the main black window. To play around with the view, press and hold the left, middle or right mouse buttons and move the mouse around. The left button controls rotation, the middle buttons controls the X and Y axes, and the right button controls the zoom function. You have to admit, it is pretty cool to play with!
To explore further, there are a bunch of other menus related to all things atomic, but I haven't the foggiest idea how to use any of them (or what they even do). I think this is best left to the atomic scientists. Check the doc directory for further instructions, and have a read through the well-constructed HTML manual pages, or head over to the GAMGI home page and converse with fellow white-coated boffins. Either way, I'm sure I'll sleep easy tonight now that I know what a propane molecule looks like and have confirmed that I am, indeed, a geek!
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John Knight is a 23-year-old drumming, climbing and music-obsessed maniac who usually can be found squeezing Audacity to within an inch of its life.
John Knight is the New Projects columnist for Linux Journal.
Practical Task Scheduling Deployment
July 20, 2016 12:00 pm CDT
One of the best things about the UNIX environment (aside from being stable and efficient) is the vast array of software tools available to help you do your job. Traditionally, a UNIX tool does only one thing, but does that one thing very well. For example, grep is very easy to use and can search vast amounts of data quickly. The find tool can find a particular file or files based on all kinds of criteria. It's pretty easy to string these tools together to build even more powerful tools, such as a tool that finds all of the .log files in the /home directory and searches each one for a particular entry. This erector-set mentality allows UNIX system administrators to seem to always have the right tool for the job.
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