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Some scientific tools on Linux

on Mar 09, 2016

For memory, and because I like to install a new Linux distribution too often, I wrote a very simple script that download and install some useful softwares. (Tested on my Manjaro, should work also on Arch, and some other distributions with pacman and yaourt if they exist.)
First, a description of the tools it installs :

For optics

  • Optical Ray Tracer is a small application that does ray tracing with mirrors and lenses. Written in Java, GPL license.

For all sciences

  • Kile KDE LaTeX editor, that does its job and have some cool features if you never remember how to make tables or add a croped image. I just never managed (and was to lazy to investigate) to make it find some packages even if they are supposed to be installed on my system, but that's not necessarily Kile's fault.

  • GNU Octave and Scilab, two open sources softwares supposed to do the same work than Matlab. I never used them long enough to know the differences between them, though. Sadly, I have my marks on Matlab and always end up going back to it.

  • ImageJ or Fiji is a small and useful software to easily analyse images, like having their spectrum, measuring angles or distance, setting scale... I have still to learn all its potential. Often used in the last labs I was in. Fiji is just ImageJ, with some other scripts on it.

  • Gnuplot is a command-line tool to make graphs. I wanted to learn to use it, but not yet had the occasion to take this time.

  • IPE : I love it ! I you don't want to draw your graphics on Powerpoint anymore, and are afraid of Inkscape, IPE is just what you need. It can draw the basic shapes, with several modes of "attraction" (to a grid, to the previous lines, to specific angles...), and has sufficient options of line widths, colors, etc, so that you are able to draw what you need. Also, you can write LateX in it, and export in eps (so that you have directly a pretty vectorial image in you paper).

To free your internet access

  • Unbound is a not too complicated to install DNS resolver. If, like me, your gouvernment is asking internet access providers to block some hostnames by DNS, then you just don't care. There is a lot of options, I didn't care to configure it very profoundly, I just wanted it to work.

The script


# Download Optical Ray Tracer
echo Optical Ray Tracer
wget http://arachnoid.com/OpticalRayTracer/resources/OpticalRayTracer.jar http://arachnoid.com/OpticalRayTracer/images/OpticalRayTracer_32x32.png
sudo mv OpticalRayTracer.jar OpticalRayTracer.png /usr/local/bin/

# Write the .desktop launcher
echo [Desktop Entry] > ~/.local/share/applications/OpticalRayTracer.desktop
echo Comment= >> ~/.local/share/applications/OpticalRayTracer.desktop
echo Exec=java -jar /usr/local/bin/OpticalRayTracer.jar >> ~/.local/share/applications/OpticalRayTracer.desktop
echo Icon=/usr/local/bin/OpticalRayTracer.png >> ~/.local/share/applications/OpticalRayTracer.desktop
echo Name=Optical Ray Tracer >> ~/.local/share/applications/OpticalRayTracer.desktop
echo NoDisplay=false >> ~/.local/share/applications/OpticalRayTracer.desktop
echo Path[$e]= >> ~/.local/share/applications/OpticalRayTracer.desktop
echo StartupNotify=true >> ~/.local/share/applications/OpticalRayTracer.desktop
echo Terminal=0 >> ~/.local/share/applications/OpticalRayTracer.desktop
echo TerminalOptions= >> ~/.local/share/applications/OpticalRayTracer.desktop
echo Type=Application >> ~/.local/share/applications/OpticalRayTracer.desktop
echo X-KDE-SubstituteUID=false >> ~/.local/share/applications/OpticalRayTracer.desktop
echo X-KDE-Username= >> ~/.local/share/applications/OpticalRayTracer.desktop

# Install by the usual way the next applications
echo Kile (LaTEX)
sudo pacman -S kile
echo Octave
sudo pacman -S octave
echo Scilab
sudo yaourt -S scilab
echo ImageJ
sudo yaourt -S imagej
echo Gnuplot
sudo pacman -S gnuplot

# Download IPE
echo IPE
sudo yaourt -S ipe
wget https://a.fsdn.com/allura/p/ipe7/icon
sudo mv icon /usr/lib/ipe/icon.png

# Write the .desktop launcher
echo [Desktop Entry] > ~/.local/share/applications/IPE.desktop
echo Comment[fr_FR]= >> ~/.local/share/applications/IPE.desktop
echo Comment=  >> ~/.local/share/applications/IPE.desktop
echo Exec=ipe >> ~/.local/share/applications/IPE.desktop
echo GenericName[fr_FR]= >> ~/.local/share/applications/IPE.desktop
echo GenericName= >> ~/.local/share/applications/IPE.desktop
echo Icon=/usr/lib/ipe/icon.png >> ~/.local/share/applications/IPE.desktop
echo MimeType=application/xml; >> ~/.local/share/applications/IPE.desktop
echo Name[fr_FR]=ipe >> ~/.local/share/applications/IPE.desktop
echo Name=ipe >> ~/.local/share/applications/IPE.desktop
echo NoDisplay=false >> ~/.local/share/applications/IPE.desktop
echo Path[$e]= >> ~/.local/share/applications/IPE.desktop
echo StartupNotify=true >> ~/.local/share/applications/IPE.desktop
echo Terminal=0 >> ~/.local/share/applications/IPE.desktop
echo TerminalOptions= >> ~/.local/share/applications/IPE.desktop
echo Type=Application >> ~/.local/share/applications/IPE.desktop
echo X-DBUS-ServiceName= >> ~/.local/share/applications/IPE.desktop
echo X-DBUS-StartupType= >> ~/.local/share/applications/IPE.desktop
echo X-KDE-SubstituteUID=false >> ~/.local/share/applications/IPE.desktop
echo X-KDE-Username= >> ~/.local/share/applications/IPE.desktop

# Install and configure Unbound
echo Unbound
sudo pacman -S unbound
sudo chmod -v 0777  unbound.conf
sudo echo 'server:' > /etc/unbound/unbound.conf
sudo echo '  use-syslog: yes' >> /etc/unbound/unbound.conf
sudo echo '  username: "unbound"' >> /etc/unbound/unbound.conf
sudo echo '  directory: "/etc/unbound"' >> /etc/unbound/unbound.conf
sudo echo 'interface:' >> /etc/unbound/unbound.conf
sudo curl -o /etc/unbound/roots.hints https://www.internic.net/domain/named.cache
sudo echo 'root-hints: "/etc/unbound/roots.hints"' >> /etc/unbound/unbound.conf
sudo echo 'nameserver' > /etc/resolv.conf
sudo unbound-control-setup
echo 'remote-control:' >> /etc/unbound/unbound.conf
echo '    control-enable: yes' >> /etc/unbound/unbound.conf
echo '    control-interface:' >> /etc/unbound/unbound.conf
echo '    control-port: 8953' >> /etc/unbound/unbound.conf
echo '    server-key-file: "/etc/unbound/unbound_server.key"' >> /etc/unbound/unbound.conf
echo '    server-cert-file: "/etc/unbound/unbound_server.pem"' >> /etc/unbound/unbound.conf
echo '    control-key-file: "/etc/unbound/unbound_control.key"' >> /etc/unbound/unbound.conf
echo '    control-cert-file: "/etc/unbound/unbound_control.pem"' >> /etc/unbound/unbound.conf
unbound-checkconf >> Reinstall.log
sudo systemctl enable unbound.service
systemctl start unbound.service

exit 0

Yeah, nothing very complicated, it's just to avoid doing everything by hand.

To use this script, just copy it in a new file, and then start it :

sudo ./script
Read more

Some useful links for optics/lasers

on Mar 06, 2016



  • Refractive index
    Very detailled database of a lot of optical glasses, with possibility to export the datas.
Read more

Some useful links for research

on Mar 05, 2016
  • Sci-hub

    The first pirate website in the world to provide mass and public access to tens of millions of research papers

    As a master/phd student, very useful when I work home searching for papers and don't want anymore to be stopped by paywalls. For now, it doesn't accept searching in the website itself, but pasting a url from a paper provider works just fine.

  • Library Genesis
    Russian online library giving access to a lot of scientific books. The classification by topics is quite well done and permits to choose directly a precise field of studies.

  • Directory of Open Access Journals
    Directory of Open Access Books
    Directory of Open Access Repositories
    Not really tested yet, but maybe the papers/books/data you are looking for are already in open access. It's worth a try.

Read more


on Mar 05, 2016 ·

Adventures of a physicist.

I don't know yet what I will talk about.

Read more
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21 hours ago · 2 min read ·
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