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Software for PHY and PAM Modules

The information on this page is intended to help students who wish to use their own computers for course work. It is likely to go out of date fairly rapidly so please report corrections and issues to CDHW (Mac OS X) JMR (Linux). Neither of us use Windows, but send recommendations/corrections to CDHW and we'll add them below.

Quick-links to sections on this page:

C compiler

Useful for PHY2027, PHY2004 and PHY3134

Linux

Linux distributions come with the Gnu Compiler Collection (GCC), and the GNU development tools. We have a separate page with details of compiling and debugging under linux.

Mac OS X

We recommend Xcode (freeware).

An installation of Xcode requires ca 1GB of disk space. It is packaged on the 'Developer Tools' disk which comes with every copy of Mac OS X. It is also available for download if you register for online membership of Apple Developer Connection which is free. We use Xcode 3.2 because it is compatible with both OS X 10.6, which is what we current use on the 'MacPhy-nn' machines.

  1. Obtain a copy of the 'Developer Tools' disk/image.
  2. Mount the image and run the 'Xcode Tools' installer.
  3. If asked, select the boot disk "Macintosh HD" as the install location.
  4. Wait tens of minutes for the installation to proceed.
  5. The Xcode application is located in:
    • /Developer/Applications/

The project template used our taught modules can be installed placing the folder Developer and its contents:

into '/Library/Application\ Support/'.

Windows

One possibility is Microsoft Visual C++ (not C#) which is apparently available at no charge to students, but check that the terms and conditions are acceptable to you:

There is a free software tool called MinGW which contains the Gnu Compiler Collection (GCC), and to which you can add the IDE Visual-MinGW.

Gnuplot

Mac OS X

Follow the installation instructions for Octave (below).

LaTeX and TeX

'LaTeX is a document preparation system for high-quality typesetting. It is most often used for medium-to-large technical or scientific documents but it can be used for almost any form of publishing.' Refer to one of the many introductory guides for more information.

Linux

Your system distribution probably includes a TeX system including LaTeX. Check your usual software source for a TeX package; otherwise install TeX Live directly. For a nice graphic frontend install:

On Linux systems, it is quite likely that dictionaries for spell-checking are already present because other programs use the same spell-check engine. However, if you need to add dictionaries:

  1. Start and quit TexWorks. (This creates the dictionary directory for the next steps.)
  2. Download the dictionary files en_GB.dic and en_GB.aff, there are copies here at Exeter.
  3. Copy both dictionary files to the folder: /usr/share/myspell/dicts (This will typically require administrative privileges.)

Mac OS X

The MacTeX distribution contains everything you will need, including a complete TeX system with LaTeX itself and integrated editors (e.g. TeXworks) to facilitate document preparation.

  1. Download the MacTeX-2011 Installer (ca 1.8GB!) from the MacTeX website.
  2. Double-click the MacTeX.mpkg installer and the installation will be placed into a new folder /Applications/TeX/.

To install the spelling dictionaries:

  1. Start and quit TexWorks. (This creates the dictionary directory for the next steps.)
  2. Download the dictionary files en_GB.dic and en_GB.aff, there are copies here at Exeter.
  3. You should find a TeXworks resources folder inside the Library folder of your Home folder. There should be a dictionaries subdirectory, but it is initially empty. Move en_GB.dic and en_GB.aff files into the empty folder 'Home:Library:TeXworks:dictionaries' , and then re-start TeXworks.

Windows

We recommend that you use the TeXlive LaTex/TeX distribution and use TeXworks as the front end:

Follow these steps:

  1. Download the 'install-tl.zip' compressed folder, there is a copy here at Exeter.
  2. Extract files (by default the files will be placed in the folder with the same name and the same location)
  3. Start the 'install-tl' batch file.
  4. Start and quit TexWorks. (This creates the dictionary directory for the next steps.)
  5. Download the dictionary files en_GB.dic and en_GB.aff, there are copies here at Exeter.
  6. Copy both dictionary files to the folder: C:\Documents and Settings\<username>\.texlive2009\texmf-config\texworks\dictionaries. N.B. The dictionaries folder may have a slightly different path for pre-XP versions of Windows.

NOTE. The installation downloads ca 1GB of files and will take a noticeable time (30mins to 1 hour, depending on the speed of the Internet link). If the installation takes place within the University firewall system two environment variables have to be set to allow communication with your computer. The modifications are the following: From the Control Panel of your computer select 'Performance and Maintenance' and then 'System'. In the opened window select Tab 'Advanced' and then 'Environment Variables'. This will open a new window where variables can be added. Select 'New' from 'User variables' and type in: ftp_proxy for variable name, and webcache.ex.ac.uk:8080 for variable value. Create one more variable with entries: http_proxy and webcache.ex.ac.uk:8080

Octave

Introduced in PHY1028 used in all stages of physics programmes for mathematics, analysis of experiment data, and project work.

Linux

  1. Install Octave by following the instructions at the OctaveForGNULinux site.
  2. Install packages as described below.

Mac OS X

Although it is possible to use the Apple X11 system as a display for Octave/Gnuplot, Aquaterm behaves in a more Mac-like manner when it comes to things like copy-and-paste of the graphs.

  1. Download the Aquaterm 1.0.1 Installer from the Aquaterm website.
  2. Double-click the AquaTerm.pkg installer and install AquaTerm into the /Applications folder.
  3. Download Octave-OS_X.zip and expand it by double-clicking it.
  4. Drag the applications it contains (Octave.app and Gnuplot.app) to your /Applications folder. This version of Octave has already had the 'miscellaneous' and 'optim' packages installed.

If you are feeling adventurous, you can install the latest version of Octave by getting it from Octave-Forge. However, the latest version at the time of writing is 3.4.0 and it seems to take a long time, ca 45 seconds, for the first 'plot' command to connect to gnuplot, so we are sticking with version 3.2.3 for now.

Windows

  1. Go to Octave-Forge website
  2. Download the installer Windows installer (Octave and Octave-Forge)
  3. Install packages as described below.

Packages for Octave

  1. Go to the Octave Packages site
  2. Download the following packages, and place in the Octave working directory:
  3. Start the Octave application and install the packages by typing:
    • pkg install -global miscellaneous-1.0.11.tar.gz
    • pkg install -global struct-1.0.9.tar.gz
    • pkg install -global optim-1.0.17.tar.gz
    (If your browser 'helpfully' uncompressed the files when downloading them the '.gz' will not be needed.)

The package version numbers increment every few months, modify the install commands to match the ones you downloaded.

Office (Word-processor, Spreadsheet, etc.)

So-called 'office productivity' software is an inescapable part of life, and most students will have learned how to use it at school. An optional class will be arranged in the Summer Term for those who wish to develop and/or refresh their skills. The market leader is currently Microsoft Office. This is available for Macs and Windows, and is supported by Academic Services. A student discount version is available but it is still quite expensive. As an alternative we recommend Libre Office:

All OS Versions

  1. Download from the Libre Office Download site.

Once Libre Office is installed, remember to run the en-GB language pack installer.

Drawing Packages

There are two basic types of drawing packages: bitmap-representation and vector-representation. Devices such as cameras and scanners produce bitmaps and to manipulate these you will need a 'bitmap graphics' application. Vector graphics formats are usually best if you are constructing technical diagrams and illustrations. Graphics packages are not easy to use, practice on simple diagrams well before that project needs to be handed-in. Graphics packages will not endow you good taste or artistic skills, but fortunately clarity and simplicity are the most important qualities of scientific diagrams.

Inkscape (Drawing - Vector Graphics)

Introduced in the IT Skills section of PHY1028, PHY1029, and PHY1030.

All Platforms

  1. Download and install the 'Stable Release' for your operating system from the Inkscape.org site.
  2. Refer to the tutorials at the Inkscape Tutorials Weblog.

Gimp (Drawing - Bitmap Graphics)

Used in in the Astrophysics Skills section of PHY1029.

All Platforms

  1. Download and install the 'Stable Release' for your operating system from the GNU Image Manipulation Progam site.
  2. Refer to the tutorials on the GIMP Tutorials page.

Spice Simulator

Useful for PHY2028 and PHY3128

Linux

Your best bet is Spice Opus (freeware). Alternatively try Ngspice (OSS, freeware).

Mac OS X

We recommend MacSpice 3f5 (freeware).

  1. Download the MacSpice.dmg
  2. Double-click MacSpice.dmg which will mount the image as a volume.
  3. Drag the MacSpice application to your /Applications folder.

Windows

You have three obvious options.

                                                                                                                                                                                                                                                                       
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