Blagh posts!

  • 01 Jan 2016 » How to build a package installer on OS X for the Cantera MATLAB interface
  • To make it easier to install certain portions of Cantera onto Macs, rather than having to install XCode and build from the source, it is possible to create an installer package. These instructions document how to do so for the MATLAB interface portion only. The user who wishes to actually build the installer will, of course, require XCode. However, downstream users shouldn’t need it.

  • 01 Jan 2016 » How to set up an encrypted .netrc file with GPG for GitHub 2FA access
  • Enabling 2 factor authentication on GitHub is a good way to protect your data, but unfortunately, it means you can’t use your password to login at the command line on Linux for pushes and pulls to HTTPS repositories. You can set up a special .netrc file to enable 2FA login from the command line.

  • 01 Jan 2016 » Installing Cantera on Ubuntu with Intel Compilers UPDATED!
  • Well, it is now 2 years since I wrote my original post on how to install Cantera with the Intel compilers, and things have changed. For one, Ubuntu has been upgraded (and will be upgraded again this summer); for another, there is a new version of Cantera to work with. Actually, there are two new versions, if you count the master branch stored at GitHub.

    This post is intended to be an update on how I install Cantera on Ubuntu using the Intel compilers. Due to some handy features in the current developer’s version, I’m going to describe instructions for the master branch. If you want the stable version, go back to the old post and use the instructions there. On with the building!

  • 01 Jan 2016 » How to build SUNDIALS 2.6.2 with Intel compilers and CMake
  • The removal of the old configure build system for SUNDIALS means that CMake must be used. This requires a few different settings than my previous posts. The commands below worked for me on Ubuntu 14.04.1 with the Intel version 15 compilers.

  • 20 Mar 2015 » How to install new Python wheels on Windows 7
  • Christopher Gohlke’s website for Python packages for Windows (he hosts many, but the most popular are probably numpy and scipy) now distributes wheels instead of exe files. This means we need the most recent version of pip and a new procedure to install them. Here’s a procedure I use to simplify installing dependencies.

  • 02 Sep 2014 » How to position images in Beamer absolutely
  • In Beamer, it is useful to position images absolutely. There are many ways to do this, but one simple one-liner can be done with tikz.

  • 24 Aug 2014 » How I set up a Cantera development environment on Windows 7
  • Setting up a development environment for Cantera on Windows 7 can be a little trickier than on Linux. This post contains instructions for how I set up my development environment on Windows 7.

  • 21 Aug 2014 » How to build Sundials on Windows 7
  • SUNDIALS is a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers. It is useful for many problems, and is needed to perform sensitivity analysis in Cantera. It can be a pain to install on Windows, so here is my procedure for installing on Windows 7 x64.

  • 13 Apr 2014 » Use pax to Extract and Include Links from External PDF files in LaTeX on Windows
  • I want to include the documentation for one of my programming projects in my thesis. The documentation is generated by Sphinx, which can generate LaTeX output. I compiled that output to PDF, which is relatively easy to include in a separate LaTeX file with the pdfpages package. Unfortunately, including a separate PDF file in this manner breaks all the internal and external clickable links in the included PDF. The solution is an experimental Java program called pax. Pax reads the PDF file before it is included and generates a .pax file. pdfTeX reads the .pax file when it includes the PDF and re-generates all of the links.

  • 07 Apr 2014 » Fixing Blank Notepad++ File Icons
  • I had a problem recently that the file icons in Windows Explorer for all the filetypes set to open in Notepad++ were coming up as the blank icon. To fix the issue, I had to reset the icon handler for Notepad++. I’m not sure if this was related to an update for Notepad++, or something I did.

  • 25 Mar 2014 » Using the same font for numbers in math mode in LaTeX
  • It really bugs me when numbers are typset with two different fonts on the same line, say in MS Word if you type 0.01 in the text and then the same in an equation field, they won’t look the same because they use different fonts. For my dissertation (written in LaTeX), I wanted to be sure to avoid this pitfall. Unfortunately, it is rather more complicated than it seems on the face. First, you must use XeLaTeX (which I am). Second, the packages fontspec and unicode-math are necessary. fontspec lets you set the main body font, while unicode-math lets you control the fonts used in math environments (between $, or in an equation environment, etc.). However, by default, unicode-math will typeset all of the numbers in whatever font you choose with that package so the default must be changed.

  • 24 Mar 2014 » Various tricks for using the LaTeX packages caption and floatrow
  • Today I had two problems with clashes between the floatrow and caption packages. The first was regarding hyperlinks and the other was regarding spacing of the subcaption of subfigures.

  • 07 Mar 2014 » How to fix broken hyperlinks to equations in LaTeX
  • While writing my dissertation in LaTeX, I was having a problem that some sub-equations were not linking to the correct place. The solution is to load the mathtools package before the hyperref package. This question on TeX.SX showed the way, even though I’m not using the \numberwithin{equation}{section} line.

  • 30 Jan 2014 » How to Install Arara with SumatraPDF Support
  • Arara is a cross platform build system written in Java. It is intended for use with TeX and various derivatives thereof, but can really be used for any build process. I’m using it to help write my dissertation in XeLaTeX. Installation is a little bit of a pain on Windows, so here are some notes to ease the process.

  • 13 Jan 2014 » How to use git-svn to rebase in a loop
  • I’m working on developing for an open source project right now. The source code is stored in a Subversion repository, but my preferred version control manager is Git. I use git-svn to access the repository so that I can still use Git as my version control.

  • 11 Jan 2014 » Installing NumPy/SciPy on Ubuntu 12.04.3 from scratch/source with Intel compilers
  • Update: The following procedure will work on Ubuntu 14.04.1 as well.

    This post will explain how to install Numpy and Scipy on Ubuntu 12.04.3 with the most recent Intel compilers as of this writing (2013 SP1 Update 1).

  • 11 Jan 2014 » Fixing small Notepad++ icons
  • I was recently annoyed by having the wrong icon for certain files that should open with Notepad++.

  • 08 Jan 2014 » Installing Cantera on Ubuntu 12.04.3 from scratch/source with Intel compilers
  • My lab typically uses the CHEMKIN-Pro software from Reaction Design to perform simulations of our experiments. Unfortunately, CHEMKIN-Pro is closed source and does not include a number of features I have found useful for my research. Thus, my labmate and I have recently endeavored to install a separate software package on our Ubuntu 12.04.3 server to perform these simulations.

  • 12 Dec 2013 » Internet Explorer Starts Opening Text Files
  • On Windows 7, Microsoft Office 2010 and 2013 will take over the file association for text-like files. The Office installer sets the default handler to use Office XML Handler for anything that was associated with Notepad++.

  • 15 Aug 2013 » Problems with libstdc++ on Ubuntu when using Intel Fortran Compiler 11.1
  • Lately, we’ve had a problem on our computational server in the lab when trying to link custom solvers to the CHEMKIN-Pro libraries. When the compiler runs, it complains about undefined references to a symbol.

  • 15 Jul 2013 » Installing Jekyll on Windows
  • Been trying to migrate this site to use Jekyll (http://jekyllrb.com) today and finally got it working with Pygments for code highlighting.

  • 06 Dec 2012 » Entering complicated n-ary Operators in Word Equation Editor 2010 or 2007
  • When adding integrals or sums to formulas in Word 2010 or 2007, the command \sum or \int will give the correct symbol, but it will not stretch to fit the argument. To avoid having to go to the toolbar and add the symbol directly, simply type \int\ofSpacefunctionSpace, where Space indicates a press on the spacebar, and where function indicates the function you wish to show. If you have a more complicated argument (for instance, one involving an operator such as plus or times), use the syntax \int\ofSpace\beginSpacefunction\endSpaceSpace.

  • 31 Jul 2012 » Get a Spotify account without Facebook connection
  • Spotify, the (supposedly, I just got an account) (Update: It is excellent, and I highly recommend paying for premium) excellent music streaming service, offers free streaming stations to your mobile device and computer, similar to Pandora. Since they just updated their Android app, I decided I wanted an account, but found that the only way to get one was to connect to Facebook. Since I didn’t want to do that, a bit of googling found this link, which details how to sign up for a German account without connecting to Facebook, then changing your country once you have an account. These instructions worked great, except I had to go to the “Subscriptions” tab of my account to actually change my country, by giving them a credit card or PayPal. Since I intend to get the premium service if I like it, I didn’t mind this, but you can delete the payment information if you so wish after you change your country.

  • 18 Jul 2012 » How to enable journal abbreviations in Mendeley bibliographies
  • UPDATE (10/10/2013): The newest version of Mendeley (1.10.1) now supports journal abbreviations, so go out there and upgrade!

  • 27 Feb 2012 » Send a text message from MATLAB
  • User Ke Feng has posted a MATLAB script to use the sendmail function within MATLAB to send a text message to US based mobile numbers.

  • 18 Jan 2012 » Please Oppose SOPA and PIPA!
  • Today there are many huge websites, including Google and Wikipedia who are blacking out their homepages to oppse two acts before Congress called SOPA and PIPA. Although I will typically have no desire to discuss politics on this forum, I want to make an exception to show my opposition to these bills as well. More formally known as the Stop Online Piracy Act (in the House) and the PROTECT IP Act (in the Senate), the details of them are too gory to go into in what I intend here to be a short post. If you want all the details, go here to Reddit or here to The Verge.