All Recent Posts

  • How to build a package installer on OS X for the Cantera MATLAB interface
    Posted in Research Revealed! on 01 Jan 2016

    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.

  • How to set up an encrypted .netrc file with GPG for GitHub 2FA access
    Posted in Research Revealed! on 01 Jan 2016

    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.

  • Installing Cantera on Ubuntu with Intel Compilers UPDATED!
    Posted in Research Revealed! on 01 Jan 2016

    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!

  • How to build SUNDIALS 2.6.2 with Intel compilers and CMake
    Posted in Research Revealed! on 01 Jan 2016

    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.

  • How to install new Python wheels on Windows 7
    Posted in Research Revealed! on 20 Mar 2015

    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.

  • How to position images in Beamer absolutely
    Posted in Research Revealed! on 02 Sep 2014

    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.

  • How I set up a Cantera development environment on Windows 7
    Posted in Research Revealed! on 24 Aug 2014

    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.

  • How to build Sundials on Windows 7
    Posted in Research Revealed! on 21 Aug 2014

    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.

  • Confined Catalysts Last Longer
    Posted in Research Revealed! on 30 Apr 2014

    I was recently appointed to be a member of the EFRC newsletter editorial board. As part of my duties, I wrote an article summarizing some research from Prof. Petra E. de Jongh’s lab at the Utrecht University. The article is available on the EFRC newsletter website,

  • Use pax to Extract and Include Links from External PDF files in LaTeX on Windows
    Posted in Research Revealed! on 13 Apr 2014

    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.

  • Fixing Blank Notepad++ File Icons
    Posted in Research Revealed! on 07 Apr 2014

    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.

  • Using the same font for numbers in math mode in LaTeX
    Posted in Research Revealed! on 25 Mar 2014

    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.

  • Various tricks for using the LaTeX packages caption and floatrow
    Posted in Research Revealed! on 24 Mar 2014

    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.

  • How to fix broken hyperlinks to equations in LaTeX
    Posted in Research Revealed! on 07 Mar 2014

    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.

  • The Advantage of Renewable Fuels in High-Efficiency Engines
    Posted in Research Revealed! on 14 Feb 2014

    I was recently appointed to be a member of the EFRC newsletter editorial board. As part of my duties, I wrote an article summarizing some research from Prof. Rolf Reitz’s lab at the University of Wisconsin. The article is available on the EFRC newsletter website,

  • How to Install Arara with SumatraPDF Support
    Posted in Research Revealed! on 30 Jan 2014

    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.

  • How to use git-svn to rebase in a loop
    Posted in Research Revealed! on 13 Jan 2014

    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.

  • Installing NumPy/SciPy on Ubuntu 12.04.3 from scratch/source with Intel compilers
    Posted in Research Revealed! on 11 Jan 2014

    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).

  • Fixing small Notepad++ icons
    Posted in Research Revealed! on 11 Jan 2014

    I was recently annoyed by having the wrong icon for certain files that should open with Notepad++.

  • Installing Cantera on Ubuntu 12.04.3 from scratch/source with Intel compilers
    Posted in Research Revealed! on 08 Jan 2014

    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.

  • Internet Explorer Starts Opening Text Files
    Posted in Research Revealed! on 12 Dec 2013

    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++.

  • Problems with libstdc++ on Ubuntu when using Intel Fortran Compiler 11.1
    Posted in Research Revealed! on 15 Aug 2013

    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.

  • Installing Jekyll on Windows
    Posted in Research Revealed! on 15 Jul 2013

    Been trying to migrate this site to use Jekyll ( today and finally got it working with Pygments for code highlighting.

  • Entering complicated n-ary Operators in Word Equation Editor 2010 or 2007
    Posted in Research Revealed! on 06 Dec 2012

    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.

  • Get a Spotify account without Facebook connection
    Posted in Research Revealed! on 31 Jul 2012

    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.

  • How to enable journal abbreviations in Mendeley bibliographies
    Posted in Research Revealed! on 18 Jul 2012

    UPDATE (10/10/2013): The newest version of Mendeley (1.10.1) now supports journal abbreviations, so go out there and upgrade!

  • Why does coffee spill when you're walking?
    Posted in Research Revealed! on 03 Jun 2012

    We’ve all been there - walking back to your table in Starbucks, hot mug of coffee in hand, trying to catch the eye of the cute girl by the window when, whoops! Coffee everywhere! Given the (probably) millions of hipsters afflicted by this scenario on a yearly basis, it seems surprising that very little research has been done into the dynamics of why the coffee ends up on on your skinny jeans instead of staying in the cup where it belongs. Never fear though, because a graduate student from the University of California at Santa Barbara has recently published a study examining the mathematics and fluid dynamics behind the spilled cup of coffee.

  • A new method for estimating secondary mass savings in vehicles could offer improved fuel economy
    Posted in Research Revealed! on 19 May 2012

    A significant determinant of the fuel economy of a vehicle, in particular automobiles, is the gross vehicle mass (GVM). Reducing the GVM can offer substantial improvements in fuel economy, varying (depending on the estimate) between 2-8% improvements in fuel economy for each 10% savings in mass. Manufacturers have many methods to reduce the GVM, including material substitution (plastic for metal) and novel designs. Although these techniques can result in substantial primary mass savings, they actually represent an underestimate of the total possible mass that can be removed. This is because as the automobile is made lighter, structural components can also be made lighter, resulting in secondary mass savings (SMS). So, for instance, a lighter car would require a smaller and lighter transmission, or smaller and lighter brakes. A new paper from Alonso et al. discusses a new method for manufacturers to estimate SMS more accurately.

  • Send a text message from MATLAB
    Posted in Research Revealed! on 27 Feb 2012

    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.

  • How the Little Ice Age was Triggered and Sustained
    Posted in Research Revealed! on 30 Jan 2012

    During the late Middle Ages, many of the glaciers in Artic Canada and Iceland experienced abrupt increases in their size, due to substantially cooler summer months. This advance of glaciers has been termed the Little Ice Age (LIA), and the expansion of the glaciers has only been undone in the last decade or two. There are several hypotheses as to the cause of the glacial expansion during the LIA, but until now, no definitive answers have emerged. However, the retreat of these glaciers over the last few decades has allowed scientists to study the plants that were killed by the advance, determine the dates of the expansion of the glaciers, and connect the timing with global events to try to assign a cause to the LIA.

  • What Role Does the Government Play in Introducing a New Biofuel to Market?
    Posted in Research Revealed! on 18 Jan 2012

    One of the ways in which climate change may be mitigated, and domestic energy security improved, is to create a new biofuel to power our cars and trucks that does not rely on traditional petroleum sources. One such fuel, ethanol, is already widely blended into gasoline in the US; another, biodiesel, is on sale in many fueling stations as a standalone fuel for diesel engines. However, due to concerns over the long-term sustainability of current production processes for biofuels (and for ethanol in particular), researchers are investigating a so called “second-generation” of biofuels. These include fuels that can be made from cellulose (the material that makes up plants’ cell walls, and comprises most of the mass of a plant) as well as fuels made from novel feedstocks, such as algae. My research in particular has focused on one such second-generation biofuel, called biobutanol. Biobutanol has many technical advantages over ethanol, but biobutanol has not been approved by the Environmental Protection Agency (EPA) for use in road vehicles. In a recent review, Slating and Kesan discussed the regulatory hurdles biobutanol must clear to be approved for everyday use.

  • Please Oppose SOPA and PIPA!
    Posted in Research Revealed! on 18 Jan 2012

    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.

  • Economists Try to Determine if Increasing Energy Efficiency Always Increases Sustainability
    Posted in Research Revealed! on 17 Jan 2012

    In the race to stop global warming and improve energy security, one of the strongest initiatives politicians can rely on is regulating the energy efficiency of an economic sector, such as manufacturing, energy generation, or transportation. Increasing energy efficiency allows us to “do more with less”, implying that increasing energy efficiency is always a good thing. Not so fast, claim some economics researchers from the UK. In a study published in 2009, they found that if energy efficiency of the Scottish economy were increased, the energy consumption of Scotland would increase as well. The authors attribute this to two effects, called rebound and backfire.

  • Rotating Detonation Engines the 'wave' of the future?
    Posted in Research Revealed! on 10 Jan 2012

    The desire for energy security and (lack of) climate change are driving two avenues of innovation to power the next generation of vehicles. The first avenue is to invent new fuels, such as bio-fuels, that change the supply dynamics of the industry. The second avenue is to invent entirely new engine concepts to improve efficiency. One such concept, using detonations (as opposed to deflagrations) to combust fuel and air mixtures, has been investigated since the 1940’s. Using detonations allows for much higher efficiency engine operation. One of the most common types of detonation engines is the Pulsed Detonation Engine (PDE). Unfortunately, due to many difficulties including the intermittent nature of thrust from such engines, no PDEs have been commercially produced to date (although the concept has flown in an Air Force test plane).