jaharvey's blog

Hello! My name is Jacob Harvey and this is my first blog post! I figured it would be best to start with an introductory post so here it goes. I am a Ph.D. graduate student in the chemistry department at the University of Massachusetts Amherst. I came to Umass with a desire to study computational chemistry and focus on, what I think is one of the earth’s biggest problems, energy research. Thus I joined Scott Auerbach’s group (samson.chem.umass.edu) as he has a number of energy related projects including studying proton transfer in proton exchange membranes (PEMs) as well as studying the formation of biofuels within a zeolite framework. My project is focused on the PEM problem. We are using molecular dynamics simulations to study thermal fluctuations and proton transfer in hydrogen bonding networks that form from oligomeric tethered functional groups (such as imidazole, triazole, and pyrazole).

When I joined the group I had only a couple of years of Fortran coding under my belt and had never been exposed to linux. In the roughly three and a half years that I have been at Umass I have grown to learn and love everything that linux has to offer. I have even become the systems administrator for our group and manage 8 desktops as well as a 40 node beowulf cluster. Our linux flavor of choice is CentOS which is a Red Hat Enterprise Linux based system. You get all the goodies of RHEL but none of the support (and none of the cost).

As I began to become more comfortable with linux, scripting, and other coding practices I soon began to realize the true power of open source projects and the benefits it can have for the computational chemistry community. As new students join our group I always tell them that linux is great for automating repetitive tasks that often occur when dealing with large text files (as are the main outputs from many of our calculations). Which means, that if I ever find myself repeating keystrokes or tasks over and over I make sure to stop and look for a better way to do what I’m trying to accomplish. It might take me longer to find a better way to do it than it would have taken me to just do it the long way, but in the end this will inevitably save me time (especially if that task is going to become common place).

Over the years I’ve picked up a number of tricks that have helped me accomplish my research faster. The goal of this blog is to share those tricks with all of you. With that, let the ride begin!