PhD life experiences, chemistry specific research discussions, and tool guides for navigating some of the software and concepts I find myself swimming through regularly.
Part 1 of X. The content of this series of posts is mainly drawn from "Atomic and Electronic Structure of Solids" by Efthimios Kaxiras, in particular Ch.2 on the single-particle approximation (SPA). What follows are my notes, interpretations, and thoughts surrounding the setup of the SPA, following the framework of Kaxiras' textbook. Outside of solids …
Continue reading Laying the Foundation for Modeling Materials – Part 1: Hamiltonian of the Solid
First in a continuum of brief news reports on Brown University's Chemistry Department Seminar series. Prof. Dequan Xiao, from the University of New Haven's Center for Integrative Materials Discovery, presented applications of his team's "inverse" design methodology, and explained its future impacts. I find myself stymied by the mountain of choices set before me, threatening …
Continue reading Inverse Design – A Path to Faster Development?
Calculations on molecular, biological, and physical systems come with a common goal: determining the lowest, most stable energetic state(s), and thus the best example of the system to study computationally. To do this, the values of interest, usually energy, need to converge: i.e., after repeated changes, each result is nearly the same as the one …
Continue reading Convergence Problems – Computer Defenestration Prevention
In order to work with a lot of physical concepts across disciplines, some level of understanding must be present regarding "energy." On an instinctive level, people tend to have a foundational understanding of "energy" just by doing and observing everyday tasks; I aim to illuminate these moments and shed some further detail on what energy …
Continue reading Understanding Energy – Potential, Kinetic, and Visualization on a “Surface”
I will be discussing a useful approach to obtaining the desired output from Gaussian calculations using "grep" on Linux. Simple technique inspired by Linux knowledge and Gaussian manuals/books (see "Note 2" at bottom of post for details). For any newbie Linux users, my quoted out comments are acting as the Terminal command line and output …
Continue reading Parsing All That Output – GREP to the Rescue!!!
Welcome to my "Chemistry and a PhD" blog, a place where I will regale you, the readers, with tales of various events throughout my time as a graduate student! Or, on a more variable excitement level, I will discuss the tidbits of knowledge and lessons I have gathered (and am still gathering) along the way. …
Len's Landing 