Since thelast update a lot of new things have happened in the Kitchin Research group. Below are some summaries of the group accomplishments, publications and activities for the past year.
1 Student accomplishments
Jacob Boes completed his PhD and began postdoctoral work with Thomas Bligaard at SLAC/Suncat at Stanford. Congratulations Jake!
Four new PhD students joined the group:
- Jenny Zhan will work on simulation of molten superalloys
- Mingjie Liu will work on the design of single atom alloy catalysts
- Yilin Yang will work on segregation in multicomponent alloys under reaction conditions
- Zhitao Guo is also joining the group and will be co-advised by Prof. Gellman. He will work on multicomponent alloy catalysts.
Welcome to the group!
Our publications and citation counts have continued to grow this year. Here is our current metrics according to Researcher ID .
We have eight new papers that are online, and two that are accepted, but not online yet. There are brief descriptions below.
2.1 Collaborative papers
- This is a modern update on the Atomic Simulation Environment Python software. We have been using and contributing to this software for about 15 years now!
- This collaborative effort with the Keith group at UPitt and Anatole von Lilienfeld explored a novel approach to estimating adsorption energies on alloy surfaces.
- We used DFT calculations to understand epitaxial stabilization of titania films on strontium titanate surfaces.
- We previously predicted that tin oxide should be able to form in the columbite phase as an epitaxial film. In this paper our collaborators show that it can be done!
- This paper finally came out in print. It shows an automated approach to sharing data. Also, it may be the only paper with data hidden inside a picture of a library in the literature.
2.2 Papers on neural networks in molecular simulation
- We used neural networks in conjunction with molecular dynamics and Monte Carlo simulations to model the coverage dependent adsorption of oxygen and initial oxidation of a Pd(111) surface.
- We used neural networks in conjunction with Monte Carlo simulations to model segregation across composition space for a Au-Pd alloy.
- We used a cluster expansion with Monte Carlo simulations to resolve some inconsistencies in simulated Cu-Pd phase diagrams. There is an interesting transition from an fcc to bcc to fcc structure across the composition space that is subtle and difficult to compute.
2.3 Papers accepted in 2017 but not yet in press
- Chen Wang, Akshay Tharval, John R. Kitchin, A density functional theory parameterized neural network model of zirconia, Accepted in Molecular Simulation, July 2017.
- Hari Thirumalai, John R. Kitchin, Investigating the Reactivity of Single Atom Alloys using Density Functional Theory, Topics in Catalysis, Accepted November 2017.
3 New courses
After a five year stint of teaching Master’s and PhD courses, I taught the undergraduate chemical engineering course again. This was the first time I taught the course using Python. All the lectures and assignments were in Jupyter notebooks. You can find the course here: https://github.com/jkitchin/s17-06364 . The whole class basically ran from a browser using a Python Flask app to serve the syllabus, lectures and assignments. Assignments were submitted and returned by email through the Flask app. It was pretty interesting. I did not like it as much as using Emacs/org-mode like I have in the past, but it was easier to get 70 undergraduates up and running.
I did not teach in the Fall, because I was on Sabbatical!
4 Sabbatical at Google
In August 2017 I started my first sabbatical! I am spending a year in the Accelerated Science group at Google in Mountain View, California. I am learning about machine learning applications in engineering and science. This is a pivotal year in my research program, so stay tuned for our new work!
It has been great for my family, who moved out here with me. We have been seeing a lot of California. I have been biking to work almost every day, usually 15-20 miles. I have logged over 1200 commuting miles already since August.
5 Emacs and org-mode
org-ref remains in the top 15% of downloaded MELPA packages, with more than 24,000 downloads since it was released. It has been pretty stable lately. It remains a cornerstone of my technical writing toolbox.
I have spent some time improving org-mode/ipython interactions including inline images, asynchronous execution and export to jupyter notebooks. It is still a work in progress.
I spent a fair bit of time learning about dynamic modules for writing compiled extensions to Emacs to bring features like linear algebra, numerical methods and database access to it. I wish I had more time to work on this. I think it will be useful to make org-mode even better for scientific research and documentation.
6 Social media
I have continued exploring the use of social media to share my work. It still seems like a worthwhile use of time, but we need continued efforts to make this really useful for science.
I use my blog to share technical knowledge and news about the group. We had 48 blog posts in 2017. A lot of them were on some use of org-mode and Emacs. I also introduced a new exporter for org-mode to make jupyter notebooks. I spent November exploring automatic differentiation and applications of it to engineering problems. Visits to the site continue to grow. Here is the growth over the past two years. The big spike in Oct 2017 is from this article on Hacker News about one of my posts!
I continue to think that technical blogging is a valuable way to communicate technical knowledge. It provides an easy way to practice writing, and with comments enabled to get feedback on your ideas. It has taken several years to develop a style for doing this effectively that is useful to me, and to others. I have integrated my blog into Twitter so that new posts are automatically tweeted, which helps publicize the new posts.
It has some limitations, e.g. it is not obvious how to cite them in ways that are compatible with the current bibliometric driven assessment tools used in promotion and tenure. Overall, I find it very complementary to formal publications though, and I wish more people did it.
I was a little less active on Github this year than last year, especially this fall as I started my sabbatical. Github remains my goto version control service though, and we continue using it for everything from code development and paper writing to course serving.
scimax finally has more Github stars than jmax does!
I have not made too many new videos this year. Hopefully there will be some new ones on the new features in scimax in the next year.
Copyright (C) 2017 by John Kitchin. See theLicense for information about copying.
Org-mode version = 9.1.3