Run Your Own DFT Calculations to Have a Better Understanding of the XAS and RIXS Experiments
Abstract
With the increasing computing power nowadays, DFT calculations are becoming popular. Coupling DFT calculations with the XAS and RIXS results will not only help you with peak/feature assignments, but will bring in more insights in the system you want to study. For those who are interested in running your own DFT calculations, but with little or no experience, we will teach you how to start from scratch, and correlate the computational results with your XAS and RIXS experiments. Attendees will be assigned access to our virtual machines for the hands session. We will also use a few simple, but insightful examples, to show what we can pull out from those calculations beyond simply reproducing your experimental results.
When? Aug 17th, 2022
Where? Virtually on zoom https://lbnl.zoom.us/meeting/register/tJ0vc-2qpjguHNNetXHfq5G0Nhwse_COoTYt
You may register for free through https://als.lbl.gov/user-meeting/
Organizers: Dr. Yang Ha (yangha@lbl.gov), Dr. Jinghua Guo, Dr. Wanli Yang
Invited speakers:
Dr. Ritimukta Sarangi (SLAC National Lab), Over 20 years' experience coupling DFT with X-ray Spectroscopy.
Dr. Wei Feinstein (IT Division, LBNL), HPC User Services Lead.
Prof. Hrant P. Hratchian (University of California, Merced), Major developer of Gaussian.
Detailed schedule (Pacific Time)
8:30 Greetings and warm up
9:00 Presentation - What can DFT do for us? (Three examples from fundamental physics, biochemistry and material science) - Yang Ha (Advanced Light Source, LBL)
10:00 Demo & Hands on session on starting your job and geometry optimization
11:00 Presentation - Current High Performance Computing Resource at Berkeley Lab - Wei Feinstein (IT, LBNL)
11:30 Lunch Break
12:30 Presentation - Coupling DFT with X-ray Spectroscopy, from experimentalist perspective - Riti Sarangi (SLAC)
13:30 Demo & Hands on session on Frequency calculations and XAS simulations
14:30 Presentation - Coupling DFT with X-ray Spectroscopy, from theoretician perspective - Hrant Hratchian (UC Merced)
16:00 Wrap up
Greetings from ALS! Welcome everyone to our second ALS users' meeting DFT workshop.
In this one day workshop, we wish to teach you some background knowledge about DFT, and you will have some hands on experience with a list of example calculations, including geometry optimization, frequency calculation and time dependent DFT to simulate spectra.
Our examples will be run using ORCA. Other software such as Gaussian or ADF will be similar. For more information about ORCA, please visit the official forum https://orcaforum.kofo.mpg.de/app.php/portal
For the hands on practice, you can either run it on our high performance computing cluster (preferred), or you can install and run ORCA on your local computer. Please check the to do list below, to have all the software installed before the workshop.
To do list before you arrive
Stay tuned by checking emails about the virtual machine access and other useful information. If you intend to run the jobs on our cluster, please make sure you get your login information and are able to login to your assigned computing cluster. If you encounter any issues, please contact us ahead of time.
Go to the ORCA website https://orcaforum.kofo.mpg.de/app.php/portal, and sign up with your email, so you can have access to download files.
The ORCA enhanced version of Avogadro is a great GUI to visualize your output results. Please download the corresponding version (PC / Mac) and install it on your local computer. (Problems?)
You could also download the ORCA manual from their forum. It is very well documented and always a great resource to refer to.
If you intend to run ORCA on your local machine, please also download the corresponding version, and install it.
In order to access our computing cluster, you will need a terminal. For Mac users, you can do so by the Terminal APP. For PC users, I personally recommend xshell (https://www.netsarang.com/en/xshell/). They have the free versions for home and school use. Or, you can use putty (https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html), which does not need your email address.
For file transfer, Mac users can still do command lines in terminal, but to have a better GUI, I recommend xftp (https://www.netsarang.com/en/xftp/). It has both PC and Mac version. Again, it is free for home and school use, with limited threads. You can also use psftp if you want to keep your privacy.
To build your own molecule, you can use your favorite software if you have. Avogadro can do the job. There is another open source software called jmol that is simple but works well. http://jmol.sourceforge.net/
If possible, please get familiar with some basic Linux commands and the vi text editor.
You may also use QMForge to visualize your output file.