realsci_nano - Network

Thank you all for tuning in, and I'll see you tomorrow for the LAST day! 👋

Thank you all for tuning in, and I'll see you tomorrow for the LAST day! 👋

Of course, none of DFT-raMO would be possible without the contributions of the following:Original DFT-raMO:Prof. Danny Fredrickson,...

Of course, none of DFT-raMO would be possible without the contributions of the following:

Original DFT-raMO:
Prof. Danny Fredrickson, concept
Dr. Vincent Yannello, lead and coding
Dr. Yiming Guo, math and coding
Dr. Erdong Lu, extra testing

For the current version of DFT-raMO, my colleague Brandon Flores was invaluable with his development of Electrum.jl (https://github.com/brainandforce/Electrum.jl/) which DFT-raMO relies on, and his knowledge of Julia and Git!

I'm still working on my DFT-raMO.jl package, but I'm excited to get it published and shared with the scientific community so anyone...

I'm still working on my DFT-raMO.jl package, but I'm excited to get it published and shared with the scientific community so anyone can use it! 🤞 Coming soon 2024...

I'd love to answer any questions you may have about computational solid state chemistry, writing scientific code/scripts, or DFT-raMO if you have any!

In the meantime, I will close with relevant further reading!

The DFT-raMO method: https://pubs.acs.org/doi/10.1021/acs.inorgchem.0c01393
Psphere update to DFT-raMO: https://pubs.acs.org/doi/10.1021/acs.inorgchem.2c03393

It's a challenging (and sometimes painful) process, but I also find it deeply rewarding, and I learn new things all the time! The...

It's a challenging (and sometimes painful) process, but I also find it deeply rewarding, and I learn new things all the time! The biggest challenge for me is trying to keep the BIG PICTURE in mind while still minding all the small details.

The coding process is usually:idea -> sketch it out -> attempt to code -> test -> debug -> debug -> debug -> debug...

The coding process is usually:

idea -> sketch it out -> attempt to code -> test -> debug -> debug -> debug -> debug -> debug ... -> commit change

It's almost similar to writing a manuscript in that aspect. 😅

I also use Github for version-control, which is something I learned a couple years ago. It has changed my life immensely, and if you are a...

I also use Github for version-control, which is something I learned a couple years ago. It has changed my life immensely, and if you are a coder but haven't used any form of version-control, what are you doing!!!

I find myself coding in short bursts rather than on a daily basis! This is because I have other tasks to do, like analyzing data or writing...

I find myself coding in short bursts rather than on a daily basis! This is because I have other tasks to do, like analyzing data or writing manuscripts!

But if you catch me on a coding day, my screen might look something like this!

Not all computational chemists write code regularly, but sometimes they write scripts to automate their tasks or process data! These scripts...

Not all computational chemists write code regularly, but sometimes they write scripts to automate their tasks or process data! These scripts are relatively simple.

When you need a collection of scripts to perform complex tasks, you might consider writing a software package.

.. and this is where we get into one aspect of computational chemistry. Coding and software!Before I begin, a disclaimer: I haven't...

.. and this is where we get into one aspect of computational chemistry. Coding and software!

Before I begin, a disclaimer: I haven't taken a single coding class since high school, so a lot is learned on-the-job or self taught! 😱

There's still more we can plan to do with DFT-raMO, and part of my work is expanding its functionality by writing code! I've been...

There's still more we can plan to do with DFT-raMO, and part of my work is expanding its functionality by writing code! I've been working on the newest version of it for almost two years now, and I am pleased to say that it's more efficient and has quality-of-life improvements.

In the story of IrIn3 polymorphism, DFT-raMO helped showed that m electrons were localized in the void spaces of CoGa3!

In the story of IrIn3 polymorphism, DFT-raMO helped showed that m electrons were localized in the void spaces of CoGa3!

This tool helped me with a lot of projects! Remember the REAl3 story? With DFT-raMO, I was able to show which orbitals were associated with...

This tool helped me with a lot of projects! Remember the REAl3 story? With DFT-raMO, I was able to show which orbitals were associated with electrons n=7 and m=1 in the 18-n+m rule!

What's important to us is that Psphere is consistent, meaning our reconstructed molecular orbitals are well-localized. When it drops...

What's important to us is that Psphere is consistent, meaning our reconstructed molecular orbitals are well-localized. When it drops sharply, it's an indication of delocalization. Or in simple terms, electrons can't be fully occupying those orbitals!

The plot here shows the output of some DFT-raMO analysis, with one dot representing one reconstructed molecular-like orbital. You can see...

The plot here shows the output of some DFT-raMO analysis, with one dot representing one reconstructed molecular-like orbital. You can see that we're able to generate atomic- and molecular orbital-like isosurfaces!

But what's that on the y-axis? That's Psphere, which is a tool that helps us evaluate the localization of our reconstructed function. It's calculated as the ratio of electron density in a defined sphere over the electron density in the whole unit cell.

To do this analysis, we wrote software in MATLAB* that does some BIG matrix math to transform wavefunction information into approximate...

To do this analysis, we wrote software in MATLAB* that does some BIG matrix math to transform wavefunction information into approximate molecular orbitals! Each of these new functions contains 2 electrons, so we have a way of doing electron-counting for our system.

* It's in MATLAB, for now, but I'm currently rewriting it in the Julia programming language.

Instead of analyzing waves that are spread out, we want to understand the electronics in a localized context. This allows us to understand...

Instead of analyzing waves that are spread out, we want to understand the electronics in a localized context. This allows us to understand the bonding in our system by making analogies to molecular orbitals.

Why do some 18-n+m compounds not show that band or pseudogap at the Fermi energy? To investigate this, I use one of our group's tools...

Why do some 18-n+m compounds not show that band or pseudogap at the Fermi energy? To investigate this, I use one of our group's tools called DFT-raMO! This is a tool that uses the occupied crystal orbitals (which we get from DFT calculations) to make molecular analogies.

DFT calculations on crystal structures use planewave basis sets to describe the information about the electrons of a system. Think sin and cosine functions!

For my research, the region around the Fermi energy (EF) is of interest! Typically, compounds that follow the 18-n+m rule have a dip in...

For my research, the region around the Fermi energy (EF) is of interest! Typically, compounds that follow the 18-n+m rule have a dip in their density of states at the EF in the form of a pseudo- or band gap. Sometimes, they don't, like in the IrIn3 type in the above image.

Once we have our equilibrium geometry, we run static calculations, where the atoms are now locked in place and we can get the data we want!...

Once we have our equilibrium geometry, we run static calculations, where the atoms are now locked in place and we can get the data we want! For example, we can get info about the electronic density of states, which can tell us things such as whether our crystal is a conductor/insulator or what kind of orbital characteristics our bands have.

Once those are set, we need to optimize our crystal's geometry! For our purposes, need to have our system at the energetic minimum to...

Once those are set, we need to optimize our crystal's geometry! For our purposes, need to have our system at the energetic minimum to extract meaningful, accurate data.

We do this geometry optimization in two steps:
(1) atoms are allowed to shift
(2) atoms and unit cell shape are allowed to shift

This two-step procedure helps the software find the equilibrium geometry efficiently.