Educational Materials



Classes I teach at UB


CHE 457/505 course: Fall 2015, Fall 2016

CHE 320 course: Spring 2017, Spring 2018

The lecture notes for this and other courses (e.g. quantum mechanics) are deposited in the Universal Lecture Notes repository. Although, different courses (e.g. PCHEM and Quantum) have different specifics, they share many common topics, especially the very basic ones such as math/physics. Moreover, these courses constitute a core every chemist should know. Therefore, I place all the topics in one repository, but the material covered in details during the lecturs may or may not include some of these topics. here.

Please use the GitHub portal to sent your feedback, corrections, and comments or to submit your own contribution.



Topic #1 Differentiation and integration: DOC PDF

Topic #2 A bit of philosophy & Mathematical notation: DOC PDF

Topic #3 Linear algebra: DOC PDF

Topic #4 Chemical kinetics: DOC PDF

Topic #5 Chemical thermodynamics: DOC PDF

Topic #6 Classical mechanics: DOC PDF

Topic #7 Statistical thermodynamics: DOC PDF

Topic #8 Quantum mechanics: DOC PDF

Part I: Intro & Mathematics PDF

Part II: Classical and Quantum Mechanics PDF

YouTube and Panopto Tutorials

Below, please find the video tutorials on various topics created in the Akimov group.


Tutorial: How to run Libra via Jupyter notebook on CCR
A DFTB+ tutorial.
Computing pDOS with Quantum Espresso.
Compute and visualized charge densities of various orbitals using Quantum Espresso and VMD.
Basics of molecular structure building with iQmol: BODIPY diad.
A tutorial showing how to analyze the charachteristic modes of a quasi-random time-series using the ACF and FT capabilities of Libra. This is the way you can use Libra to compute IR spectra or so
A small tutorial on generating time-correlated random numbers and computing the ACFs for such time series using the Libra's functionality.
A videorecording of the online stream showing how our Libra code can be used to create a molecular system.
A tutorial showing crystal slab cutting in VESTA. In this tutorial, we expose the internal (111) plane of Calcium Fluoride. Tutorial authored by Brendan A. Smith.

Tutorials

Derivatory

The purpose of this section is to provide the detailed step-by-step derivations of some important results we use routinely or less routinely in our research. Over time, I've made a lot of such write-ups/derivations, so here I publish the collection of these derivations. Since the focus on the derivations (with the hope that it'll help an interested reader to better understand the machinery of the specific topic), I've decided to call this collection the "Derivatory". I hope it'll be useful to someone. So, enjoy! I'd appreciate if you could provide some sort of feedback - be it some correction you find, or a simple note that it was useful to you.

Also, you can notice that all the files are actually hosted at the GitHub - here, - so the compete history of versions and corrections is now avialable. You can use the GitHub portal to sent your feedback, corrections, and comments or to submit your own contribution.



Time-dependent variational principle (TDVP) and the Coherent States dynamics (CSD): TDVP_and_Coherent_States_dynamics.doc TDVP_and_Coherent_States_dynamics.pdf

Quantum dynamics of Gaussian wavepackets: Gaussian_dynamics.doc Gaussian_dynamics.pdf

Quantum-to-classical mapping (Meyer-Miller-Thoss-Stock): MMTS.doc MMTS.pdf

Gaussian wavepackets: Gaussian_Wavepackets.doc Gaussian_Wavepackets.pdf

Diabatic and adiabatic representations: Diabatic_vs_Adiabatic.doc Diabatic_vs_Adiabatic.pdf

2-state TD-SE (Rabi model): analytic solution 2state_TDSE.doc 2state_TDSE.pdf

2-state TD-SE (Rabi model): numerical integration 2state_TDSE_Liouville.doc 2state_TDSE_Liouville.pdf

Rotational innvariance and the lack of it in EHT theory_rotational_invariance.doc theory_rotational_invariance.pdf

Derivative couplings and derivatives of the eigenvalues/eigenvectors theory_NAC.doc theory_NAC.pdf

Density of states (DOS) theory_DOS.doc theory_DOS.pdf