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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
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<title>The Akimov Research Group: Educational Materials</title>
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<ul class="navbar-nav">
<li class="nav-item"><a class="nav-link" href="index.html">Home</a></li>
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<br><br>
<h1><b>Educational Materials</b></h1><br>
</div>
<!-- Content -->
<div class="container" style="width:100%">
<div class="row">
<div class="col-12">
<br>
<h2>Classes I teach at UB</h2>
<br>
<p> CHE 457/505 course: Fall 2015, Fall 2016 </p>
<p> CHE 320 course: Spring 2017, Spring 2018 </p>
<p>
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.
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/" target="_new">here</a>.
</p>
<p>
Please use the GitHub portal to sent your feedback, corrections, and comments or to submit your own contribution.
</p>
</div>
</div>
<br><br>
<!-- BEGIN UNIVERSAL LECTURE NOTES -->
<div class="row">
<div class="col-6">
<p>
Topic #1 Differentiation and integration:
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_1.docx" target="_new">DOC</a>
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_1.pdf" target="_new">PDF</a>
</p>
<p>
Topic #2 A bit of philosophy & Mathematical notation:
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_2.docx" target="_new">DOC</a>
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_2.pdf" target="_new">PDF</a>
</p>
<p>
Topic #3 Linear algebra:
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_3.docx" target="_new">DOC</a>
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_3.pdf" target="_new">PDF</a>
</p>
<p>
Topic #4 Chemical kinetics:
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_4.docx" target="_new">DOC</a>
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_4.pdf" target="_new">PDF</a>
</p>
<p>
Topic #5 Chemical thermodynamics:
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_5.docx" target="_new">DOC</a>
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_5.pdf" target="_new">PDF</a>
</p>
<p>
Topic #6 Classical mechanics:
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_6.docx" target="_new">DOC</a>
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_6.pdf" target="_new">PDF</a>
</p>
<p>
Topic #7 Statistical thermodynamics:
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_7.docx" target="_new">DOC</a>
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_7.pdf" target="_new">PDF</a>
</p>
<p>
Topic #8 Quantum mechanics:
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_8.docx" target="_new">DOC</a>
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Lecture_Notes_8.pdf" target="_new">PDF</a>
</p>
</div>
<!-- END UNIVERSAL LECTURE NOTES -->
<!-- BEGIN QUANTUM MECHANICS -->
<div class="col-6">
<p>
Part I: Intro & Mathematics
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Quantum_Mechanics/Lect1.pdf" target="_new">PDF</a>
</p>
<p>
Part II: Classical and Quantum Mechanics
<a href="https://github.com/alexvakimov/Universal_Lecture_Notes/blob/master/Quantum_Mechanics/Lect2.pdf" target="_new">PDF</a>
</p>
</div>
<!-- END QUANTUM MECHANICS -->
</div> <!-- END OF: BEGIN UNIVERSAL LECTURE NOTES -->
<!-- YouTube tutorials -->
<div class="row">
<div class="col-12">
<h2>YouTube and Panopto Tutorials</h2>
<p>
Below, please find the video tutorials on various topics created in the Akimov group.
</p>
</div>
</div>
<br>
<div class="row">
<div class="col-3">
<iframe width="100%" src="https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=c0d72278-8a3c-41b3-9dec-a9f200e209ea&v=1"
frameborder="10" allowfullscreen></iframe>
Tutorial: How to run Libra via Jupyter notebook on CCR
</div>
<div class="col-3">
<iframe width="100%" src="https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=6e312fc0-1839-4043-8a57-a8e1011b3d37&v=1"
frameborder="10" allowfullscreen></iframe>
A DFTB+ tutorial.
</div>
<div class="col-3">
<iframe width="100%" src="https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=b15046dd-d8c5-4e06-848f-a8e8013b4dcd&v=1"
frameborder="10" allowfullscreen></iframe>
Computing pDOS with Quantum Espresso.
</div>
<div class="col-3">
<iframe width="100%" src="https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=9100799d-d267-4f3e-a4f5-a8f60131c57f&v=1"
frameborder="10" allowfullscreen></iframe>
Compute and visualized charge densities of various orbitals using Quantum Espresso and VMD.
</div>
</div>
<div class="row">
<div class="col-3">
<iframe width="100%" src="https://www.youtube.com/embed/BXtPtkUJVqc" frameborder="10" allowfullscreen></iframe>
Basics of molecular structure building with iQmol: BODIPY diad.
</div>
<div class="col-3">
<iframe width="100%" src="https://www.youtube.com/embed/IkSJTY8le8U" frameborder="10" allowfullscreen></iframe>
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
</div>
<div class="col-3">
<iframe width="100%" src="https://www.youtube.com/embed/vnZv9LinlYw" frameborder="10" allowfullscreen></iframe>
A small tutorial on generating time-correlated random numbers and computing the ACFs for such time series using the Libra's functionality.
</div>
<div class="col-3">
<iframe width="100%" src="https://www.youtube.com/embed/9fOB_uZgLKk" frameborder="10" allowfullscreen></iframe>
A videorecording of the online stream showing how our Libra code can be used to create a molecular system.
</div>
<div class="col-3">
<iframe width="100%" src="https://www.youtube.com/embed/2mjn-2CNEyo" frameborder="10" allowfullscreen></iframe>
A tutorial showing crystal slab cutting in VESTA. In this tutorial, we expose the
internal (111) plane of Calcium Fluoride. Tutorial authored by <b>Brendan A. Smith.</b>
</div>
</div> <!-- YouTube tutorials -->
<div class="row">
<div class="col-12">
<h2>Tutorials</h2>
</div>
</div> <!-- tutorials -->
<div class="row">
<div class="col-12">
<h2>Derivatory</h2>
<p>
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.
</p>
<p>
Also, you can notice that all the files are actually hosted at the GitHub -
<a href="https://github.com/alexvakimov/Derivatory/" target="_new">here</a>, - 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.
</p>
<br><br>
<p>
Time-dependent variational principle (TDVP) and the Coherent States dynamics (CSD):
<a href="https://github.com/alexvakimov/Derivatory/blob/master/TDVP_and_Coherent_States_dynamics.doc" target="_new">TDVP_and_Coherent_States_dynamics.doc</a>
<a href="https://github.com/alexvakimov/Derivatory/blob/master/TDVP_and_Coherent_States_dynamics.pdf" target="_new">TDVP_and_Coherent_States_dynamics.pdf</a>
</p>
<p>
Quantum dynamics of Gaussian wavepackets:
<a href="https://github.com/alexvakimov/Derivatory/blob/master/Gaussian_dynamics.doc" target="_new">Gaussian_dynamics.doc</a>
<a href="https://github.com/alexvakimov/Derivatory/blob/master/Gaussian_dynamics.pdf" target="_new">Gaussian_dynamics.pdf</a>
</p>
<p>
Quantum-to-classical mapping (Meyer-Miller-Thoss-Stock):
<a href="https://github.com/alexvakimov/Derivatory/blob/master/MMTS.doc" target="_new">MMTS.doc</a>
<a href="https://github.com/alexvakimov/Derivatory/blob/master/MMTS.pdf" target="_new">MMTS.pdf</a>
</p>
<p>
Gaussian wavepackets:
<a href="https://github.com/alexvakimov/Derivatory/blob/master/Gaussian_wavepackets.doc" target="_new">Gaussian_Wavepackets.doc</a>
<a href="https://github.com/alexvakimov/Derivatory/blob/master/Gaussian_wavepackets.pdf" target="_new">Gaussian_Wavepackets.pdf</a>
</p>
<p>
Diabatic and adiabatic representations:
<a href="https://github.com/alexvakimov/Derivatory/blob/master/Diabatic_vs_Adiabatic.doc" target="_new">Diabatic_vs_Adiabatic.doc</a>
<a href="https://github.com/alexvakimov/Derivatory/blob/master/Diabatic_vs_Adiabatic.pdf" target="_new">Diabatic_vs_Adiabatic.pdf</a>
</p>
<p>
2-state TD-SE (Rabi model): analytic solution
<a href="https://github.com/alexvakimov/Derivatory/blob/master/2state_TDSE.doc" target="_new">2state_TDSE.doc</a>
<a href="https://github.com/alexvakimov/Derivatory/blob/master/2state_TDSE.pdf" target="_new">2state_TDSE.pdf</a>
</p>
<p>
2-state TD-SE (Rabi model): numerical integration
<a href="https://github.com/alexvakimov/Derivatory/blob/master/2state_TDSE_Liouville.doc" target="_new">2state_TDSE_Liouville.doc</a>
<a href="https://github.com/alexvakimov/Derivatory/blob/master/2state_TDSE_Liouville.pdf" target="_new">2state_TDSE_Liouville.pdf</a>
</p>
<p>
Rotational innvariance and the lack of it in EHT
<a href="https://github.com/alexvakimov/Derivatory/blob/master/theory_rotational_invariance.doc" target="_new">theory_rotational_invariance.doc</a>
<a href="https://github.com/alexvakimov/Derivatory/blob/master/theory_rotational_invariance.pdf" target="_new">theory_rotational_invariance.pdf</a>
</p>
<p>
Derivative couplings and derivatives of the eigenvalues/eigenvectors
<a href="https://github.com/alexvakimov/Derivatory/blob/master/theory_NAC.doc" target="_new">theory_NAC.doc</a>
<a href="https://github.com/alexvakimov/Derivatory/blob/master/theory_NAC.pdf" target="_new">theory_NAC.pdf</a>
</p>
<p>
Density of states (DOS)
<a href="https://github.com/alexvakimov/Derivatory/blob/master/theory_DOS.doc" target="_new">theory_DOS.doc</a>
<a href="https://github.com/alexvakimov/Derivatory/blob/master/theory_DOS.pdf" target="_new">theory_DOS.pdf</a>
</p>
<br><br><br>
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