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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="Introduction to materials informatics">
<meta name="author" content="Evgeny Blokhin">
<title>Introduction to materials informatics</title>
<link rel="stylesheet" href="webassets/reveal/reset.css">
<link rel="stylesheet" href="webassets/reveal/reveal.css">
<link rel="stylesheet" href="webassets/reveal/theme/white.css">
<link rel="stylesheet" href="webassets/reveal/plugin/highlight/monokai.css">
<style>
.mpds_dot {height:22px;width:22px;border-radius:50%;display:inline-block;}
.p {background-color:#3e3f95;}
.s {background-color:#ffcc28;}
.c {background-color:#acc2b3;}
.b {background-color:#ed3237;}
</style>
</head>
<body>
<div class="reveal">
<div class="slides">
<section><!-- Slide -->
<code>Introduction to materials informatics</code>
</section>
<section data-background-iframe="https://tilde.pro/#contacts">
<div style="position:absolute;top:0;right:0;width:180px;height:180px;background:#9f3;font-size:20px;line-height:180px;border-radius:90px;">Hi, that's me 🤓<div>
</section>
<section><!-- Slide -->
<h3>Outline</h3>
<br />
<ul>
<li>data & formats</li>
<li>software & simulations</li>
<li>collaboration & sharing</li>
</ul>
<br /><br />
<small>Open the <a target="_blank" href="https://mybinder.org/v2/gh/blokhin/materials-informatics-tutorial/master?filepath=notebooks">Python notebooks</a> meanwhile.</small>
</section>
<section><!-- Slide -->
<h3>From nanometers to meters</h3>
<br />
<img src="images/bridge.png" alt="multiscale modeling bridge" />
<img src="images/multiscale.png" alt="multiscale modeling lengths" />
</section>
<section data-background-iframe="https://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid-state_physics_software" data-background-interactive></section>
<section data-background-iframe="https://tilde-lab.github.io/awesome-materials-informatics/" data-background-interactive></section><!-- Software is eating the world -->
<section><!-- Slide -->
<h3>Data formats for nanometers 🔬</h3>
<br />
<ul>
<li><code><a href="https://www.vasp.at/wiki/index.php/POSCAR" target="_blank">POSCAR</a></code></li>
<li><code><a href="https://www.iucr.org/resources/cif/dictionaries/cif_core" target="_blank">CIF</a></code></li>
<li><code><a href="https://github.com/Materials-Consortia/OPTIMADE/blob/master/optimade.rst#entry-list" target="_blank">Optimade</a></code></li>
</ul>
</section>
<section><!-- Slide -->
<code>POSCAR</code>
<br />
<pre><code class="hljs" data-trim data-noescape data-line-numbers>
https://mpds.io/entry/S251615
1.0000000000000000
0.0000 2.0245 2.0245
2.0245 0.0000 2.0245
2.0245 2.0245 0.0000
Al
1
Direct
0.000000 0.000000 0.000000
</code></pre>
</section>
<section><!-- Slide -->
<code>CIF</code>
<br />
<pre><code class="hljs" data-trim data-noescape data-line-numbers>
data_mpds_labs
_cell_length_a 15.017668
_cell_length_b 30.035337
_cell_length_c 30.035337
_cell_angle_alpha 118.543768
_cell_angle_beta 118.543768
_cell_angle_gamma 92.541335
_symmetry_space_group_name_H-M 'P1'
_symmetry_Int_Tables_number 1
loop_
_symmetry_equiv_pos_as_xyz
+x,+y,+z
loop_
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Ca 0.462 -0.342 -0.179
Be 0.362 -0.274 -0.420
...
</code></pre>
</section>
<section><!-- Slide -->
<code>Optimade</code>
<br />
<pre><code class="hljs" data-trim data-noescape data-line-numbers>
{
"attributes":{
"immutable_id":42,
"species":[
{
"chemical_symbols":[
"Au"
]
}
],
"cartesian_site_positions":[
[0,0,0]
],
"lattice_vectors":[
[0,2,2],
[2,0,2],
[2,2,0]
]
}
}
</code></pre>
</section>
<section data-background-iframe="https://nanoshow.mpds.io" data-background-interactive></section>
<section><!-- Slide -->
<h3>Python 🐍 & ASE 💎</h3>
<br />
<pre><code class="hljs" data-trim data-noescape data-line-numbers>
from ase.spacegroup import crystal
crystal_obj = crystal(
('Al', 'Y', 'Cu', 'Cu'),
basis=[
( 0.235, 0.0, 0.5 ),
( 0.5861, 0.0, 0.0 ),
( 0.333, 0.666, 0.5 ),
( 0.0, 0.0, 0.0 )
],
spacegroup=189,
cellpar=[7.033, 7.033, 4.023, 90, 90, 120],
primitive_cell=True
)
</code></pre>
<small>Have a look at the <a target="_blank" href="https://wiki.fysik.dtu.dk/ase/">ASE website</a>. Then head over to the <a target="_blank" href="https://mybinder.org/v2/gh/blokhin/materials-informatics-tutorial/master?filepath=notebooks">Python notebooks</a> you have opened earlier.</small>
</section>
<section><!-- Slide -->
<h3 style="letter-spacing:30px;">MPDS</h3>
<br />
<img src="images/mpds.png" alt="MPDS: Materials Platform for Data Science" usemap="#mpds" />
<map name="mpds">
<area shape="circle" coords="25,112,30" alt="phase diagrams" title="phase diagrams" href="https://mpds.io/inquiry/classes=binary&props=phase%20diagram&elements=Ti-O" target="_blank">
<area shape="circle" coords="112,25,30" alt="crystal structures" title="crystal structures" href="https://mpds.io/inquiry/classes=binary&props=crystal%20structure&elements=Ti-O" target="_blank">
<area shape="circle" coords="200,112,30" alt="physical properties" title="physical properties" href="https://mpds.io/inquiry/props=physical%20properties&elements=Ti-O&classes=binary%2Cpeer-reviewed" target="_blank">
<area shape="circle" coords="112,200,30" alt="published literature" title="published literature" href="https://mpds.io/inquiry/elements=Ti-O&years=1960&classes=binary" target="_blank">
<area shape="circle" coords="112,112,30" alt="MPDS platform" title="MPDS platform" href="https://mpds.io" target="_blank">
</map>
<br /><br />
<small>Phase diagrams, physical properties, and crystal structures are interlinked from the published literature. Just hover and click the colored circles <span class="mpds_dot p"></span> <span class="mpds_dot s"></span> <span class="mpds_dot b"></span> <span class="mpds_dot c"></span> at the logo.</small>
</section>
<section><!-- Slide -->
<h3>Wow, many online databases?</h3>
<img src="images/optimade_dbs.png" alt="MPDS, Materials Project, Aflowlib, OQMD, COD, Nomad" />
</section>
<section><!-- Slide -->
<h3>Let's link them all together 🤝</h3>
<img src="images/optimade-text-right-transparent-bg.png" alt="Optimade logo" />
</section>
<section><!-- Slide -->
<h3>Optimade queries</h3>
<br />
<pre><code class="hljs" data-trim data-noescape data-line-numbers>
filter=elements HAS ALL "Al","Mg","Sc","Mn","O"
filter=chemical_formula_reduced="NaCl"
filter=elements HAS ANY "Np","Cf"
AND elements HAS "O"
AND nelements=2
filter=chemical_formula_anonymous="A2B"
AND chemical_formula_anonymous="AB2"
filter=_mp_bandgap > 5.0
filter=chemical_formula_descriptive IS KNOWN
</code></pre>
<small>Let's play with them at the <a target="_blank" href="https://optimade.science">Optimade.Science</a> aggregator. Then head over to the <a target="_blank" href="https://mybinder.org/v2/gh/blokhin/materials-informatics-tutorial/master?filepath=notebooks">Python notebooks</a> you have opened earlier.</small>
</section>
<section><!-- Slide -->
<h3>Our community 👫</h3>
<br />
<ul>
<li><a target="_blank" href="https://matsci.org">matsci.org</a> forum</li>
<li><a target="_blank" href="https://mattermodeling.stackexchange.com/?tab=month">Stack Overflow</a> in materials science</li>
</ul>
</section>
<section><!-- Slide -->
<h3>Have your online profiles ready 🎓</h3>
<br />
<ul>
<li><a target="_blank" href="https://scholar.google.com/citations?user=B0h47WAAAAAJ&hl=en">Google Scholar</a></li>
<li><a target="_blank" href="https://orcid.org/0000-0001-9350-3034">ORCID</a></li>
</ul>
</section>
<section><!-- Slide -->
<h3>Conclusions 👌</h3>
<br />
<ul>
<li>materials informatics is just about how to handle materials data <span style="color:#0c0;">efficiently</span></li>
<li>Python + ASE can do anything about the nanometers for you</li>
<li>POSCAR & CIF are the most common formats for crystal structures, but the <span style="color:#0c0;">Optimade</span> is coming</li>
<li>the modern materials simulations can be prepared and even conducted fully <a href="https://absolidix.com" style="color:#0c0;border-bottom:3px solid #0c0;">online</a>.</li>
</ul>
</section>
<section><!-- Slide -->
<h3>PS</h3>
<br />
<ul>
<li><a target="_blank" href="https://tilde.pro">contact me</a> in case of any questions</li>
<li>these slides are the code on <a target="_blank" href="https://github.com/blokhin/materials-informatics-tutorial">GitHub</a> 🤓</li>
</ul>
</section>
</div>
</div>
<script src="webassets/reveal/reveal.js"></script>
<script src="webassets/reveal/plugin/highlight/highlight.js"></script>
<script>
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