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Merge pull request #5 from matlantis-pfcc/v1.2.1
Update to v1.2.1
2 parents 16b2fac + b1ccfb2 commit 81e8af6

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‎docs/README.md

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@@ -17,5 +17,6 @@ $ poetry install
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You can choose a language for build from `ja` or `en`.
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```sh
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$ poetry run python misc/split_notebook.py
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$ poetry run make html -e LANG="ja"
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```

‎docs/_static/css/cookie-consent.css

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‎docs/_static/css/custom.css

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.md-icon.md-icon--menu.md-header-nav__button {
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margin-top: 17px;
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}
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.nboutput .output_area .highlight pre {
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word-break: break-all;
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word-wrap: break-word;
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white-space: pre-wrap;
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}
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.md-typeset__table .head code.docutils{
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background: #616161;
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padding: 2px;
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white-space: nowrap;
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font-weight: bold;
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color: #FFF;
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}
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.md-typeset h1,
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.md-typeset h2 {
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color: rgba(0,0,0,.87);
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font-weight: bold;
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}

‎docs/_static/js/cookie-consent-init.umd.js

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‎docs/_static/js/cookie-consent.umd.js

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‎docs/_static/js/external-link.js

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$(document).ready(function () {
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$('a[href^="http://"], a[href^="https://"]').not('a[class*=internal]').attr({
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target: '_blank',
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referrerpolicy: "no-referrer",
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rel: "noopener noreferrer"
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});
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});

‎docs/_templates/header.html

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<span class="md-header-nav__topic"> {{ title|striptags|e }} </span>
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</div>
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</div>
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<div class="md-flex__cell md-flex__cell--shrink">
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<div style="width: 85px; height: 57px; font-size: 16px; line-height: 57px;">
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<a href="https://docs.matlantis.com/atomistic-simulation-tutorial/ja/" hreflang="ja">JA</a>
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|
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<a href="https://docs.matlantis.com/atomistic-simulation-tutorial/en/" hreflang="en">EN</a>
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</div>
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</div>
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<div class="md-flex__cell md-flex__cell--shrink">
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<label class="md-icon md-icon--search md-header-nav__button" for="__search"></label>
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{% include "searchbox.html" %}

‎docs/_templates/layout.html

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{% block htmltitle %}
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{{ super() }}
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<!-- Workaround: need to import cookie-consent library before importing require.js -->
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<script src="_static/js/cookie-consent.umd.js"></script>
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<script src="_static/js/cookie-consent-init.umd.js"></script>
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<script src="https://docs.matlantis.com/assets/js/cookie-consent.umd.js"></script>
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<script src="https://docs.matlantis.com/assets/js/cookie-consent-init.umd.js"></script>
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{% endblock %}
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{% block relbar1 %}

‎docs/conf.py

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html_css_files = [
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'css/custom.css',
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'css/cookie-consent.css',
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'https://docs.matlantis.com/assets/css/cookie-consent.css',
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]
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html_js_files = ['js/external-link.js']
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# Avoid to plotly error
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# See https://github.com/spatialaudio/nbsphinx/issues/572#issuecomment-853389268
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mathjax_path = 'https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js?config=TeX-AMS-MML_HTMLorMML'

‎docs/misc/split_notebook.py

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)
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# Copy `output` directory
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shutil.copytree(tutorials_bilingual / "output", tutorials_jp / "output")
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shutil.copytree(tutorials_bilingual / "output", tutorials_en / "output")
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shutil.copytree(tutorials_bilingual / "output", tutorials_jp / "output", dirs_exist_ok=True)
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shutil.copytree(tutorials_bilingual / "output", tutorials_en / "output", dirs_exist_ok=True)
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if args.remove_bilingual_dir:
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shutil.rmtree(tutorials_bilingual)

‎tutorials/en/1_1_welcome.ipynb

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"\n",
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"<div style=\"clear:both;display:table\">\n",
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"<figure style=\"width:30%;float:left;margin:10px\">\n",
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" <img src=\"https://matlantis.com/wp-content/themes/matlantis_theme/img/product/image_universal1.png\"/>\n",
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" <img src=\"https://matlantis.com/wp-content/themes/matlantis_theme/img/product/en_image_universal1.png\"/>\n",
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" <figcaption style=\"text-align: center\">Versatility</figcaption>\n",
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"</figure>\n",
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"<figure style=\"width:30%;float:left;margin:10px\">\n",
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" <img src=\"https://matlantis.com/wp-content/themes/matlantis_theme/img/product/image_universal2.png\"/>\n",
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" <img src=\"https://matlantis.com/wp-content/themes/matlantis_theme/img/product/en_image_universal2.png\"/>\n",
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" <figcaption style=\"text-align: center\">Speed</figcaption>\n",
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"</figure>\n",
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"<figure style=\"width:30%;float:left;margin:10px\">\n",
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" <img src=\"https://matlantis.com/wp-content/themes/matlantis_theme/img/product/image_universal3.png\"/>\n",
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" <img src=\"https://matlantis.com/wp-content/themes/matlantis_theme/img/product/en_image_universal3.png\"/>\n",
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" <figcaption style=\"text-align: center\">User-friendliness</figcaption>\n",
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"</figure>\n",
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"</div>\n",
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3.7",
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"display_name": "Python 3.8",
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"language": "python",
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"name": "python37"
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"name": "python38"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.13"
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"version": "3.8.13"
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},
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"widgets": {
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"application/vnd.jupyter.widget-state+json": {

‎tutorials/en/1_2_atomistic_simulation_intro.ipynb

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"Therefore, in atomistic simulations, it is necessary to perform appropriate **modeling** according to the phenomenon to create a simplified system that can be analyzed on a computer by extracting only the necessary elements to reproduce the desired phenomenon, rather than creating something exactly the same as the natural world.<br/>\n",
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"There are various methods for modeling, and you will be able to do them by learning through this tutorial.\n",
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"\n",
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"---\n",
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"\n",
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"[Column] Modeling\n",
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"\n",
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"For example, if you want to simulate the Earth, if you are interested in weather, you would need to focus your modeling on the Earth's surface atmosphere. \n",
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"On the other hand, if you are interested in earthquakes, you would need to concentrate your modeling on the Earth's internal structure rather than the atmosphere. \n",
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"If you want to simulate the environment on the surface of the earth, you might consider cutting out only a portion of a continent rather than the entire planet."
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"If you want to simulate the environment on the surface of the earth, you might consider cutting out only a portion of a continent rather than the entire planet.\n",
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"\n",
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"---"
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]
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},
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{
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3.7",
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"display_name": "Python 3.8",
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"language": "python",
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"name": "python37"
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"name": "python38"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.13"
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"version": "3.8.13"
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},
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"widgets": {
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"application/vnd.jupyter.widget-state+json": {

‎tutorials/en/1_3_ase_basic.ipynb

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{
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"data": {
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"text/html": [
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"<img src=\"output/H2O.png\" width=\"150\"/>"
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"<img src=\"output/H2.png\" width=\"150\"/>"
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],
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"text/plain": [
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"<IPython.core.display.Image object>"
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"from ase.io import write\n",
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"from IPython.display import Image\n",
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"\n",
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"write(\"output/H2O.png\", atoms, rotation=\"0x,0y,0z\", scale=100)\n",
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"Image(url='output/H2O.png', width=150)"
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"write(\"output/H2.png\", atoms, rotation=\"0x,0y,0z\", scale=100)\n",
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"Image(url='output/H2.png', width=150)"
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]
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},
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{
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3.7",
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"display_name": "Python 3.8",
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"language": "python",
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"name": "python37"
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"name": "python38"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.13"
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"version": "3.8.13"
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},
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"toc-autonumbering": false,
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"toc-showcode": false,

‎tutorials/en/1_4_ase_structure.ipynb

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],
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"metadata": {
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"display_name": "Python 3.7",
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"display_name": "Python 3.8",
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"language": "python",
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"name": "python38"
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},
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"language_info": {
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"name": "python",
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"nbconvert_exporter": "python",
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"version": "3.8.13"
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},
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"toc-autonumbering": false,
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"toc-showcode": false,

‎tutorials/en/1_5_ase_calculator.ipynb

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],
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"metadata": {
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"kernelspec": {
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"language": "python",
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},
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"language_info": {
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"version": "3.8.13"
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},
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"widgets": {
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"application/vnd.jupyter.widget-state+json": {

‎tutorials/en/1_6_ase_playground.ipynb

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],
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"metadata": {
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"version": "3.8.13"
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},
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"widgets": {
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"application/vnd.jupyter.widget-state+json": {

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