v1.2.0

README.md

@@ -6,9 +6,8 @@ Atomistic simulation hands on tutorial on [Matlantis](https://matlantis.com/)
 
 Please refer the document page:
 
- - https://docs.matlantis.com/atomistic-simulation-tutorial/ja/index.html
-
-Currently, only Japanese version is available.
+ - English: https://docs.matlantis.com/atomistic-simulation-tutorial/en/index.html
+ - Japanese: https://docs.matlantis.com/atomistic-simulation-tutorial/ja/index.html
 
 ## LICENSE
 <a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.

docs/_static/css/cookie-consent.css

@@ -0,0 +1,99 @@
+.cookie-consent-root.svelte-8pd0rh.svelte-8pd0rh {
+  font-size: 13px;
+  line-height: 1.5;
+}
+
+.cookie-consent-root.svelte-8pd0rh a {
+  color: rgb(13, 49, 143);
+  text-decoration: none;
+}
+
+.cookie-consent-root.svelte-8pd0rh a:hover {
+  text-decoration: underline;
+}
+
+.cookie-consent-root.svelte-8pd0rh h1 {
+  font-size: 150%;
+}
+
+.cookie-consent-root.svelte-8pd0rh p {
+  margin: 1em 0;
+}
+
+.cookie-consent-popup.svelte-8pd0rh.svelte-8pd0rh, .cookie-consent-settings-popup.svelte-8pd0rh.svelte-8pd0rh {
+  position: fixed;
+  z-index: 100000000;
+  padding: 0.5em 1.5em;
+  color: #333;
+  background-color: white;
+  box-shadow: 0 4px 15px rgba(0, 0, 0, 0.1);
+}
+
+.cookie-consent-popup.svelte-8pd0rh.svelte-8pd0rh {
+  right: 0;
+  bottom: 0;
+  left: 0;
+}
+
+.cookie-consent-settings-popup.svelte-8pd0rh.svelte-8pd0rh {
+  top: 0;
+  bottom: 0;
+  left: 0;
+  max-width: 575px;
+  overflow: auto;
+}
+
+.cookie-consent-actions.svelte-8pd0rh button, .cookie-consent-settings-actions.svelte-8pd0rh button, .cookie-consent-settings-choices-actions.svelte-8pd0rh button {
+  display: inline-block;
+  margin: 0;
+  font-family: inherit;
+  font-size: 100%;
+  line-height: inherit;
+  cursor: pointer;
+  outline: none;
+  appearance: none;
+  padding: 0.25em 0.5em;
+  color: #fff;
+  background-color: rgb(13, 49, 143);
+  border: 2px solid transparent;
+}
+
+.cookie-consent-actions.svelte-8pd0rh button:hover, .cookie-consent-settings-actions.svelte-8pd0rh button:hover, .cookie-consent-settings-choices-actions.svelte-8pd0rh button:hover {
+  background-color: rgba(13, 49, 143, 0.8);
+}
+
+.cookie-consent-actions.svelte-8pd0rh.svelte-8pd0rh {
+  text-align: right;
+}
+
+.cookie-consent-actions.svelte-8pd0rh .cookie-consent-settings-button.svelte-8pd0rh {
+  color: rgb(13, 49, 143);
+  background-color: #fff;
+  border-color: rgb(13, 49, 143);
+}
+
+.cookie-consent-actions.svelte-8pd0rh .cookie-consent-settings-button.svelte-8pd0rh:hover {
+  color: #fff;
+  background-color: rgba(13, 49, 143, 0.8);
+  border-color: transparent;
+}
+
+.cookie-consent-close.svelte-8pd0rh.svelte-8pd0rh, .cookie-consent-settings-close.svelte-8pd0rh.svelte-8pd0rh {
+  display: inline-block;
+  margin: 0;
+  font-family: inherit;
+  font-size: 100%;
+  line-height: inherit;
+  cursor: pointer;
+  outline: none;
+  appearance: none;
+  display: inline;
+  padding: 0;
+  color: inherit;
+  text-align: start;
+  background-color: transparent;
+  border: 0 none;
+  float: right;
+  padding: 0.5em;
+  font-size: 150%;
+}

docs/_templates/layout.html

@@ -1,20 +1,27 @@
 {% extends "!layout.html" %}
 
-{% block extrahead %}
-  <!-- Google Tag Manager -->
-	<script>(function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':
-	new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],
-	j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src=
-	'https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);
-	})(window,document,'script','dataLayer','GTM-W7Q4ZJV');</script>
-  <!-- End Google Tag Manager -->
+{% block htmltitle %}
   {{ super() }}
+  <!-- Workaround: need to import cookie-consent library before importing require.js -->
+  <script src="_static/js/cookie-consent.umd.js"></script>
+  <script src="_static/js/cookie-consent-init.umd.js"></script>
 {% endblock %}
 
 {% block relbar1 %}
-  <!-- Google Tag Manager (noscript) -->
-    <noscript><iframe src="https://www.googletagmanager.com/ns.html?id=GTM-W7Q4ZJV"
-	height="0" width="0" style="display:none;visibility:hidden"></iframe></noscript>
-  <!-- End Google Tag Manager (noscript) -->
+  <script>
+    const cc = cookieConsentInit(cookieConsent)({
+      onChange(result) {
+        console.log(result);
+      },
+      gtmid: 'GTM-W7Q4ZJV',
+      consentCookieOptions: {
+        domain: "matlantis.com"
+      }
+    });
+
+    function showSettings() {
+      cc.$set({ settingsShown: true });
+    }
+  </script>
   {{ super()}}
 {% endblock %}

docs/conf.py

@@ -103,6 +103,7 @@
 
 html_css_files = [
     'css/custom.css',
+    'css/cookie-consent.css',
 ]
 
 # Avoid to plotly error

docs/misc/split_notebook.py

@@ -0,0 +1,118 @@
+import argparse
+import os
+import pathlib
+import shutil
+from typing import Union
+
+import nbformat
+from nbformat.notebooknode import NotebookNode
+from distutils.util import strtobool
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--tutorials-dir", default="tutorials")
+parser.add_argument("--tutorials-bilingual-dir", default="tutorials/bilingual")
+parser.add_argument("--remove-bilingual-dir", type=strtobool, default="false")
+args = parser.parse_args()
+
+
+def split_notebook(
+        notebook: Union[str, pathlib.Path],
+        jp_notebook: Union[str, pathlib.Path],
+        en_notebook: Union[str, pathlib.Path],
+        strict: bool = True,
+) -> None:
+    # When `strict=True`, all cell must be annotated by [JP], [EN] or [ALL].
+    with open(notebook, "r") as f:
+        text = f.read().replace("\n", "")
+        notebook = nbformat.reads(text, as_version=4)
+
+    JP_cell = []
+    EN_cell = []
+
+    for i, cell in enumerate(notebook.cells):
+        if cell["cell_type"] == "markdown":
+            if cell["source"][:5] == "[EN]\n":
+                cell["source"] = cell["source"][5:]
+                if cell["source"].startswith("\n"):
+                    cell["source"] = cell["source"][1:]
+                EN_cell.append(cell)
+            elif cell["source"][:5] == "[JP]\n":
+                cell["source"] = cell["source"][5:]
+                if cell["source"].startswith("\n"):
+                    cell["source"] = cell["source"][1:]
+                JP_cell.append(cell)
+            elif cell["source"][:6] == "[ALL]\n":
+                cell["source"] = cell["source"][6:]
+                if cell["source"].startswith("\n"):
+                    cell["source"] = cell["source"][1:]
+                JP_cell.append(cell)
+                EN_cell.append(cell)
+            else:
+                if strict:
+                    raise RuntimeError(f"INFO : cannot find language annotation for cell {i}")
+                else:
+                    print(f"INFO : cannot find language annotation for cell {i}, considered as both JP & EN")
+                    JP_cell.append(cell)
+                    EN_cell.append(cell)
+        else:
+            JP_cell.append(cell)
+            EN_cell.append(cell)
+
+    if len(JP_cell) != len(EN_cell):
+        if strict:
+            raise RuntimeError(f"The number of cell is different! JP {len(JP_cell)} != EN {len(EN_cell)}.")
+        else:
+            print(f"WARNING: the number of cell is different! JP {len(JP_cell)} != EN {len(EN_cell)}.")
+
+    with open(en_notebook, mode="wt") as f:
+        EN_nb = NotebookNode(
+            {
+                "cells": EN_cell,
+                "metadata": notebook["metadata"],
+                "nbformat": notebook["nbformat"],
+                "nbformat_minor": notebook["nbformat_minor"],
+            }
+        )
+        nbformat.write(EN_nb, f)
+
+    with open(jp_notebook, mode="wt") as f:
+        JP_nb = NotebookNode(
+            {
+                "cells": JP_cell,
+                "metadata": notebook["metadata"],
+                "nbformat": notebook["nbformat"],
+                "nbformat_minor": notebook["nbformat_minor"],
+            }
+        )
+        nbformat.write(JP_nb, f)
+
+
+project_root_dir = pathlib.Path(os.path.abspath(__file__)).parent.parent.parent
+tutorials = project_root_dir / args.tutorials_dir
+tutorials_bilingual = project_root_dir / args.tutorials_bilingual_dir
+print(f"project_root_dir   : {project_root_dir}")
+print(f"tutorials          : {tutorials}")
+print(f"tutorials_bilingual: {tutorials_bilingual}")
+file_names = sorted([f.name.replace("".join(f.suffixes), "") for f in tutorials_bilingual.glob("*.ipynb")])
+print(f"file_names: {file_names}")
+tutorials_jp = tutorials / "ja"
+tutorials_en = tutorials / "en"
+
+tutorials.mkdir(exist_ok=True, parents=True)
+tutorials_jp.mkdir(exist_ok=True, parents=True)
+tutorials_en.mkdir(exist_ok=True, parents=True)
+
+for f in file_names:
+    print(f)
+    split_notebook(
+        notebook=tutorials_bilingual / f"{f}.ipynb",
+        jp_notebook=tutorials_jp / f"{f}.ipynb",
+        en_notebook=tutorials_en / f"{f}.ipynb",
+    )
+
+# Copy `output` directory
+shutil.copytree(tutorials_bilingual / "output", tutorials_jp / "output")
+shutil.copytree(tutorials_bilingual / "output", tutorials_en / "output")
+
+if args.remove_bilingual_dir:
+    shutil.rmtree(tutorials_bilingual)

docs/tutorials/en/1_1_welcome.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/1_1_welcome.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/1_2_atomistic_simulation_intro.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/1_2_atomistic_simulation_intro.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/1_3_ase_basic.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/1_3_ase_basic.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/1_4_ase_structure.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/1_4_ase_structure.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/1_5_ase_calculator.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/1_5_ase_calculator.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/1_6_ase_playground.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/1_6_ase_playground.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/1_7_ase_playground2.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/1_7_ase_playground2.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/1_8_diatomic_potential.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/1_8_diatomic_potential.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/2_1_opt.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/2_1_opt.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/2_2_opt_symmetry.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/2_2_opt_symmetry.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/2_3_opt-algorithm.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/2_3_opt-algorithm.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/3_1_bulk_energy.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/3_1_bulk_energy.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/3_2_slab_energy.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/3_2_slab_energy.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}

docs/tutorials/en/3_3_slab_adsorption_energy.nblink

@@ -0,0 +1,7 @@
+{
+	"path": "../../../tutorials/en/3_3_slab_adsorption_energy.ipynb",
+	"extra-media": [
+		"../../../tutorials/assets",
+		"../../../tutorials/en/output"
+	]
+}