Merge pull request #126 from Exabyte-io/feature/SOF-7365

feature/SOF 7365

other/materials_designer/Introduction.ipynb

@@ -17,9 +17,9 @@
     "\n",
     "This notebook lets user create an interface between two materials by finding matching superlattices and selecting optimal variants by (1) minimal strain and (2) minimal number of atoms. [Click here to open the notebook](create_interface_with_min_strain_zsl.ipynb).\n",
     "\n",
-    "#### [1.2. Relaxed interface creation with ZSL algorithm and EMT potential](create_interface_with_relaxation_ase_emt.ipynb)\n",
+    "#### [1.2. Relaxed interface creation with EMT potential](create_interface_with_relaxation_ase_emt.ipynb)\n",
     "\n",
-    "This notebook lets user create an interface between two materials and then relax it using the EMT potential. Interface creation is done in the same way as in the previous example, employing ZSL algorithm. [Click here to open the notebook](create_interface_with_relaxation_ase_emt.ipynb).\n",
+    "This notebook lets user relax an interface between two materials using the EMT potential. Interface material can be created using 1.2. notebook with ZSL algorithm or loaded from the database or a file. [Click here to open the notebook](create_interface_with_relaxation_ase_emt.ipynb).\n",
     "\n",
     "#### [1.3. Interface creation with a supercell matrix](create_interface_with_no_strain_matching.ipynb)\n",
     "\n",
@@ -35,20 +35,34 @@
     "\n",
     "This notebook demonstrates a workflow for converting materials data from the [JARVIS](https://jarvis.nist.gov/) database into ESSE format for use with Mat3ra.com platform. [Click here to open the notebook](import_material_from_jarvis_db_entry.ipynb).\n",
     "\n",
-    "## 3. Under the hood\n",
     "\n",
-    "### 3.1. Passing Data to and from the Outside Runtime\n",
+    "## 3. Under the hood\n",
+    "### <a id=\"data-exchange\">3.1. Data Exchange</a>\n",
+    "#### 3.1.1. Passing Data to and from the Outside Runtime\n",
     "The data is passed in *from* and *back to* the outside runtime (e.g. web application) using the `get_data` and `set_data` [helpers](../../utils/jupyterlite.py). The `get_data` function is used to retrieve the data from the outside runtime, while the `set_data` function is used to send the data back to the outside runtime.\n",
     "\n",
-    "### 3.2. Specific Considerations\n",
+    "#### 3.1.2. Uploads Folder\n",
+    "The **\"uploads\"** folder is used to exchange files between different notebooks when a user uploads a file, or when the notebook generates a file as part of its output.\n",
     "\n",
+    "#### 3.1.3. Passing Data between notebooks\n",
+    "When running JupyterLab (Python) locally, the files only get stored in the \"uploads\" folder and are not sent to the outside runtime. In JupyterLite (Pyodide) environment, the files are sent to the outside runtime and stored in the \"uploads\" folder.\n",
+    "\n",
+    "### 3.2. Specific Considerations\n",
     "#### 3.2.1. Interface creation\n",
     "\n",
     "The following conventions are used in the interface creation examples:\n",
     "\n",
     "3. We assume that two input materials are either in bulk form (e.g. Ni crystal) or layered (e.g. graphene). \n",
-    "1. We construct the interface along the Z-axis. The material corresponding to the bottom of the interface is referred to as the \"**substrate**\", and the top - as the \"**film**\". "
+    "1. We construct the interface along the Z-axis. The material corresponding to the bottom of the interface is referred to as the \"**substrate**\", and the top - as the \"**film**\". \n"
    ]
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [],
+   "metadata": {
+    "collapsed": false
+   }
   }
  ],
  "metadata": {