add more headlines to tutorials and fix a typo (#1126)

* try to fix the doc

* try to fix the doc

* add headlines to two tutorials

* fix spelling

* fix linting

* remove one comment

Author: JaGeo

tutorials/grueneisen_workflow.ipynb

@@ -4,14 +4,22 @@
    "cell_type": "markdown",
    "id": "0",
    "metadata": {},
+   "source": [
+    "# Grueneisen Workflow (VASP)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
    "source": [
     "This part is needed for the execution in the notebook.\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -32,7 +40,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2",
+   "id": "3",
    "metadata": {},
    "source": [
     "Let's load all required Makers."
@@ -41,7 +49,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -54,7 +62,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -74,7 +82,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -112,7 +120,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -148,7 +156,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "8",
    "metadata": {},
    "source": [
     "Then one can use the `GruneisenMaker` to generate a `Flow`."
@@ -157,7 +165,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -182,7 +190,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -191,7 +199,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "10",
+   "id": "11",
    "metadata": {},
    "source": [
     "We can then run the code with \"mock_vasp\"."
@@ -200,7 +208,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "12",
    "metadata": {
     "jupyter": {
      "is_executing": true
@@ -220,7 +228,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "12",
+   "id": "13",
    "metadata": {},
    "source": [
     "Let's then analyze outputs from the workflow."
@@ -229,7 +237,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -249,7 +257,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [

tutorials/lobster_workflow.ipynb

@@ -1,17 +1,25 @@
 {
  "cells": [
   {
-   "cell_type": "raw",
+   "cell_type": "markdown",
    "id": "0",
    "metadata": {},
+   "source": [
+    "# LOBSTER Workflow Tutorial (Using VASP for DFT)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
    "source": [
     "The first lines are needed to ensure that we can mock VASP and LOBSTER runs. The test files here might not belong to the same calculation but are good enough for testing."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -31,7 +39,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2",
+   "id": "3",
    "metadata": {},
    "source": [
     "We first load a structure that we want to analyze with bonding analysis."
@@ -40,7 +48,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -57,7 +65,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4",
+   "id": "5",
    "metadata": {},
    "source": [
     "Then, we initialize a workflow:"
@@ -66,7 +74,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -91,7 +99,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6",
+   "id": "7",
    "metadata": {},
    "source": [
     "We then run this workflow locally to show-case the capabilities. In real-life, you would omit the `mock*` parts."
@@ -100,7 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -116,7 +124,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8",
+   "id": "9",
    "metadata": {},
    "source": [
     "We can also analyze the data from the database"
@@ -125,7 +133,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [

tutorials/qha_workflow.ipynb

@@ -74,7 +74,7 @@
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "raw",
    "id": "3",
    "metadata": {},
    "source": [
@@ -166,7 +166,6 @@
     "                \"GGA\": \"PE\",\n",
     "                \"ISPIN\": 1,\n",
     "                \"KSPACING\": 0.1,\n",
-    "                # \"EDIFFG\": 1e-5,\n",
     "                \"ALGO\": \"Normal\",\n",
     "                \"LAECHG\": False,\n",
     "                \"ISMEAR\": 0,\n",

tutorials/tutorials.md

@@ -3,7 +3,7 @@
 # Tutorials
 
 The section includes tutorials for workflows in atomate2.
-They can also be found in the form of jupyternotebooks in:
+They can also be found in the form of jupyter notebooks in:
 [https://github.com/materialsproject/atomate2/tree/main/tutorials](https://github.com/materialsproject/atomate2/tree/main/tutorials)
 
 ```{toctree}