feat: HOMO/LUMO NB

.github/workflows/check_links.yml

@@ -13,4 +13,6 @@ jobs:
       - name: Link Checker
         uses: lycheeverse/lychee-action@v1.8.0
         with:
+          # materialsproject.org blocks automated requests (Cloudflare 403)
+          args: --verbose --no-progress --exclude 'materialsproject\.org' './**/*.md' './**/*.html'
           fail: true

README.md

@@ -160,7 +160,7 @@ In order to run or edit the examples:
 
 3. Optionally, for local Jupyter without OIDC, set legacy API token values in [settings.json](src/py/mat3ra/notebooks_utils/core/api/settings.json). See [Get Authentication Params](examples/system/get_authentication_params.ipynb) for details. API tokens can also be generated in [Account Preferences](https://docs.mat3ra.com/accounts/ui/preferences/api/) on the platform.
 
-NOTE: The Materials Project API key should be set in `settings.json` and obtained from [https://legacy.materialsproject.org/open](https://legacy.materialsproject.org/open).
+NOTE: The Materials Project API key should be set in `settings.json` and obtained from [https://next-gen.materialsproject.org/api](https://next-gen.materialsproject.org/api).
 
 
 ## Contribute

examples/assets/README.md

@@ -2,6 +2,6 @@
 
 This directory contains various files for the example notebooks.
 
-- `mp-978534.poscar` contains a SiGe structure from [https://legacy.materialsproject.org/materials/mp-978534](https://legacy.materialsproject.org/materials/mp-978534).
+- `mp-978534.poscar` contains a SiGe structure from [https://next-gen.materialsproject.org/materials/mp-978534](https://next-gen.materialsproject.org/materials/mp-978534).
 - `bash_workflow_template.json` contains the template JSON schema of Mat3ra workflow.
 - `Si.pz-vbc.UPF` is the pseudo potential file of silicon used in the Quantum Espresso workflow example.

other/materials_designer/uploads/H2O.json

@@ -0,0 +1,62 @@
+{
+  "name": "H2O",
+  "basis": {
+    "elements": [
+      {
+        "id": 0,
+        "value": "O"
+      },
+      {
+        "id": 1,
+        "value": "H"
+      },
+      {
+        "id": 2,
+        "value": "H"
+      }
+    ],
+    "coordinates": [
+      {
+        "id": 0,
+        "value": [
+          0.0,
+          0.5,
+          0.0
+        ]
+      },
+      {
+        "id": 1,
+        "value": [
+          0.043139,
+          0.431029,
+          0.043078
+        ]
+      },
+      {
+        "id": 2,
+        "value": [
+          0.036635,
+          0.576406,
+          0.035949
+        ]
+      }
+    ],
+    "units": "crystal",
+    "labels": [],
+    "constraints": []
+  },
+  "lattice": {
+    "a": 10.58354,
+    "b": 10.58354,
+    "c": 12.70025,
+    "alpha": 90.0,
+    "beta": 90.0,
+    "gamma": 90.0,
+    "units": {
+      "length": "angstrom",
+      "angle": "degree"
+    },
+    "type": "TRI"
+  },
+  "isNonPeriodic": true
+}

other/materials_designer/workflows/Introduction.ipynb

@@ -69,7 +69,7 @@
     "#### [6.4.1. Zero-point energy calculation.](zero_point_energy.ipynb)\n",
     "\n",
     "### 6.5. Defect Energy\n",
-    "#### 6.5.1. Defect formation energy. *(to be added)*\n",
+    "#### [6.5.1. Defect formation energy.](defect_formation_energy.ipynb)\n",
     "\n",
     "### 6.6. Formation Energy\n",
     "#### [6.6.1. Compound formation energy.](formation_energy.ipynb)\n",
@@ -84,10 +84,10 @@
     "#### 7.1.1. NEB reaction pathway calculation. *(to be added)*\n",
     "\n",
     "### 7.2. HOMO-LUMO (NWChem)\n",
-    "#### 7.2.1. HOMO-LUMO gap calculation. *(to be added)*\n",
+    "#### [7.2.1. HOMO-LUMO gap calculation.](homo_lumo_frequency.ipynb)\n",
     "\n",
     "### 7.3. Vibrational Frequency (NWChem)\n",
-    "#### 7.3.1. Vibrational frequency calculation. *(to be added)*\n",
+    "#### [7.3.1. Vibrational frequency calculation.](homo_lumo_frequency.ipynb)\n",
     "\n",
     "\n",
     "## 8. Electronics\n",