SOF-8043: Gr/Ni(111) registry and work of adhesion — Specific Example

other/experiments/jupyterlite/relax_structure_with_mlff.ipynb

@@ -82,7 +82,7 @@
    "source": [
     "from mat3ra.notebooks_utils.packages import install_packages\n",
     "from mat3ra.notebooks_utils.primitive.environment import is_pyodide_environment\n",
-    "from mat3ra.notebooks_utils.mlff import get_mlff_install_profiles\n",
+    "from mat3ra.notebooks_utils.calculators.mlff import get_mlff_install_profiles\n",
     "\n",
     "profiles = get_mlff_install_profiles(MLFF_NAME)\n",
     "await install_packages(profiles)\n",
@@ -157,7 +157,7 @@
     "from mat3ra.made.tools.convert import to_ase\n",
     "from ase.optimize import BFGS\n",
     "\n",
-    "from mat3ra.notebooks_utils.mlff import create_mlff_calculator\n",
+    "from mat3ra.notebooks_utils.calculators.mlff import create_mlff_calculator\n",
     "from mat3ra.notebooks_utils.ipython.plot._plotly import progress_callback\n",
     "\n",
     "calculator = create_mlff_calculator(MLFF_NAME, MLFF_SETTINGS[MLFF_NAME])\n",

other/materials_designer/specific_examples/Introduction.ipynb

@@ -27,7 +27,7 @@
     "| `C-2D-INT-Z` | Interface ZSL                  | [BN/Graphene 2D–2D Interface](interface_2d_2d_boron_nitride_graphene.ipynb)                                          | *To be added* | [[4]](#ref4) |\n",
     "| `C-2D-INT-Z` | Interface ZSL                  | [Graphene/SiO₂ 2D–3D Interface](interface_2d_3d_graphene_silicon_dioxide.ipynb)                                      | *To be added* | [[5]](#ref5) |\n",
     "| `C-2D-INT-Z` | Interface ZSL                  | [Cu/Cristobalite 3D–3D Interface](interface_3d_3d_copper_cristobalite.ipynb)                                         | *To be added* | [[6]](#ref6) |\n",
-    "| `C-2D-INT-Z` | Interface ZSL                  | [Graphene/Ni Interface Film XY Position Optimization](optimization_interface_film_xy_position_graphene_nickel.ipynb) | *To be added* | [[7]](#ref7) |\n",
+    "| `C-2D-INT-Z` | Interface ZSL                  | [Graphene/Ni Interface Film XY Position Optimization](optimization_interface_film_xy_position_graphene_nickel.ipynb) | [Gr/Ni(111) Registry and Work of Adhesion](optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb) | [[7]](#ref7) |\n",
     "| `C-2D-INT-T` | Interface Twisted              | *To be added*                                                                                                        | —             | — |\n",
     "| `C-2D-INT-C` | Interface Commensurate Lattice | [Twisted Commensurate MoS₂ Bilayer](interface_bilayer_twisted_commensurate_lattices_molybdenum_disulfide.ipynb)      | [Twisted MoS₂ Bilayer Band Structure](interface_bilayer_twisted_commensurate_lattices_molybdenum_disulfide_SIMULATION.ipynb) | [[8]](#ref8) |\n",
     "| `C-2D-MLT`   | Multi-Layer                    | *To be added*                                                                                                        | —             | — |\n",

other/materials_designer/specific_examples/optimization_interface_film_xy_position_graphene_nickel.ipynb

@@ -56,6 +56,8 @@
     "# Material selection\n",
     "SUBSTRATE_NAME = \"Nickel\"\n",
     "FILM_NAME = \"Graphene\"\n",
+    "# canonical name the companion SIMULATION notebook loads by\n",
+    "BASE_MATERIAL_NAME = \"Graphene_Nickel_interface\"\n",
     "\n",
     "# Slab parameters\n",
     "FILM_MILLER_INDICES = (0, 0, 1)\n",
@@ -196,7 +198,7 @@
     "    reduce_result_cell_to_primitive=REDUCE_RESULT_CELL_TO_PRIMITIVE,\n",
     ")\n",
     "\n",
-    "interface_material.name = f\"{FILM_NAME}_{SUBSTRATE_NAME}_interface\"\n",
+    "interface_material.name = BASE_MATERIAL_NAME\n",
     "\n",
     "# Visualize interface\n",
     "visualize_materials([interface_material], repetitions=STRUCTURE_REPETITIONS)\n",
@@ -264,7 +266,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mat3ra.utils.jupyterlite.plot import plot_2d_heatmap, plot_3d_surface\n",
+    "from mat3ra.notebooks_utils.ipython.plot._plotly import plot_2d_heatmap, plot_3d_surface\n",
     "\n",
     "x_values, y_values = xy_matrix\n",
     "# Plot energy landscape\n",
@@ -317,7 +319,7 @@
    "id": "16",
    "metadata": {},
    "source": [
-    "# 4. Save optimized material"
+    "# 4. Save the base and optimized materials"
    ]
   },
   {
@@ -330,6 +332,9 @@
     "from mat3ra.notebooks_utils.io import download_content_to_file\n",
     "from mat3ra.notebooks_utils.material import set_materials\n",
     "\n",
+    "set_materials(interface_material)\n",
+    "download_content_to_file(interface_material.to_json(), f\"{interface_material.name}.json\")\n",
+    "\n",
     "optimized_material.name = f\"{interface_material.name}_optimized_xy\"\n",
     "set_materials(optimized_material)\n",
     "download_content_to_file(optimized_material.to_json(), f\"{interface_material.name}_optimized_xy.json\")"