feature/SOF-8065 Feature: SE for graphene on SiO2, doping and gap at the Dirac point

other/materials_designer/specific_examples/Introduction.ipynb

@@ -25,7 +25,7 @@
     "| `C-2D-HST`   | Heterostack                    | [Si/SiO₂/HfO₂/TiN Heterostructure](heterostructure_silicon_silicon_dioxide_hafnium_dioxide_titanium_nitride.ipynb)   | *To be added* | [[3]](#ref3) |\n",
     "| `C-2D-INT-S` | Interface Simple               | *To be added*                                                                                                        | —             | — |\n",
     "| `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                  | [Graphene/SiO₂ 2D–3D Interface](interface_2d_3d_graphene_silicon_dioxide.ipynb)                                      | [Doping and Gap at the Dirac Point](interface_2d_3d_graphene_silicon_dioxide_SIMULATION.ipynb) | [[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) | [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",

other/materials_designer/specific_examples/interface_2d_3d_graphene_silicon_dioxide.ipynb

@@ -18,7 +18,7 @@
     "\n",
     "\n",
     "\n",
-    "Replicating the materials from the manuscript, FIG. 1. (b):\n",
+    "Replicating the metastable geometry of Kang et al. Sec. III: graphene 2.58 Å above the O-terminated surface, shifted from the C-over-O registry of Fig. 1(b):\n",
     "\n",
     "<img src='https://github.com/Exabyte-io/documentation/raw/12617167278ae3523adc028583b21ea4e8ebd197/images/tutorials/materials/interfaces/interface_2d_3d_graphene_silicon_dioxide/0-figure-from-manuscript.webp' width='600'/>\n"
    ]
@@ -45,12 +45,16 @@
     "FILM_VACUUM = 0.0  # in angstroms\n",
     "\n",
     "SUBSTRATE_MILLER_INDICES = (0, 0, 1)\n",
-    "SUBSTRATE_THICKNESS = 7  # in atomic layers (for 14 bilayers -- from manuscript)\n",
+    "SUBSTRATE_THICKNESS = 5  # conventional cells along c: 15 Si planes; the manuscript has 14 bilayers\n",
     "SUBSTRATE_TERMINATION_FORMULA = None  # if None, the first termination will be used\n",
     "SUBSTRATE_VACUUM = 0.0  # in angstroms\n",
     "\n",
     "INTERFACE_DISTANCE = 2.58  # Gap between substrate and film, in Angstrom -- from manuscript\n",
-    "INTERFACE_VACUUM = 20.0  # Vacuum over film, in Angstrom -- from manuscript\n",
+    "# The slab is centered, so 17.5 gives about 20 Å between periodic images, 10 Å on each side, as in the manuscript\n",
+    "INTERFACE_VACUUM = 17.5  # in Angstrom\n",
+    "# Å, in-plane; the closest a rigid shift gets to the manuscript's metastable registry (Sec. III)\n",
+    "# 3.5 prints each surface O's distance to the nearest C (0.354 / 1.095 Å)\n",
+    "REGISTRY_SHIFT = [-1.011, -0.725, 0.0]\n",
     "\n",
     "# Whether to convert materials to conventional cells before creating slabs.\n",
     "USE_CONVENTIONAL_CELL = True\n",
@@ -337,6 +341,62 @@
     ")\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 3.5. Shift graphene to the metastable registry\n",
+    "The ZSL match leaves the registry undefined; as built, both surface O atoms sit near a C atom. The film is shifted in-plane so that one surface O sits near a C atom and the other near a hexagon centre, the registry of the manuscript's metastable geometry (Sec. III).\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "from mat3ra.made.tools.modify import interface_displace_part\n",
+    "\n",
+    "interface = interface_displace_part(interface, displacement=REGISTRY_SHIFT, use_cartesian_coordinates=True)\n",
+    "\n",
+    "interface_in_cartesian = interface.clone()\n",
+    "interface_in_cartesian.to_cartesian()\n",
+    "coordinates = np.array(interface_in_cartesian.basis.coordinates.values)\n",
+    "elements = np.array(interface.basis.elements.values)\n",
+    "cell_xy = np.array(interface.lattice.vector_arrays)[:2, :2]\n",
+    "carbons = coordinates[elements == \"C\"]\n",
+    "oxygens = coordinates[elements == \"O\"]\n",
+    "for oxygen in oxygens[np.argsort(-oxygens[:, 2])[:2]]:\n",
+    "    distances = [np.linalg.norm(oxygen[:2] - carbon[:2] - i * cell_xy[0] - j * cell_xy[1])\n",
+    "                 for carbon in carbons for i in (-1, 0, 1) for j in (-1, 0, 1)]\n",
+    "    print(f\"surface O at z = {oxygen[2]:.3f} Å: nearest C in the plane {min(distances):.3f} Å\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 3.6. Set the cell to the standard hexagonal setting and center the slab\n",
+    "The ZSL interface cell comes out with γ = 60°. The cell is put in the 120° hexagonal setting (same atoms) and typed HEX, so the symbolic K point of the band path in [interface_2d_3d_graphene_silicon_dioxide_SIMULATION.ipynb](interface_2d_3d_graphene_silicon_dioxide_SIMULATION.ipynb) is graphene's K. The slab is then centered along z, so that no atom sits at z = 0, where a relaxation would wrap it to the top of the cell.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mat3ra.made.tools.helpers import create_supercell\n",
+    "from mat3ra.made.tools.modify import translate_to_center\n",
+    "\n",
+    "interface = create_supercell(interface, supercell_matrix=[[1, 0, 0], [-1, 1, 0], [0, 0, 1]])\n",
+    "interface = translate_to_center(interface, axes=[\"z\"])\n",
+    "interface.lattice.type = \"HEX\"\n",
+    "print(f\"{interface.basis.number_of_atoms} atoms, a = {interface.lattice.a:.4f} Å, \"\n",
+    "      f\"gamma = {interface.lattice.gamma:.1f}°\")"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -367,7 +427,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mat3ra.notebooks_utils.material import set_materials, download_content_to_file\n",
+    "from mat3ra.notebooks_utils.io import download_content_to_file\n",
+    "from mat3ra.notebooks_utils.material import set_materials\n",
     "\n",
     "set_materials(interface)\n",
     "download_content_to_file(interface.to_json(), f\"{interface.name}.json\")"