update: interfaces nb

Author: VsevolodX

other/materials_designer/create_interface_with_min_strain_zsl.ipynb

@@ -50,7 +50,6 @@
    "source": [
     "from mat3ra.made.tools.build.slab.configurations import SlabConfiguration\n",
     "\n",
-    "\n",
     "# Enable interactive selection of terminations via UI prompt\n",
     "IS_TERMINATIONS_SELECTION_INTERACTIVE = False\n",
     "\n",
@@ -70,19 +69,23 @@
     "SUBSTRATE_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]\n",
     "SUBSTRATE_USE_ORTHOGONAL_C = True\n",
     "\n",
+    "INTERFACE_DISTANCE = 3.0  # Gap between substrate and film, in Angstrom\n",
+    "INTERFACE_VACUUM = 10.0  # Vacuum over film, in Angstrom\n",
+    "\n",
     "# Whether to convert materials to conventional cells before creating slabs.\n",
     "# To create interfaces with smaller cells, set this flag to False. (and pass already conventional cells as input)\n",
     "USE_CONVENTIONAL_CELL = True\n",
     "\n",
-    "# Maximum area for the superlattice search algorithm\n",
-    "MAX_AREA = 50  # in Angstrom^2\n",
+    "# Maximum area for the superlattice search algorithm (the final interface area will be smaller)\n",
+    "MAX_AREA = 150  # in Angstrom^2\n",
     "# Additional fine-tuning parameters (increase values to get more strained matches):\n",
     "MAX_AREA_TOLERANCE = 0.09  # in Angstrom^2\n",
-    "MAX_ANGLE_TOLERANCE = 0.03\n",
-    "MAX_LENGTH_TOLERANCE = 0.03\n",
+    "MAX_LENGTH_TOLERANCE = 0.05\n",
+    "MAX_ANGLE_TOLERANCE = 0.02\n",
     "\n",
-    "INTERFACE_DISTANCE = 3.0  # in Angstrom\n",
-    "INTERFACE_VACUUM = 20.0  # in Angstrom"
+    "# Whether to reduce the resulting interface cell to the primitive cell after the interface creation.\n",
+    "# If the reduction causes unexpected results, try increasing the `MAX_AREA` for search.\n",
+    "REDUCE_RESULT_CELL_TO_PRIMITIVE = True"
    ],
    "outputs": [],
    "execution_count": null
@@ -203,16 +206,16 @@
    },
    "cell_type": "code",
    "source": [
-    "from mat3ra.made.tools.analyze.lattice_planes import CrystalLatticePlanesMaterialAnalyzer\n",
+    "from mat3ra.made.tools.build.slab.helpers import create_slab\n",
     "from mat3ra.made.tools.build.interface.helpers import create_zsl_interface_between_slabs\n",
     "from mat3ra.made.tools.build.slab.termination_utils import select_slab_termination\n",
     "\n",
-    "film_analyzer = CrystalLatticePlanesMaterialAnalyzer(material=film, miller_indices=FILM_MILLER_INDICES)\n",
-    "film_slabs = [film_analyzer.get_material_with_termination_without_vacuum(termination) for termination in\n",
+    "film_slabs = [create_slab(film, miller_indices=FILM_MILLER_INDICES, termination=termination, vacuum=0) for termination\n",
+    "              in\n",
     "              film_slab_terminations]\n",
     "\n",
-    "substrate_analyzer = CrystalLatticePlanesMaterialAnalyzer(material=substrate, miller_indices=SUBSTRATE_MILLER_INDICES)\n",
-    "substrate_slabs = [substrate_analyzer.get_material_with_termination_without_vacuum(termination) for termination in\n",
+    "substrate_slabs = [create_slab(substrate, miller_indices=SUBSTRATE_MILLER_INDICES, termination=termination, vacuum=0)\n",
+    "                   for termination in\n",
     "                   substrate_slab_terminations]\n",
     "\n",
     "film_slabs_with_titles = [{\"material\": slab, \"title\": str(termination)} for slab, termination in\n",
@@ -293,15 +296,15 @@
    "cell_type": "code",
    "source": [
     "from mat3ra.made.tools.analyze.interface import ZSLInterfaceAnalyzer\n",
-    "from mat3ra.made.tools.build.slab.configurations import SlabConfiguration\n",
     "\n",
     "zsl_analyzer = ZSLInterfaceAnalyzer(\n",
     "    substrate_slab_configuration=substrate_slab_config,\n",
     "    film_slab_configuration=film_slab_config,\n",
     "    max_area=MAX_AREA,\n",
     "    max_area_ratio_tol=MAX_AREA_TOLERANCE,\n",
+    "    max_length_tol=MAX_LENGTH_TOLERANCE,\n",
     "    max_angle_tol=MAX_ANGLE_TOLERANCE,\n",
-    "    max_length_tol=MAX_LENGTH_TOLERANCE\n",
+    "    reduce_result_cell=False  # Reduces supercell matrices in analyzer\n",
     ")"
    ],
    "outputs": [],
@@ -393,6 +396,10 @@
     "    vacuum=INTERFACE_VACUUM,\n",
     "    match_id=selected_index,\n",
     "    max_area=MAX_AREA,\n",
+    "    max_area_ratio_tol=MAX_AREA_TOLERANCE,\n",
+    "    max_length_tol=MAX_LENGTH_TOLERANCE,\n",
+    "    max_angle_tol=MAX_ANGLE_TOLERANCE,\n",
+    "    reduce_result_cell_to_primitive=REDUCE_RESULT_CELL_TO_PRIMITIVE,\n",
     ")"
    ],
    "outputs": [],
@@ -410,8 +417,8 @@
   {
    "cell_type": "code",
    "source": [
-    "visualize(interface, repetitions=[3, 3, 1])\n",
-    "visualize(interface, repetitions=[3, 3, 1], rotation=\"-90x\")"
+    "visualize(interface, repetitions=[1, 1, 1])\n",
+    "visualize(interface, repetitions=[1, 1, 1], rotation=\"-90x\")"
    ],
    "metadata": {
     "collapsed": false