Merge pull request #214 from Exabyte-io/feature/SOF-7549

Feature/SOF-7549 Wavejs viewer in Noteboks

Author: VsevolodX

other/materials_designer/custom_transformation.ipynb

@@ -62,7 +62,8 @@
   {
    "cell_type": "markdown",
    "source": [
-    "## 2. Load materials"
+    "## 2. Load materials\n",
+    "From the Materials Designer list, \"uploads\" folder, or Standata."
    ],
    "metadata": {
     "collapsed": false
@@ -75,7 +76,7 @@
    "source": [
     "from utils.jupyterlite import get_materials\n",
     "\n",
-    "materials = get_materials(globals())"
+    "materials = get_materials(globals()) or [Material(Materials.get_by_name_first_match(\"Graphene\"))]"
    ],
    "metadata": {
     "collapsed": false
@@ -106,10 +107,26 @@
    "execution_count": null
   },
   {
+   "metadata": {},
    "cell_type": "markdown",
+   "source": "## 4. Preview transformed materials",
+   "id": "eab6d997ef1eafd4"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
    "source": [
-    "## 4. Save transformed materials"
+    "from utils.visualize import visualize_materials\n",
+    "\n",
+    "visualize_materials(new_materials, viewer=\"wave\")"
    ],
+   "id": "1029505318aa3656"
+  },
+  {
+   "cell_type": "markdown",
+   "source": "## 5. Save transformed materials",
    "metadata": {
     "collapsed": false
    },

other/materials_designer/import_materials_from_standata.ipynb

@@ -31,7 +31,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "import sys\n",
     "\n",
@@ -47,6 +46,7 @@
     "collapsed": false
    },
    "id": "7a8c49f4612498a6",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -62,7 +62,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "from mat3ra.standata.materials import Materials\n",
     "Materials.get_names()"
@@ -71,6 +70,7 @@
     "collapsed": false
    },
    "id": "494aa9dceabed0e1",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -86,7 +86,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "from mat3ra.made.material import Material\n",
     "from utils.visualize import visualize_materials\n",
@@ -95,12 +94,13 @@
     "# returned material is a JSON object and needs to be converted to Material object\n",
     "material_by_name = Material(Materials.get_by_name(\"Graphene\")[0])\n",
     "material_by_name_first_match = Material(Materials.get_by_name_first_match(\"Graphene\"))\n",
-    "visualize_materials([material_by_name, material_by_name_first_match])"
+    "visualize_materials([material_by_name, material_by_name_first_match], viewer=\"wave\")"
    ],
    "metadata": {
     "collapsed": false
    },
    "id": "a570e2668e86dfab",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -115,7 +115,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "materials_2d_jsons = Materials.get_by_categories(\"2D\")\n",
     "materials_2d = [Material(material_json) for material_json in materials_2d_jsons]\n",
@@ -130,6 +129,7 @@
     "collapsed": false
    },
    "id": "5f192496ce7776af",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -144,7 +144,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "from utils.jupyterlite import set_materials\n",
     "\n",
@@ -154,6 +153,7 @@
     "collapsed": false
    },
    "id": "dcb45a2daead9d55",
+   "outputs": [],
    "execution_count": null
   }
  ],

other/materials_designer/specific_examples/defect_planar_grain_boundary_2d_boron_nitride.ipynb

@@ -257,8 +257,7 @@
     "print(f\"Actual angle: {actual_angle}°\")\n",
     "print(f\"Number of atoms: {len(selected_structure.basis.elements.ids)}\")\n",
     "\n",
-    "visualize_materials(selected_structure, repetitions=[1, 1, 1])\n",
-    "visualize_materials(selected_structure, repetitions=[1, 1, 1], rotation=\"-90x\")"
+    "visualize_materials(selected_structure, title=\"Grain Boundary\", viewer=\"wave\")"
    ],
    "metadata": {
     "collapsed": false

other/materials_designer/specific_examples/defect_planar_grain_boundary_3d_fcc_metals_copper.ipynb

@@ -412,10 +412,7 @@
    "metadata": {
     "collapsed": false
    },
-   "source": [
-    "visualize([grain_boundary], repetitions=[1, 1, 1])\n",
-    "visualize([grain_boundary], repetitions=[1, 1, 1], rotation=\"-90x\")"
-   ],
+   "source": "visualize([grain_boundary], repetitions=[1, 1, 1], viewer=\"wave\")",
    "outputs": [],
    "execution_count": null
   },

other/materials_designer/specific_examples/defect_point_adatom_island_molybdenum_disulfide_platinum.ipynb

@@ -36,7 +36,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "# Slab parameters\n",
     "MATERIAL_NAME = \"MoS2.*2D\"  # Name of the material (regex) to be loaded from Standata\n",
@@ -71,6 +70,7 @@
     "collapsed": false
    },
    "id": "9d8b1890b34d850a",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -86,7 +86,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "import sys\n",
     "\n",
@@ -102,6 +101,7 @@
     "collapsed": false
    },
    "id": "ef664b14457530fd",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -117,7 +117,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "from utils.visualize import visualize_materials\n",
     "from mat3ra.standata.materials import Materials\n",
@@ -133,6 +132,7 @@
     "collapsed": false
    },
    "id": "be38fdda1984c654",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -147,7 +147,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "from mat3ra.made.tools.build.slab import SlabConfiguration, get_terminations, create_slab\n",
     "from utils.visualize import visualize_materials as visualize\n",
@@ -168,6 +167,7 @@
     "collapsed": false
    },
    "id": "e2d24109d3068c9e",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -183,7 +183,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "from mat3ra.made.tools.build.defect import AdatomSlabPointDefectConfiguration\n",
     "\n",
@@ -204,6 +203,7 @@
     "collapsed": false
    },
    "id": "e385e50ae11ed2b9",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -218,7 +218,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "from mat3ra.made.tools.build.defect import create_defects\n",
     "\n",
@@ -228,6 +227,7 @@
     "collapsed": false
    },
    "id": "a990fa35742d7269",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -242,22 +242,18 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "from utils.visualize import visualize_materials as visualize\n",
     "\n",
     "visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
     "           {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defect at {PLACEMENT_METHOD} position\"}],\n",
-    "          rotation=\"-90x\"\n",
-    "          )\n",
-    "visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
-    "           {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defect at {PLACEMENT_METHOD} position\"}],\n",
-    "          )"
+    "          viewer=\"wave\")"
    ],
    "metadata": {
     "collapsed": false
    },
    "id": "509b18661a069e42",
+   "outputs": [],
    "execution_count": null
   },
   {
@@ -272,7 +268,6 @@
   },
   {
    "cell_type": "code",
-   "outputs": [],
    "source": [
     "from utils.jupyterlite import set_materials, download_content_to_file\n",
     "\n",
@@ -283,6 +278,7 @@
     "collapsed": false
    },
    "id": "61daa5afcbc078a9",
+   "outputs": [],
    "execution_count": null
   }
  ],