Merge pull request #221 from Exabyte-io/feature/SOF-7570

VsevolodX · web-flow · commit 0d9e1c91d22b · 2025-04-03T22:01:22.000-07:00
feature/SOF-7570 related -- fix Material usage
diff --git a/other/materials_designer/import_material_from_jarvis_db_entry.ipynb b/other/materials_designer/import_material_from_jarvis_db_entry.ipynb
@@ -202,7 +202,7 @@
     "# Uncomment to see the JSON\n",
     "# print(json.dumps(data, indent=4))\n",
     "\n",
-    "materials = [Material(from_poscar(poscar)) for poscar in poscars]\n",
+    "materials = [Material.create(from_poscar(poscar)) for poscar in poscars]\n",
     "\n",
     "visualize_materials(materials)"
    ],
diff --git a/other/materials_designer/import_materials_from_standata.ipynb b/other/materials_designer/import_materials_from_standata.ipynb
@@ -95,8 +95,8 @@
     "\n",
     "# use colloquial name, formula, dimensionality to select a material\n",
     "# 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",
+    "material_by_name = Material.create(Materials.get_by_name(\"Graphene\")[0])\n",
+    "material_by_name_first_match = Material.create(Materials.get_by_name_first_match(\"Graphene\"))\n",
     "visualize_materials([material_by_name, material_by_name_first_match], viewer=\"wave\")"
    ],
    "metadata": {
@@ -120,10 +120,10 @@
    "cell_type": "code",
    "source": [
     "materials_2d_jsons = Materials.get_by_categories(\"2D\")\n",
-    "materials_2d = [Material(material_json) for material_json in materials_2d_jsons]\n",
+    "materials_2d = [Material.create(material_json) for material_json in materials_2d_jsons]\n",
     "\n",
     "materials_3d_insulator_jsons = Materials.get_by_categories(\"3D\", \"Insulator\")\n",
-    "materials_3d_insulator = [Material(material_json) for material_json in materials_3d_insulator_jsons]\n",
+    "materials_3d_insulator = [Material.create(material_json) for material_json in materials_3d_insulator_jsons]\n",
     "\n",
     "visualize_materials(materials_2d)\n",
     "visualize_materials(materials_3d_insulator)"
diff --git a/other/materials_designer/specific_examples/defect_planar_grain_boundary_2d_boron_nitride.ipynb b/other/materials_designer/specific_examples/defect_planar_grain_boundary_2d_boron_nitride.ipynb
@@ -124,7 +124,7 @@
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
     "\n",
-    "material = Material(Materials.get_by_name_first_match(MATERIAL_NAME))"
+    "material = Material.create(Materials.get_by_name_first_match(MATERIAL_NAME))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/defect_planar_grain_boundary_3d_fcc_metals_copper.ipynb b/other/materials_designer/specific_examples/defect_planar_grain_boundary_3d_fcc_metals_copper.ipynb
@@ -126,7 +126,7 @@
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
     "\n",
-    "material = Material(Materials.get_by_name_first_match(MATERIAL_NAME))"
+    "material = Material.create(Materials.get_by_name_first_match(MATERIAL_NAME))"
    ],
    "outputs": [],
    "execution_count": null
diff --git a/other/materials_designer/specific_examples/defect_point_adatom_island_molybdenum_disulfide_platinum.ipynb b/other/materials_designer/specific_examples/defect_point_adatom_island_molybdenum_disulfide_platinum.ipynb
@@ -123,7 +123,7 @@
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
     "\n",
-    "substrate = Material(Materials.get_by_name_first_match(MATERIAL_NAME))\n",
+    "substrate = Material.create(Materials.get_by_name_first_match(MATERIAL_NAME))\n",
     "\n",
     "# Preview materials\n",
     "visualize_materials([substrate])\n",
diff --git a/other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide.ipynb b/other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide.ipynb
@@ -110,7 +110,7 @@
     "from mat3ra.made.material import Material\n",
     "from mat3ra.standata.materials import Materials\n",
     "\n",
-    "material = Material(Materials.get_by_name_first_match(MATERIAL_NAME))"
+    "material = Material.create(Materials.get_by_name_first_match(MATERIAL_NAME))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/defect_point_pair_gallium_nitride.ipynb b/other/materials_designer/specific_examples/defect_point_pair_gallium_nitride.ipynb
@@ -99,7 +99,7 @@
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
     "\n",
-    "material = Material(Materials.get_by_name_first_match(\"GaN\"))"
+    "material = Material.create(Materials.get_by_name_first_match(\"GaN\"))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride.ipynb b/other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride.ipynb
@@ -120,7 +120,7 @@
     "from mat3ra.made.material import Material\n",
     "from mat3ra.standata.materials import Materials\n",
     "\n",
-    "material = Material(Materials.get_by_name_and_categories(\"Boron_Nitride\", \"2D\"))"
+    "material = Material.create(Materials.get_by_name_and_categories(\"Boron_Nitride\", \"2D\"))"
    ]
   },
   {
diff --git a/other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb b/other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb
@@ -125,7 +125,7 @@
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
     "\n",
-    "material = Material(Materials.get_by_name_first_match(MATERIAL_NAME))"
+    "material = Material.create(Materials.get_by_name_first_match(MATERIAL_NAME))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/defect_surface_island_titanium_nitride.ipynb b/other/materials_designer/specific_examples/defect_surface_island_titanium_nitride.ipynb
@@ -113,7 +113,7 @@
     "from mat3ra.made.material import Material\n",
     "from mat3ra.standata.materials import Materials\n",
     "\n",
-    "material = Material(Materials.get_by_name_first_match(\"TiN\"))"
+    "material = Material.create(Materials.get_by_name_first_match(\"TiN\"))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/defect_surface_step_platinum.ipynb b/other/materials_designer/specific_examples/defect_surface_step_platinum.ipynb
@@ -104,7 +104,7 @@
     "from mat3ra.made.material import Material\n",
     "from mat3ra.standata.materials import Materials\n",
     "\n",
-    "material = Material(Materials.get_by_name_first_match(MATERIAL_NAME))"
+    "material = Material.create(Materials.get_by_name_first_match(MATERIAL_NAME))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/interface_2d_2d_boron_nitride_graphene.ipynb b/other/materials_designer/specific_examples/interface_2d_2d_boron_nitride_graphene.ipynb
@@ -111,8 +111,8 @@
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
     "\n",
-    "film = Material(Materials.get_by_name_first_match(\"Graphene\"))\n",
-    "substrate = Material(Materials.get_by_name_and_categories(\"BN\", \"2D\"))"
+    "film = Material.create(Materials.get_by_name_first_match(\"Graphene\"))\n",
+    "substrate = Material.create(Materials.get_by_name_and_categories(\"BN\", \"2D\"))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/interface_2d_3d_graphene_silicon_dioxide.ipynb b/other/materials_designer/specific_examples/interface_2d_3d_graphene_silicon_dioxide.ipynb
@@ -108,8 +108,8 @@
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
     "\n",
-    "film = Material(Materials.get_by_name_first_match(\"Graphene\"))\n",
-    "substrate = Material(Materials.get_by_name_first_match(\"SiO2\"))"
+    "film = Material.create(Materials.get_by_name_first_match(\"Graphene\"))\n",
+    "substrate = Material.create(Materials.get_by_name_first_match(\"SiO2\"))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/interface_3d_3d_copper_cristobalite.ipynb b/other/materials_designer/specific_examples/interface_3d_3d_copper_cristobalite.ipynb
@@ -113,8 +113,8 @@
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
     "\n",
-    "film = Material(Materials.get_by_name_first_match(\"Copper\"))\n",
-    "substrate = Material(Materials.get_by_name_first_match(\"Cristobalite\"))"
+    "film = Material.create(Materials.get_by_name_first_match(\"Copper\"))\n",
+    "substrate = Material.create(Materials.get_by_name_first_match(\"Cristobalite\"))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/interface_bilayer_twisted_commensurate_lattices_molybdenum_disulfide.ipynb b/other/materials_designer/specific_examples/interface_bilayer_twisted_commensurate_lattices_molybdenum_disulfide.ipynb
@@ -116,7 +116,7 @@
     "from mat3ra.standata.materials import Materials\n",
     "from utils.visualize import visualize_materials\n",
     "\n",
-    "material = Material(Materials.get_by_name_and_categories(\"MoS2\", \"2D\"))\n",
+    "material = Material.create(Materials.get_by_name_and_categories(\"MoS2\", \"2D\"))\n",
     "\n",
     "print(\"Initial material properties:\")\n",
     "print(f\"Formula: {material.formula}\")\n",
diff --git a/other/materials_designer/specific_examples/interface_bilayer_twisted_nanoribbons_boron_nitride.ipynb b/other/materials_designer/specific_examples/interface_bilayer_twisted_nanoribbons_boron_nitride.ipynb
@@ -116,7 +116,7 @@
     "from mat3ra.standata.materials import Materials\n",
     "from utils.visualize import visualize_materials\n",
     "\n",
-    "material = Material(Materials.get_by_name_first_match(\"BN\"))\n",
+    "material = Material.create(Materials.get_by_name_first_match(\"BN\"))\n",
     "\n",
     "print(\"Initial material properties:\")\n",
     "print(f\"Formula: {material.formula}\")\n",
diff --git a/other/materials_designer/specific_examples/nanocluster_gold.ipynb b/other/materials_designer/specific_examples/nanocluster_gold.ipynb
@@ -153,7 +153,7 @@
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
     "\n",
-    "material = Material(Materials.get_by_name_first_match(\"Gold\"))"
+    "material = Material.create(Materials.get_by_name_first_match(\"Gold\"))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/optimization_interface_film_xy_position_graphene_nickel.ipynb b/other/materials_designer/specific_examples/optimization_interface_film_xy_position_graphene_nickel.ipynb
@@ -123,8 +123,8 @@
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
     "\n",
-    "substrate = Material(Materials.get_by_name_first_match(SUBSTRATE_NAME))\n",
-    "film = Material(Materials.get_by_name_first_match(FILM_NAME))\n",
+    "substrate = Material.create(Materials.get_by_name_first_match(SUBSTRATE_NAME))\n",
+    "film = Material.create(Materials.get_by_name_first_match(FILM_NAME))\n",
     "\n",
     "# Preview materials\n",
     "visualize_materials([substrate, film], repetitions=STRUCTURE_REPETITIONS, rotation=\"0x\")\n"
diff --git a/other/materials_designer/specific_examples/passivation_edge_nanowire_silicon.ipynb b/other/materials_designer/specific_examples/passivation_edge_nanowire_silicon.ipynb
@@ -105,7 +105,7 @@
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
     "\n",
-    "silicon = Material(Materials.get_by_name_first_match('Silicon'))"
+    "silicon = Material.create(Materials.get_by_name_first_match('Silicon'))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/passivation_surface_silicon.ipynb b/other/materials_designer/specific_examples/passivation_surface_silicon.ipynb
@@ -118,7 +118,7 @@
     "from mat3ra.made.material import Material\n",
     "from mat3ra.standata.materials import Materials\n",
     "\n",
-    "slab = Material(Materials.get_by_name_first_match(MATERIAL_NAME))"
+    "slab = Material.create(Materials.get_by_name_first_match(MATERIAL_NAME))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/perturbation_ripple_graphene.ipynb b/other/materials_designer/specific_examples/perturbation_ripple_graphene.ipynb
@@ -166,7 +166,7 @@
     "from mat3ra.standata.materials import Materials\n",
     "from mat3ra.made.material import Material\n",
     "\n",
-    "material = Material(Materials.get_by_name_first_match(MATERIAL_NAME))"
+    "material = Material.create(Materials.get_by_name_first_match(MATERIAL_NAME))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/specific_examples/slab_strontium_titanate.ipynb b/other/materials_designer/specific_examples/slab_strontium_titanate.ipynb
@@ -100,7 +100,7 @@
     "from mat3ra.made.material import Material\n",
     "from mat3ra.standata.materials import Materials\n",
     "\n",
-    "material = Material(Materials.get_by_name_first_match(\"SrTiO3\"))"
+    "material = Material.create(Materials.get_by_name_first_match(\"SrTiO3\"))"
    ],
    "metadata": {
     "collapsed": false
diff --git a/other/materials_designer/uploads/0-Ni.json b/other/materials_designer/uploads/0-Ni.json
@@ -50,23 +50,6 @@
       }
     ],
     "units": "crystal",
-    "cell": [
-      [
-        2.146854,
-        0,
-        1.239487
-      ],
-      [
-        0.7156182,
-        2.024074,
-        1.239487
-      ],
-      [
-        0,
-        0,
-        2.478974
-      ]
-    ],
     "constraints": []
   },
   "external": {
diff --git a/other/materials_designer/uploads/1-Graphene.json b/other/materials_designer/uploads/1-Graphene.json
@@ -62,23 +62,6 @@
       }
     ],
     "units": "crystal",
-    "cell": [
-      [
-        2.464955,
-        0,
-        0
-      ],
-      [
-        -1.232478,
-        2.134715,
-        0
-      ],
-      [
-        0,
-        0,
-        19.99673
-      ]
-    ],
     "constraints": []
   },
   "external": {
diff --git a/pyproject.toml b/pyproject.toml
@@ -10,7 +10,7 @@ dependencies = [
   "matplotlib>=3.4.1",
   "pandas>=1.5.3",
   "pymatgen==2024.4.13",
-  "mat3ra-made>=2024.6.11.post0",
+  "mat3ra-made @ git+https://github.com/Exabyte-io/made.git@feature/SOF-7570",
   "mat3ra-utils>=2024.6.11.post0",
 ]
 
diff --git a/utils/jupyterlite.py b/utils/jupyterlite.py
@@ -142,7 +142,7 @@ def get_materials(globals_dict: Optional[Dict] = None) -> List[Any]:
     get_data("materials_in", globals_dict)
 
     if "materials_in" in globals_dict and globals_dict["materials_in"]:
-        materials = [Material(item) for item in globals_dict["materials_in"]]
+        materials = [Material.create(item) for item in globals_dict["materials_in"]]
         log(f"Retrieved {len(materials)} materials.")
         return materials
     else:
@@ -161,7 +161,7 @@ def set_materials(materials: List[Any]):
     from mat3ra.utils.array import convert_to_array_if_not
 
     materials = convert_to_array_if_not(materials)
-    materials_data = [material.to_json() for material in materials]
+    materials_data = [json.loads(material.to_json()) for material in materials]
     set_data("materials", materials_data)
 
 
@@ -200,7 +200,7 @@ def load_materials_from_folder(folder_path: Optional[str] = None, verbose: bool
         log(f"No data found in the '{folder_path}' folder.", SeverityLevelEnum.ERROR, force_verbose=verbose)
         return []
 
-    materials = [Material(item) for item in data_from_host]
+    materials = [Material.create(item) for item in data_from_host]
 
     if materials:
         log(
@@ -269,7 +269,7 @@ def write_materials_to_folder(materials: List[Any], folder_path: Optional[str] =
         safe_name = material.name.replace("%", "pct").replace("/", ":")
         file_path = os.path.join(folder_path, f"{safe_name}.json")
         with open(file_path, "w") as file:
-            json.dump(material.to_json(), file)
+            json.dump(material.to_dict(), file)
         log(f"Material '{material.name}' written to '{file_path}'", SeverityLevelEnum.INFO, force_verbose=verbose)
 
 
diff --git a/utils/visualize.py b/utils/visualize.py
@@ -1,5 +1,4 @@
 import io
-import json
 import time
 from enum import Enum
 from typing import Dict, List, Optional, Tuple, Union
@@ -132,7 +131,7 @@ def get_wave_js(material_json, div_id=default_div_id):
 
 def render_wave(material, properties, width=600, height=600):
     timestamp = time.time()
-    material_json = json.dumps(material.to_json(), indent=2)
+    material_json = material.to_json()
     div_id = f"wave-{timestamp}"
 
     display(HTML(get_wave_html(div_id, width, height, properties.title)))
@@ -147,7 +146,7 @@ def render_wave_grid(materials, properties, width=400, height=400, max_columns=3
 
     for i, material in enumerate(materials):
         html = get_wave_html(f"wave-{i}-{timestamp}", width, height, title=properties.title)
-        js = get_wave_js(json.dumps(material.to_json(), indent=2), f"wave-{i}-{timestamp}")
+        js = get_wave_js(material.to_json(), f"wave-{i}-{timestamp}")
         html_items.append(widgets.HTML(html))
         js_items.append(Javascript(js))
 

Original file line number	Diff line number	Diff line change
`@@ -120,7 +120,7 @@`
`120`	`120`	`"from mat3ra.made.material import Material\n",`
`121`	`121`	`"from mat3ra.standata.materials import Materials\n",`
`122`	`122`	`"\n",`
`123`		`- "material = Material(Materials.get_by_name_and_categories(\"Boron_Nitride\", \"2D\"))"`
	`123`	`+ "material = Material.create(Materials.get_by_name_and_categories(\"Boron_Nitride\", \"2D\"))"`
`124`	`124`	`]`
`125`	`125`	`},`
`126`	`126`	`{`