Merge pull request #121 from Exabyte-io/feature/SOF-7351

Feature/SOF-7351 update: show images of materials
Exabyte-io · May 7, 2024 · 9aeadce · 9aeadce
2 parents adbdf32 + 18dd9b6
commit 9aeadce
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Showing 6 changed files with 317 additions and 27 deletions.
diff --git a/other/materials_designer/create_interface_with_min_strain_zsl.ipynb b/other/materials_designer/create_interface_with_min_strain_zsl.ipynb
@@ -134,15 +134,15 @@
    "cell_type": "code",
    "outputs": [],
    "source": [
-    "from utils.jupyterlite import get_data\n",
     "from mat3ra.made.material import Material\n",
+    "from utils.jupyterlite import get_data\n",
+    "\n",
+    "from utils.visualize import visualize_materials as visualize\n",
     "\n",
     "# Get the list of input materials and load them into `materials_in` variable\n",
     "get_data(\"materials_in\", globals())\n",
-    "materials = []      \n",
-    "for material_config in globals()[\"materials_in\"]:\n",
-    "    print(material_config, \"\\n\")\n",
-    "    materials.append(Material(material_config))"
+    "materials = list(map(Material, globals()[\"materials_in\"]))\n",
+    "visualize(materials, repetitions=[1,1,1], rotation=\"0x\")"
    ],
    "metadata": {
     "collapsed": false
@@ -274,15 +274,35 @@
     "# Could be either the termination as tuple, e.g. `('Ni_P6/mmm_1', 'C_C2/m_2')` or its index: `0`\n",
     "termination_or_its_index = 0\n",
     "# select the first interface with the lowest strain and the smallest number of atoms\n",
-    "interfaces_slice_range_or_index = 0\n",
+    "interfaces_slice_range_or_index = slice(0,1)\n",
     "selected_interfaces = interface_data_holder.get_interfaces_as_materials(termination_or_its_index, interfaces_slice_range_or_index)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### 6.2. Visualize the selected interface(s)"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "visualize(selected_interfaces, repetitions=[1,1,1], rotation=\"0x\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### 6.2. Pass data to the outside runtime\n"
+    "### 6.3. Pass data to the outside runtime\n"
    ]
   },
   {
@@ -292,7 +312,6 @@
    "outputs": [],
    "source": [
     "from utils.jupyterlite import set_data\n",
-    "\n",
     "set_data(\"materials\", selected_interfaces)"
    ]
   }

diff --git a/other/materials_designer/uploads/0-Ni.json b/other/materials_designer/uploads/0-Ni.json
@@ -0,0 +1,81 @@
+{
+  "name": "Ni, Nickel, FCC (Fm-3m) 3D (Bulk), mp-23",
+  "lattice": {
+    "a": 2.478974,
+    "b": 2.478974,
+    "c": 2.478974,
+    "alpha": 60,
+    "beta": 60,
+    "gamma": 60,
+    "units": {
+      "length": "angstrom",
+      "angle": "degree"
+    },
+    "type": "FCC",
+    "vectors": {
+      "a": [
+        2.146854,
+        0,
+        1.239487
+      ],
+      "b": [
+        0.7156182,
+        2.024074,
+        1.239487
+      ],
+      "c": [
+        0,
+        0,
+        2.478974
+      ],
+      "alat": 1,
+      "units": "angstrom"
+    }
+  },
+  "basis": {
+    "elements": [
+      {
+        "id": 0,
+        "value": "Ni"
+      }
+    ],
+    "coordinates": [
+      {
+        "id": 0,
+        "value": [
+          0,
+          0,
+          0
+        ]
+      }
+    ],
+    "units": "crystal",
+    "cell": [
+      [
+        2.146854,
+        0,
+        1.239487
+      ],
+      [
+        0.7156182,
+        2.024074,
+        1.239487
+      ],
+      [
+        0,
+        0,
+        2.478974
+      ]
+    ],
+    "constraints": []
+  },
+  "external": {
+    "id": "mp-23",
+    "source": "Materials Project",
+    "doi": "10.17188/1199153",
+    "url": "https://next-gen.materialsproject.org/materials/mp-23",
+    "origin": true
+  },
+  "isNonPeriodic": false,
+  "isUpdated": true
+}
diff --git a/other/materials_designer/uploads/1-Graphene.json b/other/materials_designer/uploads/1-Graphene.json
@@ -0,0 +1,96 @@
+{
+    "name": "Graphene",
+    "basis": {
+        "elements": [
+            {
+                "id": 0,
+                "value": "C"
+            },
+            {
+                "id": 1,
+                "value": "C"
+            }
+        ],
+        "coordinates": [
+            {
+                "id": 0,
+                "value": [
+                    0,
+                    0,
+                    0
+                ]
+            },
+            {
+                "id": 1,
+                "value": [
+                    0.333333,
+                    0.666667,
+                    0
+                ]
+            }
+        ],
+        "units": "crystal",
+        "cell": [
+            [
+                2.467291,
+                0,
+                0
+            ],
+            [
+                -1.2336454999,
+                2.1367366845,
+                0
+            ],
+            [
+                0,
+                0,
+                20
+            ]
+        ],
+        "constraints": []
+    },
+    "lattice": {
+        "a": 2.467291,
+        "b": 2.467291,
+        "c": 20,
+        "alpha": 90,
+        "beta": 90,
+        "gamma": 120,
+        "units": {
+            "length": "angstrom",
+            "angle": "degree"
+        },
+        "type": "HEX",
+        "vectors": {
+            "a": [
+                2.467291,
+                0,
+                0
+            ],
+            "b": [
+                -1.233645,
+                2.136737,
+                0
+            ],
+            "c": [
+                0,
+                0,
+                20
+            ],
+            "alat": 1,
+            "units": "angstrom"
+        }
+    },
+    "isNonPeriodic": false,
+    "external": {
+        "id": "mp-1040425",
+        "source": "materials project",
+        "doi": "10.17188/1405723",
+        "url": "https://next-gen.materialsproject.org/materials/mp-1040425/",
+        "origin": true
+    },
+    "metadata": {},
+    "schemaVersion": "2022.8.16",
+    "isDefault": false,
+    "_id": ""
+}
diff --git a/pyproject.toml b/pyproject.toml
@@ -11,6 +11,7 @@ dependencies = [
   "pandas>=1.5.3",
   "pymatgen>=2024.4.13",
   "mat3ra-made>=2024.5.3.post0",
+  "mat3ra-utils"
 ]
 
 [project.optional-dependencies]

diff --git a/utils/plot.py b/utils/plot.py
@@ -1,7 +1,7 @@
 from typing import Dict, Union
 
 import plotly.graph_objs as go
-from mat3ra.made.tools.build.interface import InterfaceDataHolder
+from mat3ra.made.tools.build.interface import InterfaceDataHolder, StrainModes
 
 
 def plot_strain_vs_atoms(interface_data_holder: InterfaceDataHolder, settings: Dict[str, Union[str, int]]):
@@ -12,32 +12,31 @@ def plot_strain_vs_atoms(interface_data_holder: InterfaceDataHolder, settings: D
         interface_data_holder (InterfaceDataHolder): The interface data holder object.
         settings (Dict[str, Union[str, int]]): The settings for the plot.
     """
-    sorted_interfaces = interface_data_holder.interfaces
+    sorted_interfaces = interface_data_holder.get_interfaces_for_termination(0)
 
     data = []
-    for termination, interfaces in sorted_interfaces.items():
-        for index, interface in enumerate(interfaces):
-            strain_percentage = interface.get_mean_abs_strain() * 100
-            num_sites = interface.num_sites
-
-            hover_text = f"Index: {index}<br>Strain: {strain_percentage:.2f}%<br>Atoms: {num_sites}"
-
-            trace = go.Scatter(
-                x=[strain_percentage],
-                y=[num_sites],
-                text=[hover_text],
-                mode="markers",
-                hoverinfo="text",
-                name=f"Index: {index}",
-            )
-            data.append(trace)
+    for index, interface in enumerate(sorted_interfaces):
+        strain_percentage = interface.interface_properties[StrainModes.mean_abs_strain] * 100
+        num_sites = interface.num_sites
+
+        hover_text = f"Index: {index}<br>Strain: {strain_percentage:.2f}%<br>Atoms: {num_sites}"
+
+        trace = go.Scatter(
+            x=[strain_percentage],
+            y=[num_sites],
+            text=[hover_text],
+            mode="markers",
+            hoverinfo="text",
+            name=f"Index: {index}",
+        )
+        data.append(trace)
 
     layout = go.Layout(
         xaxis=dict(title="Strain (%)", type=settings["X_SCALE"]),
         yaxis=dict(title="Number of atoms", type=settings["Y_SCALE"]),
         hovermode="closest",
         height=settings["HEIGHT"],
-        legend_title_text="Interfaces Index Range",
+        legend_title_text="Interfaces Indices",
     )
 
     fig = go.Figure(data=data, layout=layout)