[#154] Added bond graphing (#174)

cs481-ekh · Apr 9, 2024 · 37af78f · 37af78f
1 parent e514744
commit 37af78f
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Showing 3 changed files with 52 additions and 16 deletions.
diff --git a/GoVizzy/GoVizzy.ipynb b/GoVizzy/GoVizzy.ipynb
@@ -25,10 +25,39 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "c31b2aca",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "53607c596d444a7e970ddd843418c366",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "AppLayout(children=(HBox(children=(Output(layout=Layout(height='100%', width='70%')), VBox(children=(HBox(chil…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "e07b178719f64af8ba8a442d37d4201e",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "HBox(children=(Text(value='', description='File Name:'), Button(description='Submit', style=ButtonStyle())), l…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "%run Main.py\n"
    ]
@@ -37,18 +66,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "c75f164c-2d9f-44b9-8875-82d7f34a7d4e",
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [],
-   "source": [
-    "from gv_ui import meshes\n",
-    "import cube_viskit as cv\n",
-    "\n",
-    "new_cube = cv.Cube()\n",
-    "new_cube.load_cube(\"data/rhopol.cube\")\n",
-    "new_cube.get_bonds()\n",
-    "\n",
-    "meshes.plot_bonds(new_cube)"
-   ]
+   "source": []
   }
  ],
  "metadata": {

diff --git a/GoVizzy/gv_ui/gv_ui/DisplayUI.py b/GoVizzy/gv_ui/gv_ui/DisplayUI.py
@@ -70,6 +70,7 @@ def display_cube(cube):
         elif selected_option == 'Mesh Options':
             visualizer.display_cell()
             atom_meshes = meshes.plot_atoms(cube)
+            meshes.plot_bonds(cube)
 
         # Additional View   
         elif selected_option == 'Color Options':

diff --git a/GoVizzy/gv_ui/gv_ui/meshes.py b/GoVizzy/gv_ui/gv_ui/meshes.py
@@ -94,8 +94,21 @@ def plot_bonds(cube: Cube):
     Plots the bonds between atoms in the current Cube object, using the list of atom pairs, 
     and the positions of the atoms in the graph.
     '''
+    cube.get_bonds()
+    num_pts = 1000
     for bond in cube.bonds:
-        print("Atoms: ",bond," Real Pos: ", )
-        for atom in bond:
-            print(cube.atoms.get_scaled_positions()[atom])
+        atomPos1 = cube.atoms.get_scaled_positions()[bond[0]]
+        x1, y1, z1 = tuple(p * cube.data3D.shape[idx] / Bohr for idx, p in enumerate(atomPos1))
+        atomPos2 = cube.atoms.get_scaled_positions()[bond[1]]
+        x2, y2, z2 = tuple(p * cube.data3D.shape[idx] / Bohr for idx, p in enumerate(atomPos2))
+
+        # y = x1 -> x2
+        # y = y1 -> y2
+        # z = z1 -> z2
+        X = np.linspace(x1, x2, num_pts)
+        Y = np.linspace(y1, y2, num_pts)
+        Z = np.linspace(z1, z2, num_pts)
+        p = ipv.plot(X, Y, Z)
+        p.material.visible = True
+        p.size = 3.