From 1aede50df1962719c4e1cf4f62053e2d111ab193 Mon Sep 17 00:00:00 2001
From: Taylor <taylor.baird@epfl.ch>
Date: Mon, 17 Jun 2024 20:18:07 +0200
Subject: [PATCH] Fixed issue where dispersion plot wasn't showing when
 switching to a diatomic chain.

---
 .../lattice-vibration/NGLTrajectoryClass.py   | 12 ++-
 notebook/lattice-vibration/Phonon_1D.ipynb    | 78 +++++++++++++------
 2 files changed, 64 insertions(+), 26 deletions(-)

diff --git a/notebook/lattice-vibration/NGLTrajectoryClass.py b/notebook/lattice-vibration/NGLTrajectoryClass.py
index ec1fec4..fd47348 100644
--- a/notebook/lattice-vibration/NGLTrajectoryClass.py
+++ b/notebook/lattice-vibration/NGLTrajectoryClass.py
@@ -9,7 +9,7 @@
 from ase.io.trajectory import Trajectory
 from sympy import *
 from NGLUtilsClass import NGLWidgets
-from ipywidgets import Output
+from ipywidgets import Output, AppLayout
 import sys
 sys.stdout = open('/dev/stdout', 'w')
 
@@ -62,10 +62,12 @@ def __init__(self, trajectory):
             value="monoatomic",
             disabled=False,
         )
+        self.button_chain.observe(self.show_slider_M, "value")
         self.button_chain.observe(self.compute_dispersion, "value")
         self.button_chain.observe(self.compute_trajectory_1D, "value")
+        
         self.button_chain.observe(self.band_dispersion, "value")
-        self.button_chain.observe(self.show_slider_M, "value")
+        
 
         # Output to show slider_M
         self.output_ratio = widgets.Output()
@@ -526,7 +528,6 @@ def onclick(self, event):
             self.x = event.xdata
             self.y = event.ydata
 
-       
         """
         Determine frequency and k point upon click on band dispersion figure
         """
@@ -588,4 +589,7 @@ def show_slider_M(self, *args):
             self.output_ratio.clear_output()
         elif self.button_chain.value == "diatomic":
             with self.output_ratio:
-                display(widgets.HBox([self.slider_M_description, self.slider_M]))
+                full_layout= AppLayout(left_sidebar=widgets.HBox([self.slider_M_description,self.slider_M]))
+           
+                display(full_layout)
+                #display(widgets.HBox([self.slider_M_description, self.slider_M]))
diff --git a/notebook/lattice-vibration/Phonon_1D.ipynb b/notebook/lattice-vibration/Phonon_1D.ipynb
index a30d9a3..27be46f 100644
--- a/notebook/lattice-vibration/Phonon_1D.ipynb
+++ b/notebook/lattice-vibration/Phonon_1D.ipynb
@@ -76,7 +76,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "ff2fca2da3f648a48d4eced11b3509ef",
+       "model_id": "f0b65bc10a6f44ff9a4160c1703cb6b9",
        "version_major": 2,
        "version_minor": 0
       },
@@ -106,20 +106,7 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "NameError",
-     "evalue": "name 'target_k' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[2], line 3\u001b[0m\n\u001b[1;32m      1\u001b[0m traj\u001b[38;5;241m=\u001b[39mTrajectory(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mdummy.traj\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mw\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m      2\u001b[0m traj\u001b[38;5;241m.\u001b[39mwrite(Atoms(\u001b[38;5;241m2\u001b[39m\u001b[38;5;241m*\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mC\u001b[39m\u001b[38;5;124m'\u001b[39m,[[\u001b[38;5;241m0\u001b[39m,\u001b[38;5;241m0\u001b[39m,\u001b[38;5;241m0\u001b[39m],[\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m1\u001b[39m]]))\n\u001b[0;32m----> 3\u001b[0m handler\u001b[38;5;241m=\u001b[39m\u001b[43mNGLTrajectory\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtrajectory\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mTrajectory\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mdummy.traj\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mr\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m      4\u001b[0m handler\u001b[38;5;241m.\u001b[39mview\u001b[38;5;241m.\u001b[39mstage\u001b[38;5;241m.\u001b[39mset_parameters(mouse_preset\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpymol\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      6\u001b[0m handler\u001b[38;5;241m.\u001b[39mview\u001b[38;5;241m.\u001b[39m_js(\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[1;32m      7\u001b[0m \u001b[38;5;124mthis.mouseOverDisplay(\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mblock\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m)\u001b[39m\n\u001b[1;32m      8\u001b[0m \u001b[38;5;124mvar container = this.stage.viewer.container\u001b[39m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     12\u001b[0m \u001b[38;5;124m      }, false);\u001b[39m\n\u001b[1;32m     13\u001b[0m \u001b[38;5;124m\"\"\"\u001b[39m)\n",
-      "File \u001b[0;32m~/osscar_ssh_v2/quantum-mechanics/notebook/lattice-vibration/NGLTrajectoryClass.py:79\u001b[0m, in \u001b[0;36mNGLTrajectory.__init__\u001b[0;34m(self, trajectory)\u001b[0m\n\u001b[1;32m     77\u001b[0m \u001b[38;5;66;03m#target_k=np.pi/2\u001b[39;00m\n\u001b[1;32m     78\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mka_array \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39mlinspace(\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m2\u001b[39m \u001b[38;5;241m*\u001b[39m np\u001b[38;5;241m.\u001b[39mpi, \u001b[38;5;241m2\u001b[39m \u001b[38;5;241m*\u001b[39m np\u001b[38;5;241m.\u001b[39mpi, \u001b[38;5;241m101\u001b[39m)\n\u001b[0;32m---> 79\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39midx \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mint\u001b[39m(\u001b[38;5;241m101\u001b[39m\u001b[38;5;241m*\u001b[39m(\u001b[43mtarget_k\u001b[49m\u001b[38;5;241m+\u001b[39m\u001b[38;5;241m2\u001b[39m\u001b[38;5;241m*\u001b[39mnp\u001b[38;5;241m.\u001b[39mpi)\u001b[38;5;241m/\u001b[39m(\u001b[38;5;241m4\u001b[39m\u001b[38;5;241m*\u001b[39mnp\u001b[38;5;241m.\u001b[39mpi)) \u001b[38;5;66;03m# idx corresponding to ka=0\u001b[39;00m\n\u001b[1;32m     80\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39midx \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m50\u001b[39m \u001b[38;5;66;03m# idx corresponding to ka=0\u001b[39;00m\n\u001b[1;32m     81\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39moptic \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'target_k' is not defined"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "traj=Trajectory('dummy.traj','w')\n",
     "traj.write(Atoms(2*'C',[[0,0,0],[1,1,1]]))\n",
@@ -176,9 +163,10 @@
     "chain= HBox([handler.button_chain_description,handler.button_chain])\n",
     "mass_ratio=handler.output_ratio\n",
     "click=HTMLMath(value='''Click on the plot to get the corresponding phonon''')\n",
-    "phonon = HBox(\n",
-    "    [VBox([chain,mass_ratio]), VBox([click,handler.fig.canvas])]\n",
-    ")\n",
+    "# phonon = HBox(\n",
+    "#     [VBox([chain,mass_ratio]), VBox([click,handler.fig.canvas])]\n",
+    "# )\n",
+    "phonon= AppLayout(left_sidebar=VBox([chain,mass_ratio]),center=VBox([click,handler.fig.canvas]),right=None)\n",
     "\n",
     "camera_orientation=HBox([handler.camera_orientation_description,handler.output_camera_position])\n",
     "camera_text_orientation=handler.text_orientation\n",
@@ -241,9 +229,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<style>\n",
+       ".box_style{\n",
+       "    border : 2px solid red;\n",
+       "}\n",
+       "</style>\n"
+      ],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "%%html\n",
     "<style>\n",
@@ -255,11 +260,40 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {
     "scrolled": true
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "546ceb73714c49eda44588698ece25b7",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "VBox(children=(Tab(children=(HBox(children=(VBox(children=(HBox(children=(HTMLMath(value='Atomic chain type', …"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "54e9045ba2714f91b1b621812b162fb5",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "HBox(children=(NGLWidget(max_frame=50),), layout=Layout(align_items='center', display='flex', flex_flow='colum…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "display(actions,HBox([handler.view],layout=layout).add_class(\"box_style\"))\n",
     "stop = False\n",