From 97deb91f843b666a57651a22c7fa2b2429e82c18 Mon Sep 17 00:00:00 2001
From: Taylor <taylor.baird@epfl.ch>
Date: Mon, 20 May 2024 10:42:00 +0200
Subject: [PATCH] Merged textual changes from phonon1d branch. Set default
 k-point away from gamma in a way that works with workaround for voila. Made
 arrows a bit smaller.

---
 .../lattice-vibration/NGLTrajectoryClass.py   |  15 +--
 notebook/lattice-vibration/NGLUtilsClass.py   |   2 +-
 notebook/lattice-vibration/Phonon_1D.ipynb    | 115 ++++++------------
 3 files changed, 43 insertions(+), 89 deletions(-)

diff --git a/notebook/lattice-vibration/NGLTrajectoryClass.py b/notebook/lattice-vibration/NGLTrajectoryClass.py
index c44f385..ec1fec4 100644
--- a/notebook/lattice-vibration/NGLTrajectoryClass.py
+++ b/notebook/lattice-vibration/NGLTrajectoryClass.py
@@ -22,7 +22,7 @@ def __init__(self, trajectory):
             r"Oscillations amplitude", layout=self.layout_description
         )
         self.slider_amplitude = widgets.FloatSlider(
-            value=0.12,
+            value=0.04,
             min=0.01,
             max=0.24,
             step=0.01,
@@ -70,13 +70,14 @@ def __init__(self, trajectory):
         # Output to show slider_M
         self.output_ratio = widgets.Output()
 
-        # Point is initialized at (0,0), and in acoustic mode
+        # Point is initialized at x=pi/2 and in acoustic mode
         self.x = 0
         self.y = 0
         self.ka = 0
-        #target_k=np.pi/2
+        target_k=np.pi/2
         self.ka_array = np.linspace(-2 * np.pi, 2 * np.pi, 101)
-        self.idx = 50 # idx corresponding to ka=0
+        self.idx = int(101*(target_k+2*np.pi)/(4*np.pi)) # idx corresponding to ka=0
+        #self.idx = 50 # idx corresponding to ka=0
         self.optic = False
         self.init_delay = 20
     
@@ -469,7 +470,7 @@ def band_dispersion(self, *args):
             self.x=np.pi/2
             self.idx = (np.abs(self.ka_array - self.x)).argmin()
             self.ka = self.ka_array[self.idx]
-
+            self.y=self.ka
             w = self.w[self.idx]
             self.point.set_data((self.ka, w))
 
@@ -519,8 +520,8 @@ def band_dispersion(self, *args):
     def onclick(self, event):
         if event==None:
             
-            self.x=0.0
-            self.y=0.0
+            self.x=self.x
+            self.y=self.y
         else:
             self.x = event.xdata
             self.y = event.ydata
diff --git a/notebook/lattice-vibration/NGLUtilsClass.py b/notebook/lattice-vibration/NGLUtilsClass.py
index 243c7c7..38c9b9b 100644
--- a/notebook/lattice-vibration/NGLUtilsClass.py
+++ b/notebook/lattice-vibration/NGLUtilsClass.py
@@ -477,7 +477,7 @@ def on_orientation_change(self, *args):
         with self.output_camera_position:
             self.output_camera_position.clear_output()
             position = [round(x, 1) for x in self.view._camera_orientation]
-            print(position)
+            #print(position)
 
     def change_camera_position(self, *args):
         """
diff --git a/notebook/lattice-vibration/Phonon_1D.ipynb b/notebook/lattice-vibration/Phonon_1D.ipynb
index aa3d72f..a30d9a3 100644
--- a/notebook/lattice-vibration/Phonon_1D.ipynb
+++ b/notebook/lattice-vibration/Phonon_1D.ipynb
@@ -70,9 +70,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "ff2fca2da3f648a48d4eced11b3509ef",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "import matplotlib.pyplot as plt\n",
     "%matplotlib widget\n",
@@ -91,9 +104,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "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"
+     ]
+    }
+   ],
    "source": [
     "traj=Trajectory('dummy.traj','w')\n",
     "traj.write(Atoms(2*'C',[[0,0,0],[1,1,1]]))\n",
@@ -215,26 +241,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
-   "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"
-    }
-   ],
+   "outputs": [],
    "source": [
     "%%html\n",
     "<style>\n",
@@ -246,67 +255,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {
     "scrolled": true
    },
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "d7b84f9985bc41639601a74613eceb9e",
-       "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": "1ab3a0ba628041beab40ecd5efee8549",
-       "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"
-    },
-    {
-     "ename": "TypeError",
-     "evalue": "loop() takes 1 positional argument but 2 were given",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[8], line 18\u001b[0m\n\u001b[1;32m     14\u001b[0m         view\u001b[38;5;241m.\u001b[39m_run_on_another_thread(do)\n\u001b[1;32m     17\u001b[0m hv_thread\u001b[38;5;241m=\u001b[39mhandler\u001b[38;5;241m.\u001b[39mview\u001b[38;5;241m.\u001b[39m_run_on_another_thread(init_view)\n\u001b[0;32m---> 18\u001b[0m \u001b[43mloop\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43mview\u001b[49m\u001b[43m)\u001b[49m\n",
-      "\u001b[0;31mTypeError\u001b[0m: loop() takes 1 positional argument but 2 were given"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Exception in thread Thread-10 (init_view):\n",
-      "Traceback (most recent call last):\n",
-      "  File \"/usr/lib/python3.10/threading.py\", line 1016, in _bootstrap_inner\n",
-      "    self.run()\n",
-      "  File \"/home/taylor/venvs/nb_testing/lib/python3.10/site-packages/ipykernel/ipkernel.py\", line 766, in run_closure\n",
-      "    _threading_Thread_run(self)\n",
-      "  File \"/usr/lib/python3.10/threading.py\", line 953, in run\n",
-      "    self._target(*self._args, **self._kwargs)\n",
-      "  File \"/tmp/ipykernel_27490/1732612826.py\", line 14, in init_view\n",
-      "NameError: name 'do' is not defined\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "display(actions,HBox([handler.view],layout=layout).add_class(\"box_style\"))\n",
     "stop = False\n",