From 051d2e5bd649bd55555596927616cca766784f78 Mon Sep 17 00:00:00 2001
From: Amir Mirzanejad <aqm6884@psu.edu>
Date: Thu, 7 Sep 2023 16:09:49 -0400
Subject: [PATCH] Delete plot.ipynb
---
plot.ipynb | 95 ------------------------------------------------------
1 file changed, 95 deletions(-)
delete mode 100644 plot.ipynb
diff --git a/plot.ipynb b/plot.ipynb
deleted file mode 100644
index b3ea528..0000000
--- a/plot.ipynb
+++ /dev/null
@@ -1,95 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "99d587ca-7160-4848-8ee1-858ee39ad93f",
- "metadata": {},
- "outputs": [],
- "source": [
- "# improt dependecies\n",
- "import plotly.graph_objects as go\n",
- "import numpy as np\n",
- "import scipy.ndimage\n",
- "\n",
- "# Assuming your data is in an array called \"data\"\n",
- "\n",
- "# Apply the Gaussian filter\n",
- "sigma = [1.5, 2]\n",
- "data_smooth = scipy.ndimage.gaussian_filter(data, sigma)\n",
- "\n",
- "# Mirror the data along the y-axis\n",
- "data_smooth_symmetric = np.concatenate((np.fliplr(data_smooth), data_smooth), axis=1)\n",
- "\n",
- "# Define custom color scale\n",
- "colorscale = [[0, 'orange'], [1, 'yellow']]\n",
- "\n",
- "fig = go.Figure()\n",
- "\n",
- "# Generate x and y indices\n",
- "x = np.linspace(-1, 1, data_smooth_symmetric.shape[1])\n",
- "y = np.linspace(0, 1, data_smooth_symmetric.shape[0])\n",
- "\n",
- "# Add surface trace without contours, using the symmetric data\n",
- "fig.add_trace(go.Surface(x=x, y=y, z=data_smooth_symmetric, colorscale=colorscale, showscale=True))\n",
- "\n",
- "# Add lines that correspond to constant y values\n",
- "for i in range(data_smooth_symmetric.shape[0]):\n",
- " fig.add_trace(go.Scatter3d(x=x, y=np.full_like(x, y[i]), z=data_smooth_symmetric[i, :], mode='lines', \n",
- " line=dict(color='black', width=5), showlegend=False))\n",
- "\n",
- "# Add thick blue line at x=0\n",
- "fig.add_trace(go.Scatter3d(x=np.full_like(y, 0), y=y, z=data_smooth_symmetric[:, data_smooth.shape[1]], mode='lines', \n",
- " line=dict(color='blue', width=15), showlegend=False))\n",
- "\n",
- "# Add thick red lines at x=first and x=last\n",
- "fig.add_trace(go.Scatter3d(x=np.full_like(y, -1), y=y, z=data_smooth_symmetric[:, 0], mode='lines', \n",
- " line=dict(color='red', width=10), showlegend=False))\n",
- "fig.add_trace(go.Scatter3d(x=np.full_like(y, 1), y=y, z=data_smooth_symmetric[:, -1], mode='lines', \n",
- " line=dict(color='red', width=10), showlegend=False))\n",
- "\n",
- "# Adjust position of camera\n",
- "camera_params = dict(up=dict(x=1.25,y=0,z=1), center=dict(x=0,y=0,z=0), eye=dict(x=2.25,y=-2.25,z=1.75))\n",
- "\n",
- "fig.update_layout(scene_camera=camera_params)\n",
- "\n",
- "fig.update_layout(title='3D PES', autosize=True,\n",
- " scene = dict(xaxis = dict(title='Geometry Interpolation between Paths', title_font_family=\"Arial\", title_font_color='black'), \n",
- " yaxis = dict(title='Reaction Progress / a.u.', title_font_family=\"Arial\", title_font_color='black'),\n",
- " zaxis = dict(title='Relative Energy / kcal mol', title_font_family=\"Arial\", title_font_color='black'),),\n",
- " width=1000, height=1000, margin=dict(l=65, r=100, b=65, t=90))\n",
- "\n",
- "fig.show()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "e8b23fb9-adba-416b-b21a-7cb4c3e3647a",
- "metadata": {},
- "outputs": [],
- "source": []
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3 (ipykernel)",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.10.8"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
--
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