From 58f4162cec19834c0e6375bb72875bb96cb8d909 Mon Sep 17 00:00:00 2001
From: Amir Mirzanejad <aqm6884@psu.edu>
Date: Thu, 7 Sep 2023 16:01:08 -0400
Subject: [PATCH] Notebook for Plotly plots in figures 2 and 4
---
plot.ipynb | 95 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 95 insertions(+)
create mode 100644 plot.ipynb
diff --git a/plot.ipynb b/plot.ipynb
new file mode 100644
index 0000000..b3ea528
--- /dev/null
+++ b/plot.ipynb
@@ -0,0 +1,95 @@
+{
+ "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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