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jhjensen2/noninteracting_particle_md.ipynb

Created October 30, 2018 20:42
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noninteracting_particle_MD.ipynb
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noninteracting_particle_md.ipynb
{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"name": "noninteracting_particle_MD.ipynb",
"version": "0.3.2",
"provenance": [],
"include_colab_link": true
}
},
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
},
"source": [
"<a href=\"https://colab.research.google.com/gist/jhjensen2/71bdb95ca0b12e22fa176c86b46e28b5/noninteracting_particle_md.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"metadata": {
"id": "JMMqD95zQmRq",
"colab_type": "code",
"colab": {}
},
"cell_type": "code",
"source": [
"def get_initial_coordinates():\n",
" x_coord = [np.random.random()*box_width for i in range(n_particles)]\n",
" y_coord = [np.random.random()*box_width for i in range(n_particles)]\n",
" \n",
" return x_coord, y_coord"
],
"execution_count": 0,
"outputs": []
},
{
"metadata": {
"id": "_ejOpbfWSEwt",
"colab_type": "code",
"colab": {}
},
"cell_type": "code",
"source": [
"def get_initial_velocities():\n",
" x_vel = [2*(np.random.random()-0.5)*box_width for i in range(n_particles)]\n",
" y_vel = [2*(np.random.random()-0.5)*box_width for i in range(n_particles)]\n",
" \n",
" return x_vel, y_vel"
],
"execution_count": 0,
"outputs": []
},
{
"metadata": {
"id": "8VIHckwKSvAc",
"colab_type": "code",
"colab": {}
},
"cell_type": "code",
"source": [
"def take_step(x_coord, y_coord, x_vel, y_vel):\n",
" for i in range(n_particles):\n",
" x_coord[i] += x_vel[i]*dt\n",
" y_coord[i] += y_vel[i]*dt\n",
" \n",
" if abs(x_coord[i]) > box_width:\n",
" x_vel[i] = -x_vel[i]\n",
" x_coord[i] += x_vel[i]*dt\n",
" \n",
" if abs(y_coord[i]) > box_width:\n",
" y_vel[i] = -y_vel[i]\n",
" y_coord[i] += y_vel[i]*dt\n",
" \n",
" return x_coord, y_coord, x_vel, y_vel"
],
"execution_count": 0,
"outputs": []
},
{
"metadata": {
"id": "fNwIkKkNTaDX",
"colab_type": "code",
"colab": {}
},
"cell_type": "code",
"source": [
"def add_frame(xs,ys,i):\n",
" global trajectory\n",
" if i == 0:\n",
" trajectory = ''\n",
" trajectory += str(n_particles) + '\\ntitle\\n'\n",
" for x, y in zip(xs,ys):\n",
" trajectory += ' '.join(['Ar',str(x),str(y),'0.0\\n'])\n",
" "
],
"execution_count": 0,
"outputs": []
},
{
"metadata": {
"id": "madSLHmXGOO5",
"colab_type": "code",
"colab": {}
},
"cell_type": "code",
"source": [
"import numpy as np\n",
"\n",
"n_particles = 100\n",
"box_width = 10\n",
"n_steps = 5000\n",
"dt = 0.001\n",
"global trajectory\n",
"\n",
"x_coord, y_coord = get_initial_coordinates()\n",
"\n",
"x_vel, y_vel = get_initial_velocities()\n",
"\n",
"for i in range(n_steps):\n",
" x_coord, y_coord, x_vel, y_vel = take_step(x_coord, y_coord, x_vel, y_vel)\n",
" \n",
" if i%10 == 0:\n",
" add_frame(x_coord, y_coord,i)"
],
"execution_count": 0,
"outputs": []
},
{
"metadata": {
"id": "lA45pZozRkie",
"colab_type": "code",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 860
},
"collapsed": true,
"outputId": "eae74bf5-6fed-46cf-b597-def66631fa10"
},
"cell_type": "code",
"source": [
"!pip install py3Dmol\n",
"\n"
],
"execution_count": 6,
"outputs": [
{
"output_type": "stream",
"text": [
"Requirement already satisfied: py3Dmol in /usr/local/lib/python2.7/dist-packages (0.8.0)\n",
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"Requirement already satisfied: ipython>=1.0 in /usr/local/lib/python2.7/dist-packages (from idisplay->py3Dmol) (5.5.0)\n",
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],
"name": "stdout"
}
]
},
{
"metadata": {
"id": "ELWnESw2TObR",
"colab_type": "code",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 514
},
"outputId": "1dcbb324-841d-41b9-d06a-5805bfdb3484"
},
"cell_type": "code",
"source": [
"import py3Dmol\n",
"view = py3Dmol.view()\n",
"view.addModelsAsFrames(trajectory,'xyz')\n",
"view.animate({'loop': 'forward', 'reps': 1})\n",
"view.setStyle({'sphere':{'radius': 0.5}})\n",
"view.zoomTo()"
],
"execution_count": 7,
"outputs": [
{
"output_type": "display_data",
"data": {
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