{ "cells": [ { "cell_type": "markdown", "id": "intro", "metadata": {}, "source": [ "# SimpleMD — In-Notebook Visualization\n", "\n", "This notebook runs a short Lennard-Jones simulation and visualizes the particle trajectory using [py3Dmol](https://github.com/3dmol/3Dmol.js), which renders interactively in VS Code, Jupyter, and Google Colab.\n", "\n", "For more advanced visualization (depth cueing, rendering), see the VMD instructions in the SimpleMD manual (Ch. 5).\n", "\n", "**Controls**\n", "- Drag to rotate\n", "- Scroll to zoom\n", "- Right-click drag to pan" ] }, { "cell_type": "code", "execution_count": null, "id": "colab-setup", "metadata": {}, "outputs": [], "source": [ "# --- Google Colab only: clone the repo and install py3Dmol ---\n", "# Skip this cell if running locally.\n", "import sys\n", "if 'google.colab' in sys.modules:\n", " !git clone https://github.com/emfurst/SimpleMD.git\n", " %cd SimpleMD\n", " !pip install py3Dmol --quiet" ] }, { "cell_type": "code", "execution_count": 1, "id": "imports", "metadata": {}, "outputs": [], "source": [ "import os\n", "import py3Dmol\n", "import CHEG231MD as md" ] }, { "cell_type": "markdown", "id": "sim-header", "metadata": {}, "source": [ "## Run the simulation\n", "\n", "Set up and equilibrate, then run a short production trajectory.\n", "Adjust `nn`, `rho`, and `vmax` to explore different conditions." ] }, { "cell_type": "code", "execution_count": 39, "id": "run-sim", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Equilibrated: T* = 0.614 P* = -0.392\n" ] } ], "source": [ "nn = 5 # particles per side (N = nn^3)\n", "rho = 0.4 # reduced number density\n", "vmax = 1.5 # initial max velocity\n", "\n", "sim = md.MDSimulation(nn, rho, vmax)\n", "\n", "# Equilibration\n", "for _ in range(200):\n", " sim.move()\n", "print(f\"Equilibrated: T* = {sim.T:.3f} P* = {sim.P:.3f}\")" ] }, { "cell_type": "code", "execution_count": 40, "id": "write-traj", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Wrote trajectory to MDvis.xyz (T* = 0.836, P* = -0.122)\n" ] } ], "source": [ "XYZ_FILE = \"MDvis.xyz\"\n", "\n", "def write_frame(f, sim, timestep):\n", " f.write(f\"{sim.N}\\n\")\n", " f.write(f\"Timestep: {timestep}\\n\")\n", " for row in sim.x:\n", " f.write(f\"Ar {row[0]:.6f} {row[1]:.6f} {row[2]:.6f}\\n\")\n", "\n", "# Production run — write every 5th frame\n", "with open(XYZ_FILE, \"w\") as f:\n", " for t in range(1, 501):\n", " sim.move()\n", " if t % 10 == 0:\n", " write_frame(f, sim, t)\n", "\n", "print(f\"Wrote trajectory to {XYZ_FILE} (T* = {sim.T:.3f}, P* = {sim.P:.3f})\")" ] }, { "cell_type": "markdown", "id": "vis-header", "metadata": {}, "source": [ "## Animated trajectory\n", "\n", "The viewer below plays through all saved frames.\n", "The wireframe box shows the periodic simulation cell." ] }, { "cell_type": "code", "execution_count": 50, "id": "animate", "metadata": {}, "outputs": [ { "data": { "application/3dmoljs_load.v0": "
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\n", "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "with open(XYZ_FILE) as f:\n", " xyz = f.read()\n", "\n", "view = py3Dmol.view(width=600, height=450)\n", "view.addModelsAsFrames(xyz, \"xyz\")\n", "view.setStyle({\"sphere\": {\"radius\": 0.5, \"color\": \"red\", \"opacity\": 1}})\n", "view.setBackgroundColor(\"white\")\n", "\n", "# Draw the periodic simulation box\n", "c = sim.L / 2\n", "view.addBox({\"center\": {\"x\": c, \"y\": c, \"z\": c},\n", " \"dimensions\": {\"w\": sim.L, \"h\": sim.L, \"d\": sim.L},\n", " \"color\": \"white\", \"opacity\": 0.5, \"wireframe\": False})\n", "\n", "view.zoomTo()\n", "view.animate({\"loop\": \"forward\", \"interval\": 100})\n", "view.show()" ] }, { "cell_type": "code", "execution_count": null, "id": "c6cd4574", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": ".venv", "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": "3.12.11" } }, "nbformat": 4, "nbformat_minor": 5 }