Upload v0.5

MDsim.ipynb

@@ -0,0 +1,150 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "6d6ace33-bd89-49ac-a148-06c99d7d071c",
+   "metadata": {},
+   "source": [
+    "# Getting Started with CHEG231MD\n",
+    "\n",
+    "Eric M. Furst\\\n",
+    "October 2024\n",
+    "\n",
+    "Test run of the simple MD simulation.\n",
+    "\n",
+    "The temperature will depend on density. At any density, change temp by \n",
+    "scaling max velocity by sqrt(Tnew/Told) \n",
+    "\n",
+    "$$ \\langle v^2 \\rangle = v_\\mathrm{max}^2/2 $$\n",
+    "\n",
+    "Without a thermostat, both the temperature and pressure equilibrate.\n",
+    "This makes calculating an isotherm difficult, but it shows the\n",
+    "combined contributions of potential and kinetic energy\n",
+    "\n",
+    "rho and vmax values that give results close to T+ = 2:\\\n",
+    "0.7 5.8\\\n",
+    "0.6 5.47\\\n",
+    "0.4 5.04"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c7f0016e-5ba0-45b9-9d0e-df7bde2c901f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "import CHEG231MD as md\n",
+    "\n",
+    "# create a simulation with # particles, density, and max speed\n",
+    "# N^(1/3), rho+, max vel+\n",
+    "\n",
+    "#sim = md.MDSimulation(8,0.4,5.04)\n",
+    "#sim = md.MDSimulation(8,0.6,5.47)\n",
+    "sim = md.MDSimulation(8,0.7,5.8)\n",
+    "\n",
+    "# initialize variables and lists\n",
+    "pres=[]\n",
+    "temp=[]\n",
+    "time=[]\n",
+    "Pavg = 0\n",
+    "Tavg = 0"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a14e5dc1-7601-4972-911e-0f42eb32a6c3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Run time steps of the simulation\n",
+    "for timestep in range(1,1001):\n",
+    "\n",
+    "    # advance simulation one timestep\n",
+    "    sim.move()\n",
+    "    \n",
+    "    # only average after an equilibration time\n",
+    "    if timestep > 100:\n",
+    "        # production stage\n",
+    "        Pavg += (sim.P-Pavg)/(timestep+1)\n",
+    "        Tavg += (sim.T-Tavg)/(timestep+1)\n",
+    "    else:\n",
+    "        # equilibration stage\n",
+    "        Pavg = sim.P\n",
+    "        Tavg = sim.T\n",
+    "\n",
+    "   # print timestep, ke, pe, total e, Tavg, Pavg        \n",
+    "    if timestep%50==0: # only print every 50 timesteps\n",
+    "        # timestep, <ke>, <pe>, <e>, T, P, Tavg, Pavg\n",
+    "        print(\"%4d  %6.3f  %6.3f  %6.3f  %6.3f  %6.3f  %6.3f  %6.3f\" % \n",
+    "              (timestep,sim.ke/sim.N,sim.pe/sim.N,\n",
+    "                (sim.ke+sim.pe)/sim.N,sim.T,sim.P,Tavg,Pavg))\n",
+    "\n",
+    "    pres.append(sim.P)\n",
+    "    temp.append(sim.T)\n",
+    "    time.append(timestep)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d3993efe-4dc7-4b09-9630-90201f989487",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# A different way to calculate the average pressure and temperature\n",
+    "# with standard deviations\n",
+    "\n",
+    "import numpy as np\n",
+    "\n",
+    "print(\"Pressure:    {:.2f}+/-{:.2f}\"\n",
+    "      .format(np.mean(pres[200:]),np.std(pres[200:])))\n",
+    "print(\"Temperature: {:.2f}+/-{:.2f}\"\n",
+    "      .format(np.mean(temp[200:]),np.std(temp[200:])))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "77d0de84-eb9b-4ea5-b5d3-4780335f3d7c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Plot pressure and temperature\n",
+    "\n",
+    "fig, ax = plt.subplots()\n",
+    "ax.plot(time[0:],pres[0:],label=\"P*\")\n",
+    "ax.plot(time[0:],temp[0:],label=\"T*\")\n",
+    "ax.set_xlabel(\"time step\")\n",
+    "ax.legend(frameon=False)\n",
+    "ax.set_xscale('linear')\n",
+    "plt.title(\"Dimensionless instantaneous pressure and temperature\")\n",
+    "\n",
+    "plt.show()"
+   ]
+  }
+ ],
+ "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": "3.12.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}