lammps/python/examples/ipython/dihedrals/dihedral.ipynb

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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<div style=\"text-align: center\"><a href=\"../index.ipynb\">LAMMPS Python Tutorials</a></div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Example 4: Validating a dihedral potential"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "from lammps import lammps"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L = lammps()\n",
    "cmd = L.cmd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import math\n",
    "\n",
    "cmd.units(\"real\")\n",
    "cmd.atom_style(\"molecular\")\n",
    "\n",
    "cmd.boundary(\"f f f\")\n",
    "cmd.neighbor(0.3, \"bin\")\n",
    "\n",
    "cmd.dihedral_style(\"harmonic\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cmd.read_data(\"data.dihedral\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cmd.pair_style(\"zero\", 5)\n",
    "cmd.pair_coeff(\"*\", \"*\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cmd.mass(1, 1.0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cmd.velocity(\"all\", \"set\", 0.0, 0.0, 0.0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cmd.run(0, \"post\", \"no\");"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.ipython.image(zoom=1.0,size=[320,320])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "x = L.numpy.extract_atom(\"x\")\n",
    "print(x[3])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "x[3] = (1.0, 0.0, 1.0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.ipython.image(zoom=1.0,size=[320,320])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "L.get_thermo(\"pe\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "x[3] = (1.0, 0.0, -1.0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cmd.run(0, \"post\", \"no\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "phi = [d * math.pi / 180 for d in range(360)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pos = [(1.0, math.cos(p), math.sin(p)) for p in phi]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "K = 80.0\n",
    "d = 1\n",
    "n = 2\n",
    "E_analytical = [K * (1 + d * math.cos(n*p)) for p in phi]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pe = []\n",
    "for p in pos:\n",
    "    x[3] = p\n",
    "    cmd.run(0, \"post\", \"no\");\n",
    "    pe.append(L.get_thermo(\"pe\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plt.plot(range(360), pe, range(360), E_analytical)\n",
    "plt.xlabel('angle')\n",
    "plt.ylabel('E')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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