pmpc_brush_layer.ipynb

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      "'writeandexecute' magic loaded.\n"
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    "%%writeandexecute -i pmpc_brush_layer pmpc_brush_layer.py\n",
    "from __future__ import division\n",
    "\n",
    "from numpy import pi\n",
    "\n",
    "import mbuild as mb\n",
    "\n",
    "from mbuild.lib.atoms import H\n",
    "from mbuild.lib.surfaces import Betacristobalite\n",
    "from mbuild.examples.pmpc.brush import Brush\n",
    "\n",
    "\n",
    "class PMPCLayer(mb.Monolayer):\n",
    "    \"\"\"Create a layer of grafted pMPC brushes on a beta-cristobalite surface.\"\"\"\n",
    "    def __init__(self, pattern, tile_x=1, tile_y=1, chain_length=4, alpha=pi / 4):\n",
    "        surface = Betacristobalite()\n",
    "        brush = Brush(chain_length=chain_length, alpha=alpha)\n",
    "        hydrogen = H()\n",
    "        super(PMPCLayer, self).__init__(surface, brush, backfill=hydrogen,\n",
    "                                        pattern=pattern, tile_x=tile_x,\n",
    "                                        tile_y=tile_y)"
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     "text": [
      "<PMPCLayer 3610 particles, periodicity: [ 5.3888  4.6669  0.    ], 4110 bonds, id: 4365270992>\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/ctk3b/science/python/mbuild/mbuild/recipes/monolayer.py:78: UserWarning: \n",
      " No fractions provided.  Assuming a single chain type.\n",
      "  warnings.warn(\"\\n No fractions provided.  Assuming a single chain type.\")\n",
      "/Users/ctk3b/science/python/mbuild/mbuild/recipes/monolayer.py:81: UserWarning: \n",
      " Adding 10 of chain <Brush 162 particles, non-periodic, 161 bonds, id: 4695651440>\n",
      "  warnings.warn(\"\\n Adding {} of chain {}\".format(len(pattern), chains[-1]))\n"
     ]
    }
   ],
   "source": [
    "pattern = mb.Random2DPattern(10)\n",
    "pmpc_layer = PMPCLayer(pattern=pattern, chain_length=3, alpha=pi / 4, tile_x=1, tile_y=1)\n",
    "print(pmpc_layer)\n",
    "pmpc_layer.visualize()"
   ]
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