{
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    "Color\n",
    "===============\n",
    "\n",
    "One can color the atoms using the following scheme:\n",
    "\n",
    "- Element\n",
    "- Random\n",
    "- Uniform\n",
    "- Index\n",
    "- Attribute\n",
    "\n",
    "\n",
    "Color by element\n",
    "----------------\n",
    "\n",
    "Supported style are:\n",
    "\n",
    "#. **JMOL**: http://jmol.sourceforge.net/jscolors/#color_U\n",
    "#. **VESTA**: https://jp-minerals.org/vesta/en/\n",
    "#. **CPK**: https://en.wikipedia.org/wiki/CPK_coloring\n",
    "\n",
    "\n",
    "Custom color for each species\n",
    "-----------------------------\n",
    "Use can set custom color for each species. The color can be in the form of hex code or color name.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a2a3a9a8",
   "metadata": {},
   "outputs": [],
   "source": [
    "from ase.build import molecule\n",
    "from weas_widget import WeasWidget\n",
    "\n",
    "atoms = molecule(\"C2H6SO\")\n",
    "viewer = WeasWidget()\n",
    "viewer.from_ase(atoms)\n",
    "# set the color and radius for each species\n",
    "viewer.avr.species.settings[\"C\"].update({\"color\": \"red\", \"radius\": 1.0})\n",
    "viewer.avr.species.settings[\"H\"].update({\"color\": \"green\", \"radius\": 0.5})\n",
    "viewer.avr.species.settings[\"O\"].update({\"color\": \"blue\", \"radius\": 0.6})\n",
    "viewer.avr.species.settings[\"S\"].update({\"color\": \"yellow\", \"radius\": 1.2})\n",
    "viewer"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "65780aa5",
   "metadata": {},
   "source": [
    "\n",
    "Color by attribute\n",
    "----------------------\n",
    "Coloring based on the attribute of the atoms. The attribute can be: charge, magmom, or any other attribute in the structure.\n",
    "\n",
    "Here we show how to color the atoms by their forces."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "bf6bb43e",
   "metadata": {},
   "outputs": [],
   "source": [
    "from ase.build import bulk\n",
    "from ase.calculators.emt import EMT\n",
    "import numpy as np\n",
    "from weas_widget import WeasWidget\n",
    "atoms = bulk('Au', cubic = True)\n",
    "atoms *= [3, 3, 3]\n",
    "atoms.positions += np.random.random((len(atoms), 3))\n",
    "atoms.calc = EMT()\n",
    "atoms.get_potential_energy()\n",
    "# set the forces as an attribute\n",
    "atoms.set_array(\"Force\", atoms.calc.results[\"forces\"])\n",
    "viewer = WeasWidget()\n",
    "viewer.from_ase(atoms)\n",
    "viewer.avr.color_by = \"Force\"\n",
    "viewer.avr.color_ramp = [\"red\", \"yellow\", \"blue\"]\n",
    "viewer.avr.model_style = 1\n",
    "viewer\n"
   ]
  }
 ],
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   "name": "python"
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