test-periodic-improper.ipynb

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    "import warnings\n",
    "warnings.filterwarnings(\"ignore\")\n",
    "\n",
    "import mbuild as mb\n",
    "import unyt as u\n",
    "\n",
    "import gmso\n",
    "from gmso.external import from_mbuild, to_hoomd_forcefield, to_hoomd_snapshot\n",
    "from gmso.core.forcefield import ForceField\n",
    "from gmso.parameterization import apply\n",
    "from gmso.utils.io import get_fn"
   ]
  },
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   "source": [
    "## Using GAFF with Periodic Impropers:"
   ]
  },
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    {
     "name": "stdout",
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     "text": [
      "No charged group detected, skipping electrostatics.\n"
     ]
    }
   ],
   "source": [
    "benzene = mb.load(\"c1ccccc1\", smiles=True)\n",
    "benzene.box = mb.Box([5, 5, 5,])\n",
    "top = from_mbuild(benzene)\n",
    "\n",
    "base_units = dict(mass=u.g/u.mol, length=u.nm, energy=u.kJ/u.mol)\n",
    "gaff = ForceField(get_fn(\"gmso_xmls/test_ffstyles/gaff.xml\"))\n",
    "paramaterized_top = apply(top=top, forcefields=gaff, identify_connections=True)\n",
    "snap, _ = to_hoomd_snapshot(top, base_units=base_units)\n",
    "forces, _ = to_hoomd_forcefield(top, r_cut=1.4, base_units=base_units)"
   ]
  },
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   "cell_type": "code",
   "execution_count": 5,
   "id": "7257f456-671a-4813-b2ce-34c6d02de440",
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     "name": "stdout",
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     "text": [
      "Dihedrals\n",
      "ca-ca-ca-ha\n",
      "_HOOMDDict{'k': 15.167, 'd': 1.0, 'n': 2, 'phi0': 3.141592653589793}\n",
      "ha-ca-ca-ha\n",
      "_HOOMDDict{'k': 15.167, 'd': 1.0, 'n': 2, 'phi0': 3.141592653589793}\n",
      "ca-ca-ca-ca\n",
      "_HOOMDDict{'k': 15.167, 'd': 1.0, 'n': 2, 'phi0': 3.141592653589793}\n",
      "\n",
      "Impropers\n",
      "<hoomd.md.improper.Periodic object at 0x7834ae23be10>\n",
      "ca-*-*-ha\n",
      "_HOOMDDict{'k': 4.6024, 'n': 2, 'd': 1, 'chi0': 3.141592653589793}\n"
     ]
    }
   ],
   "source": [
    "improper_force = forces[\"impropers\"][0]\n",
    "dihedral_force = forces[\"dihedrals\"][0]\n",
    "\n",
    "print(\"Dihedrals\")\n",
    "for param in dihedral_force.params:\n",
    "    print(param)\n",
    "    print(dihedral_force.params[param])\n",
    "    \n",
    "print()\n",
    "\n",
    "print(\"Impropers\")\n",
    "print(improper_force)\n",
    "for param in improper_force.params:\n",
    "    print(param)\n",
    "    print(improper_force.params[param])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "3ae98108-5796-46d1-9c69-00ee07391856",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['ca-ca-ca-ha']\n"
     ]
    }
   ],
   "source": [
    "print(snap.impropers.types)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e9efdf93-c634-4a70-9be4-c1b0b612cf34",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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