sims.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "f4a75e45-2c95-43e2-8e93-38580856c0f5",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/jbieri/miniforge3/envs/flowerMD/lib/python3.11/site-packages/mdtraj/formats/__init__.py:13: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13\n",
      "  from mdtraj.formats.trr import TRRTrajectoryFile\n"
     ]
    }
   ],
   "source": [
    "import warnings\n",
    "warnings.filterwarnings('ignore')\n",
    "import flowermd\n",
    "import hoomd\n",
    "import gsd\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import gsd.hoomd\n",
    "from flowermd.base import Lattice, Simulation, Molecule\n",
    "from flowermd.library import FF_from_file\n",
    "import unyt as u\n",
    "import hoomd\n",
    "import glob\n",
    "\n",
    "cpu = hoomd.device.CPU()\n",
    "\n",
    "# Rerun with the original seed first"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "6fbc49cf-632d-4d8c-9000-3f0a64911b63",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/jbieri/CME_lab/repos/pl-validation/ff&mol2/PIDTCPDT_C11BO.mol2\n",
      "/home/jbieri/CME_lab/repos/pl-validation/ff&mol2/PIDTCPDT_C11BO.xml\n"
     ]
    }
   ],
   "source": [
    "ff_list = []\n",
    "molecule_list = glob.glob(r\"/home/jbieri/CME_lab/repos/pl-validation/ff&mol2/*.mol2\")\n",
    "for i in range(len(molecule_list)):\n",
    "    ff_list.append((str(molecule_list[i][:-4])+ \"xml\"))\n",
    "\n",
    "print(molecule_list[10])\n",
    "print(ff_list[10])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "16cc4504-ef97-4739-9e04-1eacc7e51b6f",
   "metadata": {},
   "outputs": [
    {
     "ename": "FoyerError",
     "evalue": "For atoms representing an element, please include both the atomic_number or symbol for the atom",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mFoyerError\u001b[0m                                Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[11], line 4\u001b[0m\n\u001b[1;32m      2\u001b[0m ff \u001b[38;5;241m=\u001b[39m FF_from_file(forcefield_files\u001b[38;5;241m=\u001b[39mff_list[\u001b[38;5;241m13\u001b[39m])\n\u001b[1;32m      3\u001b[0m system \u001b[38;5;241m=\u001b[39m Lattice(molecules\u001b[38;5;241m=\u001b[39mmolecule, x \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m5\u001b[39m, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m5\u001b[39m, n \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m4\u001b[39m)\n\u001b[0;32m----> 4\u001b[0m \u001b[43msystem\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mapply_forcefield\u001b[49m\u001b[43m(\u001b[49m\u001b[43mr_cut\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m2.5\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mforce_field\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mff\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mauto_scale\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43mremove_charges\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mremove_hydrogens\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/miniforge3/envs/flowerMD/lib/python3.11/site-packages/flowermd/base/system.py:548\u001b[0m, in \u001b[0;36mSystem.apply_forcefield\u001b[0;34m(self, r_cut, force_field, auto_scale, scale_charges, remove_charges, remove_hydrogens, pppm_resolution, pppm_order, nlist_buffer)\u001b[0m\n\u001b[1;32m    544\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_gmso_forcefields_dict:\n\u001b[1;32m    545\u001b[0m     \u001b[38;5;66;03m# assign names to all the gmso sites based on mol_type to\u001b[39;00m\n\u001b[1;32m    546\u001b[0m     \u001b[38;5;66;03m# match the keys in self._gmso_forcefields_dict before applying ff\u001b[39;00m\n\u001b[1;32m    547\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_assign_site_mol_type_idx()\n\u001b[0;32m--> 548\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgmso_system \u001b[38;5;241m=\u001b[39m \u001b[43mapply\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    549\u001b[0m \u001b[43m    \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgmso_system\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    550\u001b[0m \u001b[43m    \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_gmso_forcefields_dict\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    551\u001b[0m \u001b[43m    \u001b[49m\u001b[43mmatch_ff_by\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mgroup\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m    552\u001b[0m \u001b[43m    \u001b[49m\u001b[43midentify_connections\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m    553\u001b[0m \u001b[43m    \u001b[49m\u001b[43mspeedup_by_moltag\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m    554\u001b[0m \u001b[43m    \u001b[49m\u001b[43mspeedup_by_molgraph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m    555\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    557\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m remove_charges:\n\u001b[1;32m    558\u001b[0m     \u001b[38;5;28;01mfor\u001b[39;00m site \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgmso_system\u001b[38;5;241m.\u001b[39msites:\n",
      "File \u001b[0;32m~/miniforge3/envs/flowerMD/lib/python3.11/site-packages/gmso/parameterization/parameterize.py:92\u001b[0m, in \u001b[0;36mapply\u001b[0;34m(top, forcefields, match_ff_by, identify_connections, speedup_by_molgraph, speedup_by_moltag, ignore_params, remove_untyped, fast_copy)\u001b[0m\n\u001b[1;32m     77\u001b[0m config \u001b[38;5;241m=\u001b[39m TopologyParameterizationConfig\u001b[38;5;241m.\u001b[39mmodel_validate(\n\u001b[1;32m     78\u001b[0m     \u001b[38;5;28mdict\u001b[39m(\n\u001b[1;32m     79\u001b[0m         match_ff_by\u001b[38;5;241m=\u001b[39mmatch_ff_by,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     86\u001b[0m     )\n\u001b[1;32m     87\u001b[0m )\n\u001b[1;32m     88\u001b[0m parameterizer \u001b[38;5;241m=\u001b[39m TopologyParameterizer(\n\u001b[1;32m     89\u001b[0m     topology\u001b[38;5;241m=\u001b[39mtop, forcefields\u001b[38;5;241m=\u001b[39mforcefields, config\u001b[38;5;241m=\u001b[39mconfig\n\u001b[1;32m     90\u001b[0m )\n\u001b[0;32m---> 92\u001b[0m \u001b[43mparameterizer\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun_parameterization\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     94\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m parameterizer\u001b[38;5;241m.\u001b[39mtopology\n",
      "File \u001b[0;32m~/miniforge3/envs/flowerMD/lib/python3.11/site-packages/gmso/parameterization/topology_parameterizer.py:323\u001b[0m, in \u001b[0;36mTopologyParameterizer.run_parameterization\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    318\u001b[0m             warnings\u001b[38;5;241m.\u001b[39mwarn(\n\u001b[1;32m    319\u001b[0m                 \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGroup/molecule \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mlabel\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m will not be parameterized, as the forcefield to parameterize it \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    320\u001b[0m                 \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mis missing.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    321\u001b[0m             )  \u001b[38;5;66;03m# FixMe: Will warning be enough?\u001b[39;00m\n\u001b[1;32m    322\u001b[0m         \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 323\u001b[0m             typemap \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_atomtypes\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    324\u001b[0m \u001b[43m                \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_ff\u001b[49m\u001b[43m(\u001b[49m\u001b[43mlabel\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    325\u001b[0m \u001b[43m                \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtopology\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    326\u001b[0m \u001b[43m                \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconfig\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmatch_ff_by\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    327\u001b[0m \u001b[43m                \u001b[49m\u001b[43mlabel\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    328\u001b[0m \u001b[43m                \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconfig\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mspeedup_by_moltag\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    329\u001b[0m \u001b[43m                \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconfig\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mspeedup_by_molgraph\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    330\u001b[0m \u001b[43m            \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    331\u001b[0m             \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_parameterize(\n\u001b[1;32m    332\u001b[0m                 \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtopology,\n\u001b[1;32m    333\u001b[0m                 typemap,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    336\u001b[0m                 speedup_by_moltag\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconfig\u001b[38;5;241m.\u001b[39mspeedup_by_moltag,  \u001b[38;5;66;03m# This will be removed from the future iterations\u001b[39;00m\n\u001b[1;32m    337\u001b[0m             )\n\u001b[1;32m    338\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n",
      "File \u001b[0;32m~/miniforge3/envs/flowerMD/lib/python3.11/site-packages/gmso/parameterization/topology_parameterizer.py:393\u001b[0m, in \u001b[0;36mTopologyParameterizer._get_atomtypes\u001b[0;34m(forcefield, topology, label_type, label, speedup_by_moltag, use_isomorphic_checks)\u001b[0m\n\u001b[1;32m    391\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Run atom-typing in foyer and return the typemap.\"\"\"\u001b[39;00m\n\u001b[1;32m    392\u001b[0m atom_typing_rules_provider \u001b[38;5;241m=\u001b[39m get_atomtyping_rules_provider(forcefield)\n\u001b[0;32m--> 393\u001b[0m foyer_topology_graph \u001b[38;5;241m=\u001b[39m \u001b[43mget_topology_graph\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    394\u001b[0m \u001b[43m    \u001b[49m\u001b[43mtopology\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    395\u001b[0m \u001b[43m    \u001b[49m\u001b[43mlabel_type\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    396\u001b[0m \u001b[43m    \u001b[49m\u001b[43mlabel\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    397\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    399\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m speedup_by_moltag:\n\u001b[1;32m    400\u001b[0m     \u001b[38;5;66;03m# Iterate through foyer_topology_graph, which is a subgraph of label_type\u001b[39;00m\n\u001b[1;32m    401\u001b[0m     typemap, reference \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mdict\u001b[39m(), \u001b[38;5;28mdict\u001b[39m()\n",
      "File \u001b[0;32m~/miniforge3/envs/flowerMD/lib/python3.11/site-packages/gmso/parameterization/foyer_utils.py:63\u001b[0m, in \u001b[0;36mget_topology_graph\u001b[0;34m(gmso_topology, label_type, label, atomdata_populator)\u001b[0m\n\u001b[1;32m     59\u001b[0m kwargs \u001b[38;5;241m=\u001b[39m (\n\u001b[1;32m     60\u001b[0m     atomdata_populator(gmso_topology, atom) \u001b[38;5;28;01mif\u001b[39;00m atomdata_populator \u001b[38;5;28;01melse\u001b[39;00m {}\n\u001b[1;32m     61\u001b[0m )\n\u001b[1;32m     62\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m atom\u001b[38;5;241m.\u001b[39mname\u001b[38;5;241m.\u001b[39mstartswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m_\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m atom\u001b[38;5;241m.\u001b[39melement:\n\u001b[0;32m---> 63\u001b[0m     \u001b[43mtop_graph\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43madd_atom\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m     64\u001b[0m \u001b[43m        \u001b[49m\u001b[43mname\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     65\u001b[0m \u001b[43m        \u001b[49m\u001b[43mindex\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mj\u001b[49m\u001b[43m,\u001b[49m\u001b[43m  \u001b[49m\u001b[38;5;66;43;03m# Assumes order is preserved\u001b[39;49;00m\n\u001b[1;32m     66\u001b[0m \u001b[43m        \u001b[49m\u001b[43matomic_number\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m     67\u001b[0m \u001b[43m        \u001b[49m\u001b[43msymbol\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     68\u001b[0m \u001b[43m        \u001b[49m\u001b[43mgroup\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgroup\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     69\u001b[0m \u001b[43m        \u001b[49m\u001b[43mmolecule\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmolecule\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43matom\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmolecule\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m     70\u001b[0m \u001b[43m        \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     71\u001b[0m \u001b[43m    \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     72\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m     73\u001b[0m     top_graph\u001b[38;5;241m.\u001b[39madd_atom(\n\u001b[1;32m     74\u001b[0m         name\u001b[38;5;241m=\u001b[39matom\u001b[38;5;241m.\u001b[39mname,\n\u001b[1;32m     75\u001b[0m         index\u001b[38;5;241m=\u001b[39mj,  \u001b[38;5;66;03m# Assumes order is preserved\u001b[39;00m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     80\u001b[0m         \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs,\n\u001b[1;32m     81\u001b[0m     )\n",
      "File \u001b[0;32m~/miniforge3/envs/flowerMD/lib/python3.11/site-packages/foyer/topology_graph.py:89\u001b[0m, in \u001b[0;36mTopologyGraph.add_atom\u001b[0;34m(self, index, name, atomic_number, symbol, **kwargs)\u001b[0m\n\u001b[1;32m     66\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Add an atom to the topology graph.\u001b[39;00m\n\u001b[1;32m     67\u001b[0m \n\u001b[1;32m     68\u001b[0m \u001b[38;5;124;03mParameters\u001b[39;00m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     86\u001b[0m \u001b[38;5;124;03m    The class used to store atom data\u001b[39;00m\n\u001b[1;32m     87\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m     88\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m name\u001b[38;5;241m.\u001b[39mstartswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m_\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m (atomic_number \u001b[38;5;129;01mand\u001b[39;00m symbol):\n\u001b[0;32m---> 89\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m FoyerError(\n\u001b[1;32m     90\u001b[0m         \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mFor atoms representing an element, please include \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m     91\u001b[0m         \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mboth the atomic_number or symbol for the atom\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m     92\u001b[0m     )\n\u001b[1;32m     94\u001b[0m atom_data \u001b[38;5;241m=\u001b[39m AtomData(index, name, atomic_number, symbol, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m     95\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39madd_node(index, atom_data\u001b[38;5;241m=\u001b[39matom_data)\n",
      "\u001b[0;31mFoyerError\u001b[0m: For atoms representing an element, please include both the atomic_number or symbol for the atom"
     ]
    }
   ],
   "source": [
    "molecule = (Molecule(num_mols=1, file=molecule_list[]))\n",
    "ff = FF_from_file(forcefield_files=ff_list[13])\n",
    "system = Lattice(molecules=molecule, x = 5, y = 5, n = 4)\n",
    "system.apply_forcefield(r_cut=2.5, force_field=ff, auto_scale=True,remove_charges=True, remove_hydrogens=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "7ce34fa1-8c0c-43b8-b8a8-06011885f8db",
   "metadata": {},
   "outputs": [
    {
     "ename": "FoyerError",
     "evalue": "For atoms representing an element, please include both the atomic_number or symbol for the atom",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mFoyerError\u001b[0m                                Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[3], line 5\u001b[0m\n\u001b[1;32m      3\u001b[0m ff \u001b[38;5;241m=\u001b[39m FF_from_file(forcefield_files\u001b[38;5;241m=\u001b[39mff_list[i])\n\u001b[1;32m      4\u001b[0m box \u001b[38;5;241m=\u001b[39m Lattice(molecules\u001b[38;5;241m=\u001b[39mmolecule, x \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m5\u001b[39m, y \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m5\u001b[39m, n \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m4\u001b[39m)\n\u001b[0;32m----> 5\u001b[0m \u001b[43mbox\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mapply_forcefield\u001b[49m\u001b[43m(\u001b[49m\u001b[43mr_cut\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m2.5\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mforce_field\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mff\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mauto_scale\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43mremove_charges\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mremove_hydrogens\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/miniforge3/envs/flowerMD/lib/python3.11/site-packages/flowermd/base/system.py:548\u001b[0m, in \u001b[0;36mSystem.apply_forcefield\u001b[0;34m(self, r_cut, force_field, auto_scale, scale_charges, remove_charges, remove_hydrogens, pppm_resolution, pppm_order, nlist_buffer)\u001b[0m\n\u001b[1;32m    544\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_gmso_forcefields_dict:\n\u001b[1;32m    545\u001b[0m     \u001b[38;5;66;03m# assign names to all the gmso sites based on mol_type to\u001b[39;00m\n\u001b[1;32m    546\u001b[0m     \u001b[38;5;66;03m# match the keys in self._gmso_forcefields_dict before applying ff\u001b[39;00m\n\u001b[1;32m    547\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_assign_site_mol_type_idx()\n\u001b[0;32m--> 548\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgmso_system \u001b[38;5;241m=\u001b[39m \u001b[43mapply\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    549\u001b[0m \u001b[43m    \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgmso_system\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    550\u001b[0m \u001b[43m    \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_gmso_forcefields_dict\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    551\u001b[0m \u001b[43m    \u001b[49m\u001b[43mmatch_ff_by\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mgroup\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m    552\u001b[0m \u001b[43m    \u001b[49m\u001b[43midentify_connections\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m    553\u001b[0m \u001b[43m    \u001b[49m\u001b[43mspeedup_by_moltag\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m    554\u001b[0m \u001b[43m    \u001b[49m\u001b[43mspeedup_by_molgraph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m    555\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    557\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m remove_charges:\n\u001b[1;32m    558\u001b[0m     \u001b[38;5;28;01mfor\u001b[39;00m site \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgmso_system\u001b[38;5;241m.\u001b[39msites:\n",
      "File \u001b[0;32m~/miniforge3/envs/flowerMD/lib/python3.11/site-packages/gmso/parameterization/parameterize.py:92\u001b[0m, in \u001b[0;36mapply\u001b[0;34m(top, forcefields, match_ff_by, identify_connections, speedup_by_molgraph, speedup_by_moltag, ignore_params, remove_untyped, fast_copy)\u001b[0m\n\u001b[1;32m     77\u001b[0m config \u001b[38;5;241m=\u001b[39m TopologyParameterizationConfig\u001b[38;5;241m.\u001b[39mmodel_validate(\n\u001b[1;32m     78\u001b[0m     \u001b[38;5;28mdict\u001b[39m(\n\u001b[1;32m     79\u001b[0m         match_ff_by\u001b[38;5;241m=\u001b[39mmatch_ff_by,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     86\u001b[0m     )\n\u001b[1;32m     87\u001b[0m )\n\u001b[1;32m     88\u001b[0m parameterizer \u001b[38;5;241m=\u001b[39m TopologyParameterizer(\n\u001b[1;32m     89\u001b[0m     topology\u001b[38;5;241m=\u001b[39mtop, forcefields\u001b[38;5;241m=\u001b[39mforcefields, config\u001b[38;5;241m=\u001b[39mconfig\n\u001b[1;32m     90\u001b[0m )\n\u001b[0;32m---> 92\u001b[0m \u001b[43mparameterizer\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun_parameterization\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     94\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m parameterizer\u001b[38;5;241m.\u001b[39mtopology\n",
      "File \u001b[0;32m~/miniforge3/envs/flowerMD/lib/python3.11/site-packages/gmso/parameterization/topology_parameterizer.py:323\u001b[0m, in \u001b[0;36mTopologyParameterizer.run_parameterization\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    318\u001b[0m             warnings\u001b[38;5;241m.\u001b[39mwarn(\n\u001b[1;32m    319\u001b[0m                 \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGroup/molecule \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mlabel\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m will not be parameterized, as the forcefield to parameterize it \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    320\u001b[0m                 \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mis missing.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    321\u001b[0m             )  \u001b[38;5;66;03m# FixMe: Will warning be enough?\u001b[39;00m\n\u001b[1;32m    322\u001b[0m         \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 323\u001b[0m             typemap \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_atomtypes\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    324\u001b[0m \u001b[43m                \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_ff\u001b[49m\u001b[43m(\u001b[49m\u001b[43mlabel\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    325\u001b[0m \u001b[43m                \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtopology\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    326\u001b[0m \u001b[43m                \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconfig\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmatch_ff_by\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    327\u001b[0m \u001b[43m                \u001b[49m\u001b[43mlabel\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    328\u001b[0m \u001b[43m                \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconfig\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mspeedup_by_moltag\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    329\u001b[0m \u001b[43m                \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconfig\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mspeedup_by_molgraph\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    330\u001b[0m \u001b[43m            \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    331\u001b[0m             \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_parameterize(\n\u001b[1;32m    332\u001b[0m                 \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtopology,\n\u001b[1;32m    333\u001b[0m                 typemap,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    336\u001b[0m                 speedup_by_moltag\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconfig\u001b[38;5;241m.\u001b[39mspeedup_by_moltag,  \u001b[38;5;66;03m# This will be removed from the future iterations\u001b[39;00m\n\u001b[1;32m    337\u001b[0m             )\n\u001b[1;32m    338\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n",
      "File \u001b[0;32m~/miniforge3/envs/flowerMD/lib/python3.11/site-packages/gmso/parameterization/topology_parameterizer.py:393\u001b[0m, in \u001b[0;36mTopologyParameterizer._get_atomtypes\u001b[0;34m(forcefield, topology, label_type, label, speedup_by_moltag, use_isomorphic_checks)\u001b[0m\n\u001b[1;32m    391\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Run atom-typing in foyer and return the typemap.\"\"\"\u001b[39;00m\n\u001b[1;32m    392\u001b[0m atom_typing_rules_provider \u001b[38;5;241m=\u001b[39m get_atomtyping_rules_provider(forcefield)\n\u001b[0;32m--> 393\u001b[0m foyer_topology_graph \u001b[38;5;241m=\u001b[39m \u001b[43mget_topology_graph\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    394\u001b[0m \u001b[43m    \u001b[49m\u001b[43mtopology\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    395\u001b[0m \u001b[43m    \u001b[49m\u001b[43mlabel_type\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    396\u001b[0m \u001b[43m    \u001b[49m\u001b[43mlabel\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    397\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    399\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m speedup_by_moltag:\n\u001b[1;32m    400\u001b[0m     \u001b[38;5;66;03m# Iterate through foyer_topology_graph, which is a subgraph of label_type\u001b[39;00m\n\u001b[1;32m    401\u001b[0m     typemap, reference \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mdict\u001b[39m(), \u001b[38;5;28mdict\u001b[39m()\n",
      "File \u001b[0;32m~/miniforge3/envs/flowerMD/lib/python3.11/site-packages/gmso/parameterization/foyer_utils.py:63\u001b[0m, in \u001b[0;36mget_topology_graph\u001b[0;34m(gmso_topology, label_type, label, atomdata_populator)\u001b[0m\n\u001b[1;32m     59\u001b[0m kwargs \u001b[38;5;241m=\u001b[39m (\n\u001b[1;32m     60\u001b[0m     atomdata_populator(gmso_topology, atom) \u001b[38;5;28;01mif\u001b[39;00m atomdata_populator \u001b[38;5;28;01melse\u001b[39;00m {}\n\u001b[1;32m     61\u001b[0m )\n\u001b[1;32m     62\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m atom\u001b[38;5;241m.\u001b[39mname\u001b[38;5;241m.\u001b[39mstartswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m_\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m atom\u001b[38;5;241m.\u001b[39melement:\n\u001b[0;32m---> 63\u001b[0m     \u001b[43mtop_graph\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43madd_atom\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m     64\u001b[0m \u001b[43m        \u001b[49m\u001b[43mname\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     65\u001b[0m \u001b[43m        \u001b[49m\u001b[43mindex\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mj\u001b[49m\u001b[43m,\u001b[49m\u001b[43m  \u001b[49m\u001b[38;5;66;43;03m# Assumes order is preserved\u001b[39;49;00m\n\u001b[1;32m     66\u001b[0m \u001b[43m        \u001b[49m\u001b[43matomic_number\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m     67\u001b[0m \u001b[43m        \u001b[49m\u001b[43msymbol\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     68\u001b[0m \u001b[43m        \u001b[49m\u001b[43mgroup\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgroup\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     69\u001b[0m \u001b[43m        \u001b[49m\u001b[43mmolecule\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmolecule\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mif\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43matom\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmolecule\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01melse\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m     70\u001b[0m \u001b[43m        \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m     71\u001b[0m \u001b[43m    \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     72\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m     73\u001b[0m     top_graph\u001b[38;5;241m.\u001b[39madd_atom(\n\u001b[1;32m     74\u001b[0m         name\u001b[38;5;241m=\u001b[39matom\u001b[38;5;241m.\u001b[39mname,\n\u001b[1;32m     75\u001b[0m         index\u001b[38;5;241m=\u001b[39mj,  \u001b[38;5;66;03m# Assumes order is preserved\u001b[39;00m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     80\u001b[0m         \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs,\n\u001b[1;32m     81\u001b[0m     )\n",
      "File \u001b[0;32m~/miniforge3/envs/flowerMD/lib/python3.11/site-packages/foyer/topology_graph.py:89\u001b[0m, in \u001b[0;36mTopologyGraph.add_atom\u001b[0;34m(self, index, name, atomic_number, symbol, **kwargs)\u001b[0m\n\u001b[1;32m     66\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Add an atom to the topology graph.\u001b[39;00m\n\u001b[1;32m     67\u001b[0m \n\u001b[1;32m     68\u001b[0m \u001b[38;5;124;03mParameters\u001b[39;00m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     86\u001b[0m \u001b[38;5;124;03m    The class used to store atom data\u001b[39;00m\n\u001b[1;32m     87\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m     88\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m name\u001b[38;5;241m.\u001b[39mstartswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m_\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m (atomic_number \u001b[38;5;129;01mand\u001b[39;00m symbol):\n\u001b[0;32m---> 89\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m FoyerError(\n\u001b[1;32m     90\u001b[0m         \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mFor atoms representing an element, please include \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m     91\u001b[0m         \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mboth the atomic_number or symbol for the atom\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m     92\u001b[0m     )\n\u001b[1;32m     94\u001b[0m atom_data \u001b[38;5;241m=\u001b[39m AtomData(index, name, atomic_number, symbol, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m     95\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39madd_node(index, atom_data\u001b[38;5;241m=\u001b[39matom_data)\n",
      "\u001b[0;31mFoyerError\u001b[0m: For atoms representing an element, please include both the atomic_number or symbol for the atom"
     ]
    }
   ],
   "source": [
    "for i in range(0,len(molecule_list)):\n",
    "    molecule = (Molecule(num_mols=1, file=molecule_list[i]))\n",
    "    ff = FF_from_file(forcefield_files=ff_list[i])\n",
    "    system = Lattice(molecules=molecule, x = 5, y = 5, n = 4)\n",
    "    system.apply_forcefield(r_cut=2.5, force_field=ff, auto_scale=True,remove_charges=True, remove_hydrogens=True)"
   ]
  }
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