scratch.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/var/folders/f3/zyvmf_xs32qbkl_h7913df540000gn/T/ipykernel_92949/3515135725.py:1: DeprecationWarning: \n",
      "Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),\n",
      "(to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)\n",
      "but was not found to be installed on your system.\n",
      "If this would cause problems for you,\n",
      "please provide us feedback at https://github.com/pandas-dev/pandas/issues/54466\n",
      "        \n",
      "  import pandas as pd\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "ename": "ValueError",
     "evalue": "Per-column arrays must each be 1-dimensional",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[1], line 6\u001b[0m\n\u001b[1;32m      4\u001b[0m PATCH \u001b[38;5;241m=\u001b[39m init_model(varTemp\u001b[38;5;241m=\u001b[39mVARY_TEMP, ymom\u001b[38;5;241m=\u001b[39mAEROBIC_LMWOM_GROWTH_EFFICIENCY, mortality\u001b[38;5;241m=\u001b[39mDEFAULT_MORTALITY, kmom\u001b[38;5;241m=\u001b[39mK_LMWOM)\n\u001b[1;32m      5\u001b[0m UPDATED_PATCH\u001b[38;5;241m=\u001b[39m run_model(PATCH)\n\u001b[0;32m----> 6\u001b[0m hold \u001b[38;5;241m=\u001b[39m \u001b[43mpd\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mDataFrame\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfrom_dict\u001b[49m\u001b[43m(\u001b[49m\u001b[43mUPDATED_PATCH\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/Desktop/lab_work/orphan/2024/scripts/.venv/lib/python3.11/site-packages/pandas/core/frame.py:1905\u001b[0m, in \u001b[0;36mDataFrame.from_dict\u001b[0;34m(cls, data, orient, dtype, columns)\u001b[0m\n\u001b[1;32m   1899\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[1;32m   1900\u001b[0m         \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mExpected \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m, \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcolumns\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m or \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtight\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m for orient parameter. \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m   1901\u001b[0m         \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGot \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00morient\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m instead\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m   1902\u001b[0m     )\n\u001b[1;32m   1904\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m orient \u001b[38;5;241m!=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtight\u001b[39m\u001b[38;5;124m\"\u001b[39m:\n\u001b[0;32m-> 1905\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mcls\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindex\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mindex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcolumns\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcolumns\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdtype\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdtype\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m   1906\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m   1907\u001b[0m     realdata \u001b[38;5;241m=\u001b[39m data[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdata\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n",
      "File \u001b[0;32m~/Desktop/lab_work/orphan/2024/scripts/.venv/lib/python3.11/site-packages/pandas/core/frame.py:767\u001b[0m, in \u001b[0;36mDataFrame.__init__\u001b[0;34m(self, data, index, columns, dtype, copy)\u001b[0m\n\u001b[1;32m    761\u001b[0m     mgr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_init_mgr(\n\u001b[1;32m    762\u001b[0m         data, axes\u001b[38;5;241m=\u001b[39m{\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m\"\u001b[39m: index, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcolumns\u001b[39m\u001b[38;5;124m\"\u001b[39m: columns}, dtype\u001b[38;5;241m=\u001b[39mdtype, copy\u001b[38;5;241m=\u001b[39mcopy\n\u001b[1;32m    763\u001b[0m     )\n\u001b[1;32m    765\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(data, \u001b[38;5;28mdict\u001b[39m):\n\u001b[1;32m    766\u001b[0m     \u001b[38;5;66;03m# GH#38939 de facto copy defaults to False only in non-dict cases\u001b[39;00m\n\u001b[0;32m--> 767\u001b[0m     mgr \u001b[38;5;241m=\u001b[39m \u001b[43mdict_to_mgr\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcolumns\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdtype\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdtype\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcopy\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcopy\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtyp\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmanager\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    768\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(data, ma\u001b[38;5;241m.\u001b[39mMaskedArray):\n\u001b[1;32m    769\u001b[0m     \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mnumpy\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mma\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m mrecords\n",
      "File \u001b[0;32m~/Desktop/lab_work/orphan/2024/scripts/.venv/lib/python3.11/site-packages/pandas/core/internals/construction.py:503\u001b[0m, in \u001b[0;36mdict_to_mgr\u001b[0;34m(data, index, columns, dtype, typ, copy)\u001b[0m\n\u001b[1;32m    499\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    500\u001b[0m         \u001b[38;5;66;03m# dtype check to exclude e.g. range objects, scalars\u001b[39;00m\n\u001b[1;32m    501\u001b[0m         arrays \u001b[38;5;241m=\u001b[39m [x\u001b[38;5;241m.\u001b[39mcopy() \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(x, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdtype\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;28;01melse\u001b[39;00m x \u001b[38;5;28;01mfor\u001b[39;00m x \u001b[38;5;129;01min\u001b[39;00m arrays]\n\u001b[0;32m--> 503\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43marrays_to_mgr\u001b[49m\u001b[43m(\u001b[49m\u001b[43marrays\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcolumns\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdtype\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdtype\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtyp\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtyp\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mconsolidate\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcopy\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[0;32m~/Desktop/lab_work/orphan/2024/scripts/.venv/lib/python3.11/site-packages/pandas/core/internals/construction.py:114\u001b[0m, in \u001b[0;36marrays_to_mgr\u001b[0;34m(arrays, columns, index, dtype, verify_integrity, typ, consolidate)\u001b[0m\n\u001b[1;32m    111\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m verify_integrity:\n\u001b[1;32m    112\u001b[0m     \u001b[38;5;66;03m# figure out the index, if necessary\u001b[39;00m\n\u001b[1;32m    113\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m index \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m--> 114\u001b[0m         index \u001b[38;5;241m=\u001b[39m \u001b[43m_extract_index\u001b[49m\u001b[43m(\u001b[49m\u001b[43marrays\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    115\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    116\u001b[0m         index \u001b[38;5;241m=\u001b[39m ensure_index(index)\n",
      "File \u001b[0;32m~/Desktop/lab_work/orphan/2024/scripts/.venv/lib/python3.11/site-packages/pandas/core/internals/construction.py:664\u001b[0m, in \u001b[0;36m_extract_index\u001b[0;34m(data)\u001b[0m\n\u001b[1;32m    662\u001b[0m         raw_lengths\u001b[38;5;241m.\u001b[39mappend(\u001b[38;5;28mlen\u001b[39m(val))\n\u001b[1;32m    663\u001b[0m     \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(val, np\u001b[38;5;241m.\u001b[39mndarray) \u001b[38;5;129;01mand\u001b[39;00m val\u001b[38;5;241m.\u001b[39mndim \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[0;32m--> 664\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mPer-column arrays must each be 1-dimensional\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m    666\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m indexes \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m raw_lengths:\n\u001b[1;32m    667\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mIf using all scalar values, you must pass an index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
      "\u001b[0;31mValueError\u001b[0m: Per-column arrays must each be 1-dimensional"
     ]
    }
   ],
   "source": [
    "\n",
    "import pandas as pd\n",
    "from pom_model.constants import VARY_TEMP, AEROBIC_LMWOM_GROWTH_EFFICIENCY, DEFAULT_MORTALITY, K_LMWOM\n",
    "from pom_model.pom import init_model, run_model\n",
    "PATCH = init_model(varTemp=VARY_TEMP, ymom=AEROBIC_LMWOM_GROWTH_EFFICIENCY, mortality=DEFAULT_MORTALITY, kmom=K_LMWOM)\n",
    "UPDATED_PATCH= run_model(PATCH)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'pom': array([1.23      , 0.65888131, 0.0671727 , 0.08266433, 0.09742314,\n",
       "        0.29437011, 0.11790091, 0.25497949, 0.13484163, 0.13940633,\n",
       "        0.14364794, 0.14758155, 0.1512242 , 0.1545941 , 0.15771005,\n",
       "        0.16059096, 0.16325542, 0.16572148, 0.16800642, 0.17012659,\n",
       "        0.17209735, 0.17393301, 0.17564683, 0.17725101, 0.17875674,\n",
       "        0.18017425, 0.18151283, 0.18278093, 0.18398619, 0.18513551,\n",
       "        0.18623509, 0.18729052, 0.18830684, 0.18928855, 0.19023967,\n",
       "        0.19116383, 0.19206425, 0.19294382, 0.19380512, 0.19465044,\n",
       "        0.19548184, 0.19630115, 0.19711   , 0.19790983, 0.19870195,\n",
       "        0.19948751, 0.20026752, 0.20104291, 0.20181449, 0.20258298,\n",
       "        0.20334903, 0.20411321, 0.20487603, 0.20563794, 0.20639936,\n",
       "        0.20716063, 0.20792209, 0.20868402, 0.20944668, 0.21021029,\n",
       "        0.21097507, 0.21174118, 0.21250879, 0.21327805, 0.2140491 ,\n",
       "        0.21482204, 0.21559698, 0.21637401, 0.21715323, 0.2179347 ,\n",
       "        0.2187185 , 0.21950468, 0.22029331, 0.22108444, 0.22187811,\n",
       "        0.22267436, 0.22347324, 0.22427478, 0.22507901, 0.22588597,\n",
       "        0.22669567, 0.22750816, 0.22832345, 0.22914157, 0.22996253,\n",
       "        0.23078636, 0.23161308, 0.2324427 , 0.23327525, 0.23411074,\n",
       "        0.23494918, 0.2357906 , 0.23663501, 0.23748241, 0.23833283,\n",
       "        0.23918629, 0.24004278, 0.24090233, 0.24176496, 0.24263066,\n",
       "        0.24349947, 0.24437138, 0.24524641, 0.24612458, 0.2470059 ,\n",
       "        0.24789037, 0.24877801, 0.24966884, 0.25056286, 0.25146009,\n",
       "        0.25236054, 0.25326422, 0.25417114, 0.25508132, 0.25599477,\n",
       "        0.25691149, 0.25783151, 0.25875483, 0.25968147, 0.26061144,\n",
       "        0.26154475, 0.26248141, 0.26342144, 0.26436484, 0.26531163,\n",
       "        0.26626183, 0.26721544, 0.26817247, 0.26913295, 0.27009688,\n",
       "        0.27106427, 0.27203514, 0.27300949, 0.27398736, 0.27496873,\n",
       "        0.27595363, 0.27694208, 0.27793407, 0.27892964, 0.27992878,\n",
       "        0.28093151, 0.28193785, 0.28294781, 0.28396139, 0.28497863,\n",
       "        0.28599952, 0.28702408, 0.28805232, 0.28908427, 0.29011992,\n",
       "        0.2911593 , 0.29220241, 0.29324928, 0.29429991, 0.29535432,\n",
       "        0.29641253, 0.29747454, 0.29854036, 0.29961003, 0.30068354,\n",
       "        0.30176091, 0.30284216, 0.30392729, 0.30501633, 0.30610929,\n",
       "        0.30720618, 0.30830702, 0.30941182, 0.31052059, 0.31163335,\n",
       "        0.31275011, 0.3138709 , 0.31499572, 0.31612458, 0.31725751,\n",
       "        0.31839451, 0.3195356 , 0.3206808 , 0.32183013, 0.32298359,\n",
       "        0.3241412 , 0.32530297, 0.32646893, 0.32763909, 0.32881346,\n",
       "        0.32999205, 0.33117489, 0.33236198, 0.33355335, 0.33474901,\n",
       "        0.33594897, 0.33715326, 0.33836187, 0.33957484, 0.34079218,\n",
       "        0.3420139 , 0.34324002, 0.34447056, 0.34570552, 0.34694493,\n",
       "        0.34818881, 0.34943717, 0.35069002, 0.35194738, 0.35320928,\n",
       "        0.35447571, 0.35574671, 0.35702229, 0.35830246, 0.35958724,\n",
       "        0.36087666, 0.36217071, 0.36346943, 0.36477283, 0.36608092,\n",
       "        0.36739372, 0.36871126, 0.37003354, 0.37136059, 0.37269242,\n",
       "        0.37402905, 0.37537049, 0.37671677, 0.3780679 , 0.3794239 ,\n",
       "        0.38078479, 0.38215058, 0.38352129, 0.38489695, 0.38627756,\n",
       "        0.38766315, 0.38905373, 0.39044933, 0.39184996, 0.39325563,\n",
       "        0.39466638, 0.39608221, 0.39750314, 0.3989292 , 0.4003604 ,\n",
       "        0.40179676, 0.4032383 , 0.40468504, 0.406137  , 0.40759419,\n",
       "        0.40905664, 0.41052436, 0.41199737, 0.4134757 , 0.41495936,\n",
       "        0.41644837, 0.41794275, 0.41944252, 0.4209477 , 0.42245832,\n",
       "        0.42397438, 0.42549591, 0.42702293, 0.42855546, 0.43009352,\n",
       "        0.43163713, 0.43318631, 0.43474108, 0.43630145, 0.43786747,\n",
       "        0.43943913, 0.44101646, 0.44259949, 0.44418823, 0.4457827 ,\n",
       "        0.44738293, 0.44898894, 0.45060074, 0.45221836, 0.45384182,\n",
       "        0.45547114, 0.45710635, 0.45874746, 0.46039449, 0.46204747,\n",
       "        0.46370642, 0.46537136, 0.46704231, 0.46871929, 0.47040233,\n",
       "        0.47209145, 0.47378667, 0.47548801, 0.4771955 , 0.47890915,\n",
       "        0.480629  , 0.48235506, 0.48408735, 0.4858259 , 0.48757073,\n",
       "        0.48932186, 0.49107932, 0.49284314, 0.49461332, 0.4963899 ,\n",
       "        0.4981729 , 0.49996234, 0.50175825, 0.50356065, 0.50536957,\n",
       "        0.50718502, 0.50900703, 0.51083563, 0.51267084, 0.51451268,\n",
       "        0.51636118, 0.51821636, 0.52007825, 0.52194687, 0.52382225,\n",
       "        0.52570441, 0.52759337, 0.52948917, 0.53139181, 0.53330134,\n",
       "        0.53521778, 0.53714114, 0.53907146, 0.54100877, 0.54295308,\n",
       "        0.54490442, 0.54686282, 0.5488283 , 0.5508009 , 0.55278063,\n",
       "        0.55476752, 0.55676161, 0.5587629 , 0.56077144, 0.56278725,\n",
       "        0.56481035, 0.56684077, 0.56887854, 0.57092368, 0.57297623,\n",
       "        0.5750362 , 0.57710363, 0.57917855, 0.58126097, 0.58335093,\n",
       "        0.58544846, 0.58755358, 0.58966633, 0.59178672, 0.59391479,\n",
       "        0.59605057, 0.59819408, 0.60034535, 0.60250441, 0.60467129,\n",
       "        0.60684602, 0.60902862, 0.61121913, 0.61341758, 0.61562399,\n",
       "        0.61783839, 0.62006081, 0.62229128, 0.62452984, 0.62677651,\n",
       "        0.62903131, 0.63129429, 0.63356546, 0.63584487, 0.63813254,\n",
       "        0.64042849, 0.64273277, 0.6450454 , 0.64736641, 0.64969584,\n",
       "        0.65203371, 0.65438005, 0.6567349 , 0.65909829, 0.66147025,\n",
       "        0.6638508 , 0.66623999, 0.66863784, 0.67104439, 0.67345966,\n",
       "        0.6758837 , 0.67831652, 0.68075817, 0.68320867, 0.68566807,\n",
       "        0.68813638, 0.69061365, 0.6930999 , 0.69559518, 0.69809951,\n",
       "        0.70061292, 0.70313546, 0.70566715, 0.70820802, 0.71075812,\n",
       "        0.71331747, 0.71588611, 0.71846407, 0.72105139, 0.7236481 ,\n",
       "        0.72625424, 0.72886984, 0.73149493, 0.73412956, 0.73677375,\n",
       "        0.73942754, 0.74209097, 0.74476407, 0.74744688, 0.75013943,\n",
       "        0.75284176, 0.7555539 , 0.7582759 , 0.76100778, 0.76374959,\n",
       "        0.76650136, 0.76926312, 0.77203492, 0.77481679, 0.77760877,\n",
       "        0.78041089, 0.7832232 , 0.78604572, 0.7888785 , 0.79172158,\n",
       "        0.794575  , 0.79743878, 0.80031297, 0.80319762, 0.80609275,\n",
       "        0.8089984 , 0.81191462, 0.81484144, 0.81777891, 0.82072705,\n",
       "        0.82368592, 0.82665555, 0.82963598, 0.83262725, 0.8356294 ,\n",
       "        0.83864247, 0.8416665 , 0.84470153, 0.8477476 , 0.85080476,\n",
       "        0.85387304, 0.85695248, 0.86004313, 0.86314503, 0.86625821,\n",
       "        0.86938273, 0.87251862, 0.87566592, 0.87882468, 0.88199493,\n",
       "        0.88517673, 0.88837012, 0.89157513, 0.89479181, 0.8980202 ,\n",
       "        0.90126035, 0.9045123 , 0.90777609, 0.91105177, 0.91433938,\n",
       "        0.91763896, 0.92095057, 0.92427424, 0.92761001, 0.93095794,\n",
       "        0.93431807, 0.93769045, 0.94107511, 0.9444721 , 0.94788148,\n",
       "        0.95130328, 0.95473756, 0.95818435, 0.9616437 , 0.96511567,\n",
       "        0.9686003 , 0.97209763, 0.97560771, 0.97913059, 0.98266631,\n",
       "        0.98621493, 0.9897765 , 0.99335105, 0.99693864, 1.00053931,\n",
       "        1.00415312, 1.00778012, 1.01142034, 1.01507385, 1.01874069,\n",
       "        1.02242091, 1.02611455, 1.02982168, 1.03354234, 1.03727657,\n",
       "        1.04102444, 1.04478599, 1.04856126, 1.05235033, 1.05615322,\n",
       "        1.05997   , 1.06380072, 1.06764542, 1.07150416, 1.075377  ,\n",
       "        1.07926398, 1.08316516, 1.08708059, 1.09101032, 1.09495441,\n",
       "        1.09891291, 1.10288587, 1.10687334, 1.11087539, 1.11489207,\n",
       "        1.11892342, 1.1229695 , 1.12703038, 1.1311061 , 1.13519671,\n",
       "        1.13930229, 1.14342287, 1.14755852, 1.15170929, 1.15587523,\n",
       "        1.16005642, 1.16425289, 1.16846471, 1.17269194, 1.17693463,\n",
       "        1.18119284, 1.18546663, 1.18975605, 1.19406117, 1.19838205,\n",
       "        1.20271873, 1.20707128, 1.21143977, 1.21582424, 1.22022477,\n",
       "        1.2246414 , 1.2290742 , 1.23352322, 1.23798854, 1.24247021,\n",
       "        1.24696829, 1.25148284, 1.25601392, 1.2605616 , 1.26512594,\n",
       "        1.269707  , 1.27430484, 1.27891952, 1.28355111, 1.28819967,\n",
       "        1.29286527, 1.29754796, 1.30224782, 1.3069649 , 1.31169927,\n",
       "        1.31645099, 1.32122014, 1.32600677, 1.33081095, 1.33563274,\n",
       "        1.34047221, 1.34532944, 1.35020447, 1.35509739, 1.36000825,\n",
       "        1.36493713, 1.36988409, 1.3748492 , 1.37983252, 1.38483413,\n",
       "        1.3898541 , 1.39489249, 1.39994937, 1.40502481, 1.41011888,\n",
       "        1.41523165, 1.42036319, 1.42551357, 1.43068286, 1.43587113,\n",
       "        1.44107845, 1.4463049 , 1.45155055, 1.45681546, 1.46209972,\n",
       "        1.46740338, 1.47272654, 1.47806925, 1.48343159, 1.48881363,\n",
       "        1.49421546, 1.49963714, 1.50507875, 1.51054036, 1.51602205,\n",
       "        1.52152389, 1.52704596, 1.53258834, 1.53815109, 1.54373431,\n",
       "        1.54933806, 1.55496242, 1.56060747, 1.56627329, 1.57195995,\n",
       "        1.57766753, 1.58339612, 1.58914579, 1.59491661, 1.60070868,\n",
       "        1.60652207, 1.61235685, 1.61821312, 1.62409095, 1.62999042,\n",
       "        1.63591161, 1.64185461, 1.64781949, 1.65380635, 1.65981526,\n",
       "        1.6658463 , 1.67189956, 1.67797513, 1.68407308, 1.6901935 ,\n",
       "        1.69633648, 1.7025021 , 1.70869044, 1.7149016 , 1.72113565,\n",
       "        1.72739269, 1.7336728 , 1.73997607, 1.74630258, 1.75265242,\n",
       "        1.75902569, 1.76542246, 1.77184284, 1.77828689, 1.78475473,\n",
       "        1.79124643, 1.79776209, 1.80430179, 1.81086564, 1.81745371,\n",
       "        1.8240661 , 1.8307029 , 1.83736421, 1.84405012, 1.85076071,\n",
       "        1.85749609, 1.86425635, 1.87104158, 1.87785187, 1.88468732,\n",
       "        1.89154804, 1.8984341 , 1.90534561, 1.91228266, 1.91924535,\n",
       "        1.92623378, 1.93324805, 1.94028825, 1.94735448, 1.95444684,\n",
       "        1.96156543, 1.96871034, 1.97588169, 1.98307956, 1.99030406,\n",
       "        1.99755529, 2.00483336, 2.01213835, 2.01947038, 2.02682955,\n",
       "        2.03421596, 2.04162971, 2.04907092, 2.05653967, 2.06403608,\n",
       "        2.07156025, 2.07911229, 2.08669231, 2.0943004 , 2.10193668,\n",
       "        2.10960125, 2.11729422, 2.12501571, 2.13276581, 2.14054463,\n",
       "        2.14835229, 2.1561889 , 2.16405456, 2.17194939, 2.1798735 ,\n",
       "        2.18782699, 2.19580999, 2.20382259, 2.21186493, 2.2199371 ,\n",
       "        2.22803923, 2.23617142, 2.24433379, 2.25252646, 2.26074954,\n",
       "        2.26900315]),\n",
       " 'mom': array([ 0.00000000e+00, -3.77638404e-06, -3.80270020e-06, -3.82919975e-06,\n",
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       "        108.20761665, 108.22661576, 108.24561487, 108.26461398,\n",
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       "        108.8915847 , 108.91058381, 108.92958292, 108.94858204,\n",
       "        108.96758115, 108.98658026, 109.00557938, 109.02457849,\n",
       "        109.0435776 , 109.06257671, 109.08157583, 109.10057494,\n",
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       "        109.1955705 , 109.21456961, 109.23356873, 109.25256784,\n",
       "        109.27156695, 109.29056606, 109.30956518, 109.32856429,\n",
       "        109.3475634 , 109.36656251, 109.38556163, 109.40456074,\n",
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       "        109.6515492 , 109.67054832, 109.68954743, 109.70854654,\n",
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       "        113.60336463, 113.62236374, 113.64136285, 113.66036196,\n",
       "        113.67936108]),\n",
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       "        5.        ]),\n",
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       "         8.62863457,  8.6454465 ,  8.66229174,  8.67917036,  8.69608244,\n",
       "         8.71302803,  8.73000721,  8.74702005,  8.76406661,  8.78114697,\n",
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       "         8.97128142,  8.98877279,  9.00629888,  9.02385974,  9.04145547,\n",
       "         9.05908612,  9.07675177,  9.09445249,  9.11218835,  9.12995943,\n",
       "         9.1477658 ,  9.16560753,  9.18348469,  9.20139737,  9.21934562,\n",
       "         9.23732953,  9.25534916,  9.2734046 ,  9.29149592,  9.30962318,\n",
       "         9.32778647,  9.34598586,  9.36422142,  9.38249323,  9.40080137,\n",
       "         9.4191459 ,  9.43752691,  9.45594447,  9.47439865,  9.49288953,\n",
       "         9.51141719,  9.52998171,  9.54858315,  9.5672216 ,  9.58589713,\n",
       "         9.60460982,  9.62335975,  9.64214699,  9.66097162,  9.67983372,\n",
       "         9.69873337,  9.71767064,  9.73664562,  9.75565837,  9.77470898,\n",
       "         9.79379754,  9.8129241 ,  9.83208877,  9.8512916 ,  9.87053269,\n",
       "         9.88981212,  9.90912995,  9.92848628,  9.94788118,  9.96731474,\n",
       "         9.98678703, 10.00629813, 10.02584813, 10.0454371 , 10.06506512,\n",
       "        10.08473229, 10.10443867, 10.12418436, 10.14396943, 10.16379396,\n",
       "        10.18365804, 10.20356175, 10.22350517, 10.24348839, 10.26351148,\n",
       "        10.28357454, 10.30367763, 10.32382086, 10.3440043 , 10.36422803,\n",
       "        10.38449214, 10.40479671, 10.42514184, 10.44552759, 10.46595406,\n",
       "        10.48642134, 10.5069295 , 10.52747863, 10.54806883, 10.56870017,\n",
       "        10.58937274, 10.61008662, 10.63084191, 10.65163869, 10.67247704,\n",
       "        10.69335706, 10.71427883, 10.73524244, 10.75624797, 10.77729552,\n",
       "        10.79838517, 10.819517  , 10.84069112, 10.8619076 , 10.88316654,\n",
       "        10.90446802, 10.92581213, 10.94719897, 10.96862862, 10.99010118,\n",
       "        11.01161672, 11.03317535, 11.05477715, 11.07642221, 11.09811063,\n",
       "        11.1198425 , 11.1416179 , 11.16343693, 11.18529968, 11.20720624,\n",
       "        11.2291567 , 11.25115117, 11.27318972, 11.29527245, 11.31739946,\n",
       "        11.33957083, 11.36178667, 11.38404706, 11.4063521 , 11.42870188,\n",
       "        11.4510965 , 11.47353605, 11.49602062, 11.51855032, 11.54112523,\n",
       "        11.56374545, 11.58641108, 11.60912222, 11.63187895, 11.65468138,\n",
       "        11.6775296 , 11.7004237 , 11.72336379, 11.74634997, 11.76938232,\n",
       "        11.79246095, 11.81558596, 11.83875744, 11.86197549, 11.88524021,\n",
       "        11.90855169, 11.93191005, 11.95531537, 11.97876776, 12.00226731,\n",
       "        12.02581413, 12.04940832, 12.07304997, 12.09673919, 12.12047607,\n",
       "        12.14426072, 12.16809325, 12.19197374, 12.21590231, 12.23987905,\n",
       "        12.26390407, 12.28797747, 12.31209936, 12.33626983, 12.36048898,\n",
       "        12.38475693, 12.40907378, 12.43343963, 12.45785458, 12.48231873,\n",
       "        12.50683221, 12.5313951 , 12.55600751, 12.58066955, 12.60538133,\n",
       "        12.63014295, 12.65495451, 12.67981613, 12.70472791, 12.72968995,\n",
       "        12.75470237, 12.77976527, 12.80487875, 12.83004294, 12.85525793,\n",
       "        12.88052383, 12.90584076, 12.93120882, 12.95662812, 12.98209877,\n",
       "        13.00762088, 13.03319455, 13.05881991, 13.08449706, 13.11022612,\n",
       "        13.13600718, 13.16184037, 13.1877258 , 13.21366357, 13.2396538 ,\n",
       "        13.26569661, 13.2917921 , 13.31794039, 13.34414159, 13.37039581,\n",
       "        13.39670317, 13.42306379, 13.44947777, 13.47594524, 13.5024663 ,\n",
       "        13.52904107, 13.55566967, 13.58235221, 13.60908881, 13.63587959,\n",
       "        13.66272466, 13.68962414, 13.71657814, 13.74358678, 13.77065019,\n",
       "        13.79776848, 13.82494176, 13.85217016, 13.87945379, 13.90679278,\n",
       "        13.93418724, 13.9616373 , 13.98914306, 14.01670466, 14.04432222,\n",
       "        14.07199585, 14.09972567, 14.12751181, 14.1553544 , 14.18325354,\n",
       "        14.21120937, 14.239222  , 14.26729156, 14.29541818, 14.32360197,\n",
       "        14.35184306]),\n",
       " 'bacterial_biomass': array([[2.50000000e-08, 2.51742153e-08, 2.53496447e-08, ...,\n",
       "         3.65915284e-06, 3.68465206e-06, 3.71032898e-06],\n",
       "        [1.66666667e-12, 1.67828102e-12, 1.68997631e-12, ...,\n",
       "         2.43943523e-10, 2.45643471e-10, 2.47355265e-10]]),\n",
       " 'cell_density': array([2.38732415e+09, 2.38732415e+09]),\n",
       " 'pool': 2,\n",
       " 'particle_lability': array([[150, 150]]),\n",
       " 'new_cells': 0.08333333333333333,\n",
       " 'varTemperature': True,\n",
       " 'vmax': 1.2000000000000002,\n",
       " 'km': 7.2,\n",
       " 'mortality': 2.5,\n",
       " 'schmidt_number': 1492.5373134328358}"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "UPDATED_PATCH"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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