Gillespie_MKIV.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "time step 0\n",
      "number phages: 500.0\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/opt/conda/lib/python3.7/site-packages/ipykernel_launcher.py:198: RuntimeWarning: divide by zero encountered in true_divide\n",
      "/opt/conda/lib/python3.7/site-packages/ipykernel_launcher.py:199: RuntimeWarning: divide by zero encountered in true_divide\n",
      "/opt/conda/lib/python3.7/site-packages/ipykernel_launcher.py:79: RuntimeWarning: invalid value encountered in true_divide\n",
      "/opt/conda/lib/python3.7/site-packages/ipykernel_launcher.py:80: RuntimeWarning: invalid value encountered in true_divide\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.11798288 0.09514748 0.07802094 0.05233112 0.09609897 0.10085633\n",
      " 0.13130353 0.06470029 0.13320647 0.13035205]\n",
      "chosen subpop: 5\n",
      "rx: 0.0\n",
      "time (s): 0.06423483065471516\n",
      "time step 1\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.92341818e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.06952965 0.1002045  0.09406953 0.12474437 0.14417177 0.\n",
      " 0.10224948 0.1002045  0.13599181 0.12883435]\n",
      "chosen subpop: 8\n",
      "rx: 0.0\n",
      "time (s): 0.11745655423659024\n",
      "time step 2\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.09265455e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.83912727e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [1.0475577e-10 1.0194353e-10 6.6790587e-11 5.2729411e-11 6.9602824e-11\n",
      " 1.0000000e+00 6.1166121e-11 9.3506820e-11 0.0000000e+00 9.7725175e-11]\n",
      "chosen subpop: 5\n",
      "rx: 1.0\n",
      "time (s): 0.12607772664862968\n",
      "time step 3\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.31861818e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.09029346 0.15124154 0.12866817 0.08126412 0.13431153 0.06433409\n",
      " 0.08916479 0.15349887 0.         0.10722348]\n",
      "chosen subpop: 1\n",
      "rx: 0.0\n",
      "time (s): 0.2506008467004122\n",
      "time step 4\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.74458182e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [5.21541818e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [6.9602824e-11 0.0000000e+00 9.9834356e-11 9.2100702e-11 7.1711997e-11\n",
      " 8.5773180e-11 6.1869176e-11 6.7493650e-11 1.0000000e+00 5.0620234e-11]\n",
      "chosen subpop: 8\n",
      "rx: 1.0\n",
      "time (s): 0.25537388512502635\n",
      "time step 5\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.89927273e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [9.15811801e-11 1.00000000e+00 1.01443763e-10 1.02852706e-10\n",
      " 7.74917630e-11 6.83336443e-11 9.65124716e-11 8.17185902e-11\n",
      " 8.45364681e-11 5.21308240e-11]\n",
      "chosen subpop: 1\n",
      "rx: 1.0\n",
      "time (s): 0.6388496740154568\n",
      "time step 6\n",
      "number phages: 500.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.0712963  0.12685186 0.08703704 0.0962963  0.08796296 0.06111111\n",
      " 0.13333334 0.12407408 0.08240741 0.12962963]\n",
      "chosen subpop: 1\n",
      "rx: 0.0\n",
      "time (s): 0.66644772188452\n",
      "time step 7\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.62909091e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [1.0003482e-10 1.0000000e+00 7.2560472e-11 8.1718590e-11 8.2423054e-11\n",
      " 9.0876702e-11 8.7354353e-11 6.1993410e-11 6.3402353e-11 9.1581180e-11]\n",
      "chosen subpop: 1\n",
      "rx: 1.0\n",
      "time (s): 0.8182345570255051\n",
      "time step 8\n",
      "number phages: 500.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.11337467 0.05048715 0.05845881 0.13020372 0.07263064 0.11426041\n",
      " 0.12666075 0.09477413 0.10983171 0.12931797]\n",
      "chosen subpop: 0\n",
      "rx: 0.0\n",
      "time (s): 0.9351865861202527\n",
      "time step 9\n",
      "number phages: 499.0\n",
      "prob rxn: [5.29847273e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.         0.09365559 0.12688822 0.13091642 0.12185297 0.07049346\n",
      " 0.10271903 0.11480362 0.13997985 0.09869084]\n",
      "chosen subpop: 4\n",
      "rx: 0.0\n",
      "time (s): 1.1489003046193176\n",
      "time step 10\n",
      "number phages: 498.0\n",
      "prob rxn: [2.86123636e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.67214545e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.0000000e+00 9.7022120e-11 5.1323293e-11 6.2572239e-11 1.0000000e+00\n",
      " 9.1397646e-11 8.9288472e-11 5.4135529e-11 6.1166121e-11 7.3118116e-11]\n",
      "chosen subpop: 4\n",
      "rx: 1.0\n",
      "time (s): 1.2187165504002173\n",
      "time step 11\n",
      "number phages: 499.0\n",
      "prob rxn: [3.84683636e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.         0.11135135 0.07027027 0.08864865 0.14054054 0.13945946\n",
      " 0.13621622 0.13405405 0.10702703 0.07243244]\n",
      "chosen subpop: 9\n",
      "rx: 0.0\n",
      "time (s): 1.2690653277975583\n",
      "time step 12\n",
      "number phages: 498.0\n",
      "prob rxn: [3.54938182e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [2.31796364e-11 5.15151515e-01 4.84848485e-01]\n",
      "subpop weights: [1.0000000e+00 7.6633408e-11 4.1480472e-11 8.0851763e-11 8.0148707e-11\n",
      " 9.5615994e-11 7.3118116e-11 9.4912939e-11 7.5227297e-11 0.0000000e+00]\n",
      "chosen subpop: 0\n",
      "rx: 1.0\n",
      "time (s): 1.288563930961248\n",
      "time step 13\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [5.11701818e-11 5.15151515e-01 4.84848485e-01]\n",
      "subpop weights: [9.8625885e-11 8.8763295e-11 8.7354353e-11 9.0172231e-11 6.4106824e-11\n",
      " 9.1581180e-11 9.5807993e-11 3.8041414e-11 1.0144376e-10 1.0000000e+00]\n",
      "chosen subpop: 9\n",
      "rx: 1.0\n",
      "time (s): 1.5113908107566048\n",
      "time step 14\n",
      "number phages: 500.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.13448608 0.05571566 0.09221902 0.10951009 0.13064362 0.0902978\n",
      " 0.10566763 0.13256484 0.08549472 0.06340058]\n",
      "chosen subpop: 5\n",
      "rx: 0.0\n",
      "time (s): 1.6717670966948945\n",
      "time step 15\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [2.46778182e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.13849764 0.05985915 0.14788732 0.09624413 0.12910798 0.\n",
      " 0.09037559 0.09154929 0.0798122  0.16666666]\n",
      "chosen subpop: 9\n",
      "rx: 0.0\n",
      "time (s): 1.7841021579877698\n",
      "time step 16\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.09265455e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.30996364e-11 5.15151515e-01 4.84848485e-01]\n",
      "subpop weights: [7.3821171e-11 5.6244703e-11 6.5384469e-11 9.6319064e-11 7.1711997e-11\n",
      " 0.0000000e+00 8.6476236e-11 8.3663999e-11 6.7493650e-11 1.0000000e+00]\n",
      "chosen subpop: 9\n",
      "rx: 1.0\n",
      "time (s): 1.8090332190655247\n",
      "time step 17\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.35490909e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [9.5103529e-11 5.0721882e-11 9.1581180e-11 1.0144376e-10 8.1014119e-11\n",
      " 1.0000000e+00 5.9879997e-11 5.0017410e-11 5.7062119e-11 7.6787292e-11]\n",
      "chosen subpop: 5\n",
      "rx: 1.0\n",
      "time (s): 2.1039772892519473\n",
      "time step 18\n",
      "number phages: 500.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.12359551 0.0692884  0.08052435 0.07771536 0.09363296 0.10393259\n",
      " 0.13389514 0.08988765 0.13857679 0.08895131]\n",
      "chosen subpop: 1\n",
      "rx: 0.0\n",
      "time (s): 2.144692264741238\n",
      "time step 19\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [5.40734545e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.12470588 0.         0.11411764 0.05882353 0.15882352 0.09999999\n",
      " 0.07176471 0.12117647 0.09529412 0.1552941 ]\n",
      "chosen subpop: 4\n",
      "rx: 0.0\n",
      "time (s): 2.1649999525554966\n",
      "time step 20\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.11476364e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [2.31796364e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [5.8353877e-11 0.0000000e+00 5.9760003e-11 8.5773180e-11 1.0000000e+00\n",
      " 5.1323293e-11 8.1554825e-11 6.8196705e-11 4.6401882e-11 5.8353877e-11]\n",
      "chosen subpop: 4\n",
      "rx: 1.0\n",
      "time (s): 2.3416576101468123\n",
      "time step 21\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.88712727e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [6.7629173e-11 1.0000000e+00 6.8333644e-11 6.6924709e-11 3.5928000e-11\n",
      " 6.5515766e-11 4.9312943e-11 1.0426165e-10 8.8763295e-11 3.5223529e-11]\n",
      "chosen subpop: 1\n",
      "rx: 1.0\n",
      "time (s): 2.5294715828114223\n",
      "time step 22\n",
      "number phages: 500.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.1043956  0.07509157 0.07783882 0.11355311 0.13369963 0.0952381\n",
      " 0.11080586 0.12362637 0.0934066  0.07234433]\n",
      "chosen subpop: 8\n",
      "rx: 0.0\n",
      "time (s): 2.5692832309048645\n",
      "time step 23\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.91941818e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [8.5945417e-11 7.2560472e-11 3.5223529e-11 7.4673878e-11 1.0355718e-10\n",
      " 9.9330350e-11 7.6082828e-11 8.1718590e-11 1.0000000e+00 5.7766587e-11]\n",
      "chosen subpop: 8\n",
      "rx: 1.0\n",
      "time (s): 2.596372669465805\n",
      "time step 24\n",
      "number phages: 500.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.11209965 0.12633453 0.10053382 0.12544484 0.08540926 0.07117438\n",
      " 0.0658363  0.09341638 0.11743774 0.10231318]\n",
      "chosen subpop: 3\n",
      "rx: 0.0\n",
      "time (s): 2.6621992676434982\n",
      "time step 25\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.64523636e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.06868687 0.13232324 0.08181819 0.         0.13434345 0.1050505\n",
      " 0.1010101  0.12828283 0.13939394 0.10909092]\n",
      "chosen subpop: 5\n",
      "rx: 0.0\n",
      "time (s): 3.0508811825582773\n",
      "time step 26\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [2.82501818e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.85323636e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [6.1869176e-11 9.7022120e-11 4.2886590e-11 1.0000000e+00 8.7882347e-11\n",
      " 0.0000000e+00 8.2257881e-11 9.7725175e-11 7.5930352e-11 6.2572239e-11]\n",
      "chosen subpop: 3\n",
      "rx: 1.0\n",
      "time (s): 3.239974286794877\n",
      "time step 27\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.13716364e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.1029724  0.11995754 0.12738854 0.13163483 0.07218684 0.\n",
      " 0.15180467 0.11571126 0.12208069 0.05626327]\n",
      "chosen subpop: 4\n",
      "rx: 0.0\n",
      "time (s): 3.3702487863761363\n",
      "time step 28\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.44072727e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [4.52727273e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [8.29609437e-11 1.02646586e-10 6.25722391e-11 5.20263520e-11\n",
      " 0.00000000e+00 1.00000000e+00 8.22578811e-11 4.00743536e-11\n",
      " 6.18691764e-11 4.56988232e-11]\n",
      "chosen subpop: 5\n",
      "rx: 1.0\n",
      "time (s): 3.456850900447906\n",
      "time step 29\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [5.08072727e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.15408807 0.11530399 0.12264151 0.14675054 0.         0.12473796\n",
      " 0.07966457 0.05345912 0.05765199 0.1457023 ]\n",
      "chosen subpop: 3\n",
      "rx: 0.0\n",
      "time (s): 3.748196973656604\n",
      "time step 30\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.20130909e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [2.86123636e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [5.1323293e-11 4.5698823e-11 5.6244703e-11 1.0000000e+00 0.0000000e+00\n",
      " 8.0851763e-11 4.3589646e-11 7.9445645e-11 7.8742589e-11 5.7650825e-11]\n",
      "chosen subpop: 3\n",
      "rx: 1.0\n",
      "time (s): 3.8159654484482246\n",
      "time step 31\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.88312727e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [9.1581180e-11 5.2835292e-11 5.4948705e-11 9.0172231e-11 1.0000000e+00\n",
      " 7.7491763e-11 9.4399058e-11 3.9450353e-11 8.5240939e-11 5.7062119e-11]\n",
      "chosen subpop: 4\n",
      "rx: 1.0\n",
      "time (s): 4.059937159317308\n",
      "time step 32\n",
      "number phages: 500.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.09473684 0.10263158 0.12719299 0.11491229 0.05350877 0.07368421\n",
      " 0.11842105 0.13070175 0.08596491 0.09824562]\n",
      "chosen subpop: 1\n",
      "rx: 0.0\n",
      "time (s): 4.229791131734244\n",
      "time step 33\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.81454545e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [8.6649882e-11 1.0000000e+00 3.5928000e-11 8.2423054e-11 7.6082828e-11\n",
      " 9.5807993e-11 1.0144376e-10 4.7903997e-11 9.7921407e-11 9.7216943e-11]\n",
      "chosen subpop: 1\n",
      "rx: 1.0\n",
      "time (s): 4.296042736640435\n",
      "time step 34\n",
      "number phages: 500.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.063279   0.10834133 0.12559924 0.14285715 0.0776606  0.10162991\n",
      " 0.10738256 0.11505274 0.05944391 0.09875359]\n",
      "chosen subpop: 1\n",
      "rx: 0.0\n",
      "time (s): 4.296760576993237\n",
      "time step 35\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.53636364e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.14994828 0.         0.09720785 0.11065149 0.15305066 0.1385729\n",
      " 0.08169597 0.07652533 0.07342295 0.11892451]\n",
      "chosen subpop: 2\n",
      "rx: 0.0\n",
      "time (s): 4.344159840305846\n",
      "time step 36\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.11476364e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [4.67214545e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [8.01487071e-11 1.00000000e+00 0.00000000e+00 7.73364636e-11\n",
      " 6.39783504e-11 9.13976464e-11 8.36639993e-11 1.04052704e-10\n",
      " 6.81967052e-11 5.27294111e-11]\n",
      "chosen subpop: 1\n",
      "rx: 1.0\n",
      "time (s): 4.4050296858581905\n",
      "time step 37\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.85083636e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.08208093 0.11791908 0.         0.11676302 0.11445087 0.10404625\n",
      " 0.14219654 0.11907515 0.1317919  0.07167631]\n",
      "chosen subpop: 9\n",
      "rx: 0.0\n",
      "time (s): 4.424613227274332\n",
      "time step 38\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.51316364e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.51316364e-11 5.15151515e-01 4.84848485e-01]\n",
      "subpop weights: [4.0074354e-11 4.9214115e-11 1.0000000e+00 7.1711997e-11 7.8742589e-11\n",
      " 1.0053741e-10 9.7022120e-11 5.2026352e-11 5.4135529e-11 0.0000000e+00]\n",
      "chosen subpop: 2\n",
      "rx: 1.0\n",
      "time (s): 4.538072108168351\n",
      "time step 39\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.08472727e-11 5.15151515e-01 4.84848485e-01]\n",
      "subpop weights: [9.7921407e-11 1.0355718e-10 9.0172231e-11 8.1718590e-11 4.4381648e-11\n",
      " 7.1151529e-11 6.1288939e-11 9.6512472e-11 4.8608471e-11 1.0000000e+00]\n",
      "chosen subpop: 9\n",
      "rx: 1.0\n",
      "time (s): 4.992739681413701\n",
      "time step 40\n",
      "number phages: 500.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.09349594 0.14227644 0.06808943 0.13922766 0.08028456 0.09756099\n",
      " 0.08841464 0.13414635 0.09756099 0.05894309]\n",
      "chosen subpop: 7\n",
      "rx: 0.0\n",
      "time (s): 5.437019025896851\n",
      "time step 41\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.17345455e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.09876543 0.10082304 0.15020576 0.08024691 0.13580246 0.08950617\n",
      " 0.12654321 0.         0.10390947 0.11419752]\n",
      "chosen subpop: 2\n",
      "rx: 0.0\n",
      "time (s): 5.77282721102092\n",
      "time step 42\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [5.10676364e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [2.24552727e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.11098527 0.14835785 0.         0.09513023 0.15175538 0.13023782\n",
      " 0.08607021 0.         0.10985278 0.16761042]\n",
      "chosen subpop: 4\n",
      "rx: 0.0\n",
      "time (s): 5.996633368210796\n",
      "time step 43\n",
      "number phages: 497.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.75912727e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.12058182e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.87963636e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [5.1571056e-11 3.1924942e-11 5.0000000e-01 2.8767528e-11 5.0000000e-01\n",
      " 4.1397174e-11 3.5082354e-11 0.0000000e+00 4.6308707e-11 4.8764472e-11]\n",
      "chosen subpop: 4\n",
      "rx: 1.0\n",
      "time (s): 6.1315578800979615\n",
      "time step 44\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.51316364e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.20130909e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [6.11661208e-11 8.50701107e-11 0.00000000e+00 7.45242409e-11\n",
      " 9.28037647e-11 3.79651761e-11 1.04052704e-10 1.00000000e+00\n",
      " 9.91312865e-11 4.71049415e-11]\n",
      "chosen subpop: 7\n",
      "rx: 1.0\n",
      "time (s): 6.2746456131472215\n",
      "time step 45\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.50007273e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.08062828 0.1277487  0.         0.1329843  0.1434555  0.0816754\n",
      " 0.10680629 0.14136127 0.05968586 0.12565446]\n",
      "chosen subpop: 3\n",
      "rx: 0.0\n",
      "time (s): 6.307161683660985\n",
      "time step 46\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.96189091e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [3.54938182e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [5.6244703e-11 5.2729411e-11 1.0000000e+00 0.0000000e+00 8.0851763e-11\n",
      " 6.8899761e-11 6.6790587e-11 6.8899761e-11 7.9445645e-11 8.0148707e-11]\n",
      "chosen subpop: 2\n",
      "rx: 1.0\n",
      "time (s): 6.7012278454083765\n",
      "time step 47\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.01214545e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.1390593  0.08793457 0.12474439 0.         0.11451943 0.14417179\n",
      " 0.06748466 0.06748466 0.14928426 0.10531697]\n",
      "chosen subpop: 7\n",
      "rx: 0.0\n",
      "time (s): 7.078470954503832\n",
      "time step 48\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.09265455e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.62181818e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.1740196  0.11519607 0.12990196 0.         0.08455882 0.0870098\n",
      " 0.15318626 0.         0.16666666 0.08946078]\n",
      "chosen subpop: 6\n",
      "rx: 0.0\n",
      "time (s): 7.07889681060485\n",
      "time step 49\n",
      "number phages: 497.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [2.02414545e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.33745455e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [4.44589091e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.18844566 0.15543328 0.11691885 0.         0.09766162 0.18431912\n",
      " 0.         0.         0.10866575 0.1485557 ]\n",
      "chosen subpop: 2\n",
      "rx: 0.0\n",
      "time (s): 7.260108453989542\n",
      "time step 50\n",
      "number phages: 496.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.93192727e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [4.18443636e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [2.84974545e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [4.36480000e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [2.8943058e-11 1.7272470e-11 3.3333331e-01 0.0000000e+00 1.7505880e-11\n",
      " 2.7309176e-11 3.3333331e-01 3.3333331e-01 1.3071058e-11 3.2444235e-11]\n",
      "chosen subpop: 6\n",
      "rx: 1.0\n",
      "time (s): 7.274094130349334\n",
      "time step 51\n",
      "number phages: 497.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [2.27716364e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [4.77120000e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.44589091e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [5.1921883e-11 2.1400236e-11 0.0000000e+00 5.0000000e-01 4.5256236e-11\n",
      " 4.5607060e-11 4.9115295e-11 5.0000000e-01 4.8764472e-11 2.3855999e-11]\n",
      "chosen subpop: 3\n",
      "rx: 1.0\n",
      "time (s): 7.2788821008722575\n",
      "time step 52\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.23752727e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.81701818e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "subpop weights: [0.09234508 0.10206562 0.         0.13244228 0.15674363 0.10085054\n",
      " 0.14945322 0.         0.11907655 0.14702308]\n",
      "chosen subpop: 9\n",
      "rx: 0.0\n",
      "time (s): 7.334129173918654\n",
      "time step 53\n",
      "number phages: 497.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.91570909e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.21694545e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.26516364e-11 5.15151515e-01 4.84848485e-01]\n",
      "subpop weights: [4.8062821e-11 2.2101881e-11 5.0000000e-01 4.8062821e-11 2.8416705e-11\n",
      " 2.9820001e-11 4.7010350e-11 0.0000000e+00 2.1400236e-11 5.0000000e-01]\n",
      "chosen subpop: 2\n",
      "rx: 1.0\n",
      "time (s): 7.446083134751764\n",
      "time step 54\n",
      "number phages: 498.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [3.36829091e-11 5.15151515e-01 4.84848485e-01]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [4.99810909e-11 5.15151515e-01 4.84848485e-01]\n",
      "subpop weights: [7.17119975e-11 7.94456445e-11 9.70221195e-11 1.02646586e-10\n",
      " 9.91312865e-11 4.07774127e-11 1.04052704e-10 0.00000000e+00\n",
      " 9.56159943e-11 1.00000000e+00]\n",
      "chosen subpop: 9\n",
      "rx: 1.0\n",
      "time (s): 7.536534512337842\n",
      "time step 55\n",
      "number phages: 499.0\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n",
      "prob rxn: [1.]\n"
     ]
    }
   ],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "import random\n",
    "#np.show_config() use threads?\n",
    "\n",
    "def update_data(sub_pops, max_receptors):\n",
    "    #rows that says how many bacteria have nonperm\n",
    "    #columns that say how many bacteria have perm\n",
    "    #this will be MxM sized matrix\n",
    "    #flatten this matrix into array?\n",
    "    # -- > row i and col j --> number bacteria with\n",
    "    data = np.zeros((max_receptors,max_receptors),dtype=np.int32)\n",
    "    sub_pop_keys = list(sub_pops.keys())\n",
    "\n",
    "    for i in sub_pop_keys:\n",
    "        pop = sub_pops[i]\n",
    "        receptors = pop[:,-1] #the last column of pop is number of receptors\n",
    "        #0 == free receptors\n",
    "        #1 == nonperm receptors\n",
    "        #2 == perm receptors\n",
    "        #3 == number of receptors for that bacteria\n",
    "        species, count = np.unique(pop[:,1:3], axis = 0, return_counts = True)\n",
    "        for s in enumerate(species):\n",
    "            spc = s[1]\n",
    "            i = int(spc[0]) #nonperm bounded\n",
    "            j = int(spc[1]) #perm bounded\n",
    "            data[i,j] = count[s[0]]\n",
    "    return data;\n",
    "\n",
    "#suppose m receptors\n",
    "#suppose x bacteria\n",
    "#suppose y phages\n",
    "#each bacteria may have n phages bound to it\n",
    "#each bacteria may have n' phages permanently bound to it\n",
    "#n+n'<=m\n",
    "\n",
    "#initialize an array containing all the available bacteria and their receptors\n",
    "def initiate_bacteria(num_bacteria, receptors):\n",
    "    #different rows represent different bacteria\n",
    "    #different columns represent receptor freedom\n",
    "    #3 states of receptor freedom\n",
    "    #0 == free\n",
    "    #1 == nonperm bounded\n",
    "    #2 == perm bounded\n",
    "    #The sum of these must be less than or equal to m\n",
    "    #m must be less than or equal to M\n",
    "    M = receptors\n",
    "    #each bacteria can have a stochastic number of m receptors less than or equal to M\n",
    "    #A healthy, non phage challenged bacteria may have up to 150+ receptors\n",
    "    m_rows = np.random.randint(low = 50, high = 150, size = (num_bacteria,1),dtype=np.int32) #generates random number of receptors\n",
    "    free_m = m_rows\n",
    "    non_perm_m = np.zeros((num_bacteria,1), dtype = np.int32)\n",
    "    perm_m = np.zeros((num_bacteria,1), dtype=np.int32)\n",
    "\n",
    "    pop = np.hstack((free_m,non_perm_m))\n",
    "    pop = np.hstack((pop,perm_m))\n",
    "    pop = np.hstack((pop,m_rows))\n",
    "    #the last column of pop will tell you the number of receptors for each bacteria\n",
    "    #when we update m, it must not be lower than the sum of the first 3 columns of pop for each bacteria\n",
    "    return pop;\n",
    "\n",
    "#for large numbers of bacteria, we must divide population into subpops\n",
    "def define_pop(num_bacteria, receptors):\n",
    "    #divide bacteria population into subpops, each size 100,000\n",
    "    num_bacteria = int(num_bacteria)\n",
    "    n = num_bacteria/100000\n",
    "    n = int(n)\n",
    "    sub_pops = {}\n",
    "    for i in range(n):\n",
    "        sub_pops[i] = initiate_bacteria(num_bacteria, receptors)\n",
    "\n",
    "    return sub_pops;\n",
    "\n",
    "def prob_matrix(P0,rx1,rx2,rx3,N,k1,k2,k3,MOI,pop):\n",
    "    reactions = np.stack((rx1,rx2,rx3),axis=1)\n",
    "    P = P0*reactions\n",
    "    p_choose1 = P[:,0]/np.nansum(P[:,0])\n",
    "    p_choose2 = P[:,1]/np.nansum(P[:,1])\n",
    "    p_choose3 = P[:,2]/np.nansum(P[:,2])\n",
    "    choices_i = {}\n",
    "    #randomly choose from 0 to N for each reaction if reactions are possible:\n",
    "    if np.nansum(P[:,0]) != 0:\n",
    "        chooser1 = np.random.choice(list(range(0,N)),p = p_choose1)\n",
    "        #exception of impossible indices\n",
    "        choices_i[0] = chooser1\n",
    "    if np.nansum(P[:,1]) != 0:\n",
    "        chooser2 = np.random.choice(list(range(0,N)),p = p_choose2)\n",
    "        #exception of impossible indices\n",
    "        choices_i[1] = chooser2\n",
    "    if np.nansum(P[:,2]) != 0:\n",
    "        chooser3 = np.random.choice(list(range(0,N)),p = p_choose3)\n",
    "        #exception of impossible indices\n",
    "        choices_i[2] = chooser3\n",
    "\n",
    "    prob_ind = list(range(len(choices_i)))\n",
    "    p_choose_f = []\n",
    "    for u in prob_ind:\n",
    "        p_choose_f.append(P[:,u][choices_i[u]])\n",
    "\n",
    "    p_choose_f = np.array(p_choose_f)\n",
    "    p_choose_f = p_choose_f/np.nansum(p_choose_f)\n",
    "    print('prob rxn: {}'.format(p_choose_f))\n",
    "    choosej = np.random.choice(prob_ind, p = p_choose_f)\n",
    "    \n",
    "    j_f = choosej  #which reaction on the bacteria will occur (r1,r2,r3)\n",
    "    i_f = choices_i[choosej] #this is the row index of the selected bacteria\n",
    "    bact = pop[i_f]\n",
    "    if j_f == 0:\n",
    "        w = MOI*k1*bact[0]\n",
    "    if j_f == 1:\n",
    "        w = k2*bact[1]\n",
    "    if j_f == 2:\n",
    "        w = k3*bact[2]\n",
    "    return  [j_f, i_f, w];\n",
    "\n",
    "\n",
    "def gillespie_reaction_weights(sub_pops,num_phages,tau,MOI,k1,k2,k3):\n",
    "    #calculate P0\n",
    "\n",
    "    candidates = np.zeros((len(sub_pops),3),dtype=np.float32) #sized 12000 max\n",
    "    reactions = 0\n",
    "    for i in range(len(sub_pops)):\n",
    "        pop = sub_pops[i]\n",
    "        N = pop.shape[0]\n",
    "        rx1 = np.nansum(pop[:,0])*MOI*k1\n",
    "        rx2 = np.nansum(pop[:,1])*k2\n",
    "        rx3 = np.nansum(pop[:,1])*k3\n",
    "        reactions += (rx1+rx2+rx3)\n",
    "\n",
    "    del rx1, rx2, rx3, pop\n",
    "\n",
    "    P0 = np.exp(-tau*reactions)\n",
    "\n",
    "    for i in range(len(sub_pops)):\n",
    "        pop = sub_pops[i]\n",
    "        N = pop.shape[0]\n",
    "        rx1 = pop[:,0]*MOI*k1\n",
    "        rx2 = pop[:,1]*k2\n",
    "        rx3 = pop[:,1]*k3\n",
    "        candidates[i] = prob_matrix(P0,rx1,rx2,rx3,N,k1,k2,k3,MOI,pop)\n",
    "\n",
    "    del rx1, rx2, rx3, pop\n",
    "    #for each subpop, choose the a candidate bacteria\n",
    "    #for each bacteria, choose the heaviest reaction on each\n",
    "    #choose the heaviest bacteria\n",
    "    weights = candidates[:,2]/np.nansum(candidates[:,2])\n",
    "    print('subpop weights: {}'.format(weights))\n",
    "    bacteria_ind = np.random.choice(range(0,len(weights)), p=weights)\n",
    "    print('chosen subpop: {}'.format(bacteria_ind))\n",
    "    #bacteria_ind is both the subpop index chosen, and location of values in candidates\n",
    "    bacteria = candidates[bacteria_ind]\n",
    "    pop = sub_pops[bacteria_ind]\n",
    "    j_f = bacteria[0] #which reaction is occuring\n",
    "    i_f = bacteria[1] #which bacteria in the chosen subpop\n",
    "    i_f = int(i_f)\n",
    "    bact = pop[i_f]\n",
    "    print('rx: {}'.format(j_f))\n",
    "    if j_f == 0:  #rx1 occurs\n",
    "        bact[0]-=1\n",
    "        bact[1]+=1\n",
    "        num_phages-=1\n",
    "    if j_f == 1:  #rx2 occurs\n",
    "        bact[1]-=1\n",
    "        bact[0]+=1\n",
    "        num_phages+=1\n",
    "    if j_f == 2:   #rx3 occurs\n",
    "        bact[1]-=1\n",
    "        bact[2]+=1\n",
    "    #update\n",
    "    pop[i_f] = bact\n",
    "    sub_pops[bacteria_ind] = pop\n",
    "    del bact, pop\n",
    "    return sub_pops,num_phages;\n",
    "\n",
    "def gillespie_time(pop,MOI,num_phages,k1,k2,k3): #returns a tau for each subpop\n",
    "    #receives subpop...  3x100000 sized population matrix\n",
    "    #find smallest tau for each subpop\n",
    "    N = pop.shape[0]\n",
    "    tau_j = np.random.uniform(size=(N,3))\n",
    "\n",
    "    rx1 = pop[:,0]*num_phages*k1\n",
    "    rx2 = pop[:,1]*k2\n",
    "    rx3 = pop[:,2]*k3\n",
    "    #we must decide which reactions are possible for a_u\n",
    "    #find any impossible reactions and exclude them from analysis and choice\n",
    "    #reactions that are impossible are those that have no reactants\n",
    "    #thus au = hu*ku == 0\n",
    "    #check rx1\n",
    "    inclusion_r1 = np.where(rx1!=0)\n",
    "    #check rx2\n",
    "    inclusion_r2 = np.where(rx2!=0)\n",
    "    #check rx3\n",
    "    inclusion_r3 = np.where(rx3!=0)\n",
    "    #each tau is weighted by its respective reaction for each bacteria\n",
    "    tau_j[:,0] = (1/rx1) * np.log(1/(tau_j[:,0]))\n",
    "    #issue:  if X molecules of species S == 0, then tau--> -inf\n",
    "    tau_j[:,1] = (1/rx2) * np.log(1/tau_j[:,1])\n",
    "    tau_j[:,2] = (1/rx3) * np.log(1/tau_j[:,2])\n",
    "    #if tau == -inf --> np.nan\n",
    "    tau_j[:,0][np.where(tau_j[:,0] == -np.inf)] = np.nan\n",
    "    tau_j[:,1][np.where(tau_j[:,1] == -np.inf)] = np.nan\n",
    "    tau_j[:,2][np.where(tau_j[:,2] == -np.inf)] = np.nan\n",
    "    #only choose those that are not np.nan because they are impossible\n",
    "    min_i = np.nanmin(tau_j,axis=1)  #set of all mins for each bacteria\n",
    "    i = np.nanargmin(min_i) #min of all mins, the index of this is within N --> says what row it belongs to\n",
    "    j = np.nanargmin(tau_j[i])\n",
    "    #print(min_i)\n",
    "    mintau = tau_j[i,j] #final tau for all calculations\n",
    "\n",
    "    return mintau;\n",
    "\n",
    "\n",
    "def gillespie(sub_pops,num_phages,k1,k2,k3):\n",
    "    #k1 = assoicate\n",
    "    #k2 = dissociate\n",
    "    #k3 = perm\n",
    "\n",
    "    #generate set of 3 taus for each bacteria based on receptor status\n",
    "    #must do this for all subpops\n",
    "    #define new dictionary for time respective to each sub_pops\n",
    "    sub_pop_keys = list(sub_pops.keys())\n",
    "    N = 0\n",
    "    for t in sub_pop_keys:\n",
    "        N+=list(sub_pops[t].shape)[0] #number of bacteria each iteration\n",
    "        #in the future, bacteria may die and be unavailable\n",
    "    MOI = num_phages/N\n",
    "    phages = MOI\n",
    "\n",
    "    tau = np.zeros((len(sub_pop_keys)))\n",
    "    for t in sub_pop_keys:\n",
    "        tau[t] = gillespie_time(sub_pops[t],MOI,num_phages,k1,k2,k3)\n",
    "    tau = np.nanmin(tau) #find minimum tau from subpops\n",
    "    #mutate pop\n",
    "    sub_pops,num_phages = gillespie_reaction_weights(sub_pops,num_phages,tau,MOI,k1,k2,k3)\n",
    "    return sub_pops,num_phages,tau;\n",
    "\n",
    "def run_gillespie():\n",
    "    tot_time = 10000\n",
    "    num_bacteria = 1e+6\n",
    "    num_phages = num_bacteria*5e-4\n",
    "    k1,k2,k3 = 1.2e-11,8.5e-4,8e-4\n",
    "    max_receptors = 100\n",
    "    time = np.zeros((tot_time))\n",
    "    data_all = np.zeros((tot_time,max_receptors,max_receptors),dtype=np.int32)\n",
    "    free_phages = np.zeros((tot_time),dtype=np.int32)\n",
    "\n",
    "    sub_pops = define_pop(num_bacteria, max_receptors)\n",
    "\n",
    "\n",
    "    for t in range(tot_time):\n",
    "        print('time step {}'.format(t))\n",
    "        print('number phages: {}'.format(num_phages))\n",
    "        sub_pops,num_phages,tau = gillespie(sub_pops,num_phages,k1,k2,k3)\n",
    "        data_all[t] = update_data(sub_pops, max_receptors)\n",
    "        free_phages[t] = num_phages\n",
    "        time[t] = time[t-1]+tau\n",
    "        print('time (s): {}'.format(time[t]))\n",
    "        if num_phages == 0:\n",
    "            break;\n",
    "    return data_all,free_phages,time\n",
    "\n",
    "data_all,free_phages,time = run_gillespie()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'time' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-4-8e6486dae6cf>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mplt\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplot\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtime\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mfree_phages\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0mplt\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplot\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtime\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mdata_all\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m10000\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0mplt\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshow\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mNameError\u001b[0m: name 'time' is not defined"
     ]
    }
   ],
   "source": [
    "\n",
    "plt.plot(time,free_phages)\n",
    "plt.plot(time,data_all[0:10000,0,1])\n",
    "plt.show()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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