trapping/notebooks/cross-sections.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-04-08T18:49+0000",
     "start_time": "2018-04-08T18:49+0000"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "b3666d93-1a9f-47f6-b272-8c9cde5eb9eb",
       "version_major": 2,
       "version_minor": 0
      },
      "method": "display_data"
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "0e65aaab-812e-45f3-98df-43ed93255c5e",
       "version_major": 2,
       "version_minor": 0
      },
      "method": "display_data"
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%classpath add jar ../build/install/trapping/lib/commons-math3-3.6.1.jar\n",
    "%classpath add jar ../build/install/trapping/lib/trapping-dev.jar"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2018-04-08T18:58+0000",
     "start_time": "2018-04-08T18:58+0000"
    }
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "8e62373b-9e28-4669-937f-06f5c908a4bd",
       "version_major": 2,
       "version_minor": 0
      },
      "method": "display_data"
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "scatter = inr.numass.trapping.Scatter.INSTANCE\n",
    "\n",
    "def e = (1..20) // energy in keV\n",
    "\n",
    "factor = 1e-22\n",
    "sigmaEl = e.collect{scatter.sigmael(it*1000)/factor}\n",
    "sigmaIon = e.collect{scatter.sigmaion(it*1000)/factor}\n",
    "sigmaExc = e.collect{scatter.sigmaexc(it*1000)/factor}\n",
    "\n",
    "def plot = new Plot(logY: true, yLogBase: 10)\n",
    "plot << new Line(x: e, y: sigmaEl, displayName: \"Elastic\")\n",
    "plot << new Line(x: e, y: sigmaIon, displayName: \"Ionization\")\n",
    "plot << new Line(x: e, y: sigmaExc, displayName: \"Excitation\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "E(keV)\telastic\tion\texc\n",
      "12.0\t0.43948540252301355\t2.7362696996880764\t2.2754271467658227\n",
      "12.1\t0.4360219815420227\t2.716347129996631\t2.259247553470829\n",
      "12.2\t0.4326153394877464\t2.6967291910800784\t2.2433117665045716\n",
      "12.3\t0.42926409223681455\t2.6774088086825643\t2.227614186457129\n",
      "12.4\t0.42596690029168804\t2.6583791281775273\t2.212149386181278\n",
      "12.5\t0.4227224669965498\t2.639633506055748\t2.1969121041685504\n",
      "12.6\t0.41952953683810995\t2.621165501807934\t2.1818972382301722\n",
      "12.7\t0.4163868938266485\t2.602968870180603\t2.1670998394665926\n",
      "12.8\t0.4132933599529065\t2.585037553785318\t2.1525151065102723\n",
      "12.9\t0.4102477937167139\t2.567365676042546\t2.138138380027344\n",
      "13.0\t0.4072490887234942\t2.5499475344425586\t2.123965137464613\n",
      "13.1\t0.4042961723450181\t2.532777594106803\t2.1099909880291814\n",
      "13.2\t0.40138800444100226\t2.515850481634202\t2.096211667888705\n",
      "13.3\t0.3985235761383543\t2.4991609792177183\t2.082623035581028\n",
      "13.4\t0.3957019086650494\t2.4827040190174023\t2.069221067622563\n",
      "13.5\t0.39292205223581\t2.466474677776929\t2.0560018543054204\n",
      "13.6\t0.39018308498692494\t2.4504681716713828\t2.042961595673853\n",
      "13.7\t0.3874841119576961\t2.434679851374739\t2.0300965976711156\n",
      "13.8\t0.3848242641161482\t2.419105197336177\t2.0174032684483527\n",
      "13.9\t0.3822026974267757\t2.403739815254919\t2.00487811482759\n",
      "14.0\t0.3796185919582249\t2.3885794317439313\t1.9925177389113418\n",
      "14.1\t0.3770711510289289\t2.373619890173301\t1.9803188348317768\n",
      "14.2\t0.3745596003888268\t2.358857146684646\t1.9682781856327505\n",
      "14.3\t0.3720831874354002\t2.3442872663683785\t1.9563926602783916\n",
      "14.4\t0.36964118046236066\t2.32990641959609\t1.9446592107822769\n",
      "14.5\t0.36723286793941123\t2.315710878500726\t1.9330748694515214\n",
      "14.6\t0.3648575578215951\t2.3016970135976464\t1.9216367462404509\n",
      "14.7\t0.36251457688682004\t2.287861290540006\t1.910342026208781\n",
      "14.8\t0.3602032701002296\t2.274200267002247\t1.8991879670794969\n",
      "14.9\t0.357923000004158\t2.26071058968582\t1.8881718968918926\n",
      "15.0\t0.3556731461324769\t2.2473889914415754\t1.8772912117454528\n",
      "15.1\t0.353453104448203\t2.234232288503513\t1.8665433736304802\n",
      "15.2\t0.35126228680329497\t2.221237377828907\t1.8559259083415982\n",
      "15.3\t0.3491001204196282\t2.2084012345400286\t1.845436403470438\n",
      "15.4\t0.3469660473901797\t2.1957209094629615\t1.835072506474014\n",
      "15.5\t0.3448595241995173\t2.1831935267592297\t1.824831922815469\n",
      "15.6\t0.3427800212627204\t2.170816281646157\t1.8147124141740314\n",
      "15.7\t0.34072702248191666\t2.158586438202101\t1.8047117967211865\n",
      "15.8\t0.33870002481965195\t2.1465013272528792\t1.7948279394602165\n",
      "15.9\t0.3366985378883526\t2.134558344335901\t1.7850587626263867\n",
      "16.0\t0.33472208355517563\t2.122754947738674\t1.7754022361452126\n",
      "16.1\t0.33277019556158083\t2.111088656608532\t1.7658563781463463\n",
      "16.2\t0.33084241915698676\t2.0995570491305764\t1.7564192535307461\n",
      "16.3\t0.32893831074590485\t2.0881577607709536\t1.7470889725889123\n",
      "16.4\t0.3270574375479805\t2.0768884825827687\t1.7378636896680617\n",
      "16.5\t0.3251993772703896\t2.0657469595720115\t1.7287416018862318\n",
      "16.6\t0.32336371779207285\t2.054730989121034\t1.7197209478913829\n",
      "16.7\t0.3215500568593091\t2.043838419467228\t1.7108000066636726\n",
      "16.8\t0.31975800179215863\t2.0330671482346325\t1.7019770963591483\n",
      "16.9\t0.3179871692013229\t2.022415121016355\t1.693250573193194\n",
      "17.0\t0.3162371847149949\t2.011880330005736\t1.684618830362136\n",
      "17.1\t0.3145076827152896\t2.0014608126743285\t1.6760802970014965\n",
      "17.2\t0.31279830608386505\t1.991154650494809\t1.6676334371794341\n",
      "17.3\t0.31110870595636253\t1.9809599677070577\t1.6592767489239986\n",
      "17.4\t0.3094385414853119\t1.9708749301257074\t1.6510087632828718\n",
      "17.5\t0.3077874796111622\t1.9608977439875288\t1.6428280434143254\n",
      "17.6\t0.30615519484111486\t1.9510266548371218\t1.6347331837082066\n",
      "17.7\t0.3045413690354524\t1.9412599464494087\t1.6267228089357717\n",
      "17.8\t0.3029456912010658\t1.9315959397875393\t1.6187955734272899\n",
      "17.9\t0.3013678572919011\t1.9220329919948316\t1.6109501602763423\n",
      "18.0\t0.29980757001605496\t1.9125694954194674\t1.603185280569817\n",
      "18.1\t0.29826453864926233\t1.9032038766707016\t1.5954996726426307\n",
      "18.2\t0.29673847885453164\t1.8939345957053948\t1.5878921013562524\n",
      "18.3\t0.29522911250768985\t1.8847601449437406\t1.5803613574001418\n",
      "18.4\t0.2937361675286164\t1.8756790484131034\t1.5729062566152603\n",
      "18.5\t0.2922593777179467\t1.866689860918917\t1.565525639338836\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "null"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "println \"E(keV)\\telastic\\tion\\texc\"\n",
    "for(d = 12.0; d < 18.6; d += 0.1){\n",
    "    def sigmaEl = scatter.sigmael(d*1000)/factor\n",
    "    def sigmaIon = scatter.sigmaion(d*1000)/factor\n",
    "    def sigmaExc = scatter.sigmaexc(d*1000)/factor\n",
    "    println \"$d\\t$sigmaEl\\t$sigmaIon\\t$sigmaExc\"\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "b29b147e-ab0d-473b-b9db-909013996ad7",
       "version_major": 2,
       "version_minor": 0
      },
      "method": "display_data"
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import com.twosigma.beakerx.table.*\n",
    "\n",
    "def list = []\n",
    "    \n",
    "for(d = 12.0; d < 18.6; d += 0.1){\n",
    "    list << [\n",
    "        \"x\": d,\n",
    "        \"el\": scatter.sigmael(d*1000)/factor,\n",
    "        \"ion\": scatter.sigmaion(d*1000)/factor,\n",
    "        \"exc\": scatter.sigmaexc(d*1000)/factor \n",
    "    ]\n",
    "}\n",
    "beakerx[\"table\"] = new TableDisplay(list)\n",
    "list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{'x': 12.0,\n",
       "  'el': 0.43948540252301355,\n",
       "  'ion': 2.7362696996880764,\n",
       "  'exc': 2.2754271467658227},\n",
       " {'x': 12.1,\n",
       "  'el': 0.4360219815420227,\n",
       "  'ion': 2.716347129996631,\n",
       "  'exc': 2.259247553470829},\n",
       " {'x': 12.2,\n",
       "  'el': 0.4326153394877464,\n",
       "  'ion': 2.6967291910800784,\n",
       "  'exc': 2.2433117665045716},\n",
       " {'x': 12.3,\n",
       "  'el': 0.42926409223681455,\n",
       "  'ion': 2.6774088086825643,\n",
       "  'exc': 2.227614186457129},\n",
       " {'x': 12.4,\n",
       "  'el': 0.42596690029168804,\n",
       "  'ion': 2.6583791281775273,\n",
       "  'exc': 2.212149386181278},\n",
       " {'x': 12.5,\n",
       "  'el': 0.4227224669965498,\n",
       "  'ion': 2.639633506055748,\n",
       "  'exc': 2.1969121041685504},\n",
       " {'x': 12.6,\n",
       "  'el': 0.41952953683810995,\n",
       "  'ion': 2.621165501807934,\n",
       "  'exc': 2.1818972382301722},\n",
       " {'x': 12.7,\n",
       "  'el': 0.4163868938266485,\n",
       "  'ion': 2.602968870180603,\n",
       "  'exc': 2.1670998394665926},\n",
       " {'x': 12.8,\n",
       "  'el': 0.4132933599529065,\n",
       "  'ion': 2.585037553785318,\n",
       "  'exc': 2.1525151065102723},\n",
       " {'x': 12.9,\n",
       "  'el': 0.4102477937167139,\n",
       "  'ion': 2.567365676042546,\n",
       "  'exc': 2.138138380027344},\n",
       " {'x': 13.0,\n",
       "  'el': 0.4072490887234942,\n",
       "  'ion': 2.5499475344425586,\n",
       "  'exc': 2.123965137464613},\n",
       " {'x': 13.1,\n",
       "  'el': 0.4042961723450181,\n",
       "  'ion': 2.532777594106803,\n",
       "  'exc': 2.1099909880291814},\n",
       " {'x': 13.2,\n",
       "  'el': 0.40138800444100226,\n",
       "  'ion': 2.515850481634202,\n",
       "  'exc': 2.096211667888705},\n",
       " {'x': 13.3,\n",
       "  'el': 0.3985235761383543,\n",
       "  'ion': 2.4991609792177183,\n",
       "  'exc': 2.082623035581028},\n",
       " {'x': 13.4,\n",
       "  'el': 0.3957019086650494,\n",
       "  'ion': 2.4827040190174023,\n",
       "  'exc': 2.069221067622563},\n",
       " {'x': 13.5,\n",
       "  'el': 0.39292205223581,\n",
       "  'ion': 2.466474677776929,\n",
       "  'exc': 2.0560018543054204},\n",
       " {'x': 13.6,\n",
       "  'el': 0.39018308498692494,\n",
       "  'ion': 2.4504681716713828,\n",
       "  'exc': 2.042961595673853},\n",
       " {'x': 13.7,\n",
       "  'el': 0.3874841119576961,\n",
       "  'ion': 2.434679851374739,\n",
       "  'exc': 2.0300965976711156},\n",
       " {'x': 13.8,\n",
       "  'el': 0.3848242641161482,\n",
       "  'ion': 2.419105197336177,\n",
       "  'exc': 2.0174032684483527},\n",
       " {'x': 13.9,\n",
       "  'el': 0.3822026974267757,\n",
       "  'ion': 2.403739815254919,\n",
       "  'exc': 2.00487811482759},\n",
       " {'x': 14.0,\n",
       "  'el': 0.3796185919582249,\n",
       "  'ion': 2.3885794317439313,\n",
       "  'exc': 1.9925177389113418},\n",
       " {'x': 14.1,\n",
       "  'el': 0.3770711510289289,\n",
       "  'ion': 2.373619890173301,\n",
       "  'exc': 1.9803188348317768},\n",
       " {'x': 14.2,\n",
       "  'el': 0.3745596003888268,\n",
       "  'ion': 2.358857146684646,\n",
       "  'exc': 1.9682781856327505},\n",
       " {'x': 14.3,\n",
       "  'el': 0.3720831874354002,\n",
       "  'ion': 2.3442872663683785,\n",
       "  'exc': 1.9563926602783916},\n",
       " {'x': 14.4,\n",
       "  'el': 0.36964118046236066,\n",
       "  'ion': 2.32990641959609,\n",
       "  'exc': 1.9446592107822769},\n",
       " {'x': 14.5,\n",
       "  'el': 0.36723286793941123,\n",
       "  'ion': 2.315710878500726,\n",
       "  'exc': 1.9330748694515214},\n",
       " {'x': 14.6,\n",
       "  'el': 0.3648575578215951,\n",
       "  'ion': 2.3016970135976464,\n",
       "  'exc': 1.9216367462404509},\n",
       " {'x': 14.7,\n",
       "  'el': 0.36251457688682004,\n",
       "  'ion': 2.287861290540006,\n",
       "  'exc': 1.910342026208781},\n",
       " {'x': 14.8,\n",
       "  'el': 0.3602032701002296,\n",
       "  'ion': 2.274200267002247,\n",
       "  'exc': 1.8991879670794969},\n",
       " {'x': 14.9,\n",
       "  'el': 0.357923000004158,\n",
       "  'ion': 2.26071058968582,\n",
       "  'exc': 1.8881718968918926},\n",
       " {'x': 15.0,\n",
       "  'el': 0.3556731461324769,\n",
       "  'ion': 2.2473889914415754,\n",
       "  'exc': 1.8772912117454528},\n",
       " {'x': 15.1,\n",
       "  'el': 0.353453104448203,\n",
       "  'ion': 2.234232288503513,\n",
       "  'exc': 1.8665433736304802},\n",
       " {'x': 15.2,\n",
       "  'el': 0.35126228680329497,\n",
       "  'ion': 2.221237377828907,\n",
       "  'exc': 1.8559259083415982},\n",
       " {'x': 15.3,\n",
       "  'el': 0.3491001204196282,\n",
       "  'ion': 2.2084012345400286,\n",
       "  'exc': 1.845436403470438},\n",
       " {'x': 15.4,\n",
       "  'el': 0.3469660473901797,\n",
       "  'ion': 2.1957209094629615,\n",
       "  'exc': 1.835072506474014},\n",
       " {'x': 15.5,\n",
       "  'el': 0.3448595241995173,\n",
       "  'ion': 2.1831935267592297,\n",
       "  'exc': 1.824831922815469},\n",
       " {'x': 15.6,\n",
       "  'el': 0.3427800212627204,\n",
       "  'ion': 2.170816281646157,\n",
       "  'exc': 1.8147124141740314},\n",
       " {'x': 15.7,\n",
       "  'el': 0.34072702248191666,\n",
       "  'ion': 2.158586438202101,\n",
       "  'exc': 1.8047117967211865},\n",
       " {'x': 15.8,\n",
       "  'el': 0.33870002481965195,\n",
       "  'ion': 2.1465013272528792,\n",
       "  'exc': 1.7948279394602165},\n",
       " {'x': 15.9,\n",
       "  'el': 0.3366985378883526,\n",
       "  'ion': 2.134558344335901,\n",
       "  'exc': 1.7850587626263867},\n",
       " {'x': 16.0,\n",
       "  'el': 0.33472208355517563,\n",
       "  'ion': 2.122754947738674,\n",
       "  'exc': 1.7754022361452126},\n",
       " {'x': 16.1,\n",
       "  'el': 0.33277019556158083,\n",
       "  'ion': 2.111088656608532,\n",
       "  'exc': 1.7658563781463463},\n",
       " {'x': 16.2,\n",
       "  'el': 0.33084241915698676,\n",
       "  'ion': 2.0995570491305764,\n",
       "  'exc': 1.7564192535307461},\n",
       " {'x': 16.3,\n",
       "  'el': 0.32893831074590485,\n",
       "  'ion': 2.0881577607709536,\n",
       "  'exc': 1.7470889725889123},\n",
       " {'x': 16.4,\n",
       "  'el': 0.3270574375479805,\n",
       "  'ion': 2.0768884825827687,\n",
       "  'exc': 1.7378636896680617},\n",
       " {'x': 16.5,\n",
       "  'el': 0.3251993772703896,\n",
       "  'ion': 2.0657469595720115,\n",
       "  'exc': 1.7287416018862318},\n",
       " {'x': 16.6,\n",
       "  'el': 0.32336371779207285,\n",
       "  'ion': 2.054730989121034,\n",
       "  'exc': 1.7197209478913829},\n",
       " {'x': 16.7,\n",
       "  'el': 0.3215500568593091,\n",
       "  'ion': 2.043838419467228,\n",
       "  'exc': 1.7108000066636726},\n",
       " {'x': 16.8,\n",
       "  'el': 0.31975800179215863,\n",
       "  'ion': 2.0330671482346325,\n",
       "  'exc': 1.7019770963591483},\n",
       " {'x': 16.9,\n",
       "  'el': 0.3179871692013229,\n",
       "  'ion': 2.022415121016355,\n",
       "  'exc': 1.693250573193194},\n",
       " {'x': 17.0,\n",
       "  'el': 0.3162371847149949,\n",
       "  'ion': 2.011880330005736,\n",
       "  'exc': 1.684618830362136},\n",
       " {'x': 17.1,\n",
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       " {'x': 17.2,\n",
       "  'el': 0.31279830608386505,\n",
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       "  'exc': 1.6676334371794341},\n",
       " {'x': 17.3,\n",
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       " {'x': 17.4,\n",
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       " {'x': 17.7,\n",
       "  'el': 0.3045413690354524,\n",
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       "  'exc': 1.6267228089357717},\n",
       " {'x': 17.8,\n",
       "  'el': 0.3029456912010658,\n",
       "  'ion': 1.9315959397875393,\n",
       "  'exc': 1.6187955734272899},\n",
       " {'x': 17.9,\n",
       "  'el': 0.3013678572919011,\n",
       "  'ion': 1.9220329919948316,\n",
       "  'exc': 1.6109501602763423},\n",
       " {'x': 18.0,\n",
       "  'el': 0.29980757001605496,\n",
       "  'ion': 1.9125694954194674,\n",
       "  'exc': 1.603185280569817},\n",
       " {'x': 18.1,\n",
       "  'el': 0.29826453864926233,\n",
       "  'ion': 1.9032038766707016,\n",
       "  'exc': 1.5954996726426307},\n",
       " {'x': 18.2,\n",
       "  'el': 0.29673847885453164,\n",
       "  'ion': 1.8939345957053948,\n",
       "  'exc': 1.5878921013562524},\n",
       " {'x': 18.3,\n",
       "  'el': 0.29522911250768985,\n",
       "  'ion': 1.8847601449437406,\n",
       "  'exc': 1.5803613574001418},\n",
       " {'x': 18.4,\n",
       "  'el': 0.2937361675286164,\n",
       "  'ion': 1.8756790484131034,\n",
       "  'exc': 1.5729062566152603},\n",
       " {'x': 18.5,\n",
       "  'el': 0.2922593777179467,\n",
       "  'ion': 1.866689860918917,\n",
       "  'exc': 1.565525639338836}]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%%python\n",
    "from beakerx.object import beakerx\n",
    "import pandas as pd\n",
    "beakerx.table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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