plot_ver_thfo2-cla.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import NCrystal as NC\n",
    "import numpy as np\n",
    "from plotly.subplots import make_subplots\n",
    "import plotly.graph_objects as go"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "T = 2 # temperature "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "dcutoff = 0.5 # AA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "wavelength = np.linspace(0.01, 25, 1000)\n",
    "E = NC.wl2ekin(wavelength)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "nc_O2   = 'ncplugin-MagScat_O2_pdos_hydrogenated_THFO2-hydrate_mag.ncmat'\n",
    "nc_ept  = 'HighNESS_1088H2O_64THF_0O2_sg1_ClathrateHydrate-sII.ncmat'\n",
    "nc_cla  = 'HighNESS_1088H2O_64THF_128O2_sg1_ClathrateHydrate-sII.ncmat'\n",
    "nc_comb = 'HighNESS_1088H2O_64THF_128O2_sg1_ClathrateHydrate-sII_mag.ncmat'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NCrystal::NCMATLoader WARNING: Loading NCMAT data which has @CUSTOM_ section(s). This is OK if intended.\n",
      "2\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "36036.385139129285"
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     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "O2info = NC.createInfo(nc_O2+';temp={}K'.format(T))\n",
    "print(O2info.getAtomInfo()[0].count.as_integer_ratio()[0])\n",
    "O2V = 192 * O2info.getAtomInfo()[0].count.as_integer_ratio()[0] * O2info.getAtomInfo()[0].atomData.averageMassAMU() / O2info.density\n",
    "O2V"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "H(cohSL=-3.739fm cohXS=1.75679barn incXS=80.26barn absXS=0.3326barn mass=1.00798amu Z=1)\n",
      "2176 1.007975973752\n",
      "H(cohSL=-3.739fm cohXS=1.75679barn incXS=80.26barn absXS=0.3326barn mass=1.00798amu Z=1)\n",
      "512 1.007975973752\n",
      "C(cohSL=6.646fm cohXS=5.55048barn incXS=0.001barn absXS=0.0035barn mass=12.011amu Z=6)\n",
      "256 12.0110369031873\n",
      "O(cohSL=5.803fm cohXS=4.2317barn incXS=0.0008barn absXS=0.00019barn mass=15.9993amu Z=8)\n",
      "1088 15.999304712099\n",
      "O(cohSL=5.803fm cohXS=4.2317barn incXS=0.0008barn absXS=0.00019barn mass=15.9993amu Z=8)\n",
      "64 15.999304712099\n"
     ]
    },
    {
     "data": {
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      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "eptinfo = NC.createInfo(nc_ept+';temp={}K'.format(T))\n",
    "Mtot = 0\n",
    "for i in range(len(eptinfo.getAtomInfo())):\n",
    "    print(eptinfo.getAtomInfo()[i].atomData.description())\n",
    "    N = eptinfo.getAtomInfo()[i].count.as_integer_ratio()[0]\n",
    "    M = eptinfo.getAtomInfo()[i].atomData.averageMassAMU()\n",
    "    print(N, M)\n",
    "    Mtot += N * M\n",
    "eptV = Mtot / eptinfo.density\n",
    "eptV"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.5980847448023815"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "vf_O2 = O2V / (eptV + O2V)\n",
    "vf_O2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.4019152551976185"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "vf_ept = 1 - vf_O2\n",
    "vf_ept"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NCrystal WARNING: Discarding 188 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 186 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 195 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 196 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 198 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 207 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 186 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 195 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 196 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 198 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 207 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 188 edges of provided kernel data due to missing S values.\n",
      "NCrystal::NCMATLoader WARNING: Loading NCMAT data which has @CUSTOM_ section(s). This is OK if intended.\n",
      "NCrystal WARNING: Discarding 186 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 195 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 196 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 198 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 207 edges of provided kernel data due to missing S values.\n",
      "NCrystal WARNING: Discarding 188 edges of provided kernel data due to missing S values.\n"
     ]
    }
   ],
   "source": [
    "O2    = NC.createScatter(nc_O2+';coh_elas=0;temp={}K'.format(T))\n",
    "ept   = NC.createScatter(nc_ept+';temp={}K;dcutoff={}'.format(T,dcutoff))\n",
    "cla   = NC.createScatter(nc_cla+';temp={}K;dcutoff={}'.format(T,dcutoff))\n",
    "comb  = NC.createScatter(nc_comb+';temp={}K;dcutoff={}'.format(T,dcutoff))\n",
    "\n",
    "xs_O2   = O2.crossSectionNonOriented(E)\n",
    "xs_ept  = ept.crossSectionNonOriented(E)\n",
    "xs_cla  = cla.crossSectionNonOriented(E)\n",
    "xs_comb = comb.crossSectionNonOriented(E)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
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     },
     "metadata": {},
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    }
   ],
   "source": [
    "fig = make_subplots(rows = 1, cols = 1)\n",
    "fig.add_trace(\n",
    "    go.Scatter(\n",
    "        x = wavelength,\n",
    "        y = xs_O2,\n",
    "        mode = 'lines',\n",
    "        name = 'O2',\n",
    "    ),\n",
    "    row = 1, col = 1\n",
    ")\n",
    "fig.add_trace(\n",
    "    go.Scatter(\n",
    "        x = wavelength,\n",
    "        y = xs_ept,\n",
    "        mode = 'lines',\n",
    "        name = 'THF-hydrate',\n",
    "    ),\n",
    "    row = 1, col = 1\n",
    ")\n",
    "fig.add_trace(\n",
    "    go.Scatter(\n",
    "        x = wavelength,\n",
    "        y = xs_cla,\n",
    "        mode = 'lines',\n",
    "        name = 'THF+O2-hydrate',\n",
    "    ),\n",
    "    row = 1, col = 1\n",
    ")\n",
    "fig.add_trace(\n",
    "    go.Scatter(\n",
    "        x = wavelength,\n",
    "        y = xs_comb,\n",
    "        mode = 'lines',\n",
    "        name = 'Combined',\n",
    "    ),\n",
    "    row = 1, col = 1\n",
    ")\n",
    "fig.add_trace(\n",
    "    go.Scatter(\n",
    "        x = wavelength,\n",
    "        y = xs_ept*(17*3+13)/(17*3+13+3*2)+xs_O2*(3*2)/(17*3+13+3*2),\n",
    "        mode = 'lines',\n",
    "        line_dash = 'dash',\n",
    "        name = 'Combined calc',\n",
    "    ),\n",
    "    row = 1, col = 1\n",
    ")\n",
    "fig.update_xaxes(tickfont = dict(size = 20), linecolor = 'black', mirror = True, \n",
    "                 ticks = 'outside', exponentformat = 'power', row = 1, col = 1, \n",
    "                 #type = 'log', \n",
    "                 #range=[0,25],\n",
    "                 title = r'$\\Large \\textrm{Incident neutron wavelength } (\\mathring{\\textrm{A}})$', \n",
    "                 showgrid=True, gridwidth=.5, gridcolor='grey')\n",
    "fig.update_yaxes(tickfont = dict(size = 20), linecolor = 'black', mirror = True, \n",
    "                 ticks = 'outside', exponentformat = 'power', row = 1, col = 1, \n",
    "                 #type = 'log', \n",
    "                 #range = [0,9],\n",
    "                 title = r'$\\Large \\textrm{Scattering cross section per atom (barn)}$',\n",
    "                 showgrid=True, gridwidth=.5, gridcolor='grey')\n",
    "#fig.add_annotation(xref='paper',yref='paper',x=.5, y=.85, \n",
    "#                   text=r'$\\Large \\textrm{O2-D2O clathrates}$', showarrow=False)\n",
    "#fig.add_annotation(xref='paper',yref='paper',x=.5, y=.75, \n",
    "#                   text=r'$\\Large \\textrm{SII structure}$', showarrow=False)\n",
    "#fig.add_annotation(xref='paper',yref='paper',x=.5, y=.62, \n",
    "#                   text=r'$\\Large T=2\\textrm{ K}$', showarrow=False)\n",
    "fig.update_layout(\n",
    "    #paper_bgcolor = 'rgba(0,0,0,0)',\n",
    "    plot_bgcolor = 'rgba(0,0,0,0)',\n",
    "    font = dict(family = 'Times new roman', size = 24),\n",
    "    legend = dict(x = 0.7, y = 0.15, bordercolor = \"Black\", borderwidth = 1, font = dict(size = 18)),\n",
    "    margin = dict(l = 80, r = 20, t = 20, b = 60),\n",
    "    autosize=False,\n",
    "    width=700,\n",
    "    height=600\n",
    ")\n",
    "fig.show('svg')\n",
    "#fig.write_image('TDF-D2O-clathrates_XS_wavelength.eps',width=700,height=500)\n",
    "#fig.write_image('TDF-D2O-clathrates_XS_wavelength.png',width=700,height=500)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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