openmc extra material segfault

openmc-extra-material-segfault.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Small Lattice\n",
    "\n",
    "Using the the tools so far, simulate a small 3x3 lattice where the center rod is a control rod made of boron carbide (B$_4$C).\n",
    "\n",
    "Compute the flux in each rod, including the control rod."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/scopatz/miniconda/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.\n",
      "  from ._conv import register_converters as _register_converters\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.10.0\n"
     ]
    }
   ],
   "source": [
    "import openmc\n",
    "print(openmc.__version__)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Materials"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "b4c = openmc.Material(name=\"b4c\")\n",
    "b4c.set_density('g/cm3', 2.52)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "b4c.add_element('B', 4.0)\n",
    "b4c.add_element('C', 1.0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Material\n",
       "\tID             =\t1\n",
       "\tName           =\tb4c\n",
       "\tTemperature    =\tNone\n",
       "\tDensity        =\t2.52 [g/cm3]\n",
       "\tS(a,b) Tables  \n",
       "\tNuclides       \n",
       "\tB10            =\t0.7928       [ao]\n",
       "\tB11            =\t3.2072       [ao]\n",
       "\tC0             =\t1.0          [ao]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "b4c"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "uo2 = openmc.Material(name=\"uo2\")\n",
    "uo2.set_density('g/cm3', 10.7)\n",
    "uo2.add_nuclide('U235', 0.03)\n",
    "uo2.add_nuclide('U238', 0.97)\n",
    "uo2.add_element('O', 2.0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "clad = openmc.Material(name=\"cladding\")\n",
    "clad.set_density('g/cm3', 6.6)\n",
    "clad.add_element('Zr', 1.0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "cool = openmc.Material(name=\"coolant\")\n",
    "cool.set_density('g/cm3', 1.0)\n",
    "cool.add_element('H', 2.0)\n",
    "cool.add_element('O', 1.0)\n",
    "cool.add_s_alpha_beta('c_H_in_H2O')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# !!! NOTE If b4c is removed from the mats list, since it is unused, the segfault will disappear"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "mats = openmc.Materials([b4c, uo2, clad, cool])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "mats.export_to_xml()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Surfaces"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "r_fuel = 0.39\n",
    "r_clad_in = 0.4\n",
    "r_clad_out = 0.46\n",
    "pitch = 1.26"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "# top left\n",
    "rod1_fuel = openmc.ZCylinder(R=r_fuel, x0=-pitch, y0=pitch)\n",
    "rod1_clad_in = openmc.ZCylinder(R=r_clad_in, x0=-pitch, y0=pitch)\n",
    "rod1_clad_out = openmc.ZCylinder(R=r_clad_out, x0=-pitch, y0=pitch)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "# top center\n",
    "rod2_fuel = openmc.ZCylinder(R=r_fuel, x0=0.0, y0=pitch)\n",
    "rod2_clad_in = openmc.ZCylinder(R=r_clad_in, x0=0.0, y0=pitch)\n",
    "rod2_clad_out = openmc.ZCylinder(R=r_clad_out, x0=0.0, y0=pitch)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# top right\n",
    "rod3_fuel = openmc.ZCylinder(R=r_fuel, x0=pitch, y0=pitch)\n",
    "rod3_clad_in = openmc.ZCylinder(R=r_clad_in, x0=pitch, y0=pitch)\n",
    "rod3_clad_out = openmc.ZCylinder(R=r_clad_out, x0=pitch, y0=pitch)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "# center left\n",
    "rod4_fuel = openmc.ZCylinder(R=r_fuel, x0=-pitch, y0=0.0)\n",
    "rod4_clad_in = openmc.ZCylinder(R=r_clad_in, x0=-pitch, y0=0.0)\n",
    "rod4_clad_out = openmc.ZCylinder(R=r_clad_out, x0=-pitch, y0=0.0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "# center center\n",
    "rod5_fuel = openmc.ZCylinder(R=r_fuel, x0=0.0, y0=0.0)\n",
    "rod5_clad_in = openmc.ZCylinder(R=r_clad_in, x0=0.0, y0=0.0)\n",
    "rod5_clad_out = openmc.ZCylinder(R=r_clad_out, x0=0.0, y0=0.0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "# center right\n",
    "rod6_fuel = openmc.ZCylinder(R=r_fuel, x0=pitch, y0=0.0)\n",
    "rod6_clad_in = openmc.ZCylinder(R=r_clad_in, x0=pitch, y0=0.0)\n",
    "rod6_clad_out = openmc.ZCylinder(R=r_clad_out, x0=pitch, y0=0.0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "# bottom left\n",
    "rod7_fuel = openmc.ZCylinder(R=r_fuel, x0=-pitch, y0=-pitch)\n",
    "rod7_clad_in = openmc.ZCylinder(R=r_clad_in, x0=-pitch, y0=-pitch)\n",
    "rod7_clad_out = openmc.ZCylinder(R=r_clad_out, x0=-pitch, y0=-pitch)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "# bottom center\n",
    "rod8_fuel = openmc.ZCylinder(R=r_fuel, x0=0.0, y0=-pitch)\n",
    "rod8_clad_in = openmc.ZCylinder(R=r_clad_in, x0=0.0, y0=-pitch)\n",
    "rod8_clad_out = openmc.ZCylinder(R=r_clad_out, x0=0.0, y0=-pitch)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "# bottom right\n",
    "rod9_fuel = openmc.ZCylinder(R=r_fuel, x0=pitch, y0=-pitch)\n",
    "rod9_clad_in = openmc.ZCylinder(R=r_clad_in, x0=pitch, y0=-pitch)\n",
    "rod9_clad_out = openmc.ZCylinder(R=r_clad_out, x0=pitch, y0=-pitch)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "box = openmc.get_rectangular_prism(width=3*pitch, height=3*pitch, \n",
    "                                   boundary_type='reflective')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Cells"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "fuel_rods = (rod1_fuel, rod2_fuel, rod3_fuel, rod4_fuel, \n",
    "             rod6_fuel, rod7_fuel, rod8_fuel, rod9_fuel)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "fuel_region = -rod1_fuel\n",
    "for fuel_rod in fuel_rods[1:]:\n",
    "    fuel_region = fuel_region | -fuel_rod"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "control_region = -rod5_fuel"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "gap_region = (+rod1_fuel & -rod1_clad_in)\n",
    "gap_region = gap_region | (+rod2_fuel & -rod2_clad_in)\n",
    "gap_region = gap_region | (+rod3_fuel & -rod3_clad_in)\n",
    "gap_region = gap_region | (+rod4_fuel & -rod4_clad_in)\n",
    "gap_region = gap_region | (+rod5_fuel & -rod5_clad_in)\n",
    "gap_region = gap_region | (+rod6_fuel & -rod6_clad_in)\n",
    "gap_region = gap_region | (+rod7_fuel & -rod7_clad_in)\n",
    "gap_region = gap_region | (+rod8_fuel & -rod8_clad_in)\n",
    "gap_region = gap_region | (+rod9_fuel & -rod9_clad_in)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [],
   "source": [
    "clad_region = (+rod1_clad_in & -rod1_clad_out)\n",
    "clad_region = clad_region | (+rod2_clad_in & -rod2_clad_out)\n",
    "clad_region = clad_region | (+rod3_clad_in & -rod3_clad_out)\n",
    "clad_region = clad_region | (+rod4_clad_in & -rod4_clad_out)\n",
    "clad_region = clad_region | (+rod5_clad_in & -rod5_clad_out)\n",
    "clad_region = clad_region | (+rod6_clad_in & -rod6_clad_out)\n",
    "clad_region = clad_region | (+rod7_clad_in & -rod7_clad_out)\n",
    "clad_region = clad_region | (+rod8_clad_in & -rod8_clad_out)\n",
    "clad_region = clad_region | (+rod9_clad_in & -rod9_clad_out)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "cool_region = box & +rod1_clad_out & +rod2_clad_out & +rod3_clad_out \\\n",
    "                  & +rod4_clad_out & +rod5_clad_out & +rod6_clad_out \\\n",
    "                  & +rod7_clad_out & +rod8_clad_out & +rod9_clad_out"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Cells"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "fuel_cell = openmc.Cell(name=\"Fuel\", fill=uo2, region=fuel_region)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# !!! Note that using a material other than b4c in the control rod cell causes a segfault, presumably due to an unused material"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "control_cell = openmc.Cell(name=\"Control\", fill=clad,  region=control_region)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "gap_cell = openmc.Cell(name=\"Gap\", region=gap_region)\n",
    "clad_cell = openmc.Cell(name=\"Cladding\", fill=clad, region=clad_region)\n",
    "cool_cell = openmc.Cell(name=\"Coolant\", fill=cool, region=cool_region)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Universies and Geomtery"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "root = openmc.Universe(cells=(fuel_cell, control_cell, gap_cell, \n",
    "                              clad_cell, cool_cell))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "geom = openmc.Geometry(root)\n",
    "geom.export_to_xml()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Stats and Sources"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "src1 = openmc.Source(space=openmc.stats.Point((-pitch, pitch, 0)))\n",
    "src2 = openmc.Source(space=openmc.stats.Point((0.0, pitch, 0)))\n",
    "src3 = openmc.Source(space=openmc.stats.Point((pitch, pitch, 0)))\n",
    "src4 = openmc.Source(space=openmc.stats.Point((-pitch, 0, 0)))\n",
    "# no source in center\n",
    "src6 = openmc.Source(space=openmc.stats.Point((pitch, 0, 0)))\n",
    "src7 = openmc.Source(space=openmc.stats.Point((-pitch, -pitch, 0)))\n",
    "src8 = openmc.Source(space=openmc.stats.Point((0.0, -pitch, 0)))\n",
    "src9 = openmc.Source(space=openmc.stats.Point((pitch, -pitch, 0)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": [
    "settings = openmc.Settings()\n",
    "settings.source = [src1, src2, src3, src4, src6, src7, src8, src9]\n",
    "settings.batches = 1000\n",
    "settings.inactive = 10\n",
    "settings.particles = 1000"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [],
   "source": [
    "settings.export_to_xml()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Tallies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "cell_filter = openmc.CellFilter(fuel_cell)\n",
    "t = openmc.Tally()\n",
    "t.filters = [cell_filter]\n",
    "t.scores = ['flux']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [],
   "source": [
    "control_filter = openmc.CellFilter(control_cell)\n",
    "u = openmc.Tally()\n",
    "u.filters = [control_filter]\n",
    "u.scores = ['flux']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "tallies = openmc.Tallies([t, u])\n",
    "tallies.export_to_xml()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Execute!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "                               %%%%%%%%%%%%%%%\n",
      "                          %%%%%%%%%%%%%%%%%%%%%%%%\n",
      "                       %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n",
      "                     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n",
      "                   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n",
      "                  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n",
      "                                   %%%%%%%%%%%%%%%%%%%%%%%%\n",
      "                                    %%%%%%%%%%%%%%%%%%%%%%%%\n",
      "                ###############      %%%%%%%%%%%%%%%%%%%%%%%%\n",
      "               ##################     %%%%%%%%%%%%%%%%%%%%%%%\n",
      "               ###################     %%%%%%%%%%%%%%%%%%%%%%%\n",
      "               ####################     %%%%%%%%%%%%%%%%%%%%%%\n",
      "               #####################     %%%%%%%%%%%%%%%%%%%%%\n",
      "               ######################     %%%%%%%%%%%%%%%%%%%%\n",
      "               #######################     %%%%%%%%%%%%%%%%%%\n",
      "                #######################     %%%%%%%%%%%%%%%%%\n",
      "                ######################     %%%%%%%%%%%%%%%%%\n",
      "                 ####################     %%%%%%%%%%%%%%%%%\n",
      "                   #################     %%%%%%%%%%%%%%%%%\n",
      "                    ###############     %%%%%%%%%%%%%%%%\n",
      "                      ############     %%%%%%%%%%%%%%%\n",
      "                         ########     %%%%%%%%%%%%%%\n",
      "                                     %%%%%%%%%%%\n",
      "\n",
      "                   | The OpenMC Monte Carlo Code\n",
      "         Copyright | 2011-2018 Massachusetts Institute of Technology\n",
      "           License | http://openmc.readthedocs.io/en/latest/license.html\n",
      "           Version | 0.10.0\n",
      "          Git SHA1 | 9ecf2df9b520b632394f4071b14188f07336e6be\n",
      "         Date/Time | 2018-03-05 18:40:08\n",
      "    OpenMP Threads | 4\n",
      "\n",
      " Reading settings XML file...\n",
      " Reading cross sections XML file...\n",
      " Reading materials XML file...\n",
      " Reading geometry XML file...\n",
      " Building neighboring cells lists for each surface...\n",
      " Reading B10 from /home/scopatz/nndc_hdf5/B10.h5\n",
      " Reading B11 from /home/scopatz/nndc_hdf5/B11.h5\n",
      " Reading C0 from /home/scopatz/nndc_hdf5/C0.h5\n",
      " Reading U235 from /home/scopatz/nndc_hdf5/U235.h5\n",
      " Reading U238 from /home/scopatz/nndc_hdf5/U238.h5\n",
      " Reading O16 from /home/scopatz/nndc_hdf5/O16.h5\n",
      " Reading O17 from /home/scopatz/nndc_hdf5/O17.h5\n",
      " Reading Zr90 from /home/scopatz/nndc_hdf5/Zr90.h5\n",
      " Reading Zr91 from /home/scopatz/nndc_hdf5/Zr91.h5\n",
      " Reading Zr92 from /home/scopatz/nndc_hdf5/Zr92.h5\n",
      " Reading Zr94 from /home/scopatz/nndc_hdf5/Zr94.h5\n",
      " Reading Zr96 from /home/scopatz/nndc_hdf5/Zr96.h5\n",
      " Reading H1 from /home/scopatz/nndc_hdf5/H1.h5\n",
      " Reading H2 from /home/scopatz/nndc_hdf5/H2.h5\n",
      " Reading c_H_in_H2O from /home/scopatz/nndc_hdf5/c_H_in_H2O.h5\n",
      "\n",
      "Program received signal SIGSEGV: Segmentation fault - invalid memory reference.\n",
      "\n",
      "Backtrace for this error:\n",
      "#0  0x7F4711F36407\n",
      "#1  0x7F4711F36A0E\n",
      "#2  0x7F4710EA713F\n",
      "#3  0x7F4713660D55\n",
      "#4  0x7F471367C78A\n",
      "#5  0x7F471365C37A\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "-11"
      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "openmc.run()"
   ]
  }
 ],
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