geometry-marking.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "416ac23a",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import subprocess\n",
    "\n",
    "import alphashape\n",
    "import gmsh\n",
    "import h5py\n",
    "import matplotlib.pyplot as plt\n",
    "import meshio\n",
    "import numpy as np\n",
    "import shapely\n",
    "import warnings\n",
    "\n",
    "from concavehull import concavehull\n",
    "from descartes import PolygonPatch\n",
    "from dolfinx import cpp, fem, io, mesh, nls, plot\n",
    "from mpi4py import MPI\n",
    "from petsc4py import PETSc\n",
    "\n",
    "import commons, geometry, grapher, utils\n",
    "warnings.simplefilter('ignore')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "cf4a9ef4",
   "metadata": {},
   "outputs": [],
   "source": [
    "markers = commons.SurfaceMarkers()\n",
    "cell_types = commons.CellTypes()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0c9fed67",
   "metadata": {},
   "source": [
    "### 2D Irregular Surface"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "ea13dc35",
   "metadata": {},
   "outputs": [],
   "source": [
    "def mesh_surface(coords, xmax=470, ymax=470):\n",
    "    points = {}\n",
    "    new_points = {}\n",
    "    count = 0\n",
    "    for row in coords:\n",
    "        points[(row[0], row[1])] = count\n",
    "        count += 1\n",
    "    points_set = set(points.keys())\n",
    "    no_full_neighbors = set()\n",
    "    triangles = []\n",
    "    for (x0, y0) in points_set:\n",
    "        p0 = points[(x0, y0)]\n",
    "        neighbors = [\n",
    "            (int(x0 + 1), y0),\n",
    "            (int(x0 + 1), int(y0 + 1)),\n",
    "            (x0, int(y0 + 1))\n",
    "        ]\n",
    "        neighbor_points = [p0]\n",
    "        for p in neighbors:\n",
    "            v = points.get(p)\n",
    "            neighbor_points.append(v)\n",
    "\n",
    "        midpoint = (x0 + 0.5, y0 + 0.5)\n",
    "        if midpoint[0] > xmax or midpoint[1] > ymax:\n",
    "            continue\n",
    "        points[midpoint] = count\n",
    "        p2 = count\n",
    "        count += 1\n",
    "        for i in range(4):\n",
    "            p0 = neighbor_points[i]\n",
    "            if i == 3:\n",
    "                p1 = neighbor_points[0]\n",
    "            else:\n",
    "                p1 = neighbor_points[i + 1]\n",
    "            if not p0 is None and not p1 is None:\n",
    "                triangles.append(\n",
    "                    (p0, p1, p2)\n",
    "                )\n",
    "                \n",
    "\n",
    "    return triangles, points"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "b22efc47",
   "metadata": {},
   "outputs": [],
   "source": [
    "img = np.asarray(plt.imread('data/current_constriction/test11.tif')[:, :, 0], dtype=np.uint8)\n",
    "img2 = img.copy()\n",
    "img2[0:5, :] = 0\n",
    "img2[-5:, :] = 0\n",
    "img2[:, 0:5] = 0\n",
    "img2[:, -5:,] = 0\n",
    "coords = np.asarray(np.argwhere(img2 == 1), dtype=np.int32)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "973ec64d",
   "metadata": {},
   "outputs": [],
   "source": [
    "triangles, points = mesh_surface(coords)\n",
    "cell_type = cell_types.triangle\n",
    "cells = np.asarray(triangles, dtype=np.int32)\n",
    "max_row_idx = max(points.values())\n",
    "new_points = np.zeros((max_row_idx + 1, 2))\n",
    "\n",
    "for k, v in points.items():\n",
    "    new_points[v, :] = k\n",
    "cell_data = np.zeros((len(triangles),), dtype=np.int32).tolist()\n",
    "out_mesh = meshio.Mesh(points=new_points, cells={cell_type: cells}, cell_data={\"name_to_read\": [cell_data]})\n",
    "out_mesh.write(\"trial.xdmf\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fbbac472",
   "metadata": {},
   "source": [
    "### 3D Surface Marking"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "be7c5a4e",
   "metadata": {},
   "source": [
    "### Irregular Surface Using gmsh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "27512968",
   "metadata": {},
   "outputs": [],
   "source": [
    "coords = np.asarray(np.argwhere(img2 == 1), dtype=np.int32)\n",
    "xmax = 470\n",
    "ymax = 470\n",
    "all_points = {}\n",
    "corner_points = [\n",
    "    (0, 0, 0),\n",
    "    (xmax, 0, 0),\n",
    "    (xmax, ymax, 0),\n",
    "    (0, ymax, 0)\n",
    "]\n",
    "other_points = []\n",
    "count = 0\n",
    "for row in coords:\n",
    "    all_points[(row[0], row[1])] = count\n",
    "    count += 1\n",
    "gmsh_points = []\n",
    "points_view = {int(v): (int(k[0]), int(k[1])) for k, v in all_points.items()}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "2ff381de",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "120"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "graph = grapher.PixelGraph(points=points_view)\n",
    "graph.build_graph()\n",
    "graph.get_graph_pieces()\n",
    "graph.n_pieces"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4bf9bd8f",
   "metadata": {},
   "source": [
    "#### Meshing with GMSH"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "1a9b1c8f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[21]\n",
      "(235.0, 0.0, 12.5) 22\n",
      "(235.0, 470.0, 12.5) 23\n",
      "(470.0, 235.0, 12.5) 24\n",
      "(0.0, 235.0, 12.5) 25\n",
      "Info    : Healing shapes (tolerance: 1e-08)\n",
      "Info    :  - Fixing degenerated edges and faces\n",
      "Info    :  . Repaired face\n",
      "Info    :  . Orientation of wires fixed\n",
      "Info    :  - Fixing small edges\n",
      "Info    :  - Fixing spot and strip faces\n",
      "Info    :  - Sewing faces\n",
      "Info    :  - Making solids\n",
      "Info    : Done healing shapes (Wall 3.02095s, CPU 3.02364s):\n",
      "Info    :  - Compounds          : 0 (1)\n",
      "Info    :  - Composite solids   : 0 (0)\n",
      "Info    :  - Solids             : 1 (0)\n",
      "Info    :  - Shells             : 1 (0)\n",
      "Info    :  - Wires              : 46 (26)\n",
      "Info    :  - Faces              : 26 (26)\n",
      "Info    :  - Edges              : 2095 (2095)\n",
      "Info    :  - Vertices           : 2091 (2091)\n",
      "Info    :  - Total surface area : 488800 (646119)\n",
      "Info    : Meshing 1D...\n",
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      "Info    : [ 40%] Meshing curve 666 (Line)\n",
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      "Info    : [ 40%] Meshing curve 668 (Line)\n",
      "Info    : [ 40%] Meshing curve 669 (Line)\n",
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      "Info    : [ 40%] Meshing curve 680 (Line)\n",
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      "Info    : [ 40%] Meshing curve 720 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1055 (Line)\n",
      "Info    : [ 60%] Meshing curve 1056 (Line)\n",
      "Info    : [ 60%] Meshing curve 1057 (Line)\n",
      "Info    : [ 60%] Meshing curve 1058 (Line)\n",
      "Info    : [ 60%] Meshing curve 1059 (Line)\n",
      "Info    : [ 60%] Meshing curve 1060 (Line)\n",
      "Info    : [ 60%] Meshing curve 1061 (Line)\n",
      "Info    : [ 60%] Meshing curve 1062 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1065 (Line)\n",
      "Info    : [ 60%] Meshing curve 1066 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1069 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1072 (Line)\n",
      "Info    : [ 60%] Meshing curve 1073 (Line)\n",
      "Info    : [ 60%] Meshing curve 1074 (Line)\n",
      "Info    : [ 60%] Meshing curve 1075 (Line)\n",
      "Info    : [ 60%] Meshing curve 1076 (Line)\n",
      "Info    : [ 60%] Meshing curve 1077 (Line)\n",
      "Info    : [ 60%] Meshing curve 1078 (Line)\n",
      "Info    : [ 60%] Meshing curve 1079 (Line)\n",
      "Info    : [ 60%] Meshing curve 1080 (Line)\n",
      "Info    : [ 60%] Meshing curve 1081 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1083 (Line)\n",
      "Info    : [ 60%] Meshing curve 1084 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1086 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1092 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1096 (Line)\n",
      "Info    : [ 60%] Meshing curve 1097 (Line)\n",
      "Info    : [ 60%] Meshing curve 1098 (Line)\n",
      "Info    : [ 60%] Meshing curve 1099 (Line)\n",
      "Info    : [ 60%] Meshing curve 1100 (Line)\n",
      "Info    : [ 60%] Meshing curve 1101 (Line)\n",
      "Info    : [ 60%] Meshing curve 1102 (Line)\n",
      "Info    : [ 60%] Meshing curve 1103 (Line)\n",
      "Info    : [ 60%] Meshing curve 1104 (Line)\n",
      "Info    : [ 60%] Meshing curve 1105 (Line)\n",
      "Info    : [ 60%] Meshing curve 1106 (Line)\n",
      "Info    : [ 60%] Meshing curve 1107 (Line)\n",
      "Info    : [ 60%] Meshing curve 1108 (Line)\n",
      "Info    : [ 60%] Meshing curve 1109 (Line)\n",
      "Info    : [ 60%] Meshing curve 1110 (Line)\n",
      "Info    : [ 60%] Meshing curve 1111 (Line)\n",
      "Info    : [ 60%] Meshing curve 1112 (Line)\n",
      "Info    : [ 60%] Meshing curve 1113 (Line)\n",
      "Info    : [ 60%] Meshing curve 1114 (Line)\n",
      "Info    : [ 60%] Meshing curve 1115 (Line)\n",
      "Info    : [ 60%] Meshing curve 1116 (Line)\n",
      "Info    : [ 60%] Meshing curve 1117 (Line)\n",
      "Info    : [ 60%] Meshing curve 1118 (Line)\n",
      "Info    : [ 60%] Meshing curve 1119 (Line)\n",
      "Info    : [ 60%] Meshing curve 1120 (Line)\n",
      "Info    : [ 60%] Meshing curve 1121 (Line)\n",
      "Info    : [ 60%] Meshing curve 1122 (Line)\n",
      "Info    : [ 60%] Meshing curve 1123 (Line)\n",
      "Info    : [ 60%] Meshing curve 1124 (Line)\n",
      "Info    : [ 60%] Meshing curve 1125 (Line)\n",
      "Info    : [ 60%] Meshing curve 1126 (Line)\n",
      "Info    : [ 60%] Meshing curve 1127 (Line)\n",
      "Info    : [ 60%] Meshing curve 1128 (Line)\n",
      "Info    : [ 60%] Meshing curve 1129 (Line)\n",
      "Info    : [ 60%] Meshing curve 1130 (Line)\n",
      "Info    : [ 60%] Meshing curve 1131 (Line)\n",
      "Info    : [ 60%] Meshing curve 1132 (Line)\n",
      "Info    : [ 60%] Meshing curve 1133 (Line)\n",
      "Info    : [ 60%] Meshing curve 1134 (Line)\n",
      "Info    : [ 60%] Meshing curve 1135 (Line)\n",
      "Info    : [ 60%] Meshing curve 1136 (Line)\n",
      "Info    : [ 60%] Meshing curve 1137 (Line)\n",
      "Info    : [ 60%] Meshing curve 1138 (Line)\n",
      "Info    : [ 60%] Meshing curve 1139 (Line)\n",
      "Info    : [ 60%] Meshing curve 1140 (Line)\n",
      "Info    : [ 60%] Meshing curve 1141 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1145 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1147 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1150 (Line)\n",
      "Info    : [ 60%] Meshing curve 1151 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1153 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1155 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1159 (Line)\n",
      "Info    : [ 60%] Meshing curve 1160 (Line)\n",
      "Info    : [ 60%] Meshing curve 1161 (Line)\n",
      "Info    : [ 60%] Meshing curve 1162 (Line)\n",
      "Info    : [ 60%] Meshing curve 1163 (Line)\n",
      "Info    : [ 60%] Meshing curve 1164 (Line)\n",
      "Info    : [ 60%] Meshing curve 1165 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1167 (Line)\n",
      "Info    : [ 60%] Meshing curve 1168 (Line)\n",
      "Info    : [ 60%] Meshing curve 1169 (Line)\n",
      "Info    : [ 60%] Meshing curve 1170 (Line)\n",
      "Info    : [ 60%] Meshing curve 1171 (Line)\n",
      "Info    : [ 60%] Meshing curve 1172 (Line)\n",
      "Info    : [ 60%] Meshing curve 1173 (Line)\n",
      "Info    : [ 60%] Meshing curve 1174 (Line)\n",
      "Info    : [ 60%] Meshing curve 1175 (Line)\n",
      "Info    : [ 60%] Meshing curve 1176 (Line)\n",
      "Info    : [ 60%] Meshing curve 1177 (Line)\n",
      "Info    : [ 60%] Meshing curve 1178 (Line)\n",
      "Info    : [ 60%] Meshing curve 1179 (Line)\n",
      "Info    : [ 60%] Meshing curve 1180 (Line)\n",
      "Info    : [ 60%] Meshing curve 1181 (Line)\n",
      "Info    : [ 60%] Meshing curve 1182 (Line)\n",
      "Info    : [ 60%] Meshing curve 1183 (Line)\n",
      "Info    : [ 60%] Meshing curve 1184 (Line)\n",
      "Info    : [ 60%] Meshing curve 1185 (Line)\n",
      "Info    : [ 60%] Meshing curve 1186 (Line)\n",
      "Info    : [ 60%] Meshing curve 1187 (Line)\n",
      "Info    : [ 60%] Meshing curve 1188 (Line)\n",
      "Info    : [ 60%] Meshing curve 1189 (Line)\n",
      "Info    : [ 60%] Meshing curve 1190 (Line)\n",
      "Info    : [ 60%] Meshing curve 1191 (Line)\n",
      "Info    : [ 60%] Meshing curve 1192 (Line)\n",
      "Info    : [ 60%] Meshing curve 1193 (Line)\n",
      "Info    : [ 60%] Meshing curve 1194 (Line)\n",
      "Info    : [ 60%] Meshing curve 1195 (Line)\n",
      "Info    : [ 60%] Meshing curve 1196 (Line)\n",
      "Info    : [ 60%] Meshing curve 1197 (Line)\n",
      "Info    : [ 60%] Meshing curve 1198 (Line)\n",
      "Info    : [ 60%] Meshing curve 1199 (Line)\n",
      "Info    : [ 60%] Meshing curve 1200 (Line)\n",
      "Info    : [ 60%] Meshing curve 1201 (Line)\n",
      "Info    : [ 60%] Meshing curve 1202 (Line)\n",
      "Info    : [ 60%] Meshing curve 1203 (Line)\n",
      "Info    : [ 60%] Meshing curve 1204 (Line)\n",
      "Info    : [ 60%] Meshing curve 1205 (Line)\n",
      "Info    : [ 60%] Meshing curve 1206 (Line)\n",
      "Info    : [ 60%] Meshing curve 1207 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1211 (Line)\n",
      "Info    : [ 60%] Meshing curve 1212 (Line)\n",
      "Info    : [ 60%] Meshing curve 1213 (Line)\n",
      "Info    : [ 60%] Meshing curve 1214 (Line)\n",
      "Info    : [ 60%] Meshing curve 1215 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1217 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1221 (Line)\n",
      "Info    : [ 60%] Meshing curve 1222 (Line)\n",
      "Info    : [ 60%] Meshing curve 1223 (Line)\n",
      "Info    : [ 60%] Meshing curve 1224 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1226 (Line)\n",
      "Info    : [ 60%] Meshing curve 1227 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1231 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1233 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1239 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1241 (Line)\n",
      "Info    : [ 60%] Meshing curve 1242 (Line)\n",
      "Info    : [ 60%] Meshing curve 1243 (Line)\n",
      "Info    : [ 60%] Meshing curve 1244 (Line)\n",
      "Info    : [ 60%] Meshing curve 1245 (Line)\n",
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      "Info    : [ 60%] Meshing curve 1247 (Line)\n",
      "Info    : [ 60%] Meshing curve 1248 (Line)\n",
      "Info    : [ 60%] Meshing curve 1249 (Line)\n",
      "Info    : [ 60%] Meshing curve 1250 (Line)\n",
      "Info    : [ 60%] Meshing curve 1251 (Line)\n",
      "Info    : [ 60%] Meshing curve 1252 (Line)\n",
      "Info    : [ 60%] Meshing curve 1253 (Line)\n",
      "Info    : [ 60%] Meshing curve 1254 (Line)\n",
      "Info    : [ 60%] Meshing curve 1255 (Line)\n",
      "Info    : [ 60%] Meshing curve 1256 (Line)\n",
      "Info    : [ 60%] Meshing curve 1257 (Line)\n",
      "Info    : [ 60%] Meshing curve 1258 (Line)\n",
      "Info    : [ 70%] Meshing curve 1259 (Line)\n",
      "Info    : [ 70%] Meshing curve 1260 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1262 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1264 (Line)\n",
      "Info    : [ 70%] Meshing curve 1265 (Line)\n",
      "Info    : [ 70%] Meshing curve 1266 (Line)\n",
      "Info    : [ 70%] Meshing curve 1267 (Line)\n",
      "Info    : [ 70%] Meshing curve 1268 (Line)\n",
      "Info    : [ 70%] Meshing curve 1269 (Line)\n",
      "Info    : [ 70%] Meshing curve 1270 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1276 (Line)\n",
      "Info    : [ 70%] Meshing curve 1277 (Line)\n",
      "Info    : [ 70%] Meshing curve 1278 (Line)\n",
      "Info    : [ 70%] Meshing curve 1279 (Line)\n",
      "Info    : [ 70%] Meshing curve 1280 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1282 (Line)\n",
      "Info    : [ 70%] Meshing curve 1283 (Line)\n",
      "Info    : [ 70%] Meshing curve 1284 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1286 (Line)\n",
      "Info    : [ 70%] Meshing curve 1287 (Line)\n",
      "Info    : [ 70%] Meshing curve 1288 (Line)\n",
      "Info    : [ 70%] Meshing curve 1289 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1291 (Line)\n",
      "Info    : [ 70%] Meshing curve 1292 (Line)\n",
      "Info    : [ 70%] Meshing curve 1293 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1295 (Line)\n",
      "Info    : [ 70%] Meshing curve 1296 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1298 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1300 (Line)\n",
      "Info    : [ 70%] Meshing curve 1301 (Line)\n",
      "Info    : [ 70%] Meshing curve 1302 (Line)\n",
      "Info    : [ 70%] Meshing curve 1303 (Line)\n",
      "Info    : [ 70%] Meshing curve 1304 (Line)\n",
      "Info    : [ 70%] Meshing curve 1305 (Line)\n",
      "Info    : [ 70%] Meshing curve 1306 (Line)\n",
      "Info    : [ 70%] Meshing curve 1307 (Line)\n",
      "Info    : [ 70%] Meshing curve 1308 (Line)\n",
      "Info    : [ 70%] Meshing curve 1309 (Line)\n",
      "Info    : [ 70%] Meshing curve 1310 (Line)\n",
      "Info    : [ 70%] Meshing curve 1311 (Line)\n",
      "Info    : [ 70%] Meshing curve 1312 (Line)\n",
      "Info    : [ 70%] Meshing curve 1313 (Line)\n",
      "Info    : [ 70%] Meshing curve 1314 (Line)\n",
      "Info    : [ 70%] Meshing curve 1315 (Line)\n",
      "Info    : [ 70%] Meshing curve 1316 (Line)\n",
      "Info    : [ 70%] Meshing curve 1317 (Line)\n",
      "Info    : [ 70%] Meshing curve 1318 (Line)\n",
      "Info    : [ 70%] Meshing curve 1319 (Line)\n",
      "Info    : [ 70%] Meshing curve 1320 (Line)\n",
      "Info    : [ 70%] Meshing curve 1321 (Line)\n",
      "Info    : [ 70%] Meshing curve 1322 (Line)\n",
      "Info    : [ 70%] Meshing curve 1323 (Line)\n",
      "Info    : [ 70%] Meshing curve 1324 (Line)\n",
      "Info    : [ 70%] Meshing curve 1325 (Line)\n",
      "Info    : [ 70%] Meshing curve 1326 (Line)\n",
      "Info    : [ 70%] Meshing curve 1327 (Line)\n",
      "Info    : [ 70%] Meshing curve 1328 (Line)\n",
      "Info    : [ 70%] Meshing curve 1329 (Line)\n",
      "Info    : [ 70%] Meshing curve 1330 (Line)\n",
      "Info    : [ 70%] Meshing curve 1331 (Line)\n",
      "Info    : [ 70%] Meshing curve 1332 (Line)\n",
      "Info    : [ 70%] Meshing curve 1333 (Line)\n",
      "Info    : [ 70%] Meshing curve 1334 (Line)\n",
      "Info    : [ 70%] Meshing curve 1335 (Line)\n",
      "Info    : [ 70%] Meshing curve 1336 (Line)\n",
      "Info    : [ 70%] Meshing curve 1337 (Line)\n",
      "Info    : [ 70%] Meshing curve 1338 (Line)\n",
      "Info    : [ 70%] Meshing curve 1339 (Line)\n",
      "Info    : [ 70%] Meshing curve 1340 (Line)\n",
      "Info    : [ 70%] Meshing curve 1341 (Line)\n",
      "Info    : [ 70%] Meshing curve 1342 (Line)\n",
      "Info    : [ 70%] Meshing curve 1343 (Line)\n",
      "Info    : [ 70%] Meshing curve 1344 (Line)\n",
      "Info    : [ 70%] Meshing curve 1345 (Line)\n",
      "Info    : [ 70%] Meshing curve 1346 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1348 (Line)\n",
      "Info    : [ 70%] Meshing curve 1349 (Line)\n",
      "Info    : [ 70%] Meshing curve 1350 (Line)\n",
      "Info    : [ 70%] Meshing curve 1351 (Line)\n",
      "Info    : [ 70%] Meshing curve 1352 (Line)\n",
      "Info    : [ 70%] Meshing curve 1353 (Line)\n",
      "Info    : [ 70%] Meshing curve 1354 (Line)\n",
      "Info    : [ 70%] Meshing curve 1355 (Line)\n",
      "Info    : [ 70%] Meshing curve 1356 (Line)\n",
      "Info    : [ 70%] Meshing curve 1357 (Line)\n",
      "Info    : [ 70%] Meshing curve 1358 (Line)\n",
      "Info    : [ 70%] Meshing curve 1359 (Line)\n",
      "Info    : [ 70%] Meshing curve 1360 (Line)\n",
      "Info    : [ 70%] Meshing curve 1361 (Line)\n",
      "Info    : [ 70%] Meshing curve 1362 (Line)\n",
      "Info    : [ 70%] Meshing curve 1363 (Line)\n",
      "Info    : [ 70%] Meshing curve 1364 (Line)\n",
      "Info    : [ 70%] Meshing curve 1365 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1369 (Line)\n",
      "Info    : [ 70%] Meshing curve 1370 (Line)\n",
      "Info    : [ 70%] Meshing curve 1371 (Line)\n",
      "Info    : [ 70%] Meshing curve 1372 (Line)\n",
      "Info    : [ 70%] Meshing curve 1373 (Line)\n",
      "Info    : [ 70%] Meshing curve 1374 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1379 (Line)\n",
      "Info    : [ 70%] Meshing curve 1380 (Line)\n",
      "Info    : [ 70%] Meshing curve 1381 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1389 (Line)\n",
      "Info    : [ 70%] Meshing curve 1390 (Line)\n",
      "Info    : [ 70%] Meshing curve 1391 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1399 (Line)\n",
      "Info    : [ 70%] Meshing curve 1400 (Line)\n",
      "Info    : [ 70%] Meshing curve 1401 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1406 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1410 (Line)\n",
      "Info    : [ 70%] Meshing curve 1411 (Line)\n",
      "Info    : [ 70%] Meshing curve 1412 (Line)\n",
      "Info    : [ 70%] Meshing curve 1413 (Line)\n",
      "Info    : [ 70%] Meshing curve 1414 (Line)\n",
      "Info    : [ 70%] Meshing curve 1415 (Line)\n",
      "Info    : [ 70%] Meshing curve 1416 (Line)\n",
      "Info    : [ 70%] Meshing curve 1417 (Line)\n",
      "Info    : [ 70%] Meshing curve 1418 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1421 (Line)\n",
      "Info    : [ 70%] Meshing curve 1422 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1424 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1426 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1428 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1431 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1441 (Line)\n",
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      "Info    : [ 70%] Meshing curve 1443 (Line)\n",
      "Info    : [ 70%] Meshing curve 1444 (Line)\n",
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      "Info    : [ 90%] Meshing curve 1830 (Line)\n",
      "Info    : [ 90%] Meshing curve 1831 (Line)\n",
      "Info    : [ 90%] Meshing curve 1832 (Line)\n",
      "Info    : [ 90%] Meshing curve 1833 (Line)\n",
      "Info    : [ 90%] Meshing curve 1834 (Line)\n",
      "Info    : [ 90%] Meshing curve 1835 (Line)\n",
      "Info    : [ 90%] Meshing curve 1836 (Line)\n",
      "Info    : [ 90%] Meshing curve 1837 (Line)\n",
      "Info    : [ 90%] Meshing curve 1838 (Line)\n",
      "Info    : [ 90%] Meshing curve 1839 (Line)\n",
      "Info    : [ 90%] Meshing curve 1840 (Line)\n",
      "Info    : [ 90%] Meshing curve 1841 (Line)\n",
      "Info    : [ 90%] Meshing curve 1842 (Line)\n",
      "Info    : [ 90%] Meshing curve 1843 (Line)\n",
      "Info    : [ 90%] Meshing curve 1844 (Line)\n",
      "Info    : [ 90%] Meshing curve 1845 (Line)\n",
      "Info    : [ 90%] Meshing curve 1846 (Line)\n",
      "Info    : [ 90%] Meshing curve 1847 (Line)\n",
      "Info    : [ 90%] Meshing curve 1848 (Line)\n",
      "Info    : [ 90%] Meshing curve 1849 (Line)\n",
      "Info    : [ 90%] Meshing curve 1850 (Line)\n",
      "Info    : [ 90%] Meshing curve 1851 (Line)\n",
      "Info    : [ 90%] Meshing curve 1852 (Line)\n",
      "Info    : [ 90%] Meshing curve 1853 (Line)\n",
      "Info    : [ 90%] Meshing curve 1854 (Line)\n",
      "Info    : [ 90%] Meshing curve 1855 (Line)\n",
      "Info    : [ 90%] Meshing curve 1856 (Line)\n",
      "Info    : [ 90%] Meshing curve 1857 (Line)\n",
      "Info    : [ 90%] Meshing curve 1858 (Line)\n",
      "Info    : [ 90%] Meshing curve 1859 (Line)\n",
      "Info    : [ 90%] Meshing curve 1860 (Line)\n",
      "Info    : [ 90%] Meshing curve 1861 (Line)\n",
      "Info    : [ 90%] Meshing curve 1862 (Line)\n",
      "Info    : [ 90%] Meshing curve 1863 (Line)\n",
      "Info    : [ 90%] Meshing curve 1864 (Line)\n",
      "Info    : [ 90%] Meshing curve 1865 (Line)\n",
      "Info    : [ 90%] Meshing curve 1866 (Line)\n",
      "Info    : [ 90%] Meshing curve 1867 (Line)\n",
      "Info    : [ 90%] Meshing curve 1868 (Line)\n",
      "Info    : [ 90%] Meshing curve 1869 (Line)\n",
      "Info    : [ 90%] Meshing curve 1870 (Line)\n",
      "Info    : [ 90%] Meshing curve 1871 (Line)\n",
      "Info    : [ 90%] Meshing curve 1872 (Line)\n",
      "Info    : [ 90%] Meshing curve 1873 (Line)\n",
      "Info    : [ 90%] Meshing curve 1874 (Line)\n",
      "Info    : [ 90%] Meshing curve 1875 (Line)\n",
      "Info    : [ 90%] Meshing curve 1876 (Line)\n",
      "Info    : [ 90%] Meshing curve 1877 (Line)\n",
      "Info    : [ 90%] Meshing curve 1878 (Line)\n",
      "Info    : [ 90%] Meshing curve 1879 (Line)\n",
      "Info    : [ 90%] Meshing curve 1880 (Line)\n",
      "Info    : [ 90%] Meshing curve 1881 (Line)\n",
      "Info    : [ 90%] Meshing curve 1882 (Line)\n",
      "Info    : [ 90%] Meshing curve 1883 (Line)\n",
      "Info    : [ 90%] Meshing curve 1884 (Line)\n",
      "Info    : [ 90%] Meshing curve 1885 (Line)\n",
      "Info    : [ 90%] Meshing curve 1886 (Line)\n",
      "Info    : [100%] Meshing curve 1887 (Line)\n",
      "Info    : [100%] Meshing curve 1888 (Line)\n",
      "Info    : [100%] Meshing curve 1889 (Line)\n",
      "Info    : [100%] Meshing curve 1890 (Line)\n",
      "Info    : [100%] Meshing curve 1891 (Line)\n",
      "Info    : [100%] Meshing curve 1892 (Line)\n",
      "Info    : [100%] Meshing curve 1893 (Line)\n",
      "Info    : [100%] Meshing curve 1894 (Line)\n",
      "Info    : [100%] Meshing curve 1895 (Line)\n",
      "Info    : [100%] Meshing curve 1896 (Line)\n",
      "Info    : [100%] Meshing curve 1897 (Line)\n",
      "Info    : [100%] Meshing curve 1898 (Line)\n",
      "Info    : [100%] Meshing curve 1899 (Line)\n",
      "Info    : [100%] Meshing curve 1900 (Line)\n",
      "Info    : [100%] Meshing curve 1901 (Line)\n",
      "Info    : [100%] Meshing curve 1902 (Line)\n",
      "Info    : [100%] Meshing curve 1903 (Line)\n",
      "Info    : [100%] Meshing curve 1904 (Line)\n",
      "Info    : [100%] Meshing curve 1905 (Line)\n",
      "Info    : [100%] Meshing curve 1906 (Line)\n",
      "Info    : [100%] Meshing curve 1907 (Line)\n",
      "Info    : [100%] Meshing curve 1908 (Line)\n",
      "Info    : [100%] Meshing curve 1909 (Line)\n",
      "Info    : [100%] Meshing curve 1910 (Line)\n",
      "Info    : [100%] Meshing curve 1911 (Line)\n",
      "Info    : [100%] Meshing curve 1912 (Line)\n",
      "Info    : [100%] Meshing curve 1913 (Line)\n",
      "Info    : [100%] Meshing curve 1914 (Line)\n",
      "Info    : [100%] Meshing curve 1915 (Line)\n",
      "Info    : [100%] Meshing curve 1916 (Line)\n",
      "Info    : [100%] Meshing curve 1917 (Line)\n",
      "Info    : [100%] Meshing curve 1918 (Line)\n",
      "Info    : [100%] Meshing curve 1919 (Line)\n",
      "Info    : [100%] Meshing curve 1920 (Line)\n",
      "Info    : [100%] Meshing curve 1921 (Line)\n",
      "Info    : [100%] Meshing curve 1922 (Line)\n",
      "Info    : [100%] Meshing curve 1923 (Line)\n",
      "Info    : [100%] Meshing curve 1924 (Line)\n",
      "Info    : [100%] Meshing curve 1925 (Line)\n",
      "Info    : [100%] Meshing curve 1926 (Line)\n",
      "Info    : [100%] Meshing curve 1927 (Line)\n",
      "Info    : [100%] Meshing curve 1928 (Line)\n",
      "Info    : [100%] Meshing curve 1929 (Line)\n",
      "Info    : [100%] Meshing curve 1930 (Line)\n",
      "Info    : [100%] Meshing curve 1931 (Line)\n",
      "Info    : [100%] Meshing curve 1932 (Line)\n",
      "Info    : [100%] Meshing curve 1933 (Line)\n",
      "Info    : [100%] Meshing curve 1934 (Line)\n",
      "Info    : [100%] Meshing curve 1935 (Line)\n",
      "Info    : [100%] Meshing curve 1936 (Line)\n",
      "Info    : [100%] Meshing curve 1937 (Line)\n",
      "Info    : [100%] Meshing curve 1938 (Line)\n",
      "Info    : [100%] Meshing curve 1939 (Line)\n",
      "Info    : [100%] Meshing curve 1940 (Line)\n",
      "Info    : [100%] Meshing curve 1941 (Line)\n",
      "Info    : [100%] Meshing curve 1942 (Line)\n",
      "Info    : [100%] Meshing curve 1943 (Line)\n",
      "Info    : [100%] Meshing curve 1944 (Line)\n",
      "Info    : [100%] Meshing curve 1945 (Line)\n",
      "Info    : [100%] Meshing curve 1946 (Line)\n",
      "Info    : [100%] Meshing curve 1947 (Line)\n",
      "Info    : [100%] Meshing curve 1948 (Line)\n",
      "Info    : [100%] Meshing curve 1949 (Line)\n",
      "Info    : [100%] Meshing curve 1950 (Line)\n",
      "Info    : [100%] Meshing curve 1951 (Line)\n",
      "Info    : [100%] Meshing curve 1952 (Line)\n",
      "Info    : [100%] Meshing curve 1953 (Line)\n",
      "Info    : [100%] Meshing curve 1954 (Line)\n",
      "Info    : [100%] Meshing curve 1955 (Line)\n",
      "Info    : [100%] Meshing curve 1956 (Line)\n",
      "Info    : [100%] Meshing curve 1957 (Line)\n",
      "Info    : [100%] Meshing curve 1958 (Line)\n",
      "Info    : [100%] Meshing curve 1959 (Line)\n",
      "Info    : [100%] Meshing curve 1960 (Line)\n",
      "Info    : [100%] Meshing curve 1961 (Line)\n",
      "Info    : [100%] Meshing curve 1962 (Line)\n",
      "Info    : [100%] Meshing curve 1963 (Line)\n",
      "Info    : [100%] Meshing curve 1964 (Line)\n",
      "Info    : [100%] Meshing curve 1965 (Line)\n",
      "Info    : [100%] Meshing curve 1966 (Line)\n",
      "Info    : [100%] Meshing curve 1967 (Line)\n",
      "Info    : [100%] Meshing curve 1968 (Line)\n",
      "Info    : [100%] Meshing curve 1969 (Line)\n",
      "Info    : [100%] Meshing curve 1970 (Line)\n",
      "Info    : [100%] Meshing curve 1971 (Line)\n",
      "Info    : [100%] Meshing curve 1972 (Line)\n",
      "Info    : [100%] Meshing curve 1973 (Line)\n",
      "Info    : [100%] Meshing curve 1974 (Line)\n",
      "Info    : [100%] Meshing curve 1975 (Line)\n",
      "Info    : [100%] Meshing curve 1976 (Line)\n",
      "Info    : [100%] Meshing curve 1977 (Line)\n",
      "Info    : [100%] Meshing curve 1978 (Line)\n",
      "Info    : [100%] Meshing curve 1979 (Line)\n",
      "Info    : [100%] Meshing curve 1980 (Line)\n",
      "Info    : [100%] Meshing curve 1981 (Line)\n",
      "Info    : [100%] Meshing curve 1982 (Line)\n",
      "Info    : [100%] Meshing curve 1983 (Line)\n",
      "Info    : [100%] Meshing curve 1984 (Line)\n",
      "Info    : [100%] Meshing curve 1985 (Line)\n",
      "Info    : [100%] Meshing curve 1986 (Line)\n",
      "Info    : [100%] Meshing curve 1987 (Line)\n",
      "Info    : [100%] Meshing curve 1988 (Line)\n",
      "Info    : [100%] Meshing curve 1989 (Line)\n",
      "Info    : [100%] Meshing curve 1990 (Line)\n",
      "Info    : [100%] Meshing curve 1991 (Line)\n",
      "Info    : [100%] Meshing curve 1992 (Line)\n",
      "Info    : [100%] Meshing curve 1993 (Line)\n",
      "Info    : [100%] Meshing curve 1994 (Line)\n",
      "Info    : [100%] Meshing curve 1995 (Line)\n",
      "Info    : [100%] Meshing curve 1996 (Line)\n",
      "Info    : [100%] Meshing curve 1997 (Line)\n",
      "Info    : [100%] Meshing curve 1998 (Line)\n",
      "Info    : [100%] Meshing curve 1999 (Line)\n",
      "Info    : [100%] Meshing curve 2000 (Line)\n",
      "Info    : [100%] Meshing curve 2001 (Line)\n",
      "Info    : [100%] Meshing curve 2002 (Line)\n",
      "Info    : [100%] Meshing curve 2003 (Line)\n",
      "Info    : [100%] Meshing curve 2004 (Line)\n",
      "Info    : [100%] Meshing curve 2005 (Line)\n",
      "Info    : [100%] Meshing curve 2006 (Line)\n",
      "Info    : [100%] Meshing curve 2007 (Line)\n",
      "Info    : [100%] Meshing curve 2008 (Line)\n",
      "Info    : [100%] Meshing curve 2009 (Line)\n",
      "Info    : [100%] Meshing curve 2010 (Line)\n",
      "Info    : [100%] Meshing curve 2011 (Line)\n",
      "Info    : [100%] Meshing curve 2012 (Line)\n",
      "Info    : [100%] Meshing curve 2013 (Line)\n",
      "Info    : [100%] Meshing curve 2014 (Line)\n",
      "Info    : [100%] Meshing curve 2015 (Line)\n",
      "Info    : [100%] Meshing curve 2016 (Line)\n",
      "Info    : [100%] Meshing curve 2017 (Line)\n",
      "Info    : [100%] Meshing curve 2018 (Line)\n",
      "Info    : [100%] Meshing curve 2019 (Line)\n",
      "Info    : [100%] Meshing curve 2020 (Line)\n",
      "Info    : [100%] Meshing curve 2021 (Line)\n",
      "Info    : [100%] Meshing curve 2022 (Line)\n",
      "Info    : [100%] Meshing curve 2023 (Line)\n",
      "Info    : [100%] Meshing curve 2024 (Line)\n",
      "Info    : [100%] Meshing curve 2025 (Line)\n",
      "Info    : [100%] Meshing curve 2026 (Line)\n",
      "Info    : [100%] Meshing curve 2027 (Line)\n",
      "Info    : [100%] Meshing curve 2028 (Line)\n",
      "Info    : [100%] Meshing curve 2029 (Line)\n",
      "Info    : [100%] Meshing curve 2030 (Line)\n",
      "Info    : [100%] Meshing curve 2031 (Line)\n",
      "Info    : [100%] Meshing curve 2032 (Line)\n",
      "Info    : [100%] Meshing curve 2033 (Line)\n",
      "Info    : [100%] Meshing curve 2034 (Line)\n",
      "Info    : [100%] Meshing curve 2035 (Line)\n",
      "Info    : [100%] Meshing curve 2036 (Line)\n",
      "Info    : [100%] Meshing curve 2037 (Line)\n",
      "Info    : [100%] Meshing curve 2038 (Line)\n",
      "Info    : [100%] Meshing curve 2039 (Line)\n",
      "Info    : [100%] Meshing curve 2040 (Line)\n",
      "Info    : [100%] Meshing curve 2041 (Line)\n",
      "Info    : [100%] Meshing curve 2042 (Line)\n",
      "Info    : [100%] Meshing curve 2043 (Line)\n",
      "Info    : [100%] Meshing curve 2044 (Line)\n",
      "Info    : [100%] Meshing curve 2045 (Line)\n",
      "Info    : [100%] Meshing curve 2046 (Line)\n",
      "Info    : [100%] Meshing curve 2047 (Line)\n",
      "Info    : [100%] Meshing curve 2048 (Line)\n",
      "Info    : [100%] Meshing curve 2049 (Line)\n",
      "Info    : [100%] Meshing curve 2050 (Line)\n",
      "Info    : [100%] Meshing curve 2051 (Line)\n",
      "Info    : [100%] Meshing curve 2052 (Line)\n",
      "Info    : [100%] Meshing curve 2053 (Line)\n",
      "Info    : [100%] Meshing curve 2054 (Line)\n",
      "Info    : [100%] Meshing curve 2055 (Line)\n",
      "Info    : [100%] Meshing curve 2056 (Line)\n",
      "Info    : [100%] Meshing curve 2057 (Line)\n",
      "Info    : [100%] Meshing curve 2058 (Line)\n",
      "Info    : [100%] Meshing curve 2059 (Line)\n",
      "Info    : [100%] Meshing curve 2060 (Line)\n",
      "Info    : [100%] Meshing curve 2061 (Line)\n",
      "Info    : [100%] Meshing curve 2062 (Line)\n",
      "Info    : [100%] Meshing curve 2063 (Line)\n",
      "Info    : [100%] Meshing curve 2064 (Line)\n",
      "Info    : [100%] Meshing curve 2065 (Line)\n",
      "Info    : [100%] Meshing curve 2066 (Line)\n",
      "Info    : [100%] Meshing curve 2067 (Line)\n",
      "Info    : [100%] Meshing curve 2068 (Line)\n",
      "Info    : [100%] Meshing curve 2069 (Line)\n",
      "Info    : [100%] Meshing curve 2070 (Line)\n",
      "Info    : [100%] Meshing curve 2071 (Line)\n",
      "Info    : [100%] Meshing curve 2072 (Line)\n",
      "Info    : [100%] Meshing curve 2073 (Line)\n",
      "Info    : [100%] Meshing curve 2074 (Line)\n",
      "Info    : [100%] Meshing curve 2075 (Line)\n",
      "Info    : [100%] Meshing curve 2076 (Line)\n",
      "Info    : [100%] Meshing curve 2077 (Line)\n",
      "Info    : [100%] Meshing curve 2078 (Line)\n",
      "Info    : [100%] Meshing curve 2079 (Line)\n",
      "Info    : [100%] Meshing curve 2080 (Line)\n",
      "Info    : [100%] Meshing curve 2081 (Line)\n",
      "Info    : [100%] Meshing curve 2082 (Line)\n",
      "Info    : [100%] Meshing curve 2083 (Line)\n",
      "Info    : [100%] Meshing curve 2084 (Line)\n",
      "Info    : [100%] Meshing curve 2085 (Line)\n",
      "Info    : [100%] Meshing curve 2086 (Line)\n",
      "Info    : [100%] Meshing curve 2087 (Line)\n",
      "Info    : [100%] Meshing curve 2088 (Line)\n",
      "Info    : [100%] Meshing curve 2089 (Line)\n",
      "Info    : [100%] Meshing curve 2090 (Line)\n",
      "Info    : [100%] Meshing curve 2091 (Line)\n",
      "Info    : [100%] Meshing curve 2092 (Line)\n",
      "Info    : [100%] Meshing curve 2093 (Line)\n",
      "Info    : [100%] Meshing curve 2094 (Line)\n",
      "Info    : [100%] Meshing curve 2095 (Line)\n",
      "Info    : Done meshing 1D (Wall 0.09732s, CPU 0.102726s)\n",
      "Info    : Meshing 2D...\n",
      "Info    : [  0%] Meshing surface 1 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 10%] Meshing surface 2 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 10%] Meshing surface 3 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 20%] Meshing surface 4 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 20%] Meshing surface 5 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 20%] Meshing surface 6 (Plane, Frontal-Delaunay)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Info    : [ 30%] Meshing surface 7 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 30%] Meshing surface 8 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 40%] Meshing surface 9 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 40%] Meshing surface 10 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 40%] Meshing surface 11 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 50%] Meshing surface 12 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 50%] Meshing surface 13 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 50%] Meshing surface 14 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 60%] Meshing surface 15 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 60%] Meshing surface 16 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 70%] Meshing surface 17 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 70%] Meshing surface 18 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 70%] Meshing surface 19 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 80%] Meshing surface 20 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 80%] Meshing surface 21 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 90%] Meshing surface 22 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 90%] Meshing surface 23 (Plane, Frontal-Delaunay)\n",
      "Info    : [ 90%] Meshing surface 24 (Plane, Frontal-Delaunay)\n",
      "Info    : [100%] Meshing surface 25 (Plane, Frontal-Delaunay)\n",
      "Info    : [100%] Meshing surface 26 (Plane, Frontal-Delaunay)\n",
      "Info    : Done meshing 2D (Wall 2.31139s, CPU 2.31344s)\n",
      "Info    : Meshing 3D...\n",
      "Info    : 3D Meshing 1 volume with 1 connected component\n",
      "Info    : Tetrahedrizing 58675 nodes...\n",
      "Info    : Done tetrahedrizing 58683 nodes (Wall 0.40287s, CPU 0.379725s)\n",
      "Info    : Reconstructing mesh...\n",
      "Info    :  - Creating surface mesh\n",
      "Info    :  - Identifying boundary edges\n",
      "Info    :  - Recovering boundary\n",
      "Info    : Done reconstructing mesh (Wall 6.23076s, CPU 6.17359s)\n",
      "Info    : Found volume 1\n",
      "Info    : It. 0 - 0 nodes created - worst tet radius 3.58857 (nodes removed 0 0)\n",
      "Info    : It. 500 - 19 nodes created - worst tet radius 2.18533 (nodes removed 0 481)\n",
      "Info    : It. 1000 - 22 nodes created - worst tet radius 2.07383 (nodes removed 0 978)\n",
      "Info    : It. 1500 - 23 nodes created - worst tet radius 2.02089 (nodes removed 0 1477)\n",
      "Info    : It. 2000 - 24 nodes created - worst tet radius 1.98725 (nodes removed 0 1976)\n",
      "Info    : It. 2500 - 24 nodes created - worst tet radius 1.9591 (nodes removed 0 2476)\n",
      "Info    : It. 3000 - 24 nodes created - worst tet radius 1.93732 (nodes removed 0 2976)\n",
      "Info    : It. 3500 - 24 nodes created - worst tet radius 1.91791 (nodes removed 0 3476)\n",
      "Info    : It. 4000 - 24 nodes created - worst tet radius 1.90146 (nodes removed 0 3976)\n",
      "Info    : It. 4500 - 24 nodes created - worst tet radius 1.88637 (nodes removed 0 4476)\n",
      "Info    : It. 5000 - 25 nodes created - worst tet radius 1.87494 (nodes removed 0 4975)\n",
      "Info    : It. 5500 - 26 nodes created - worst tet radius 1.86327 (nodes removed 0 5474)\n",
      "Info    : It. 6000 - 26 nodes created - worst tet radius 1.85259 (nodes removed 0 5974)\n",
      "Info    : It. 6500 - 26 nodes created - worst tet radius 1.84153 (nodes removed 0 6474)\n",
      "Info    : It. 7000 - 26 nodes created - worst tet radius 1.83015 (nodes removed 0 6974)\n",
      "Info    : It. 7500 - 26 nodes created - worst tet radius 1.81917 (nodes removed 0 7474)\n",
      "Info    : It. 8000 - 26 nodes created - worst tet radius 1.80937 (nodes removed 0 7974)\n",
      "Info    : It. 8500 - 26 nodes created - worst tet radius 1.79988 (nodes removed 0 8474)\n",
      "Info    : It. 9000 - 27 nodes created - worst tet radius 1.79048 (nodes removed 0 8973)\n",
      "Info    : It. 9500 - 27 nodes created - worst tet radius 1.78099 (nodes removed 0 9473)\n",
      "Info    : It. 10000 - 27 nodes created - worst tet radius 1.77167 (nodes removed 0 9973)\n",
      "Info    : It. 10500 - 27 nodes created - worst tet radius 1.76393 (nodes removed 0 10473)\n",
      "Info    : It. 11000 - 27 nodes created - worst tet radius 1.75545 (nodes removed 0 10973)\n",
      "Info    : It. 11500 - 27 nodes created - worst tet radius 1.74692 (nodes removed 0 11473)\n",
      "Info    : It. 12000 - 27 nodes created - worst tet radius 1.73847 (nodes removed 0 11973)\n",
      "Info    : It. 12500 - 28 nodes created - worst tet radius 1.73027 (nodes removed 0 12472)\n",
      "Info    : It. 13000 - 28 nodes created - worst tet radius 1.72267 (nodes removed 0 12972)\n",
      "Info    : It. 13500 - 29 nodes created - worst tet radius 1.71524 (nodes removed 0 13471)\n",
      "Info    : It. 14000 - 29 nodes created - worst tet radius 1.70735 (nodes removed 0 13971)\n",
      "Info    : It. 14500 - 30 nodes created - worst tet radius 1.69966 (nodes removed 0 14470)\n",
      "Info    : It. 15000 - 32 nodes created - worst tet radius 1.69207 (nodes removed 0 14968)\n",
      "Info    : It. 15500 - 32 nodes created - worst tet radius 1.68504 (nodes removed 0 15468)\n",
      "Info    : It. 16000 - 35 nodes created - worst tet radius 1.67793 (nodes removed 0 15965)\n",
      "Info    : It. 16500 - 39 nodes created - worst tet radius 1.67224 (nodes removed 0 16461)\n",
      "Info    : It. 17000 - 43 nodes created - worst tet radius 1.66633 (nodes removed 0 16957)\n",
      "Info    : It. 17500 - 44 nodes created - worst tet radius 1.65984 (nodes removed 0 17456)\n",
      "Info    : It. 18000 - 45 nodes created - worst tet radius 1.65243 (nodes removed 0 17955)\n",
      "Info    : It. 18500 - 46 nodes created - worst tet radius 1.64507 (nodes removed 0 18454)\n",
      "Info    : It. 19000 - 48 nodes created - worst tet radius 1.6381 (nodes removed 0 18952)\n",
      "Info    : It. 19500 - 51 nodes created - worst tet radius 1.63173 (nodes removed 0 19449)\n",
      "Info    : It. 20000 - 52 nodes created - worst tet radius 1.70293 (nodes removed 0 19948)\n",
      "Info    : It. 20500 - 54 nodes created - worst tet radius 1.61529 (nodes removed 0 20446)\n",
      "Info    : It. 21000 - 55 nodes created - worst tet radius 1.60805 (nodes removed 0 20945)\n",
      "Info    : It. 21500 - 59 nodes created - worst tet radius 1.74844 (nodes removed 0 21441)\n",
      "Info    : It. 22000 - 59 nodes created - worst tet radius 1.5909 (nodes removed 0 21941)\n",
      "Info    : It. 22500 - 62 nodes created - worst tet radius 1.58688 (nodes removed 0 22438)\n",
      "Info    : It. 23000 - 68 nodes created - worst tet radius 1.58296 (nodes removed 0 22932)\n",
      "Info    : It. 23500 - 73 nodes created - worst tet radius 1.57589 (nodes removed 0 23427)\n",
      "Info    : It. 24000 - 78 nodes created - worst tet radius 1.56292 (nodes removed 0 23922)\n",
      "Info    : It. 24500 - 80 nodes created - worst tet radius 1.55052 (nodes removed 0 24420)\n",
      "Info    : It. 25000 - 89 nodes created - worst tet radius 1.53816 (nodes removed 0 24911)\n",
      "Info    : It. 25500 - 96 nodes created - worst tet radius 1.52817 (nodes removed 0 25404)\n",
      "Info    : It. 26000 - 112 nodes created - worst tet radius 1.50884 (nodes removed 0 25888)\n",
      "Info    : It. 26500 - 124 nodes created - worst tet radius 1.6671 (nodes removed 0 26376)\n",
      "Info    : It. 27000 - 140 nodes created - worst tet radius 1.51013 (nodes removed 0 26860)\n",
      "Info    : It. 27500 - 155 nodes created - worst tet radius 1.45177 (nodes removed 0 27345)\n",
      "Info    : It. 28000 - 201 nodes created - worst tet radius 1.38327 (nodes removed 0 27799)\n",
      "Info    : It. 28500 - 621 nodes created - worst tet radius 1.6031 (nodes removed 0 27879)\n",
      "Info    : It. 29000 - 1106 nodes created - worst tet radius 1.21339 (nodes removed 0 27894)\n",
      "Info    : It. 29500 - 1587 nodes created - worst tet radius 1.16226 (nodes removed 0 27913)\n",
      "Info    : It. 30000 - 2071 nodes created - worst tet radius 1.13303 (nodes removed 0 27929)\n",
      "Info    : It. 30500 - 2562 nodes created - worst tet radius 1.09989 (nodes removed 0 27938)\n",
      "Info    : It. 31000 - 3053 nodes created - worst tet radius 1.11946 (nodes removed 0 27947)\n",
      "Info    : It. 31500 - 3546 nodes created - worst tet radius 1.09728 (nodes removed 0 27954)\n",
      "Info    : It. 32000 - 4026 nodes created - worst tet radius 1.18048 (nodes removed 0 27974)\n",
      "Info    : 3D refinement terminated (63165 nodes total):\n",
      "Info    :  - 177 Delaunay cavities modified for star shapeness\n",
      "Info    :  - 27976 nodes could not be inserted\n",
      "Info    :  - 172382 tetrahedra created in 13.3958 sec. (12868 tets/s)\n",
      "Info    : Done meshing 3D (Wall 22.2151s, CPU 22.1883s)\n",
      "Info    : Optimizing mesh...\n",
      "Info    : Optimizing volume 1\n",
      "Info    : Optimization starts (volume = 5.5225e+06) with worst = 1.84334e-08 / average = 0.376792:\n",
      "Info    : 0.00 < quality < 0.10 :      1930 elements\n",
      "Info    : 0.10 < quality < 0.20 :      8765 elements\n",
      "Info    : 0.20 < quality < 0.30 :     49704 elements\n",
      "Info    : 0.30 < quality < 0.40 :     63981 elements\n",
      "Info    : 0.40 < quality < 0.50 :     24325 elements\n",
      "Info    : 0.50 < quality < 0.60 :      4924 elements\n",
      "Info    : 0.60 < quality < 0.70 :      3451 elements\n",
      "Info    : 0.70 < quality < 0.80 :      5091 elements\n",
      "Info    : 0.80 < quality < 0.90 :      6280 elements\n",
      "Info    : 0.90 < quality < 1.00 :      3931 elements\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Info    : 8217 edge swaps, 5706 node relocations (volume = 5.5225e+06): worst = 5.59492e-06 / average = 0.388804 (Wall 3.09823s, CPU 3.0988s)\n",
      "Info    : 10733 edge swaps, 9547 node relocations (volume = 5.5225e+06): worst = 6.34305e-06 / average = 0.389977 (Wall 5.6185s, CPU 5.61992s)\n",
      "Info    : 0.00 < quality < 0.10 :       568 elements\n",
      "Info    : 0.10 < quality < 0.20 :      4629 elements\n",
      "Info    : 0.20 < quality < 0.30 :     41437 elements\n",
      "Info    : 0.30 < quality < 0.40 :     62723 elements\n",
      "Info    : 0.40 < quality < 0.50 :     26737 elements\n",
      "Info    : 0.50 < quality < 0.60 :      5696 elements\n",
      "Info    : 0.60 < quality < 0.70 :      3338 elements\n",
      "Info    : 0.70 < quality < 0.80 :      4832 elements\n",
      "Info    : 0.80 < quality < 0.90 :      6003 elements\n",
      "Info    : 0.90 < quality < 1.00 :      3695 elements\n",
      "Info    : Done optimizing mesh (Wall 5.96243s, CPU 5.95687s)\n",
      "Info    : 63165 nodes 289521 elements\n",
      "Info    : Writing 'trial.msh'...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Warning : 1 ill-shaped tets are still in the mesh\n",
      "Warning : ------------------------------\n",
      "Warning : Mesh generation error summary\n",
      "Warning :     1 warning\n",
      "Warning :     0 errors\n",
      "Warning : Check the full log for details\n",
      "Warning : ------------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Info    : Done writing 'trial.msh'\n"
     ]
    }
   ],
   "source": [
    "Lx = 470\n",
    "Ly = 470\n",
    "Lz = 25\n",
    "try:\n",
    "    gmsh.finalize()\n",
    "except:\n",
    "    pass\n",
    "\n",
    "gmsh.initialize()\n",
    "gmsh.model.add('area')\n",
    "z0_points = [\n",
    "    (0, 0, 0),\n",
    "    (Lx, 0, 0),\n",
    "    (Lx, Ly, 0),\n",
    "    (0, Ly, 0),\n",
    "]\n",
    "zL_points = [\n",
    "    (0, 0, Lz),\n",
    "    (Lx, 0, Lz),\n",
    "    (Lx, Ly, Lz),\n",
    "    (0, Ly, Lz),\n",
    "]\n",
    "points0 = []\n",
    "points1 = []\n",
    "lines = []\n",
    "\n",
    "for i in range(4):\n",
    "    idx = gmsh.model.occ.addPoint(*z0_points[i])\n",
    "    points0.append(idx)\n",
    "for i in range(4):\n",
    "    idx = gmsh.model.occ.addPoint(*zL_points[i])\n",
    "    points1.append(\n",
    "        idx\n",
    "    )\n",
    "gmsh.model.occ.synchronize()\n",
    "for i in range(-1, 3):\n",
    "    idx = gmsh.model.occ.addLine(points0[i], points0[i + 1])\n",
    "    lines.append(\n",
    "        idx\n",
    "    )\n",
    "\n",
    "for i in range(-1, 3):\n",
    "    idx = gmsh.model.occ.addLine(points1[i], points1[i + 1])\n",
    "    lines.append(\n",
    "        idx\n",
    "    )\n",
    "\n",
    "# 1 --> 5\n",
    "idx = gmsh.model.occ.addLine(points0[1], points1[1])\n",
    "lines.append(\n",
    "    idx\n",
    ")\n",
    "\n",
    "# 2 --> 6\n",
    "idx = gmsh.model.occ.addLine(points0[2], points1[2])\n",
    "lines.append(\n",
    "    idx\n",
    ")\n",
    "\n",
    "# 3 --> 7\n",
    "idx = gmsh.model.occ.addLine(points0[3], points1[3])\n",
    "lines.append(\n",
    "    idx\n",
    ")\n",
    "\n",
    "# 0 --> 4\n",
    "idx = gmsh.model.occ.addLine(points0[0], points1[0])\n",
    "lines.append(\n",
    "    idx\n",
    ")\n",
    "\n",
    "gmsh.model.occ.synchronize()\n",
    "\n",
    "loops = []\n",
    "# xy sides\n",
    "idx = gmsh.model.occ.addCurveLoop(lines[:4])\n",
    "loops.append(\n",
    "    idx\n",
    ")\n",
    "\n",
    "idx = gmsh.model.occ.addCurveLoop(lines[4:8])\n",
    "loops.append(\n",
    "    idx\n",
    ")\n",
    "\n",
    "# xz sides\n",
    "idx = gmsh.model.occ.addCurveLoop([lines[1]] + [lines[8]] + [lines[5]] + [lines[11]])\n",
    "loops.append(\n",
    "    idx\n",
    ")\n",
    "\n",
    "idx = gmsh.model.occ.addCurveLoop([lines[3]] + [lines[9]] + [lines[7]] + [lines[10]])\n",
    "loops.append(\n",
    "    idx\n",
    ")\n",
    "\n",
    "# yz sides\n",
    "idx = gmsh.model.occ.addCurveLoop([lines[2]] + [lines[8]] + [lines[6]] + [lines[9]])\n",
    "loops.append(\n",
    "    idx\n",
    ")\n",
    "\n",
    "idx = gmsh.model.occ.addCurveLoop([lines[0]] + [lines[11]] + [lines[4]] + [lines[10]])\n",
    "loops.append(\n",
    "    idx\n",
    ")\n",
    "\n",
    "gmsh.model.occ.synchronize()\n",
    "\n",
    "side_loops = []\n",
    "insulated = []\n",
    "right = []\n",
    "left = []\n",
    "process_count = 0\n",
    "for p in graph.pieces:\n",
    "    if len(p) < 50:\n",
    "        continue\n",
    "    arr = []\n",
    "    for c in p:\n",
    "        arr.append(points_view[c])\n",
    "    alpha_shape = alphashape.alphashape(arr, 0.25)\n",
    "    exterior = alpha_shape.exterior\n",
    "    hull = []\n",
    "    for c in exterior.coords:\n",
    "        hull.append((c[0], c[1]))\n",
    "    hull_arr = np.asarray(hull)\n",
    "    hull_points = []\n",
    "    for pp in hull[:-1]:\n",
    "        idx = gmsh.model.occ.addPoint(int(pp[0]), int(pp[1]), 0)\n",
    "        hull_points.append(\n",
    "            idx\n",
    "        )\n",
    "    gmsh.model.occ.synchronize()\n",
    "    hull_lines = []\n",
    "    for i in range(-1, len(hull_points) - 1):\n",
    "        idx = gmsh.model.occ.addLine(hull_points[i], hull_points[i + 1])\n",
    "        hull_lines.append(\n",
    "            idx\n",
    "        )\n",
    "\n",
    "    gmsh.model.occ.synchronize()\n",
    "    idx = gmsh.model.occ.addCurveLoop(hull_lines)\n",
    "    side_loops.append(idx)\n",
    "    idx2 = gmsh.model.occ.addPlaneSurface((idx, ))\n",
    "    left.append(idx2)\n",
    "    gmsh.model.occ.synchronize()\n",
    "\n",
    "right = [gmsh.model.occ.addPlaneSurface((loops[1], ))]\n",
    "gmsh.model.occ.synchronize()\n",
    "\n",
    "for vv in loops[2:]:\n",
    "    idx = gmsh.model.occ.addPlaneSurface((vv, ))\n",
    "    insulated.append(\n",
    "        idx\n",
    "    )\n",
    "    gmsh.model.occ.synchronize()\n",
    "\n",
    "insulated += [gmsh.model.occ.addPlaneSurface((loops[0], *side_loops))]\n",
    "\n",
    "gmsh.model.occ.healShapes()\n",
    "gmsh.model.occ.synchronize()\n",
    "max_surf_id = np.max([vv[1] for vv in gmsh.model.occ.getEntities(2)])\n",
    "lefttag = gmsh.model.addPhysicalGroup(2, list(range(7, max_surf_id)), markers.left_cc)\n",
    "righttag = gmsh.model.addPhysicalGroup(2, [1], markers.right_cc)\n",
    "insulatedtag = gmsh.model.addPhysicalGroup(2, [2, 3, 4, 5, 6], markers.insulated)\n",
    "gmsh.model.occ.synchronize()\n",
    "sloop = gmsh.model.occ.addSurfaceLoop(tuple(left + insulated + right))\n",
    "gmsh.model.occ.synchronize()\n",
    "physvol = gmsh.model.addPhysicalGroup(3, [1], 1)\n",
    "gmsh.model.occ.synchronize()\n",
    "#     gmsh.model.occ.healShapes()\n",
    "gmsh.model.mesh.generate(3)\n",
    "gmsh.write(\"trial.msh\")\n",
    "gmsh.finalize()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "e2d56484",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n"
     ]
    }
   ],
   "source": [
    "outdir = f'mesh/study_2/470-470-{Lz}_000-000-000/'\n",
    "utils.make_dir_if_missing(outdir)\n",
    "scale_factor = [0.045, 0.045, 0.05]\n",
    "msh = meshio.read(\"trial.msh\")\n",
    "\n",
    "tria_mesh_unscaled = geometry.create_mesh(msh, cell_types.triangle)\n",
    "tria_mesh_unscaled.write(f\"{outdir}\" + 'tria.xdmf')\n",
    "tria_mesh_scaled = geometry.scale_mesh(tria_mesh_unscaled, cell_types.triangle, scale_factor=scale_factor)\n",
    "tria_mesh_scaled.write(f\"{outdir}\" + 'tria.xdmf')\n",
    "\n",
    "tetr_mesh_unscaled = geometry.create_mesh(msh, cell_types.tetra)\n",
    "tetr_mesh_unscaled.write(f\"{outdir}\" + 'tetr.xdmf')\n",
    "tetr_mesh_scaled = geometry.scale_mesh(tetr_mesh_unscaled, cell_types.tetra, scale_factor=scale_factor)\n",
    "tetr_mesh_scaled.write(f\"{outdir}\" + 'tetr.xdmf')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "fda1c7d1",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "DEBUG:mesh/study_2/470-470-25_000-000-000:Loading tetrahedra (dim = 3) mesh..\n",
      "DEBUG:mesh/study_2/470-470-25_000-000-000:Solving problem..\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:**************************RESULTS-SUMMARY******************************************\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Contact Area @ left cc [sq. um]                 : 1.5915e+02\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Contact Area @ right cc [sq. um]                : 4.4732e+02\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Current density @ left cc                       : -9.8859e-02\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Current density @ right cc                      : 4.2398e-02\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Insulated Area [sq. um]                         : 3.9379e+02\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Total Area [sq. um]                             : 1.0003e+03\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Electrolyte Volume [cu. um]                     : 5.5915e+02\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Electrolyte Volume Fraction                     : 102.44%\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Bulk conductivity [S.m-1]                       : 1.0000e-01\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Effective conductivity [S.m-1]                  : 4.1507e-02\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Insulated Current [A] : -9.32e-01\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Deviation in current at two current collectors  : 18.63%\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Voltage                                         : 1\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:Time elapsed                                    : 32.00000s\n",
      "INFO:mesh/study_2/470-470-25_000-000-000:*************************END-OF-SUMMARY*******************************************\n"
     ]
    }
   ],
   "source": [
    "res = subprocess.check_call('mpirun python3 transport.py --grid_extents 470-470-25_000-000-000', shell=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6565ae6d",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f6caaac5",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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