title: Gmsh issue with physical entities
body: <p>I have a <code>*.geo</code> file that I have written with a python script. The main use of this <code>*.geo</code> file is to construct and save a triangular mesh. In gmsh you can label interest entities with the command Physical. For example <code>Physical Point</code>, <code>Physical Line</code>, etc.</p>
  
  <p>Here comes the <code>*.geo</code> file:</p>
  
  <pre><code>// This is a test for *.geo
  h = 1.00E+01 ;
  
  Point( 1 ) = { 1.00E+00 , 1.00E+00 , 0.00E+00 ,h};
  Point( 2 ) = { 7.00E+01 , 1.00E+00 , 0.00E+00 ,h};
  Point( 3 ) = { 7.00E+01 , 7.00E+01 , 0.00E+00 ,h};
  Point( 4 ) = { 1.00E+00 , 7.00E+01 , 0.00E+00 ,h};
  Point( 5 ) = { 3.80E+01 , 2.70E+01 , 0.00E+00 ,h*0.5};
  Point( 6 ) = { 3.80E+01 , 2.80E+01 , 0.00E+00 ,h*0.5};
  Point( 7 ) = { 3.80E+01 , 2.90E+01 , 0.00E+00 ,h*0.5};
  Point( 8 ) = { 3.80E+01 , 3.00E+01 , 0.00E+00 ,h*0.5};
  Point( 9 ) = { 3.80E+01 , 3.10E+01 , 0.00E+00 ,h*0.5};
  Point( 10 ) = { 3.80E+01 , 3.20E+01 , 0.00E+00 ,h*0.5};
  Point( 11 ) = { 3.80E+01 , 3.30E+01 , 0.00E+00 ,h*0.5};
  Point( 12 ) = { 3.90E+01 , 3.30E+01 , 0.00E+00 ,h*0.5};
  Point( 13 ) = { 3.90E+01 , 3.40E+01 , 0.00E+00 ,h*0.5};
  Point( 14 ) = { 3.90E+01 , 3.50E+01 , 0.00E+00 ,h*0.5};
  Point( 15 ) = { 3.90E+01 , 3.60E+01 , 0.00E+00 ,h*0.5};
  Point( 16 ) = { 4.00E+01 , 3.60E+01 , 0.00E+00 ,h*0.5};
  Point( 17 ) = { 4.00E+01 , 3.70E+01 , 0.00E+00 ,h*0.5};
  Point( 18 ) = { 4.10E+01 , 3.70E+01 , 0.00E+00 ,h*0.5};
  Point( 19 ) = { 4.10E+01 , 3.80E+01 , 0.00E+00 ,h*0.5};
  Point( 20 ) = { 4.10E+01 , 3.90E+01 , 0.00E+00 ,h*0.5};
  Point( 21 ) = { 4.20E+01 , 3.90E+01 , 0.00E+00 ,h*0.5};
  Point( 22 ) = { 4.20E+01 , 4.00E+01 , 0.00E+00 ,h*0.5};
  Point( 23 ) = { 4.30E+01 , 4.00E+01 , 0.00E+00 ,h*0.5};
  Point( 24 ) = { 4.40E+01 , 4.00E+01 , 0.00E+00 ,h*0.5};
  Point( 25 ) = { 4.40E+01 , 4.10E+01 , 0.00E+00 ,h*0.5};
  Point( 26 ) = { 4.50E+01 , 4.10E+01 , 0.00E+00 ,h*0.5};
  Point( 27 ) = { 4.50E+01 , 4.20E+01 , 0.00E+00 ,h*0.5};
  Point( 28 ) = { 4.60E+01 , 4.20E+01 , 0.00E+00 ,h*0.5};
  Point( 29 ) = { 4.70E+01 , 4.20E+01 , 0.00E+00 ,h*0.5};
  Point( 30 ) = { 4.80E+01 , 4.20E+01 , 0.00E+00 ,h*0.5};
  Point( 31 ) = { 4.80E+01 , 4.30E+01 , 0.00E+00 ,h*0.5};
  Point( 32 ) = { 4.90E+01 , 4.30E+01 , 0.00E+00 ,h*0.5};
  Point( 33 ) = { 5.00E+01 , 4.30E+01 , 0.00E+00 ,h*0.5};
  Point( 34 ) = { 5.10E+01 , 4.30E+01 , 0.00E+00 ,h*0.5};
  Point( 35 ) = { 5.20E+01 , 4.30E+01 , 0.00E+00 ,h*0.5};
  Point( 36 ) = { 5.30E+01 , 4.30E+01 , 0.00E+00 ,h*0.5};
  Point( 37 ) = { 5.40E+01 , 4.30E+01 , 0.00E+00 ,h*0.5};
  Point( 38 ) = { 5.40E+01 , 4.20E+01 , 0.00E+00 ,h*0.5};
  Point( 39 ) = { 5.50E+01 , 4.20E+01 , 0.00E+00 ,h*0.5};
  Point( 40 ) = { 5.60E+01 , 4.20E+01 , 0.00E+00 ,h*0.5};
  Point( 41 ) = { 5.70E+01 , 4.20E+01 , 0.00E+00 ,h*0.5};
  Point( 42 ) = { 5.70E+01 , 4.10E+01 , 0.00E+00 ,h*0.5};
  Point( 43 ) = { 5.80E+01 , 4.10E+01 , 0.00E+00 ,h*0.5};
  Point( 44 ) = { 5.80E+01 , 4.00E+01 , 0.00E+00 ,h*0.5};
  Point( 45 ) = { 5.90E+01 , 4.00E+01 , 0.00E+00 ,h*0.5};
  Point( 46 ) = { 6.00E+01 , 4.00E+01 , 0.00E+00 ,h*0.5};
  Point( 47 ) = { 6.00E+01 , 3.90E+01 , 0.00E+00 ,h*0.5};
  Point( 48 ) = { 6.10E+01 , 3.90E+01 , 0.00E+00 ,h*0.5};
  Point( 49 ) = { 6.10E+01 , 3.80E+01 , 0.00E+00 ,h*0.5};
  Point( 50 ) = { 6.10E+01 , 3.70E+01 , 0.00E+00 ,h*0.5};
  Point( 51 ) = { 6.20E+01 , 3.70E+01 , 0.00E+00 ,h*0.5};
  Point( 52 ) = { 6.20E+01 , 3.60E+01 , 0.00E+00 ,h*0.5};
  Point( 53 ) = { 6.30E+01 , 3.60E+01 , 0.00E+00 ,h*0.5};
  Point( 54 ) = { 6.30E+01 , 3.50E+01 , 0.00E+00 ,h*0.5};
  Point( 55 ) = { 6.30E+01 , 3.40E+01 , 0.00E+00 ,h*0.5};
  Point( 56 ) = { 6.30E+01 , 3.30E+01 , 0.00E+00 ,h*0.5};
  Point( 57 ) = { 6.40E+01 , 3.30E+01 , 0.00E+00 ,h*0.5};
  Point( 58 ) = { 6.40E+01 , 3.20E+01 , 0.00E+00 ,h*0.5};
  Point( 59 ) = { 6.40E+01 , 3.10E+01 , 0.00E+00 ,h*0.5};
  Point( 60 ) = { 6.40E+01 , 3.00E+01 , 0.00E+00 ,h*0.5};
  Point( 61 ) = { 6.40E+01 , 2.90E+01 , 0.00E+00 ,h*0.5};
  Point( 62 ) = { 6.40E+01 , 2.80E+01 , 0.00E+00 ,h*0.5};
  Point( 63 ) = { 6.40E+01 , 2.70E+01 , 0.00E+00 ,h*0.5};
  Point( 64 ) = { 6.30E+01 , 2.70E+01 , 0.00E+00 ,h*0.5};
  Point( 65 ) = { 6.30E+01 , 2.60E+01 , 0.00E+00 ,h*0.5};
  Point( 66 ) = { 6.30E+01 , 2.50E+01 , 0.00E+00 ,h*0.5};
  Point( 67 ) = { 6.30E+01 , 2.40E+01 , 0.00E+00 ,h*0.5};
  Point( 68 ) = { 6.20E+01 , 2.40E+01 , 0.00E+00 ,h*0.5};
  Point( 69 ) = { 6.20E+01 , 2.30E+01 , 0.00E+00 ,h*0.5};
  Point( 70 ) = { 6.10E+01 , 2.30E+01 , 0.00E+00 ,h*0.5};
  Point( 71 ) = { 6.10E+01 , 2.20E+01 , 0.00E+00 ,h*0.5};
  Point( 72 ) = { 6.10E+01 , 2.10E+01 , 0.00E+00 ,h*0.5};
  Point( 73 ) = { 6.00E+01 , 2.10E+01 , 0.00E+00 ,h*0.5};
  Point( 74 ) = { 6.00E+01 , 2.00E+01 , 0.00E+00 ,h*0.5};
  Point( 75 ) = { 5.90E+01 , 2.00E+01 , 0.00E+00 ,h*0.5};
  Point( 76 ) = { 5.80E+01 , 2.00E+01 , 0.00E+00 ,h*0.5};
  Point( 77 ) = { 5.80E+01 , 1.90E+01 , 0.00E+00 ,h*0.5};
  Point( 78 ) = { 5.70E+01 , 1.90E+01 , 0.00E+00 ,h*0.5};
  Point( 79 ) = { 5.70E+01 , 1.80E+01 , 0.00E+00 ,h*0.5};
  Point( 80 ) = { 5.60E+01 , 1.80E+01 , 0.00E+00 ,h*0.5};
  Point( 81 ) = { 5.50E+01 , 1.80E+01 , 0.00E+00 ,h*0.5};
  Point( 82 ) = { 5.40E+01 , 1.80E+01 , 0.00E+00 ,h*0.5};
  Point( 83 ) = { 5.40E+01 , 1.70E+01 , 0.00E+00 ,h*0.5};
  Point( 84 ) = { 5.30E+01 , 1.70E+01 , 0.00E+00 ,h*0.5};
  Point( 85 ) = { 5.20E+01 , 1.70E+01 , 0.00E+00 ,h*0.5};
  Point( 86 ) = { 5.10E+01 , 1.70E+01 , 0.00E+00 ,h*0.5};
  Point( 87 ) = { 5.00E+01 , 1.70E+01 , 0.00E+00 ,h*0.5};
  Point( 88 ) = { 4.90E+01 , 1.70E+01 , 0.00E+00 ,h*0.5};
  Point( 89 ) = { 4.80E+01 , 1.70E+01 , 0.00E+00 ,h*0.5};
  Point( 90 ) = { 4.80E+01 , 1.80E+01 , 0.00E+00 ,h*0.5};
  Point( 91 ) = { 4.70E+01 , 1.80E+01 , 0.00E+00 ,h*0.5};
  Point( 92 ) = { 4.60E+01 , 1.80E+01 , 0.00E+00 ,h*0.5};
  Point( 93 ) = { 4.50E+01 , 1.80E+01 , 0.00E+00 ,h*0.5};
  Point( 94 ) = { 4.50E+01 , 1.90E+01 , 0.00E+00 ,h*0.5};
  Point( 95 ) = { 4.40E+01 , 1.90E+01 , 0.00E+00 ,h*0.5};
  Point( 96 ) = { 4.40E+01 , 2.00E+01 , 0.00E+00 ,h*0.5};
  Point( 97 ) = { 4.30E+01 , 2.00E+01 , 0.00E+00 ,h*0.5};
  Point( 98 ) = { 4.20E+01 , 2.00E+01 , 0.00E+00 ,h*0.5};
  Point( 99 ) = { 4.20E+01 , 2.10E+01 , 0.00E+00 ,h*0.5};
  Point( 100 ) = { 4.10E+01 , 2.10E+01 , 0.00E+00 ,h*0.5};
  Point( 101 ) = { 4.10E+01 , 2.20E+01 , 0.00E+00 ,h*0.5};
  Point( 102 ) = { 4.10E+01 , 2.30E+01 , 0.00E+00 ,h*0.5};
  Point( 103 ) = { 4.00E+01 , 2.30E+01 , 0.00E+00 ,h*0.5};
  Point( 104 ) = { 4.00E+01 , 2.40E+01 , 0.00E+00 ,h*0.5};
  Point( 105 ) = { 3.90E+01 , 2.40E+01 , 0.00E+00 ,h*0.5};
  Point( 106 ) = { 3.90E+01 , 2.50E+01 , 0.00E+00 ,h*0.5};
  Point( 107 ) = { 3.90E+01 , 2.60E+01 , 0.00E+00 ,h*0.5};
  Point( 108 ) = { 3.90E+01 , 2.70E+01 , 0.00E+00 ,h*0.5};
  Point( 109 ) = { 3.80E+01 , 2.70E+01 , 0.00E+00 ,h*0.5};
  
  // Writing stuff for domain: 4
  
  Line( 110 ) = { 1 , 2 , 3 , 4 , 1 };
  Line Loop( 111 ) = { 110 };
  Physical Line( "Border_0" ) = { 111 };
  
  // Writing stuff for domain: 105
  
  BSpline( 112 ) = {   5,   6,   7,   8,   9,  10,  11,  12,  13,  14,  15,  16,  17,  18,
    19,  20,  21,  22,  23,  24,  25,  26,  27,  28,  29,  30,  31,  32,
    33,  34,  35,  36,  37,  38,  39,  40,  41,  42,  43,  44,  45,  46,
    47,  48,  49,  50,  51,  52,  53,  54,  55,  56,  57,  58,  59,  60,
    61,  62,  63,  64,  65,  66,  67,  68,  69,  70,  71,  72,  73,  74,
    75,  76,  77,  78,  79,  80,  81,  82,  83,  84,  85,  86,  87,  88,
    89,  90,  91,  92,  93,  94,  95,  96,  97,  98,  99, 100, 101, 102,
   103, 104, 105, 106, 107, 108, 109, 5};
  Line Loop( 113 ) = { 112 };
  Physical Line( "Border_1" ) = { 113 };
  Plane Surface( 114 ) = { 113 };
  Physical Surface( "Inclusion_1" ) = { 114 };
  
  Plane Surface( 115 ) = {111,113};
  Physical Surface( "Matrix_domain" ) = { 115 };
  </code></pre>
  
  <p>The created <code>*.msh</code> file, contains the mesh, has identified the Physical labels, but I can not find the corresponding element sets.</p>