Unexpected…

homogenized_plate.geo
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			el_size = 0.02;
			inclusion_radius = 0.25;
			box_size = 1.0; // this is the edge length of the box

			Point(1) = {-box_size/2, -box_size/2, 0, el_size};
			Point(2) = {-box_size/2 + inclusion_radius, -box_size/2, 0, el_size};
			Point(3) = {-box_size/2, -box_size/2 + inclusion_radius, 0, el_size};
			Point(4) = {-box_size/2 - inclusion_radius, -box_size/2, 0, el_size};
			Point(5) = {-box_size/2, -box_size/2 - inclusion_radius, 0, el_size};

			Point(6) = {0, 0, 0, el_size};
			Point(7) = {-box_size, 0, 0, el_size};
			Point(8) = {-box_size, -box_size, 0, el_size};
			Point(9) = {0, -box_size, 0, el_size};
			Circle(1) = {2, 1, 3};
			Circle(2) = {3, 1, 4};
			Circle(3) = {4, 1, 5};
			Circle(4) = {5, 1, 2};
			Line(5) = {9, 6};
			Line(6) = {6, 7};
			Line(7) = {7, 8};
			Line(8) = {8, 9};
			Line Loop(9) = {4, 1, 2, 3};
			Plane Surface(10) = {9};
			Line Loop(11) = {5, 6, 7, 8};
			Plane Surface(12) = {9, -11};
			Physical Surface("inclusion") = {10};
			Physical Surface("matrix") = {12};
			Physical Line("bottom") = {8};
			Physical Line("right") = {5};
			Physical Line("top") = {6};
			Physical Line("left") = {7};