change mesh origin to crystal lower left corner

src/nos/data/helmholtz/mesh/crystal_builder.py

@@ -69,8 +69,7 @@ def __init__(self, description: Description):
         # define center of crystals
         offset = self.crystal_description.grid_size / 2.0
         self.centers_x = [
-            offset + col * self.crystal_description.grid_size + self.description.left_width
-            for col in range(self.crystal_description.n)
+            offset + col * self.crystal_description.grid_size for col in range(self.crystal_description.n)
         ]
         self.center_y = offset
 

src/nos/data/helmholtz/mesh/crystal_domain_builder.py

@@ -46,9 +46,7 @@ def define_basic_shape(self) -> int:
         Returns:
             gmsh index to the rectangle.
         """
-        domain = self.factory.addRectangle(
-            self.description.left_width, 0.0, 0.0, self.description.domain_width, self.description.height
-        )
+        domain = self.factory.addRectangle(0.0, 0.0, 0.0, self.description.domain_width, self.description.height)
         return domain
 
     def define_tools(self) -> List[int]:

src/nos/data/helmholtz/mesh/mesh_builder.py

@@ -69,12 +69,16 @@ def build_basic_shapes(self) -> List[int]:
         tags = []
         # left space, domain, right space
         if self.description.left_width > 0:
-            tags.append(self.factory.addRectangle(0.0, 0.0, 0.0, self.description.left_width, self.description.height))
+            tags.append(
+                self.factory.addRectangle(
+                    -self.description.left_width, 0.0, 0.0, self.description.left_width, self.description.height
+                )
+            )
         tags.append(self.domain_builder.build())
         if self.description.right_width > 0:
             tags.append(
                 self.factory.addRectangle(
-                    self.description.left_width + self.description.domain_width,
+                    self.description.domain_width,
                     0.0,
                     0.0,
                     self.description.right_width,
@@ -84,11 +88,15 @@ def build_basic_shapes(self) -> List[int]:
         # absorbers
         absorber_depth = self.description.absorber.lambda_depth * max(self.description.wave_lengths)
         # left
-        tags.append(self.factory.add_rectangle(-absorber_depth, 0.0, 0.0, absorber_depth, self.description.height))
+        tags.append(
+            self.factory.add_rectangle(
+                -absorber_depth - self.description.left_width, 0.0, 0.0, absorber_depth, self.description.height
+            )
+        )
         # right
         tags.append(
             self.factory.add_rectangle(
-                self.description.left_width + self.description.domain_width + self.description.right_width,
+                self.description.domain_width + self.description.right_width,
                 0.0,
                 0.0,
                 absorber_depth,
@@ -121,9 +129,9 @@ def get_physical_groups(self) -> List[Tuple[int, List[int], int]]:
         all_surfaces = self.factory.get_entities(2)
         surf_categories = defaultdict(list)
         domain_bbox = BoundingBox2D(
+            -self.description.left_width,
             0.0,
-            0.0,
-            self.description.left_width + self.description.domain_width + self.description.right_width,
+            self.description.domain_width + self.description.right_width,
             self.description.height,
         )  # left space, domain, right space
         for _, surf in all_surfaces:
@@ -138,7 +146,7 @@ def get_physical_groups(self) -> List[Tuple[int, List[int], int]]:
                 surf_categories["left_side"].append(surf)
                 continue
             # domain
-            if com[0, 0] < self.description.left_width + self.description.domain_width:
+            if com[0, 0] < self.description.domain_width:
                 surf_categories["crystal_domain"].append(surf)
                 continue
             # right spacer
@@ -147,17 +155,6 @@ def get_physical_groups(self) -> List[Tuple[int, List[int], int]]:
         for name, indices in surf_categories.items():
             categories.append((2, indices, self.description.indices[name]))
 
-        # lines
-        lines = self.factory.get_entities(1)
-        excitation_boundary = None
-        for _, line in lines:
-            com = np.array(self.factory.getCenterOfMass(1, line))
-            if np.allclose(com, [0, self.description.height / 2.0, 0]):
-                excitation_boundary = line
-                break
-
-        categories.append((1, [excitation_boundary], self.description.indices["excitation"]))
-
         return categories
 
     def set_physical_groups(self, groups: List[Tuple[int, List[int], int]]) -> None:

src/nos/data/helmholtz/solver/adiabatic_absorber.py

@@ -17,7 +17,7 @@ class AdiabaticAbsorber(WaveNumberFunction):
 
     def __init__(self, description: Description):
         self.bbox = BoundingBox2D(
-            0.0, 0.0, description.left_width + description.domain_width + description.right_width, description.height
+            -description.left_width, 0.0, description.domain_width + description.right_width, description.height
         )
         self.depth = description.absorber.lambda_depth
         self.round_trip = description.absorber.round_trip

test/data/helmholtz/solver/test_adiabatic_layer.py

@@ -24,14 +24,16 @@ def all_sides_absorber():
     )
     absorber = AdiabaticAbsorber(des)
 
-    assert absorber.bbox.x_max == 3.0
+    assert absorber.bbox.x_max == 2.5
+    assert absorber.bbox.x_min == -0.5
     assert absorber.bbox.y_max == 1.0
+    assert absorber.bbox.y_min == 0.0
 
     return absorber
 
 
 def test_inside_zero(all_sides_absorber):
-    x = np.random.random((1000, 2)) @ np.array([[3.0, 0.0], [0.0, 1.0]])  # scale to match all inside
+    x = np.random.random((1000, 2)) @ np.array([[3.0, 0.0], [0.0, 1.0]]) - np.array([0.5, 0])  # all inside
     assert np.allclose(all_sides_absorber.eval(x), 0)
 
 
@@ -51,6 +53,6 @@ def test_correct_value(all_sides_absorber):
     x = np.array([[4.0, 1.0], [-1, -1]])
 
     sigma_0 = -3 * np.log(10) / 2.0
-    sol = sigma_0 * 1j * np.array([1.0, np.sqrt(2)]) ** 2
+    sol = sigma_0 * 1j * np.array([1.5, np.sqrt(1.25)]) ** 2
 
     assert np.allclose(all_sides_absorber.eval(x), sol)