fix bugs

src/data/helmholtz/helmholtz.py

@@ -1,7 +1,7 @@
 import pathlib
 
-from domain_properties import read_config
-from solver import HelmholtzSolver
+from .domain_properties import read_config
+from .solver import HelmholtzSolver
 
 
 class Helmholtz:

src/data/helmholtz/solver/solver.py

@@ -2,6 +2,7 @@
 
 import dolfinx
 import ufl
+from dolfinx.fem.petsc import LinearProblem
 from mpi4py import MPI
 from petsc4py import PETSc
 
@@ -49,16 +50,14 @@ def __call__(self, description: Description):
 
         for i, (k0, f) in enumerate(zip(description.ks, description.frequencies)):
             # update k
-            k.x.array[:] = k0 * crystals(v, cell_tags).x.array + trunc(v, cell_tags).x.array
+            k.x.array[:] = k0 * crystals.eval(v, cell_tags).x.array + trunc.eval(v, cell_tags).x.array
 
             # assemble problem
             lhs = ufl.inner(ufl.grad(p), ufl.grad(xi)) * ufl.dx - k**2 * ufl.inner(p, xi) * ufl.dx
             rhs = k * s * ufl.inner(v_f, xi) * d_excitation
 
             # compute solution
-            problem = dolfinx.fem.petsc.LinearProblem(
-                lhs, rhs, u=p_sol, petsc_options={"ksp_type": "preonly", "pc_type": "lu"}
-            )
+            problem = LinearProblem(lhs, rhs, u=p_sol, petsc_options={"ksp_type": "preonly", "pc_type": "lu"})
             problem.solve()
 
             # write solution

src/data/helmholtz/solver/wave_number.py

@@ -22,8 +22,8 @@ class AdiabaticLayer(WaveNumberModifier):
     """
 
     def __init__(self, pd: Description, degree: int = 2):
-        self.box_min = np.array([0.0, 0.0])
-        self.box_max = np.array([pd.width + pd.right_width, pd.height])
+        self.box_min = np.array([0.0, 0.0, 0.0])
+        self.box_max = np.array([pd.width + pd.right_width, pd.height, 0.0])
         self.depth = pd.absorber_depth
         self.degree = degree
         rt = pd.round_trip
@@ -45,15 +45,15 @@ def eval(self, function_space: dolfinx.fem.FunctionSpace, ct: dolfinx.mesh.MeshT
 
         def wave_mod(x: np.array) -> np.array:
             # Clamp point coordinates to the range defined by the box
-            clamped = np.maximum(self.box_min, np.minimum(x, self.box_max))
+            clamped = np.maximum(self.box_min[:, np.newaxis], np.minimum(x, self.box_max[:, np.newaxis]))
 
-            # Compute the distance from the clamped point to the original point
-            dist = np.linalg.norm(clamped - x)
+            # Compute the distance from the clamped points to the original points
+            dist = np.linalg.norm(clamped - x, axis=0)
 
             # Relative distance inside absorber
             dist = dist / self.depth
 
-            return self.sigma_0 * 1j * np.sum(dist**self.degree)
+            return self.sigma_0 * 1j * dist**self.degree
 
         f = dolfinx.fem.Function(function_space)
         f.interpolate(wave_mod)