fixing other v_inner/outer to the active ones

tardis/montecarlo/montecarlo_numba/formal_integral.py

@@ -67,8 +67,8 @@ def numba_formal_integral(
     # global read-only values
     size_line, size_shell = tau_sobolev.shape
     size_tau = size_line * size_shell
-    R_ph = geometry.r_inner[0]  # make sure these are cgs
-    R_max = geometry.r_outer[size_shell - 1]
+    R_ph = geometry.r_inner_active[0]  # make sure these are cgs
+    R_max = geometry.r_outer_active[size_shell - 1]
     pp = np.zeros(N, dtype=np.float64)  # check
     exp_tau = np.zeros(size_tau, dtype=np.float64)
     exp_tau = np.exp(-tau_sobolev.T.ravel())  # maybe make this 2D?
@@ -660,13 +660,13 @@ def populate_z(geometry, model, p, oz, oshell_id):
         :oshell_id: (int64) will be set with the corresponding shell_ids
     """
     # abbreviations
-    r = geometry.r_outer
-    N = len(geometry.r_inner)  # check
+    r = geometry.r_outer_active
+    N = len(geometry.r_inner_active)  # check
     inv_t = 1 / model.time_explosion
     z = 0
     offset = N
 
-    if p <= geometry.r_inner[0]:
+    if p <= geometry.r_inner_active[0]:
         # intersect the photosphere
         for i in range(N):
             oz[i] = 1 - calculate_z(r[i], p, inv_t)

tardis/montecarlo/montecarlo_numba/formal_integral_cuda.py

@@ -41,9 +41,9 @@ def cuda_formal_integral(
     Parameters
     ----------
     r_inner : array(float64, 1d, C)
-        self.geometry.r_inner
+        self.geometry.r_inner_active
     r_outer : array(float64, 1d, C)
-        self.geometry.r_outer
+        self.geometry.r_outer_active
     time_explosion: float64
         self.geometry.time_explosion
     line_list_nu : array(float64, 1d, A)
@@ -246,7 +246,7 @@ def formal_integral(
         exp_tau = np.zeros(size_tau, dtype=np.float64)  # array(float64, 1d, C)
         exp_tau = np.exp(-tau_sobolev.T.ravel())  # array(float64, 1d, C)
         pp[::] = calculate_p_values(
-            self.geometry.r_outer[size_shell - 1], N
+            self.geometry.r_outer_active[size_shell - 1], N
         )  # array(float64, 1d, C)
 
         I_nu = np.zeros(
@@ -262,8 +262,8 @@ def formal_integral(
         blocks_per_grid = (inu_size // THREADS_PER_BLOCK) + 1
 
         cuda_formal_integral[blocks_per_grid, THREADS_PER_BLOCK](
-            self.geometry.r_inner,
-            self.geometry.r_outer,
+            self.geometry.r_inner_active,
+            self.geometry.r_outer_active,
             self.model.time_explosion,
             self.plasma.line_list_nu,
             iT.value,

tardis/montecarlo/montecarlo_numba/tests/test_packet.py

@@ -75,7 +75,7 @@ def test_calculate_distance_boundary(packet_params, expected_params, geometry):
     r = packet_params["r"]
 
     d_boundary = calculate_distances.calculate_distance_boundary(
-        r, mu, geometry.r_inner[0], geometry.r_outer[0]
+        r, mu, geometry.r_inner_active[0], geometry.r_outer_active[0]
     )
 
     # Accuracy to within 0.1cm

tardis/visualization/tools/sdec_plot.py

@@ -165,7 +165,7 @@ def from_simulation(cls, sim, packets_mode):
             "line_id"
         )
         transport_state = sim.transport.transport_state
-        r_inner = sim.simulation_state.geometry.r_inner
+        r_inner = sim.simulation_state.geometry.r_inner_active
         t_inner = sim.simulation_state.packet_source.temperature
         time_of_simulation = (
             transport_state.packet_collection.time_of_simulation * u.s