From eab51811c7c1195836d21a2c427463f361bd3979 Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Wed, 25 Oct 2023 10:52:42 -0400
Subject: [PATCH] facet indices not dofs

---
 festim/hydrogen_transport_problem.py  | 15 +++++++++------
 festim/subdomain/surface_subdomain.py | 12 ++++++------
 2 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/festim/hydrogen_transport_problem.py b/festim/hydrogen_transport_problem.py
index 471e42e4d..a9a9447ac 100644
--- a/festim/hydrogen_transport_problem.py
+++ b/festim/hydrogen_transport_problem.py
@@ -139,7 +139,8 @@ def defing_export_writers(self):
 
     def define_function_space(self):
         """Creates the function space of the model, creates a mixed element if
-        model is multispecies. Creates the main solution and previous solution function u and u_n."""
+        model is multispecies. Creates the main solution and previous solution
+        function u and u_n."""
         element_CG = basix.ufl.element(
             basix.ElementFamily.P,
             self.mesh.mesh.basix_cell(),
@@ -193,7 +194,7 @@ def assign_functions_to_species(self):
     def define_markers_and_measures(self):
         """Defines the markers and measures of the model"""
 
-        dofs_facets, tags_facets = [], []
+        facet_indices, tags_facets = [], []
 
         # find all cells in domain and mark them as 0
         num_cells = self.mesh.mesh.topology.index_map(self.mesh.vdim).size_local
@@ -202,8 +203,10 @@ def define_markers_and_measures(self):
 
         for sub_dom in self.subdomains:
             if isinstance(sub_dom, F.SurfaceSubdomain1D):
-                dof = sub_dom.locate_dof(self.mesh.mesh, self.mesh.fdim)
-                dofs_facets.append(dof)
+                facet_index = sub_dom.locate_boundary_facet_indices(
+                    self.mesh.mesh, self.mesh.fdim
+                )
+                facet_indices.append(facet_index)
                 tags_facets.append(sub_dom.id)
             if isinstance(sub_dom, F.VolumeSubdomain1D):
                 # find all cells in subdomain and mark them as sub_dom.id
@@ -218,12 +221,12 @@ def define_markers_and_measures(self):
             self.mesh.check_borders(self.volume_subdomains)
 
         # dofs and tags need to be in np.in32 format for meshtags
-        dofs_facets = np.array(dofs_facets, dtype=np.int32)
+        facet_indices = np.array(facet_indices, dtype=np.int32)
         tags_facets = np.array(tags_facets, dtype=np.int32)
 
         # define mesh tags
         self.facet_meshtags = meshtags(
-            self.mesh.mesh, self.mesh.fdim, dofs_facets, tags_facets
+            self.mesh.mesh, self.mesh.fdim, facet_indices, tags_facets
         )
         self.volume_meshtags = meshtags(
             self.mesh.mesh, self.mesh.vdim, mesh_cell_indices, tags_volumes
diff --git a/festim/subdomain/surface_subdomain.py b/festim/subdomain/surface_subdomain.py
index f1ee32839..80fd082aa 100644
--- a/festim/subdomain/surface_subdomain.py
+++ b/festim/subdomain/surface_subdomain.py
@@ -1,4 +1,3 @@
-from dolfinx import fem
 import dolfinx.mesh
 import numpy as np
 
@@ -23,18 +22,19 @@ def __init__(self, id, x) -> None:
         self.id = id
         self.x = x
 
-    def locate_dof(self, mesh, fdim):
+    def locate_boundary_facet_indices(self, mesh, fdim):
         """Locates the dof of the surface subdomain within the function space
+        and return the index of the dof
 
         Args:
             mesh (dolfinx.mesh.Mesh): the mesh of the simulation
             fdim (int): the dimension of the model facets
 
         Returns:
-            dof (np.array): the first value in the list of dofs of the surface
-                subdomain
+            index (np.array): the first value in the list of surface facet
+                indices of the subdomain
         """
-        dofs = dolfinx.mesh.locate_entities_boundary(
+        indices = dolfinx.mesh.locate_entities_boundary(
             mesh, fdim, lambda x: np.isclose(x[0], self.x)
         )
-        return dofs[0]
+        return indices[0]