solve with different solver - might work with Robin bcs + removing as…

…sertion for the cellular cases (unecessesary)
aashildte · Sep 26, 2024 · 5a296b6 · 5a296b6
1 parent d97d28a
commit 5a296b6
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Showing 2 changed files with 7 additions and 10 deletions.
diff --git a/emimechanicalmodel/cardiac_model.py b/emimechanicalmodel/cardiac_model.py
@@ -405,9 +405,8 @@ def _define_kinematic_variables(self):
 
         if self.experiment_str == "contraction":
             state, test_state = self.state, self.test_state
-            weak_form += self._remove_rigid_motion_term(u, r, state, test_state)
-            #weak_form += self._add_robin_bnd_term()
-            #weak_form += df.inner(self.u, self.v)*self.ds
+            #weak_form += self._remove_rigid_motion_term(u, r, state, test_state)
+            weak_form += self._add_robin_bnd_term()
 
         (self.F, self.E, self.sigma, self.P, self.u, self.weak_form,) = (
             F,
@@ -497,7 +496,7 @@ def _add_robin_bnd_term(self):
 
         """
         robin_value = df.Constant(1.0)
-        robin_bcs_term = df.inner(robin_value * self.u, self.v) * self.ds(1)      # in all directions
+        robin_bcs_term = df.inner(robin_value * self.u, self.v) * df.ds
 
         return robin_bcs_term
 
@@ -519,7 +518,7 @@ def solve(self, project=False):
         # as per default we are using the manual implementation which
         # should be at least as fast; however, we will
         # just keep a simple version here for easy comparison:
-
+        """ 
         df.solve(
             self.weak_form == 0,
             self.state,
@@ -535,7 +534,7 @@ def solve(self, project=False):
         
         """
         self._solver.solve(self.problem, self.state.vector())
-        """
+
         # save stress and strain to fenics functions
         if project:
             for proj_fun in self.projections:

diff --git a/emimechanicalmodel/emi_model.py b/emimechanicalmodel/emi_model.py
@@ -212,8 +212,7 @@ def evaluate_cellular_strain_magnitude(self):
         Returns:
             ..math:: || \overline{E} || integrated over the extracellular space
         """
-        assert isinstance(self.mat_model, EMIMatrixHolzapfelMaterial), "Error: Collagen fibers not defined."
-
+
         e1, e2 = self.fiber_dir, self.sheet_dir
 
         E11 = df.inner(e1, self.E * e1)**2
@@ -235,8 +234,7 @@ def evaluate_cellular_stress_magnitude(self):
             ..math:: || \overline{E} || integrated over the extracellular space
 
         """
-        assert isinstance(self.mat_model, EMIMatrixHolzapfelMaterial), "Error: Collagen fibers not defined."
-
+
         e1, e2 = self.fiber_dir, self.sheet_dir
 
         sigma11 = df.inner(e1, self.sigma * e1)**2