add back D_constant (oops)

RangamaniLabUCSD · Aug 17, 2024 · 2c8bb87 · 2c8bb87
1 parent 3254d41
commit 2c8bb87
Showing 1 changed file with 18 additions and 17 deletions.
diff --git a/smart/model.py b/smart/model.py
@@ -49,7 +49,7 @@
 )
 
 from .solvers import smartSNESProblem
-from .units import unit
+from . import unit
 
 
 logger = logging.getLogger(__name__)
@@ -641,11 +641,11 @@ def _init_2_5_link_compartments_to_species(self):
         for species in self.sc:
             species.compartment = self.cc[species.compartment_name]
             species.dimensionality = self.cc[species.compartment_name].dimensionality
-            # convert diffusion coeff to units consistent with mesh
-            diffusion_conversion = species.diffusion_units.to(
-                species.compartment.compartment_units**2 / unit.s
+            # convert diffusion coeff to  consistent with mesh
+            diffusion_conversion = species.diffusion_.to(
+                species.compartment.compartment_**2 / unit.s
             )
-            species.diffusion_units = species.compartment.compartment_units**2 / unit.s
+            species.diffusion_ = species.compartment.compartment_**2 / unit.s
             species.D *= diffusion_conversion.magnitude
 
     def _init_2_6_link_species_to_compartments(self):
@@ -1084,7 +1084,7 @@ def _init_5_2_create_variational_forms(self):
         for flux in self.fc:
             # -1 factor in flux.form means this is a lhs term
             form_type = "boundary_reaction" if flux.is_boundary_condition else "domain_reaction"
-            flux_form_units = flux.equation_units * flux.measure_units
+            flux_form_ = flux.equation_ * flux.measure_
             # Determine if flux is linear w.r.t. compartment functions
             # Use flux.is_linear_wrt_comp and combine with linear_wrt_comp
             # (prioritizing former). If compartment is not relevant to flux then it is linear
@@ -1097,7 +1097,7 @@ def _init_5_2_create_variational_forms(self):
                     flux.form,
                     flux.destination_species,
                     form_type,
-                    flux_form_units,
+                    flux_form_,
                     True,
                     linearity_dict,
                 )
@@ -1112,15 +1112,15 @@ def _init_5_2_create_variational_forms(self):
             v = species.v
             D = species.D
             dx = species.compartment.mesh.dx
-            Dform_units = (
-                species.diffusion_units
-                * species.concentration_units
-                * species.compartment.compartment_units ** (species.compartment.dimensionality - 2)
+            Dform_ = (
+                species.diffusion_
+                * species.concentration_
+                * species.compartment.compartment_ ** (species.compartment.dimensionality - 2)
             )
-            mass_form_units = (
-                species.concentration_units
+            mass_form_ = (
+                species.concentration_
                 / unit.s
-                * species.compartment.compartment_units**species.compartment.dimensionality
+                * species.compartment.compartment_**species.compartment.dimensionality
             )
             # diffusion term
             if species.D == 0:
@@ -1130,6 +1130,7 @@ def _init_5_2_create_variational_forms(self):
                     extra=dict(format_type="log"),
                 )
             else:
+                D_constant = d.Constant(D, name=f"D_{species.name}")
                 if self.config.flags["axisymmetric_model"]:
                     Dform = x[0] * D_constant * d.inner(d.grad(u), d.grad(v)) * dx
                 else:
@@ -1142,7 +1143,7 @@ def _init_5_2_create_variational_forms(self):
                         Dform,
                         species,
                         "diffusion",
-                        Dform_units,
+                        Dform_,
                         True,
                         linear_wrt_comp,
                     )
@@ -1159,7 +1160,7 @@ def _init_5_2_create_variational_forms(self):
                     Muform,
                     species,
                     "mass_u",
-                    mass_form_units,
+                    mass_form_,
                     True,
                     linear_wrt_comp,
                 )
@@ -1174,7 +1175,7 @@ def _init_5_2_create_variational_forms(self):
                     Munform,
                     species,
                     "mass_un",
-                    mass_form_units,
+                    mass_form_,
                     True,
                     linear_wrt_comp,
                 )