Fix: VCML writer dropped species velocity components equal to "0.0"

pyvcell/vcml/vcml_writer.py

@@ -410,19 +410,17 @@ def write_species_mapping(self, mapping: SpeciesMapping, parent: _Element) -> No
         elif boundary_value_count > 0:
             raise ValueError(f"SpeciesMapping {mapping.species_name} has {boundary_value_count} boundary values")
         if mapping.velocity_x is not None or mapping.velocity_y is not None or mapping.velocity_z is not None:
+            # Emit every component that is set, INCLUDING a literal "0.0". Dropping zero components broke the
+            # Moving Boundary solver, which reads the VCML directly and requires each needed component to be
+            # present (an axis-aligned advection like velocity=(v, 0) lost its Y and failed with "VelocityY is
+            # null"). The FV reader defaults a missing component to 0, so emitting "0.0" stays round-trip-faithful.
             velocity_element = Element("Velocity")
             if mapping.velocity_x is not None:
-                str_val_x = str(mapping.velocity_x)
-                if str_val_x != "0.0":
-                    velocity_element.set("X", str_val_x)
+                velocity_element.set("X", str(mapping.velocity_x))
             if mapping.velocity_y is not None:
-                str_val_y = str(mapping.velocity_y)
-                if str_val_y != "0.0":
-                    velocity_element.set("Y", str_val_y)
+                velocity_element.set("Y", str(mapping.velocity_y))
             if mapping.velocity_z is not None:
-                str_val_z = str(mapping.velocity_z)
-                if str_val_z != "0.0":
-                    velocity_element.set("Z", str_val_z)
+                velocity_element.set("Z", str(mapping.velocity_z))
             parent.append(velocity_element)
 
     @staticmethod

tests/vcml/test_moving_boundary.py

@@ -80,6 +80,23 @@ def test_moving_boundary_vcml_round_trip() -> None:
     assert sim.moving_boundary_options.redistribution_frequency == 5
 
 
+def test_species_advection_velocity_emits_zero_components() -> None:
+    # Regression: the writer dropped a velocity component equal to "0.0", so an axis-aligned species
+    # advection v = (vx, 0) lost its Y attribute and the Moving Boundary solver (which requires each
+    # component) failed with "VelocityY is null". The component must be emitted, and round-trip.
+    biomodel = _moving_boundary_biomodel()
+    sm = biomodel.applications[0].get_species_mapping("C")
+    sm.velocity_x = "0.5"
+    sm.velocity_y = "0.0"  # the dropped-on-write case
+
+    vcml = to_vcml_str(biomodel, regenerate=False)
+    assert 'X="0.5"' in vcml and 'Y="0.0"' in vcml  # both present (Y no longer dropped)
+
+    reloaded_sm = load_vcml_str(vcml).applications[0].get_species_mapping("C")
+    assert reloaded_sm.velocity_x is not None and float(reloaded_sm.velocity_x) == 0.5
+    assert reloaded_sm.velocity_y is not None and float(reloaded_sm.velocity_y) == 0.0
+
+
 def test_simulate_moving_boundary_rejects_non_moving_boundary_sim() -> None:
     biomodel = _moving_boundary_biomodel()
     app = biomodel.applications[0]