..

dweindl · Apr 23, 2024 · d3c4fc4 · d3c4fc4
1 parent 4fd7a30
commit d3c4fc4
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/python/sdist/amici/de_model.py b/python/sdist/amici/de_model.py
@@ -1400,7 +1400,8 @@ def _compute_equation(self, name: str) -> None:
                                 if not s.has_conservation_law()
                             ),
                             self.sym("dx"),
-                            strict=True,
+                            # dx contains extra elements for algebraic states
+                            strict=False,
                         )
                     ]
                     + [eq.get_val() for eq in self._algebraic_equations]

diff --git a/python/sdist/amici/sbml_import.py b/python/sdist/amici/sbml_import.py
@@ -556,9 +556,13 @@ def _build_ode_model(
         dxdt = smart_multiply(
             self.stoichiometric_matrix, MutableDenseMatrix(fluxes)
         )
+        # there may be an additional 0-entry at the end of the
+        #  stoichiometric matrix / flux vector
+        assert dxdt.shape[0] - len(self.symbols[SymbolId.SPECIES]) in (0, 1)
+
         # correct time derivatives for compartment changes
         for ix, ((species_id, species), formula) in enumerate(
-            zip(self.symbols[SymbolId.SPECIES].items(), dxdt, strict=True)
+            zip(self.symbols[SymbolId.SPECIES].items(), dxdt, strict=False)
         ):
             # rate rules and amount species don't need to be updated
             if "dt" in species: