fix(parsers): Fix Jaguar Hessian unit bug + Check 1 validation test

q2mm/models/hessian.py

@@ -254,7 +254,7 @@ def replace_neg_eigenvalue(
     eigenvalues: np.ndarray,
     replace_with: float = 1.0,
     zer_out_neg: bool = False,
-    units: int = co.KJMOLA,
+    units: str = co.GAUSSIAN,
     strict: bool = True,
 ) -> np.ndarray:
     """Replace the most negative eigenvalue to invert TS curvature (Method C).
@@ -264,9 +264,10 @@ def replace_neg_eigenvalue(
     large positive value so that the TS is treated as an energy minimum by
     the MM force field.
 
-    The default replacement is 1.0 Hartree/Bohr², converted to
-    kJ/(mol·Å²) via :func:`~q2mm.models.units.hessian_au_to_kjmola2`
-    (≈ 9376).  This operates on **Cartesian** Hessian eigenvalues —
+    The default replacement is 1.0 Hartree/Bohr² (atomic units).  When
+    *units* is ``co.KJMOLA``, the replacement is converted via
+    :func:`~q2mm.models.units.hessian_au_to_kjmola2` (≈ 9376) to
+    kJ/mol/Ų.  This operates on **Cartesian** Hessian eigenvalues —
     not mass-weighted ones.
 
     Note: Limé & Norrby showed that "Method D" (fitting the natural eigenvalue
@@ -280,8 +281,9 @@ def replace_neg_eigenvalue(
         replace_with (float): Replacement value in Hartree/Bohr². Defaults to 1.0.
         zer_out_neg (bool): If True, zero out remaining negative eigenvalues after
             replacing the most negative. Defaults to False.
-        units (int): Target units for the replacement. If ``co.KJMOLA``
-            (default), *replace_with* is converted via
+        units (str): Unit system of the eigenvalues.  If ``co.GAUSSIAN``
+            (default), *replace_with* is used as-is (Hartree/Bohr²).
+            If ``co.KJMOLA``, *replace_with* is converted via
             :func:`~q2mm.models.units.hessian_au_to_kjmola2`.
         strict (bool): If True, raise ValueError when more than one negative
             eigenvalue is found (indicates a higher-order saddle point or

q2mm/parsers/jaguar.py

@@ -27,8 +27,12 @@
 class JaguarIn(File):
     """Retrieve data from Jaguar ``.in`` files.
 
-    The Hessian is not mass-weighted. Hessian units are assumed to be
-    kJ/(mol·Å²).
+    The Hessian is **not** mass-weighted and is returned in atomic units
+    (Hartree/Bohr²), matching the convention used by Gaussian .fchk and
+    Psi4 outputs.  Jaguar stores the Hessian in the ``&hess`` section of
+    its ``.in`` file in Hartree/Bohr² (confirmed empirically: raw diagonal
+    elements give frequencies that match the Jaguar ``.out`` exactly when
+    treated as atomic units).
     """
 
     def __init__(self, path: str) -> None:
@@ -57,7 +61,8 @@ def get_hessian(self, num_atoms: int) -> np.ndarray:
 
         Returns:
             (numpy.ndarray): 2-D Hessian matrix of shape
-                ``(num_atoms * 3, num_atoms * 3)`` after unit conversion.
+                ``(num_atoms * 3, num_atoms * 3)`` in Hartree/Bohr²
+                (atomic units, no additional conversion applied).
 
         """
         if self._hessian is None:
@@ -85,7 +90,11 @@ def get_hessian(self, num_atoms: int) -> np.ndarray:
 
             logger.log(1, f">>> hessian:\n{hessian}")
             logger.log(5, f"  -- Created {hessian.shape} Hessian matrix (w/o dummy atoms).")
-            self._hessian = hessian * co.HESSIAN_CONVERSION  # Hartree/Bohr² → kJ/(mol·Å²); see constants.py
+            # Jaguar stores the Hessian in atomic units (Hartree/Bohr²).
+            # We return it as-is to match the convention of other QM parsers
+            # (Gaussian .fchk, Psi4).  Downstream code (Seminario, frequency
+            # computation) expects AU when au_hessian=True / au_units=True.
+            self._hessian = hessian
             logger.log(1, f">>> hessian.shape: {hessian.shape}")
         return self._hessian