Fix bug with Lr leading to an

CHANGELOG.md

@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Unit conversion for (currenly unused) vdW radii from the original Fortran project
 - minor print output issues (no new line breaks, more consistent verbosity differentiation, ...)
 - bug in `postprocess_mol` which led to an unassigned return variable in the single-point case
+- bug with all atom lists being initialized with a length of 102 instead of 103
 
 ### Added
 - Support for the novel "g-xTB" method (working title: GP3-xTB)

src/mindlessgen/molecules/generate_molecule.py

@@ -73,8 +73,8 @@ def generate_atom_list(cfg: GenerateConfig, verbosity: int = 1) -> np.ndarray:
         valid_elems = set_all_elem
 
     natoms = np.zeros(
-        102, dtype=int
-    )  # 102 is the number of accessible elements in the periodic table
+        103, dtype=int
+    )  # 103 is the number of accessible elements in the periodic table
 
     # Some sanity checks:
     # - Check if the minimum number of atoms is smaller than the maximum number of atoms

src/mindlessgen/molecules/molecule.py

@@ -547,7 +547,7 @@ def read_xyz_from_file(self, filename: str | Path) -> None:
             # read the atomic coordinates
             self.xyz = np.zeros((self.num_atoms, 3))
             self.ati = np.zeros(self.num_atoms, dtype=int)
-            self.atlist = np.zeros(102, dtype=int)
+            self.atlist = np.zeros(103, dtype=int)
             for i in range(self.num_atoms):
                 line = lines[i + 2].split()
                 self.ati[i] = PSE_NUMBERS[line[0].lower()] - 1

src/mindlessgen/molecules/refinement.py

@@ -197,7 +197,7 @@ def detect_fragments(
         # Remove the atoms that are not in the fragment from ati
         fragment_molecule.ati = np.array([mol.ati[i] for i in fragment])
         # Update atlist by going through ati and add the occurences of each atom onto an empty array
-        fragment_molecule.atlist = np.zeros(102, dtype=int)
+        fragment_molecule.atlist = np.zeros(103, dtype=int)
         for atom in fragment_molecule.ati:
             fragment_molecule.atlist[atom] += 1
         # Update the charge of the fragment molecule

src/mindlessgen/prog/config.py

@@ -779,7 +779,9 @@ def check_config(self, verbosity: int = 1) -> None:
                         for elem in self.generate.element_composition
                     ):
                         warnings.warn(
-                            "f-block elements could be within the molecule. xTB does not treat f electrons explicitly. In this case UHF is set to 0."
+                            "f-block elements could be within the molecule. "
+                            + "xTB does not treat f electrons explicitly. "
+                            + "UHF is temporarily set to 0."
                         )
 
             # Check for super heavy elements in forbidden elements

test/test_generate/test_generate_molecule.py

@@ -35,7 +35,7 @@ def test_generate_atom_list(min_atoms, max_atoms, default_generate_config):
 
     # Common assertions for atom count range
     assert isinstance(atom_list, np.ndarray)
-    assert atom_list.shape == (102,)
+    assert atom_list.shape == (103,)
     assert np.sum(atom_list) > 0
     assert np.sum(atom_list) >= min_atoms
     assert np.sum(atom_list) <= max_atoms