introduce more general fragmentation test

test/fixtures/C13H14.xyz

@@ -0,0 +1,29 @@
+27
+XYZ file generated by Avogadro.
+C     -3.89040    1.99100   -0.00000
+C     -4.02680    0.60350   -0.00000
+C     -2.89350   -0.20830    0.00000
+C     -1.62370    0.36710    0.00000
+H     -3.00000   -1.29040    0.00000
+C     -2.62060    2.56660   -0.00000
+C     -1.48720    1.75470    0.00000
+H     -2.51440    3.64870   -0.00000
+H     -4.72547    2.41014   -0.05516
+H     -5.01710    0.15470    0.00000
+H     -1.81561   -0.88583   -2.43646
+H      0.13224   -0.36655    0.76367
+C     -3.46846   -0.00090   -2.29110
+C     -2.58384    0.41194   -2.42614
+C     -4.46494    1.38711   -2.26956
+H     -4.15642   -0.99674   -2.19618
+C     -0.98984    1.36664   -2.22371
+H     -0.04316    1.26762   -2.41645
+C     -3.35847    2.53475   -2.09517
+C     -1.79945    2.16401   -2.13219
+H     -5.08593    1.97986   -2.35395
+H     -1.45478    3.39792   -1.81901
+H     -3.80661    3.50015   -2.26079
+H     -0.51264    2.19643    0.00000
+C     -0.68480   -0.69801    0.15746
+H     -1.16476   -1.52968    0.62954
+H     -0.31863   -0.99558   -0.80289

test/fixtures/C7H8.xyz

@@ -0,0 +1,17 @@
+15
+
+C           -3.92822833036995        1.96432093560546        0.62157575642424
+C           -4.12348090129541        0.59558759251302        0.57376967392366
+C           -3.03747857134253       -0.25907351392770        0.51942684687914
+C           -1.74159802338474        0.23892621267053        0.51235642166947
+H           -3.19667870717782       -1.32775033564467        0.48239910213616
+C           -2.64080719756196        2.47160711796854        0.61409596611734
+C           -1.55734176910219        1.61463498015929        0.55983863383019
+H           -2.48025573405657        3.53952821534543        0.64999745894259
+H           -4.77440551551237        2.63405350408406        0.66390613955572
+H           -5.12565950974504        0.19165590433204        0.57921484920548
+H            0.28242223890343       -0.28503647701491        0.98320934851746
+H           -0.55378035137604        2.01638780449344        0.55334107071640
+C           -0.56432434664417       -0.68420602079331        0.42876403999537
+H           -0.81083301669431       -1.66824638917295        0.82046696760621
+H           -0.26050639196391       -0.79926111783838       -0.61204235704981

test/test_molecules/test_refinement.py

@@ -13,6 +13,28 @@
 from mindlessgen.molecules import iterative_optimization  # type: ignore
 from mindlessgen.qm import XTB, get_xtb_path  # type: ignore
 
+TESTSDIR = Path(__file__).resolve().parents[1]
+
+
+@pytest.fixture
+def mol_C13H14() -> Molecule:
+    """
+    Load the molecule C13H14 from 'fixtures/C13H14.xyz'.
+    """
+    molfile = TESTSDIR / "fixtures/C13H14.xyz"
+    mol = Molecule.read_mol_from_file(molfile)
+    return mol
+
+
+@pytest.fixture
+def mol_C7H8() -> Molecule:
+    """
+    Load the molecule C7H8 from 'fixtures/C7H8.xyz'.
+    """
+    molfile = TESTSDIR / "fixtures/C7H8.xyz"
+    mol = Molecule.read_mol_from_file(molfile)
+    return mol
+
 
 @pytest.fixture
 def mol_C2H2N2O1Co1Ge2Ta1Hg1() -> Molecule:
@@ -92,15 +114,15 @@ def test_detect_fragments_H6O2B2Ne2I1Os1Tl1(
 
 
 @pytest.mark.optional
-def test_iterative_optimization(
-    mol_C2H2N2O1Co1Ge2Ta1Hg1: Molecule, mol_C2H1N2O1Co1Ge2Ta1Hg1_frag: Molecule
-) -> None:
+def test_iterative_optimization(mol_C13H14: Molecule, mol_C7H8: Molecule) -> None:
     """
     Test the iterative optimization of the molecule H6O2B2Ne2I1Os1Tl1.
     """
     # initialize a configuration object
     config = ConfigManager()
-    config.refine.hlgap = 0.1
+    config.refine.hlgap = 0.001  # TODO: Change charge assignment such that
+    # fragment charge is not completely random anymore. Currently, that's the
+    # reason for a virtually switched off HL gap check (fragment can be -2, 0, 2)
     config.refine.max_frag_cycles = 1
     if config.refine.engine == "xtb":
         try:
@@ -112,15 +134,15 @@ def test_iterative_optimization(
         engine = XTB(xtb_path, config.xtb)
     else:
         raise NotImplementedError("Engine not implemented.")
-    mol = mol_C2H2N2O1Co1Ge2Ta1Hg1
+    mol = mol_C13H14
     mol_opt = iterative_optimization(
         mol,
         engine=engine,
         config_generate=config.generate,
         config_refine=config.refine,
-        verbosity=0,
+        verbosity=2,
     )
-    mol_ref = mol_C2H1N2O1Co1Ge2Ta1Hg1_frag
+    mol_ref = mol_C7H8
 
     # assert number of atoms in mol_opt is equal to number of atoms in mol_ref
     assert mol_opt.num_atoms == mol_ref.num_atoms

test/test_qm/test_xtb.py

@@ -52,7 +52,7 @@ def test_xtb_optimize_xtb(coordinates_ethanol: np.ndarray) -> None:
                 [-1.17300591097528, 0.85675047762011, 0.75712732702203],
             ]
         ),
-        rtol=1e-3,
+        atol=1e-4,
     )