implemented the warnings at the right position

Signed-off-by: Jonathan Schöps <[email protected]>

src/mindlessgen/generator/main.py

@@ -8,12 +8,10 @@
 from pathlib import Path
 import multiprocessing as mp
 import warnings
-import numpy as np
 
-from ..molecules import generate_random_molecule, Molecule, get_lanthanides
+from ..molecules import generate_random_molecule, Molecule
 from ..qm import XTB, get_xtb_path, QMMethod, ORCA, get_orca_path, GP3, get_gp3_path
 from ..molecules import iterative_optimization, postprocess_mol
-from ..molecules.miscellaneous import get_actinides
 from ..prog import ConfigManager
 
 from .. import __version__
@@ -59,31 +57,9 @@ def generator(config: ConfigManager) -> tuple[list[Molecule] | None, int]:
 
     if config.general.verbosity > 0:
         print(config)
+        config.check_config()
 
-    # lower number of the available cores and the configured parallelism
     num_cores = min(mp.cpu_count(), config.general.parallel)
-    if config.general.parallel > mp.cpu_count():
-        warnings.warn(
-            f"Number of cores requested ({config.general.parallel}) is greater "
-            + f"than the number of available cores ({mp.cpu_count()})."
-            + f"Using {num_cores} cores instead."
-        )
-    if config.general.verbosity > 0:
-        print(f"Running with {num_cores} cores.")
-
-    if num_cores > 1 and config.general.verbosity > 0:
-        # raise warning that parallelization will disable verbosity
-        warnings.warn(
-            "Parallelization will disable verbosity during iterative search. "
-            + "Set '--verbosity 0' or '-P 1' to avoid this warning, or simply ignore it."
-        )
-    if num_cores > 1 and config.postprocess.debug:
-        # raise warning that debugging of postprocessing will disable parallelization
-        warnings.warn(
-            "Debug output might seem to be redundant due to the parallel processes "
-            + "with possibly similar errors in parallel mode. "
-            + "Don't be confused!"
-        )
 
     # Check if the file "mindless.molecules" exists. If yes, append to it.
     if Path(MINDLESS_MOLECULES_FILE).is_file():
@@ -242,16 +218,6 @@ def single_molecule_generator(
         if config.general.verbosity > 1:
             print("Postprocessing successful.")
 
-    if isinstance(refine_engine, XTB):
-        if np.any(np.isin(optimized_molecule.ati, get_lanthanides() + get_actinides())):
-            print(config.warnings.get_warning()[0])
-
-        if np.any(optimized_molecule.ati > 85):
-            print(config.warnings.get_warning()[1])
-
-        if postprocess_engine is None:
-            print(config.warnings.get_warning()[2])
-
     if not stop_event.is_set():
         stop_event.set()  # Signal other processes to stop
         return optimized_molecule

src/mindlessgen/molecules/miscellaneous.py

@@ -34,7 +34,7 @@ def set_random_charge(ati: np.ndarray, verbosity: int = 1) -> tuple[int, int]:
                 ln_protons += (
                     atom - 3 + 1
                 )  # subtract 3 to get the number of protons in the Ln3+ ion
-            if atom in get_actinides():
+            elif atom in get_actinides():
                 if atom < 96:
                     uhf += atom - 88
                 else:

src/mindlessgen/prog/config.py

@@ -6,6 +6,8 @@
 
 from pathlib import Path
 from abc import ABC, abstractmethod
+import warnings
+import multiprocessing as mp
 import toml
 
 from ..molecules import PSE_NUMBERS
@@ -716,25 +718,6 @@ def scf_cycles(self, max_scf_cycles: int):
         self._scf_cycles = max_scf_cycles
 
 
-class WarningConfig:
-    """
-    This class handles warnings related to xTB calculations.
-    """
-
-    def __init__(self) -> None:
-        self.warnings = [
-            "WARNING: f-block elements are within the molecule. xTB does not treat f electrons explicitly. UHF is set to 0.",
-            "WARNING: Super heavy elements are within the molecule. xTB does not treat super havy elements. Atomic numbers are reduced by 32.",
-            "WARNING: Postproccessing is turned off the structure will not be relaxed.",
-        ]
-
-    def get_warning(self) -> list[str]:
-        """
-        Get the list of warnings.
-        """
-        return self.warnings
-
-
 class ConfigManager:
     """
     Overall configuration manager for the program.
@@ -750,11 +733,65 @@ def __init__(self, config_file: str | Path | None = None):
         self.refine = RefineConfig()
         self.postprocess = PostProcessConfig()
         self.generate = GenerateConfig()
-        self.warnings = WarningConfig()
 
         if config_file:
             self.load_from_toml(config_file)
 
+    def check_config(self):
+        """
+        Checks ConfigClass for any incompatibilities that are imaginable
+        """
+        # lower number of the available cores and the configured parallelism
+        num_cores = min(mp.cpu_count(), self.general.parallel)
+        if self.general.parallel > mp.cpu_count():
+            warnings.warn(
+                f"Number of cores requested ({self.general.parallel}) is greater "
+                + f"than the number of available cores ({mp.cpu_count()})."
+                + f"Using {num_cores} cores instead."
+            )
+        if self.general.verbosity > 0:
+            print(f"Running with {num_cores} cores.")
+
+        if num_cores > 1 and self.general.verbosity > 0:
+            # raise warning that parallelization will disable verbosity
+            warnings.warn(
+                "Parallelization will disable verbosity during iterative search. "
+                + "Set '--verbosity 0' or '-P 1' to avoid this warning, or simply ignore it."
+            )
+        if num_cores > 1 and self.postprocess.debug:
+            # raise warning that debugging of postprocessing will disable parallelization
+            warnings.warn(
+                "Debug output might seem to be redundant due to the parallel processes "
+                + "with possibly similar errors in parallel mode. "
+                + "Don't be confused!"
+            )
+
+        # Check for f-block elements in forbidden elements
+        if self.generate.forbidden_elements:
+            f_block_elements = set(range(56, 70)) | set(range(88, 102))
+            if any(
+                elem not in f_block_elements
+                for elem in self.generate.forbidden_elements
+            ):
+                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."
+                )
+
+        # Check for super heavy elements in forbidden elements
+        super_heavy_elements = set(range(86, 102))
+        if self.generate.element_composition and any(
+            elem in super_heavy_elements for elem in self.generate.element_composition
+        ):
+            warnings.warn(
+                "Super heavy elements are within the molecule. xTB does not treat super heavy elements. Atomic numbers are reduced by 32."
+            )
+
+        # Check if postprocessing is turned off
+        if not self.general.postprocess:
+            warnings.warn(
+                "Postprocessing is turned off. The structure will not be relaxed."
+            )
+
     def get_all_identifiers(self):
         """
         Returns the identifiers of all subconfiguration classes, e.g. "orca", "refinement", ...

src/mindlessgen/qm/xtb.py

@@ -90,7 +90,6 @@ def optimize(
             if super_heavy_elements:
                 # Reset the atomic numbers to the original values before returning the optimized molecule.
                 optimized_molecule.ati = ati_original
-                molecule.ati = ati_original
                 optimized_molecule.atlist = molecule.atlist
             return optimized_molecule