Elements 87 to 103 are now accessible via the element composition

CHANGELOG.md

@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Support for the novel "g-xTB" method (working title: GP3-xTB)
 - A function which contracts the coordinates after the initial generation.
 - A function which is able to printout the xyz coordinates to the terminal similar to the `.xyz` layout.
+- Elements 87 to 103 are accessible via the element composition. If `xtb` is the engine, the elements will be replaced by their lighter homologues.
 
 ### Breaking Changes
 - Removal of the `dist_threshold` flag and in the `-toml` file.

src/mindlessgen/generator/main.py

@@ -8,10 +8,12 @@
 from pathlib import Path
 import multiprocessing as mp
 import warnings
+import numpy as np
 
-from ..molecules import generate_random_molecule, Molecule
+from ..molecules import generate_random_molecule, Molecule, get_lanthanides
 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__
@@ -209,6 +211,7 @@ def single_molecule_generator(
             config_refine=config.refine,
             verbosity=config.general.verbosity,
         )
+
     except RuntimeError as e:
         if config.general.verbosity > 0:
             print(f"Refinement failed for cycle {cycle + 1}.")
@@ -239,6 +242,16 @@ 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

@@ -16,14 +16,15 @@ def set_random_charge(ati: np.ndarray, verbosity: int = 1) -> tuple[int, int]:
     if verbosity > 1:
         print(f"Number of protons in molecule: {nel}")
 
-    if np.any(np.isin(ati, get_lanthanides())):
-        ### Special mode for lanthanides
+    if np.any(np.isin(ati, get_lanthanides() + get_actinides())):
+        ### Special mode for lanthanides and actinides
         # -> always high spin
-        # -> Divide the molecule into Ln3+ ions and negative "ligands"
+        # -> Divide the molecule into Ln3+/Ac3+ ions and negative "ligands"
         # -> The ligands are the remaining protons are assumed to be low spin
         uhf = 0
         charge = 0
         ln_protons = 0
+        ac_protons = 0
         for atom in ati:
             if atom in get_lanthanides():
                 if atom < 64:
@@ -33,9 +34,20 @@ 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
-        ligand_protons = nel - ln_protons
+            if atom in get_actinides():
+                if atom < 96:
+                    uhf += atom - 88
+                else:
+                    uhf += 102 - atom
+                ac_protons += (
+                    atom - 3 + 1
+                )  # subtract 3 to get the number of protons in the Ln3+ ion
+        ligand_protons = nel - ln_protons - ac_protons
         if verbosity > 2:
-            print(f"Number of protons from Ln^3+ ions: {ln_protons}")
+            if np.any(np.isin(ati, get_lanthanides())):
+                print(f"Number of protons from Ln^3+ ions: {ln_protons}")
+            if np.any(np.isin(ati, get_actinides())):
+                print(f"Number of protons from Ac^3+ ions: {ac_protons}")
             print(
                 f"Number of protons from ligands (assuming negative charge): {ligand_protons}"
             )

src/mindlessgen/prog/config.py

@@ -716,6 +716,25 @@ 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.
@@ -731,6 +750,7 @@ 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)

src/mindlessgen/qm/xtb.py

@@ -36,6 +36,11 @@ def optimize(
         """
         Optimize a molecule using xtb.
         """
+        super_heavy_elements = False
+        ati_original = molecule.ati.copy()
+        if np.any(molecule.ati > 85):
+            super_heavy_elements = True
+            molecule.ati[molecule.ati > 85] -= 32
         if np.any(np.isin(molecule.ati, get_lanthanides())):
             check_ligand_uhf(molecule.ati, molecule.charge)
             # Store the original UHF value and set uhf to 0
@@ -82,12 +87,22 @@ def optimize(
             if np.any(np.isin(molecule.ati, get_lanthanides())):
                 # Reset the UHF value to the original value before returning the optimized molecule.
                 optimized_molecule.uhf = uhf_original
+            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
 
     def singlepoint(self, molecule: Molecule, verbosity: int = 1) -> str:
         """
         Perform a single-point calculation using xtb.
         """
+        super_heavy_elements = False
+        ati_original = molecule.ati.copy()
+        if np.any(molecule.ati > 85):
+            super_heavy_elements = True
+            molecule.ati[molecule.ati > 85] -= 32
         if np.any(np.isin(molecule.ati, get_lanthanides())):
             check_ligand_uhf(molecule.ati, molecule.charge)
             # Store the original UHF value and set uhf to 0
@@ -128,6 +143,9 @@ def singlepoint(self, molecule: Molecule, verbosity: int = 1) -> str:
 
             if np.any(np.isin(molecule.ati, get_lanthanides())):
                 molecule.uhf = uhf_original
+            if super_heavy_elements:
+                # Reset the atomic numbers to the original values before returning the optimized molecule.
+                molecule.ati = ati_original
             return xtb_log_out
 
     def check_gap(