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

@@ -58,31 +58,12 @@ def generator(config: ConfigManager) -> tuple[list[Molecule] | None, int]:
     if config.general.verbosity > 0:
         print(config)
 
-    # lower number of the available cores and the configured parallelism
+    config.check_config(verbosity=config.general.verbosity)
+
     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():
         if config.general.verbosity > 0:

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
+            elif 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

@@ -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
@@ -735,6 +737,68 @@ def __init__(self, config_file: str | Path | None = None):
         if config_file:
             self.load_from_toml(config_file)
 
+    def check_config(self, verbosity: int = 1) -> None:
+        """
+        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() and verbosity > -1:
+            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 num_cores > 1 and self.postprocess.debug and verbosity > -1:
+            # 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!"
+            )
+
+        if num_cores > 1 and 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 self.refine.engine == "xtb":
+            # Check for f-block elements in forbidden elements
+            if self.generate.forbidden_elements:
+                if verbosity > 0:
+                    f_block_elements = set(range(56, 71)) | set(range(88, 103))
+                    lanthanides = set(range(56, 71))
+                    if not all(
+                        elem in self.generate.forbidden_elements for elem in lanthanides
+                    ) or any(
+                        elem in f_block_elements
+                        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."
+                        )
+
+            # 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
+            ):
+                if verbosity > 0:
+                    warnings.warn(
+                        "xTB does not treat super heavy elements. Atomic numbers are temporarily reduced by 32 to their lighter homologues and then replaced with the correct atom number."
+                    )
+                # Check if postprocessing is turned off
+                if not self.general.postprocess:
+                    if verbosity > 0:
+                        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

@@ -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 +87,21 @@ 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
+                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 +142,9 @@ 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(

test/test_molecules/test_miscellaneous.py

@@ -37,7 +37,18 @@
             7,
         ),  # Gd (64), C, C -> Lanthanide case, UHF = 7, CHRG = 1
         (np.array([57, 7, 0]), [0], 1),  # Ce (58), O, H -> Lanthanide case, UHF = 1
-        (np.array([69, 7, 0]), [0], 1),  # Ce (58), O, H -> Lanthanide case, UHF = 1
+        (np.array([69, 7, 0]), [0], 1),  # Yb (70), O, H -> Lanthanide case, UHF = 1
+        (np.array([5, 7, 0, 98]), [0], 4),  # Es(99), O, C, H -> Actinides case, UHF = 4
+        (
+            np.array([59, 92, 0, 0]),
+            [0],
+            7,
+        ),  # Nd(60), Np(93), H, H -> Lanthanide and Actinide case, UHF = 7
+        (
+            np.array([59, 91, 92, 5, 7, 0]),
+            [0],
+            10,
+        ),  # Nd(60), U(92), Np(93), H, H -> Lanthanide and Actinides case, UHF = 10
     ],
     ids=[
         "B-N-H (standard, odd)",
@@ -49,6 +60,9 @@
         "Gd-C-N (lanthanide)",
         "Ce-O-H (lanthanide)",
         "Yb-O-H (lanthanide)",
+        "Es-O-C-H (actinides)",
+        "Nd-Np-H-H (lanthanide and actinide)",
+        "Nd-Eu-Np-H-H (lanthanide and actinides)",
     ],
 )
 def test_set_random_charge(atom_types, expected_charges, expected_uhf):