GFN2 Core Hamiltonian

.pre-commit-config.yaml

@@ -45,9 +45,10 @@ repos:
     hooks:
       - id: isort
         name: isort (python)
-        args: ["--profile", "black", "--filter-files"]
+        args: ["--profile", "black", "--line-length", "80", "--filter-files"]
 
   - repo: https://github.com/psf/black
     rev: 24.10.0
     hooks:
       - id: black
+        args: ["--line-length", "80"]

setup.cfg

@@ -47,7 +47,7 @@ install_requires =
     scipy
     tad-dftd3>=0.3.0
     tad-dftd4>=0.2.0
-    tad-mctc>=0.2.0
+    tad-mctc>=0.3.0
     tad-multicharge
     tomli
     tomli-w

src/dxtb/_src/basis/slater.py

@@ -125,7 +125,7 @@ def slater_to_gauss(
     # <φ|φ> = (2i-1)!!(2j-1)!!(2k-1)!!/(4α)^(i+j+k) · sqrt(π/2α)³
     # N² = (4α)^(i+j+k)/((2i-1)!!(2j-1)!!(2k-1)!!)  · sqrt(2α/π)³
     # N = (4α)^((i+j+k)/2) / sqrt((2i-1)!!(2j-1)!!(2k-1)!!) · (2α/π)^(3/4)
-    if norm:
+    if norm is True:
         coeff = coeff * (
             (top * alpha) ** 0.75
             * torch.sqrt(4 * alpha) ** l

src/dxtb/_src/calculators/gfn1.py

@@ -57,6 +57,7 @@ def __init__(
         # pylint: disable=import-outside-toplevel
         from dxtb import GFN1_XTB
 
+        # constructor can be found in src/dxtb/_src/calculators/types/base.py
         super().__init__(
             numbers,
             GFN1_XTB,

src/dxtb/_src/calculators/gfn2.py

@@ -57,6 +57,7 @@ def __init__(
         # pylint: disable=import-outside-toplevel
         from dxtb import GFN2_XTB
 
+        # constructor can be found in src/dxtb/_src/calculators/types/base.py
         super().__init__(
             numbers,
             GFN2_XTB,
@@ -66,5 +67,3 @@ def __init__(
             device=device,
             dtype=dtype,
         )
-
-        raise NotImplementedError("GFN2-xTB is not yet implemented.")

src/dxtb/_src/components/classicals/list.py

@@ -146,10 +146,10 @@
 
         gradients = {}
         for classical in self.components:
             timer.start(f"{classical.label} Gradient")
             gradients[classical.label] = classical.get_gradient(
                 energy[classical.label], positions
             )
             timer.stop(f"{classical.label} Gradient")
 
         return gradients
@@ -157,16 +157,10 @@
     ###########################################################################
 
     @overload
-    def get_interaction(
-        self,
-        name: Literal["Halogen"],
-    ) -> Halogen: ...
+    def get_interaction(self, name: Literal["Halogen"]) -> Halogen: ...
 
     @overload
-    def get_interaction(
-        self,
-        name: Literal["Repulsion"],
-    ) -> Repulsion: ...
+    def get_interaction(self, name: Literal["Repulsion"]) -> Repulsion: ...
 
     @override  # generic implementation for typing
     def get_interaction(self, name: str) -> Classical:

src/dxtb/_src/components/classicals/repulsion/factory.py

@@ -74,7 +74,9 @@ def new_repulsion(
     """
 
     if hasattr(par, "repulsion") is False or par.repulsion is None:
-        # TODO: Repulsion is used in all models, so error or just warning?
+        # Although repulsion is used in all models, we do not want to exit
+        # for custom models that are loaded from a parameter file. Hence, we
+        # only issue a warning here, not an error.
         warnings.warn("No repulsion scheme found.", ParameterWarning)
         return None
 

src/dxtb/_src/components/interactions/coulomb/thirdorder.py

@@ -188,9 +188,9 @@ def get_cache(
         Note
         ----
         If the :class:`.ES3` interaction is evaluated within the
-        :class:`dxtb.components.InteractionList`, ``positions`` will be passed
-        as an argument, too. Hence, it is necessary in signature
-        of the function to absorb it (also see
+        :class:`dxtb.components.InteractionList`, ``positions`` will be
+        passed as an argument, too. Hence, it is necessary to absorb
+        the ``positions`` in the signature of the function (also see
         :meth:`dxtb.components.Interaction.get_cache`).
         """
         if numbers is None:
@@ -297,7 +297,7 @@ def new_es3(
     if device is not None:
         if device != numbers.device:
             raise DeviceError(
-                f"Passed device ({device}) and device of electric field "
+                f"Passed device ({device}) and device of `numbers` tensor "
                 f"({numbers.device}) do not match."
             )
 

src/dxtb/_src/components/interactions/solvation/alpb.py

@@ -270,10 +270,11 @@ def get_cache(
 
         Note
         ----
-        If the :class:`.GeneralizedBorn` interaction is evaluated within the
-        :class:`dxtb.components.InteractionList`, the :class:`dxtb.IndexHelper`
-        will be passed as an argument, too. Hence, it is necessary in signature
-        of the function to absorb it.
+        If the :class:`.GeneralizedBorn` interaction is evaluated
+        within the :class:`dxtb.components.InteractionList`, the
+        :class:`dxtb.IndexHelper` will be passed as an argument, too. Hence,
+        it is necessary to absorb the ``positions`` in the signature of the
+        function.
         """
         if numbers is None:
             raise ValueError("Atomic numbers are required for cache.")

src/dxtb/_src/components/list.py

@@ -75,10 +75,10 @@ def restore(self) -> None:
         """
         pass
 
-    def __str__(self) -> str:
+    def __str__(self) -> str:  # pragma: no cover
         return f"{self.__class__.__name__}({list(self.keys())})"
 
-    def __repr__(self) -> str:
+    def __repr__(self) -> str:  # pragma: no cover
         return str(self)
 
 
@@ -238,7 +238,8 @@ def reset_all(self) -> None:
 
     @property
     def labels(self) -> list[str]:
-        return [component.label for component in self.components]
+        """Alphabetically sorted list of all components labels."""
+        return sorted([component.label for component in self.components])
 
     def get_interaction(self, name: str) -> C:
         """
@@ -265,10 +266,13 @@ def get_interaction(self, name: str) -> C:
 
         raise ValueError(f"The component named '{name}' is not in the list.")
 
-    def __str__(self) -> str:
+    def __len__(self) -> int:
+        return len(self.components)
+
+    def __str__(self) -> str:  # pragma: no cover
         return f"{self.__class__.__name__}({self.labels})"
 
-    def __repr__(self) -> str:
+    def __repr__(self) -> str:  # pragma: no cover
         return str(self)
 
     @override

src/dxtb/_src/integral/container.py

@@ -482,6 +482,23 @@ def reset_all(self) -> None:
             if isinstance(i, BaseIntegral) or isinstance(i, BaseHamiltonian):
                 i.clear()
 
+    @property
+    def labels(self) -> list[str]:
+        """Return all initialized integrals by label."""
+        return [
+            slot[1:]
+            for slot in self.__slots__
+            if slot.startswith("_") and getattr(self, slot) is not None
+        ]
+
+    def __len__(self) -> int:
+        """Print all initialized integrals."""
+        return sum(
+            1
+            for slot in self.__slots__
+            if slot.startswith("_") and getattr(self, slot) is not None
+        )
+
     # pretty print
 
     def __str__(self) -> str:

src/dxtb/_src/xtb/abc.py

@@ -36,6 +36,28 @@ class HamiltonianABC(ABC):
     Abstract base class for Hamiltonians.
     """
 
+    @abstractmethod
+    def _get_hscale(self) -> Tensor:
+        """
+        Obtain the off-site scaling factor for the Hamiltonian.
+
+        Returns
+        -------
+        Tensor
+            Off-site scaling factor for the Hamiltonian.
+        """
+
+    @abstractmethod
+    def _get_elem_valence(self) -> Tensor:
+        """
+        Obtain a mask for valence and non-valence shells. This is only required for GFN1-xTB's second hydrogen s-function.
+
+        Returns
+        -------
+        Tensor
+            Mask indicating valence shells for each unique species.
+        """
+
     @abstractmethod
     def build(self, positions: Tensor, overlap: Tensor | None = None) -> Tensor:
         """