Fix alchemical model

src/metatrain/experimental/alchemical_model/trainer.py

@@ -5,7 +5,6 @@
 import torch
 from metatensor.learn.data import DataLoader
 
-from ...utils.composition import calculate_composition_weights
 from ...utils.data import (
     CombinedDataLoader,
     Dataset,
@@ -23,6 +22,7 @@
 from ...utils.neighbor_lists import get_system_with_neighbor_lists
 from ...utils.per_atom import average_by_num_atoms
 from . import AlchemicalModel
+from .utils.composition import calculate_composition_weights
 from .utils.normalize import (
     get_average_number_of_atoms,
     get_average_number_of_neighbors,

src/metatrain/experimental/alchemical_model/utils/composition.py

@@ -0,0 +1,69 @@
+from typing import List, Tuple, Union
+
+import torch
+
+from ....utils.data.dataset import Dataset, get_atomic_types
+
+
+def calculate_composition_weights(
+    datasets: Union[Dataset, List[Dataset]], property: str
+) -> Tuple[torch.Tensor, List[int]]:
+    """Calculate the composition weights for a dataset.
+
+    It assumes per-system properties.
+
+    :param dataset: Dataset to calculate the composition weights for.
+    :returns: Composition weights for the dataset, as well as the
+        list of species that the weights correspond to.
+    """
+    if not isinstance(datasets, list):
+        datasets = [datasets]
+
+    # Note: `atomic_types` are sorted, and the composition weights are sorted as
+    # well, because the species are sorted in the composition features.
+    atomic_types = sorted(get_atomic_types(datasets))
+
+    targets = torch.stack(
+        [sample[property].block().values for dataset in datasets for sample in dataset]
+    )
+    targets = targets.squeeze(dim=(1, 2))  # remove component and property dimensions
+
+    total_num_structures = sum([len(dataset) for dataset in datasets])
+    dtype = datasets[0][0]["system"].positions.dtype
+    composition_features = torch.empty(
+        (total_num_structures, len(atomic_types)), dtype=dtype
+    )
+    structure_index = 0
+    for dataset in datasets:
+        for sample in dataset:
+            structure = sample["system"]
+            for j, s in enumerate(atomic_types):
+                composition_features[structure_index, j] = torch.sum(
+                    structure.types == s
+                )
+            structure_index += 1
+
+    regularizer = 1e-20
+    while regularizer:
+        if regularizer > 1e5:
+            raise RuntimeError(
+                "Failed to solve the linear system to calculate the "
+                "composition weights. The dataset is probably too small "
+                "or ill-conditioned."
+            )
+        try:
+            solution = torch.linalg.solve(
+                composition_features.T @ composition_features
+                + regularizer
+                * torch.eye(
+                    composition_features.shape[1],
+                    dtype=composition_features.dtype,
+                    device=composition_features.device,
+                ),
+                composition_features.T @ targets,
+            )
+            break
+        except torch._C._LinAlgError:
+            regularizer *= 10.0
+
+    return solution, atomic_types