GNN cvs module merge

mlcolvar/core/nn/graph/gnn.py

@@ -0,0 +1,135 @@
+import torch
+import lightning
+from torch import nn
+import numpy as np
+import torch_geometric as tg
+from typing import List, Dict, Tuple, Any
+
+# from mlcolvar.graph import data as gdata
+from mlcolvar.core.nn.graph import radial
+# from mlcolvar.graph.core.nn import schnet
+# from mlcolvar.graph.core.nn import gvp_layer
+# from mlcolvar.graph.utils import torch_tools
+
+"""
+GNN models.
+"""
+
+__all__ = ['BaseGNN']
+
+
+class BaseGNN(nn.Module):
+    """
+    The commen GNN interface for mlcolvar.
+
+    Parameters
+    ----------
+    n_out: int
+        Size of the output node features.
+    cutoff: float
+        Cutoff radius of the basis functions. Should be the same as the cutoff
+        radius used to build the graphs.
+    atomic_numbers: List[int]
+        The atomic numbers mapping, e.g. the `atomic_numbers` attribute of a
+        `mlcolvar.graph.data.GraphDataSet` instance.
+    n_bases: int
+        Size of the basis set.
+    n_polynomials: bool
+        Order of the polynomials in the basis functions.
+    basis_type: str
+        Type of the basis function.
+    """
+
+    def __init__(
+        self,
+        n_out: int,
+        cutoff: float,
+        atomic_numbers: List[int],
+        n_bases: int = 6,
+        n_polynomials: int = 6,
+        basis_type: str = 'bessel'
+    ) -> None:
+        super().__init__()
+        self._model_type = 'gnn'
+
+        self._n_out = n_out
+        self._radial_embedding = radial.RadialEmbeddingBlock(
+            cutoff, n_bases, n_polynomials, basis_type
+        )
+        self.register_buffer(
+            'n_out', torch.tensor(n_out, dtype=torch.int64)
+        )
+        self.register_buffer(
+            'cutoff', torch.tensor(cutoff, dtype=torch.get_default_dtype())
+        )
+        self.register_buffer(
+            'atomic_numbers', torch.tensor(atomic_numbers, dtype=torch.int64)
+        )
+
+    def embed_edge(
+        self, data: Dict[str, torch.Tensor], normalize: bool = True
+    ) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
+        """
+        Perform the edge embedding.
+
+        Parameters
+        ----------
+        data: Dict[str, torch.Tensor]
+            The data dict. Usually came from the `to_dict` method of a
+            `torch_geometric.data.Batch` object.
+        normalize: bool
+            If return the normalized distance vectors.
+
+        Returns
+        -------
+        edge_lengths: torch.Tensor (shape: [n_edges, 1])
+            The edge lengths.
+        edge_length_embeddings: torch.Tensor (shape: [n_edges, n_bases])
+            The edge length embeddings.
+        edge_unit_vectors: torch.Tensor (shape: [n_edges, 3])
+            The normalized edge vectors.
+        """
+        vectors, lengths = get_edge_vectors_and_lengths(
+            positions=data['positions'],
+            edge_index=data['edge_index'],
+            shifts=data['shifts'],
+            normalize=normalize,
+        )
+        return lengths, self._radial_embedding(lengths), vectors
+
+def get_edge_vectors_and_lengths(
+    positions: torch.Tensor,
+    edge_index: torch.Tensor,
+    shifts: torch.Tensor,
+    normalize: bool = True,
+) -> Tuple[torch.Tensor, torch.Tensor]:
+    """
+    Calculate edge vectors and lengths by indices and shift vectors.
+
+    Parameters
+    ----------
+    position: torch.Tensor (shape: [n_atoms, 3])
+        The position vector.
+    edge_index: torch.Tensor (shape: [2, n_edges])
+        The edge indices.
+    shifts: torch.Tensor (shape: [n_edges, 3])
+        The shift vector.
+    normalize: bool
+        If return the normalized distance vectors.
+
+    Returns
+    -------
+    vectors: torch.Tensor (shape: [n_edges, 3])
+        The distance vectors.
+    lengths: torch.Tensor (shape: [n_edges, 1])
+        The edge lengths.
+    """
+    sender = edge_index[0]
+    receiver = edge_index[1]
+    vectors = positions[receiver] - positions[sender] + shifts  # [n_edges, 3]
+    lengths = torch.linalg.norm(vectors, dim=-1, keepdim=True)  # [n_edges, 1]
+
+    if normalize:
+        vectors = torch.nan_to_num(torch.div(vectors, lengths))
+
+    return vectors, lengths