import torch import torch.nn as nn from torch_scatter import scatter_sum from torch_geometric.nn import radius_graph, knn_graph from ..common import GaussianSmearing, MLP class EnBaseLayer(nn.Module): def __init__(self, hidden_dim, edge_feat_dim, num_r_gaussian, update_x=True, act_fn='relu', norm=False): super().__init__() self.r_min = 0. self.r_max = 10. ** 2 self.hidden_dim = hidden_dim self.num_r_gaussian = num_r_gaussian self.edge_feat_dim = edge_feat_dim self.update_x = update_x self.act_fn = act_fn self.norm = norm if num_r_gaussian > 1: self.r_expansion = GaussianSmearing(self.r_min, self.r_max, num_gaussians=num_r_gaussian, fixed_offset=False) self.edge_mlp = MLP(2 * hidden_dim + edge_feat_dim + num_r_gaussian, hidden_dim, hidden_dim, num_layer=2, norm=norm, act_fn=act_fn, act_last=True) self.edge_inf = nn.Sequential(nn.Linear(hidden_dim, 1), nn.Sigmoid()) if self.update_x: self.x_mlp = MLP(hidden_dim, 1, hidden_dim, num_layer=2, norm=norm, act_fn=act_fn) self.node_mlp = MLP(2 * hidden_dim, hidden_dim, hidden_dim, num_layer=2, norm=norm, act_fn=act_fn) def forward(self, h, edge_index, edge_attr): dst, src = edge_index hi, hj = h[dst], h[src] # \phi_e in Eq(3) mij = self.edge_mlp(torch.cat([edge_attr, hi, hj], -1)) eij = self.edge_inf(mij) mi = scatter_sum(mij * eij, dst, dim=0, dim_size=h.shape[0]) # h update in Eq(6) # h = h + self.node_mlp(torch.cat([mi, h], -1)) output = self.node_mlp(torch.cat([mi, h], -1)) # if self.update_x: # # x update in Eq(4) # xi, xj = x[dst], x[src] # delta_x = scatter_sum((xi - xj) * self.x_mlp(mij), dst, dim=0) # x = x + delta_x return output class EnEquiEncoder(nn.Module): def __init__(self, num_layers, hidden_dim, edge_feat_dim, num_r_gaussian, k=32, cutoff=10.0, update_x=True, act_fn='relu', norm=False): super().__init__() # Build the network self.num_layers = num_layers self.hidden_dim = hidden_dim self.edge_feat_dim = edge_feat_dim self.num_r_gaussian = num_r_gaussian self.update_x = update_x self.act_fn = act_fn self.norm = norm self.k = k self.cutoff = cutoff self.distance_expansion = GaussianSmearing(stop=cutoff, num_gaussians=num_r_gaussian, fixed_offset=False) self.net = self._build_network() def _build_network(self): # Equivariant layers layers = [] for l_idx in range(self.num_layers): layer = EnBaseLayer(self.hidden_dim, self.edge_feat_dim, self.num_r_gaussian, update_x=self.update_x, act_fn=self.act_fn, norm=self.norm) layers.append(layer) return nn.ModuleList(layers) def forward(self, node_attr, pos, batch): # edge_index = radius_graph(pos, self.cutoff, batch=batch, loop=False) edge_index = knn_graph(pos, k=self.k, batch=batch, flow='target_to_source') edge_length = torch.norm(pos[edge_index[0]] - pos[edge_index[1]], dim=1) edge_attr = self.distance_expansion(edge_length) h = node_attr for interaction in self.net: h = h + interaction(h, edge_index, edge_attr) return h