import torch import torch.nn as nn import torch.nn.functional as F from cdvae.pl_modules.embeddings import MAX_ATOMIC_NUM from cdvae.pl_modules.gemnet.gemnet import GemNetT def build_mlp(in_dim, hidden_dim, fc_num_layers, out_dim): mods = [nn.Linear(in_dim, hidden_dim), nn.ReLU()] for i in range(fc_num_layers-1): mods += [nn.Linear(hidden_dim, hidden_dim), nn.ReLU()] mods += [nn.Linear(hidden_dim, out_dim)] return nn.Sequential(*mods) class GemNetTDecoder(nn.Module): """Decoder with GemNetT.""" def __init__( self, hidden_dim=128, latent_dim=256, max_neighbors=20, radius=6., scale_file=None, ): super(GemNetTDecoder, self).__init__() self.cutoff = radius self.max_num_neighbors = max_neighbors self.gemnet = GemNetT( num_targets=1, latent_dim=latent_dim, emb_size_atom=hidden_dim, emb_size_edge=hidden_dim, regress_forces=True, cutoff=self.cutoff, max_neighbors=self.max_num_neighbors, otf_graph=True, scale_file=scale_file, ) self.fc_atom = nn.Linear(hidden_dim, MAX_ATOMIC_NUM) def forward(self, z, pred_frac_coords, pred_atom_types, num_atoms, lengths, angles): """ args: z: (N_cryst, num_latent) pred_frac_coords: (N_atoms, 3) pred_atom_types: (N_atoms, ), need to use atomic number e.g. H = 1 num_atoms: (N_cryst,) lengths: (N_cryst, 3) angles: (N_cryst, 3) returns: atom_frac_coords: (N_atoms, 3) atom_types: (N_atoms, MAX_ATOMIC_NUM) """ # (num_atoms, hidden_dim) (num_crysts, 3) h, pred_cart_coord_diff = self.gemnet( z=z, frac_coords=pred_frac_coords, atom_types=pred_atom_types, num_atoms=num_atoms, lengths=lengths, angles=angles, edge_index=None, to_jimages=None, num_bonds=None, ) pred_atom_types = self.fc_atom(h) return pred_cart_coord_diff, pred_atom_types