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def forward(self, batch): h = self.emb_in(batch.x) # (n,) -> (n, d) #pos = batch.pos # (n, 3) batch.pos = torch.autograd.Variable(batch.pos, requires_grad=True) distances = self.make_dist(batch.pos, batch.edge_index, batch.cell_offset ,batch.unit_cell[:3]) for conv in self.convs: # Message passing layer h_update = conv(h, batch.edge_index, distances) # Update node features (n, d) -> (n, d) h = h + h_update if self.residual else h_update # Update node coordinates (no residual) (n, 3) -> (n, 3) out = h if self.pool is not None: out = self.pool(h, batch.batch) energy = self.pred(out) #### Necemo to tako implementirat jer cemo imat pos1,pos2 blabla al oke force = -1.0 * torch.autograd.grad( energy, batch.pos, grad_outputs=torch.ones_like(energy), create_graph=True, retain_graph=True )[0] return energy, force # (batch_size, out_features) class PBCConvLayer(nn.Module): def __init__(self): super(PBCConvLayer, self).__init__() def forward(self, pos, edge_index, offsets, cell_vectors): # pos: Positions of nodes (N, 3) # edge_index: Indices of edges (2, E) # offsets: Offsets for PBC (E, 3), values like -1, 0, 1 for each edge considering PBC # cell_vectors: Cell vectors defining the unit cell (3, 3) # Calculate edge vectors considering initial positions to_move = pos[edge_index[1]] # Shape (E, 3) # Apply PBC corrections using offsets and cell vectors pbc_adjustments = torch.matmul(offsets, cell_vectors) corrected = to_move - pbc_adjustments # Compute distances distances = torch.linalg.vector_norm(corrected - pos[edge_index[0]],dim=-1) return distances
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