dimenet_pp.py

import torch
import torch.nn as nn
from modules.activations import swish
from modules.bessel_basis_layer import BesselBasisLayer
from modules.embedding_block import EmbeddingBlock
from modules.interaction_pp_block import InteractionPPBlock
from modules.output_pp_block import OutputPPBlock
from modules.spherical_basis_layer import SphericalBasisLayer


class DimeNetPP(nn.Module):
    """
    DimeNet++ model.

    Parameters
    ----------
    emb_size
        Embedding size used for the messages
    out_emb_size
        Embedding size used for atoms in the output block
    int_emb_size
        Embedding size used for interaction triplets
    basis_emb_size
        Embedding size used inside the basis transformation
    num_blocks
        Number of building blocks to be stacked
    num_spherical
        Number of spherical harmonics
    num_radial
        Number of radial basis functions
    cutoff
        Cutoff distance for interatomic interactions
    envelope_exponent
        Shape of the smooth cutoff
    num_before_skip
        Number of residual layers in interaction block before skip connection
    num_after_skip
        Number of residual layers in interaction block after skip connection
    num_dense_output
        Number of dense layers for the output blocks
    num_targets
        Number of targets to predict
    activation
        Activation function
    extensive
        Whether the output should be extensive (proportional to the number of atoms)
    output_init
        Initial function in output block
    """

    def __init__(
        self,
        emb_size,
        out_emb_size,
        int_emb_size,
        basis_emb_size,
        num_blocks,
        num_spherical,
        num_radial,
        cutoff=5.0,
        envelope_exponent=5,
        num_before_skip=1,
        num_after_skip=2,
        num_dense_output=3,
        num_targets=12,
        activation=swish,
        extensive=True,
        output_init=nn.init.zeros_,
    ):
        super(DimeNetPP, self).__init__()

        self.num_blocks = num_blocks
        self.num_radial = num_radial

        # cosine basis function expansion layer
        self.rbf_layer = BesselBasisLayer(
            num_radial=num_radial,
            cutoff=cutoff,
            envelope_exponent=envelope_exponent,
        )

        self.sbf_layer = SphericalBasisLayer(
            num_spherical=num_spherical,
            num_radial=num_radial,
            cutoff=cutoff,
            envelope_exponent=envelope_exponent,
        )

        # embedding block
        self.emb_block = EmbeddingBlock(
            emb_size=emb_size,
            num_radial=num_radial,
            bessel_funcs=self.sbf_layer.get_bessel_funcs(),
            cutoff=cutoff,
            envelope_exponent=envelope_exponent,
            activation=activation,
        )

        # output block
        self.output_blocks = nn.ModuleList(
            {
                OutputPPBlock(
                    emb_size=emb_size,
                    out_emb_size=out_emb_size,
                    num_radial=num_radial,
                    num_dense=num_dense_output,
                    num_targets=num_targets,
                    activation=activation,
                    extensive=extensive,
                    output_init=output_init,
                )
                for _ in range(num_blocks + 1)
            }
        )

        # interaction block
        self.interaction_blocks = nn.ModuleList(
            {
                InteractionPPBlock(
                    emb_size=emb_size,
                    int_emb_size=int_emb_size,
                    basis_emb_size=basis_emb_size,
                    num_radial=num_radial,
                    num_spherical=num_spherical,
                    num_before_skip=num_before_skip,
                    num_after_skip=num_after_skip,
                    activation=activation,
                )
                for _ in range(num_blocks)
            }
        )

    def edge_init(self, edges):
        # Calculate angles k -> j -> i
        R1, R2 = edges.src["o"], edges.dst["o"]
        x = torch.sum(R1 * R2, dim=-1)
        y = torch.cross(R1, R2)
        y = torch.norm(y, dim=-1)
        angle = torch.atan2(y, x)
        # Transform via angles
        cbf = [f(angle) for f in self.sbf_layer.get_sph_funcs()]
        cbf = torch.stack(cbf, dim=1)  # [None, 7]
        cbf = cbf.repeat_interleave(self.num_radial, dim=1)  # [None, 42]
        # Notice: it's dst, not src
        sbf = edges.dst["rbf_env"] * cbf  # [None, 42]
        return {"sbf": sbf}

    def forward(self, g, l_g):
        # add rbf features for each edge in one batch graph, [num_radial,]
        g = self.rbf_layer(g)
        # Embedding block
        g = self.emb_block(g)
        # Output block
        P = self.output_blocks[0](g)  # [batch_size, num_targets]
        # Prepare sbf feature before the following blocks
        for k, v in g.edata.items():
            l_g.ndata[k] = v

        l_g.apply_edges(self.edge_init)
        # Interaction blocks
        for i in range(self.num_blocks):
            g = self.interaction_blocks[i](g, l_g)
            P += self.output_blocks[i + 1](g)

        return P