polymerlearn/models/gnn/schnet/model.py

import os
import os.path as osp
import warnings
from math import pi as PI
from typing import Optional

import numpy as np
import torch
import torch.nn.functional as F
from torch.nn import Embedding, Linear, ModuleList, Sequential
from torch_scatter import scatter

from torch_geometric.data import Dataset, download_url, extract_zip
from torch_geometric.data.makedirs import makedirs
from torch_geometric.nn import MessagePassing, radius_graph

qm9_target_dict = {
    0: 'dipole_moment',
    1: 'isotropic_polarizability',
    2: 'homo',
    3: 'lumo',
    4: 'gap',
    5: 'electronic_spatial_extent',
    6: 'zpve',
    7: 'energy_U0',
    8: 'energy_U',
    9: 'enthalpy_H',
    10: 'free_energy',
    11: 'heat_capacity',
}


class SchNet(torch.nn.Module):
    r"""The continuous-filter convolutional neural network SchNet from the
    `"SchNet: A Continuous-filter Convolutional Neural Network for Modeling
    Quantum Interactions" <https://arxiv.org/abs/1706.08566>`_ paper that uses
    the interactions blocks of the form
    .. math::
        \mathbf{x}^{\prime}_i = \sum_{j \in \mathcal{N}(i)} \mathbf{x}_j \odot
        h_{\mathbf{\Theta}} ( \exp(-\gamma(\mathbf{e}_{j,i} - \mathbf{\mu}))),
    here :math:`h_{\mathbf{\Theta}}` denotes an MLP and
    :math:`\mathbf{e}_{j,i}` denotes the interatomic distances between atoms.
    .. note::
        For an example of using a pretrained SchNet variant, see
        `examples/qm9_pretrained_schnet.py
        <https://github.com/pyg-team/pytorch_geometric/blob/master/examples/
        qm9_pretrained_schnet.py>`_.
    Args:
        hidden_channels (int, optional): Hidden embedding size.
            (default: :obj:`128`)
        num_filters (int, optional): The number of filters to use.
            (default: :obj:`128`)
        num_interactions (int, optional): The number of interaction blocks.
            (default: :obj:`6`)
        num_gaussians (int, optional): The number of gaussians :math:`\mu`.
            (default: :obj:`50`)
        cutoff (float, optional): Cutoff distance for interatomic interactions.
            (default: :obj:`10.0`)
        max_num_neighbors (int, optional): The maximum number of neighbors to
            collect for each node within the :attr:`cutoff` distance.
            (default: :obj:`32`)
        readout (string, optional): Whether to apply :obj:`"add"` or
            :obj:`"mean"` global aggregation. (default: :obj:`"add"`)
        dipole (bool, optional): If set to :obj:`True`, will use the magnitude
            of the dipole moment to make the final prediction, *e.g.*, for
            target 0 of :class:`torch_geometric.datasets.QM9`.
            (default: :obj:`False`)
        mean (float, optional): The mean of the property to predict.
            (default: :obj:`None`)
        std (float, optional): The standard deviation of the property to
            predict. (default: :obj:`None`)
        atomref (torch.Tensor, optional): The reference of single-atom
            properties.
            Expects a vector of shape :obj:`(max_atomic_number, )`.
        get_embedding (bool, optional): If true, forward outputs an embedding
            rather than singular value
    """

    url = 'http://www.quantum-machine.org/datasets/trained_schnet_models.zip'

    def __init__(self, hidden_channels: int = 128, num_filters: int = 128,
                 num_interactions: int = 6, num_gaussians: int = 50,
                 cutoff: float = 10.0, max_num_neighbors: int = 32,
                 readout: str = 'add', dipole: bool = False,
                 mean: Optional[float] = None, std: Optional[float] = None,
                 atomref: Optional[torch.Tensor] = None, get_embedding = False):
        super().__init__()

        import ase

        self.hidden_channels = hidden_channels
        self.num_filters = num_filters
        self.num_interactions = num_interactions
        self.num_gaussians = num_gaussians
        self.cutoff = cutoff
        self.max_num_neighbors = max_num_neighbors
        self.readout = readout
        self.dipole = dipole
        self.readout = 'add' if self.dipole else self.readout
        self.mean = mean
        self.std = std
        self.scale = None
        self.get_embedding = get_embedding

        atomic_mass = torch.from_numpy(ase.data.atomic_masses)
        self.register_buffer('atomic_mass', atomic_mass)

        self.embedding = Embedding(100, hidden_channels)
        self.distance_expansion = GaussianSmearing(0.0, cutoff, num_gaussians)

        self.interactions = ModuleList()
        for _ in range(num_interactions):
            block = InteractionBlock(hidden_channels, num_gaussians,
                                     num_filters, cutoff)
            self.interactions.append(block)

        self.lin1 = Linear(hidden_channels, hidden_channels // 2)
        self.act = ShiftedSoftplus()
        self.lin2 = Linear(hidden_channels // 2, 1)

        self.register_buffer('initial_atomref', atomref)
        self.atomref = None
        if atomref is not None:
            self.atomref = Embedding(100, 1)
            self.atomref.weight.data.copy_(atomref)

        self.reset_parameters()

    def reset_parameters(self):
        self.embedding.reset_parameters()
        for interaction in self.interactions:
            interaction.reset_parameters()
        torch.nn.init.xavier_uniform_(self.lin1.weight)
        self.lin1.bias.data.fill_(0)
        torch.nn.init.xavier_uniform_(self.lin2.weight)
        self.lin2.bias.data.fill_(0)
        if self.atomref is not None:
            self.atomref.weight.data.copy_(self.initial_atomref)

    @staticmethod
    def from_qm9_pretrained(root: str, dataset: Dataset, target: int):
        import ase
        import schnetpack as spk  # noqa

        assert target >= 0 and target <= 12

        units = [1] * 12
        units[0] = ase.units.Debye
        units[1] = ase.units.Bohr**3
        units[5] = ase.units.Bohr**2

        root = osp.expanduser(osp.normpath(root))
        makedirs(root)
        folder = 'trained_schnet_models'
        if not osp.exists(osp.join(root, folder)):
            path = download_url(SchNet.url, root)
            extract_zip(path, root)
            os.unlink(path)

        name = f'qm9_{qm9_target_dict[target]}'
        path = osp.join(root, 'trained_schnet_models', name, 'split.npz')

        split = np.load(path)
        train_idx = split['train_idx']
        val_idx = split['val_idx']
        test_idx = split['test_idx']

        # Filter the splits to only contain characterized molecules.
        idx = dataset.data.idx
        assoc = idx.new_empty(idx.max().item() + 1)
        assoc[idx] = torch.arange(idx.size(0))

        train_idx = assoc[train_idx[np.isin(train_idx, idx)]]
        val_idx = assoc[val_idx[np.isin(val_idx, idx)]]
        test_idx = assoc[test_idx[np.isin(test_idx, idx)]]

        path = osp.join(root, 'trained_schnet_models', name, 'best_model')

        with warnings.catch_warnings():
            warnings.simplefilter('ignore')
            state = torch.load(path, map_location='cpu')

        net = SchNet(hidden_channels=128, num_filters=128, num_interactions=6,
                     num_gaussians=50, cutoff=10.0,
                     atomref=dataset.atomref(target))

        net.embedding.weight = state.representation.embedding.weight

        for int1, int2 in zip(state.representation.interactions,
                              net.interactions):
            int2.mlp[0].weight = int1.filter_network[0].weight
            int2.mlp[0].bias = int1.filter_network[0].bias
            int2.mlp[2].weight = int1.filter_network[1].weight
            int2.mlp[2].bias = int1.filter_network[1].bias
            int2.lin.weight = int1.dense.weight
            int2.lin.bias = int1.dense.bias

            int2.conv.lin1.weight = int1.cfconv.in2f.weight
            int2.conv.lin2.weight = int1.cfconv.f2out.weight
            int2.conv.lin2.bias = int1.cfconv.f2out.bias

        net.lin1.weight = state.output_modules[0].out_net[1].out_net[0].weight
        net.lin1.bias = state.output_modules[0].out_net[1].out_net[0].bias
        net.lin2.weight = state.output_modules[0].out_net[1].out_net[1].weight
        net.lin2.bias = state.output_modules[0].out_net[1].out_net[1].bias

        mean = state.output_modules[0].atom_pool.average
        net.readout = 'mean' if mean is True else 'add'

        dipole = state.output_modules[0].__class__.__name__ == 'DipoleMoment'
        net.dipole = dipole

        net.mean = state.output_modules[0].standardize.mean.item()
        net.std = state.output_modules[0].standardize.stddev.item()

        if state.output_modules[0].atomref is not None:
            net.atomref.weight = state.output_modules[0].atomref.weight
        else:
            net.atomref = None

        net.scale = 1. / units[target]

        return net, (dataset[train_idx], dataset[val_idx], dataset[test_idx])

    def forward(self, z, pos, batch=None):
        """"""
        assert z.dim() == 1 and z.dtype == torch.long
        batch = torch.zeros_like(z) if batch is None else batch

        #print('batch', batch)

        h = self.embedding(z)

        edge_index = radius_graph(pos, r=self.cutoff, batch=batch,
                                  max_num_neighbors=self.max_num_neighbors)
        row, col = edge_index
        edge_weight = (pos[row] - pos[col]).norm(dim=-1)
        edge_attr = self.distance_expansion(edge_weight)

        for interaction in self.interactions:
            h = h + interaction(h, edge_index, edge_weight, edge_attr)

        h = self.lin1(h)
        h = self.act(h)

        if self.get_embedding:
            return h 
            # h is vector after activation

        h = self.lin2(h)

        if self.dipole:
            # Get center of mass.
            mass = self.atomic_mass[z].view(-1, 1)
            c = scatter(mass * pos, batch, dim=0) / scatter(mass, batch, dim=0)
            h = h * (pos - c.index_select(0, batch))

        if not self.dipole and self.mean is not None and self.std is not None:
            h = h * self.std + self.mean

        if not self.dipole and self.atomref is not None:
            h = h + self.atomref(z)

        out = scatter(h, batch, dim=0, reduce=self.readout)

        if self.dipole:
            out = torch.norm(out, dim=-1, keepdim=True)

        if self.scale is not None:
            out = self.scale * out

        return out

    def __repr__(self):
        return (f'{self.__class__.__name__}('
                f'hidden_channels={self.hidden_channels}, '
                f'num_filters={self.num_filters}, '
                f'num_interactions={self.num_interactions}, '
                f'num_gaussians={self.num_gaussians}, '
                f'cutoff={self.cutoff})')


class InteractionBlock(torch.nn.Module):
    def __init__(self, hidden_channels, num_gaussians, num_filters, cutoff):
        super().__init__()
        self.mlp = Sequential(
            Linear(num_gaussians, num_filters),
            ShiftedSoftplus(),
            Linear(num_filters, num_filters),
        )
        self.conv = CFConv(hidden_channels, hidden_channels, num_filters,
                           self.mlp, cutoff)
        self.act = ShiftedSoftplus()
        self.lin = Linear(hidden_channels, hidden_channels)

        self.reset_parameters()

    def reset_parameters(self):
        torch.nn.init.xavier_uniform_(self.mlp[0].weight)
        self.mlp[0].bias.data.fill_(0)
        torch.nn.init.xavier_uniform_(self.mlp[2].weight)
        self.mlp[2].bias.data.fill_(0)
        self.conv.reset_parameters()
        torch.nn.init.xavier_uniform_(self.lin.weight)
        self.lin.bias.data.fill_(0)

    def forward(self, x, edge_index, edge_weight, edge_attr):
        x = self.conv(x, edge_index, edge_weight, edge_attr)
        x = self.act(x)
        x = self.lin(x)
        return x


class CFConv(MessagePassing):
    def __init__(self, in_channels, out_channels, num_filters, nn, cutoff):
        super().__init__(aggr='add')
        self.lin1 = Linear(in_channels, num_filters, bias=False)
        self.lin2 = Linear(num_filters, out_channels)
        self.nn = nn
        self.cutoff = cutoff

        self.reset_parameters()

    def reset_parameters(self):
        torch.nn.init.xavier_uniform_(self.lin1.weight)
        torch.nn.init.xavier_uniform_(self.lin2.weight)
        self.lin2.bias.data.fill_(0)

    def forward(self, x, edge_index, edge_weight, edge_attr):
        C = 0.5 * (torch.cos(edge_weight * PI / self.cutoff) + 1.0)
        W = self.nn(edge_attr) * C.view(-1, 1)

        x = self.lin1(x)
        x = self.propagate(edge_index, x=x, W=W)
        x = self.lin2(x)
        return x

    def message(self, x_j, W):
        return x_j * W


class GaussianSmearing(torch.nn.Module):
    def __init__(self, start=0.0, stop=5.0, num_gaussians=50):
        super().__init__()
        offset = torch.linspace(start, stop, num_gaussians)
        self.coeff = -0.5 / (offset[1] - offset[0]).item()**2
        self.register_buffer('offset', offset)

    def forward(self, dist):
        dist = dist.view(-1, 1) - self.offset.view(1, -1)
        return torch.exp(self.coeff * torch.pow(dist, 2))


class ShiftedSoftplus(torch.nn.Module):
    def __init__(self):
        super().__init__()
        self.shift = torch.log(torch.tensor(2.0)).item()

    def forward(self, x):
        return F.softplus(x) - self.shift