modeling_atomformer.py

"""Implementation of the Atomformer model."""

from typing import Any, Optional, Tuple

import torch
import torch.nn.functional as f
from torch import nn
from transformers.modeling_utils import PreTrainedModel
from .configuration_atomformer import AtomformerConfig


ATOM_METADATA = [
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@torch.jit.script
def gaussian(x: torch.Tensor, mean: torch.Tensor, std: torch.Tensor) -> torch.Tensor:
    """Compute the Gaussian distribution probability density."""
    pi = 3.14159
    a = (2 * pi) ** 0.5
    output: torch.Tensor = torch.exp(-0.5 * (((x - mean) / std) ** 2)) / (a * std)
    return output


class GaussianLayer(nn.Module):
    """Gaussian pairwise positional embedding layer."""

    def __init__(self, k: int = 128, edge_types: int = 1024):
        super().__init__()
        self.k = k
        self.means = nn.Embedding(1, k)
        self.stds = nn.Embedding(1, k)
        self.mul = nn.Embedding(edge_types, 1)
        self.bias = nn.Embedding(edge_types, 1)
        nn.init.uniform_(self.means.weight, 0, 3)
        nn.init.uniform_(self.stds.weight, 0, 3)
        nn.init.constant_(self.bias.weight, 0)
        nn.init.constant_(self.mul.weight, 1)

    def forward(self, x: torch.Tensor, edge_types: int) -> torch.Tensor:
        """Forward pass to compute the Gaussian pos. embeddings."""
        mul = self.mul(edge_types)
        bias = self.bias(edge_types)
        x = mul * x.unsqueeze(-1) + bias
        x = x.expand(-1, -1, -1, self.k)
        mean = self.means.weight.float().view(-1)
        std = self.stds.weight.float().view(-1).abs() + 1e-5
        output: torch.Tensor = gaussian(x.float(), mean, std).type_as(self.means.weight)
        return output


class ParallelBlock(nn.Module):
    """Parallel transformer block (MLP & Attention in parallel).

    Based on:
      'Scaling Vision Atomformers to 22 Billion Parameters` - https://arxiv.org/abs/2302.05442

    Adapted from TIMM implementation.
    """

    def __init__(
        self,
        dim: int,
        num_heads: int,
        mlp_ratio: int = 4,
        dropout: float = 0.0,
        k: int = 128,
        gradient_checkpointing: bool = False,
    ):
        super().__init__()
        assert (
            dim % num_heads == 0
        ), f"dim {dim} should be divisible by num_heads {num_heads}"
        self.num_heads = num_heads
        self.head_dim = dim // num_heads
        self.scale = self.head_dim**-0.5
        self.mlp_hidden_dim = int(mlp_ratio * dim)
        self.proj_drop = nn.Dropout(dropout)
        self.attn_drop = nn.Dropout(dropout)
        self.gradient_checkpointing = gradient_checkpointing

        self.in_proj_in_dim = dim
        self.in_proj_out_dim = self.mlp_hidden_dim + 3 * dim
        self.out_proj_in_dim = self.mlp_hidden_dim + dim
        self.out_proj_out_dim = 2 * dim

        self.in_split = [self.mlp_hidden_dim] + [dim] * 3
        self.out_split = [dim] * 2

        self.in_norm = nn.LayerNorm(dim)
        self.q_norm = nn.LayerNorm(self.head_dim)
        self.k_norm = nn.LayerNorm(self.head_dim)
        self.in_proj = nn.Linear(self.in_proj_in_dim, self.in_proj_out_dim, bias=False)
        self.act_fn = nn.GELU()
        self.out_proj = nn.Linear(
            self.out_proj_in_dim, self.out_proj_out_dim, bias=False
        )
        self.gaussian_proj = nn.Linear(k, 1)
        self.pos_embed_ff_norm = nn.LayerNorm(k)

    def forward(
        self,
        x: torch.Tensor,
        pos_embed: torch.Tensor,
        attention_mask: Optional[torch.Tensor] = None,
    ) -> Tuple[torch.Tensor, torch.Tensor]:
        """Forward pass for the parallel block."""
        b, n, c = x.shape
        res = x

        # Combined MLP fc1 & qkv projections
        x = self.in_proj(self.in_norm(x))
        x, q, k, v = torch.split(x, self.in_split, dim=-1)
        x = self.act_fn(x)
        x = self.proj_drop(x)

        # Dot product attention
        q = self.q_norm(q.view(b, n, self.num_heads, self.head_dim).transpose(1, 2))
        k = self.k_norm(k.view(b, n, self.num_heads, self.head_dim).transpose(1, 2))
        v = v.view(b, n, self.num_heads, self.head_dim).transpose(1, 2)

        x_attn = (
            f.scaled_dot_product_attention(
                q,
                k,
                v,
                attn_mask=attention_mask
                + self.gaussian_proj(self.pos_embed_ff_norm(pos_embed)).permute(
                    0, 3, 1, 2
                ),
                is_causal=False,
            )
            .transpose(1, 2)
            .reshape(b, n, c)
        )

        # Combined MLP fc2 & attn_output projection
        x_mlp, x_attn = self.out_proj(torch.cat([x, x_attn], dim=-1)).split(
            self.out_split, dim=-1
        )
        # Residual connections
        x = x_mlp + x_attn + res
        del x_mlp, x_attn, res

        return x, pos_embed


class AtomformerEncoder(nn.Module):
    """Atomformer encoder.

    The transformer encoder consists of a series of parallel blocks,
    each containing a multi-head self-attention mechanism and a feed-forward network.
    """

    def __init__(self, config: AtomformerConfig):
        super().__init__()
        self.vocab_size = config.vocab_size
        self.dim = config.dim
        self.num_heads = config.num_heads
        self.depth = config.depth
        self.mlp_ratio = config.mlp_ratio
        self.dropout = config.dropout
        self.k = config.k
        self.gradient_checkpointing = config.gradient_checkpointing

        self.metadata_vocab = nn.Embedding(self.vocab_size, 17)
        self.metadata_vocab.weight.requires_grad = False
        self.metadata_vocab.weight.fill_(-1)
        self.metadata_vocab.weight[1:-4] = torch.tensor(
            ATOM_METADATA, dtype=torch.float32
        )
        self.embed_metadata = nn.Linear(17, self.dim)

        self.gaussian_embed = GaussianLayer(
            k=self.k, edge_types=(self.vocab_size + 1) ** 2
        )

        self.embed_tokens = nn.Embedding(config.vocab_size, config.dim)
        nn.init.normal_(self.embed_tokens.weight, std=0.02)

        self.blocks = nn.ModuleList()
        for _ in range(self.depth):
            self.blocks.append(
                ParallelBlock(
                    self.dim,
                    self.num_heads,
                    self.mlp_ratio,
                    self.dropout,
                    self.k,
                    self.gradient_checkpointing,
                )
            )

    def _expand_mask(
        self,
        mask: torch.Tensor,
        dtype: torch.dtype,
        device: torch.device,
        tgt_len: Optional[int] = None,
    ) -> torch.Tensor:
        """
        Expand attention mask.

        Expands attention_mask from `[bsz, seq_len]` to
        `[bsz, 1, tgt_seq_len, src_seq_len]`.
        """
        bsz, src_len = mask.size()
        tgt_len = tgt_len if tgt_len is not None else src_len

        expanded_mask = (
            mask[:, None, None, :].expand(bsz, 1, tgt_len, src_len).to(dtype)
        )

        inverted_mask: torch.Tensor = 1.0 - expanded_mask

        return inverted_mask.masked_fill(
            inverted_mask.to(torch.bool), torch.finfo(dtype).min
        ).to(device)

    def forward(
        self,
        input_ids: torch.Tensor,
        coords: torch.Tensor,
        attention_mask: Optional[torch.Tensor] = None,
    ) -> Tuple[torch.Tensor, torch.Tensor]:
        """Forward pass for the transformer encoder."""
        # pad coords by zeros for graph token
        coords_center = torch.sum(coords, dim=1, keepdim=True) / coords.shape[1]
        coords = torch.cat([coords_center, coords], dim=1)

        r_ij = torch.cdist(coords, coords, p=2)  # [B, N, N]
        # pad input_ids by graph token
        input_ids = torch.cat(
            [
                torch.zeros(
                    input_ids.size(0), 1, dtype=torch.long, device=input_ids.device
                ).fill_(122),
                input_ids,
            ],
            dim=1,
        )
        edge_type = input_ids.unsqueeze(-1) * self.vocab_size + input_ids.unsqueeze(
            -2
        )  # [B, N, N]
        pos_embeds = self.gaussian_embed(r_ij, edge_type)  # [B, N, N, K]

        input_embeds = self.embed_tokens(input_ids)
        atom_metadata = self.metadata_vocab(input_ids)
        input_embeds = input_embeds + self.embed_metadata(atom_metadata)  # [B, N, C]

        attention_mask = (
            torch.cat(
                [
                    torch.ones(
                        attention_mask.size(0),
                        1,
                        dtype=torch.bool,
                        device=attention_mask.device,
                    ),
                    attention_mask.bool(),
                ],
                dim=1,
            )
            if attention_mask is not None
            else None
        )

        attention_mask = (
            self._expand_mask(attention_mask, input_embeds.dtype, input_embeds.device)
            if attention_mask is not None
            else None
        )

        for blk in self.blocks:
            input_embeds, pos_embeds = blk(input_embeds, pos_embeds, attention_mask)

        return input_embeds, pos_embeds


class AtomformerPreTrainedModel(PreTrainedModel):  # type: ignore
    """Base class for all transformer models."""

    config_class = AtomformerConfig
    base_model_prefix = "model"
    supports_gradient_checkpointing = True
    _no_split_modules = ["ParallelBlock"]

    def _set_gradient_checkpointing(
        self, module: nn.Module, value: bool = False
    ) -> None:
        if isinstance(module, (AtomformerEncoder)):
            module.gradient_checkpointing = value


class AtomformerModel(AtomformerPreTrainedModel):
    """Atomformer model for atom modeling."""

    def __init__(self, config: AtomformerConfig):
        super().__init__(config)
        self.config = config
        self.encoder = AtomformerEncoder(config)

    def forward(
        self,
        input_ids: torch.Tensor,
        coords: torch.Tensor,
        attention_mask: Optional[torch.Tensor] = None,
    ) -> torch.Tensor:
        """Forward function call for the transformer model."""
        output: torch.Tensor = self.encoder(input_ids, coords, attention_mask)
        return output[0][:, :-1]


class AtomformerForMaskedAM(AtomformerPreTrainedModel):
    """Atomformer with an atom modeling head on top for masked atom modeling."""

    def __init__(self, config: AtomformerConfig):
        super().__init__(config)
        self.config = config
        self.encoder = AtomformerEncoder(config)
        self.am_head = nn.Linear(config.dim, config.vocab_size, bias=False)

    def forward(
        self,
        input_ids: torch.Tensor,
        coords: torch.Tensor,
        labels: Optional[torch.Tensor] = None,
        fixed: Optional[torch.Tensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
    ) -> Tuple[Optional[torch.Tensor], torch.Tensor]:
        """Forward function call for the masked atom modeling model."""
        hidden_states = self.encoder(input_ids, coords, attention_mask)
        logits = self.am_head(hidden_states)

        loss = None
        if labels is not None:
            loss_fct = nn.CrossEntropyLoss()
            logits, labels = logits.view(-1, self.config.vocab_size), labels.view(-1)
            loss = loss_fct(logits, labels)

        return loss, logits


class AtomformerForCoordinateAM(AtomformerPreTrainedModel):
    """Atomformer with an atom coordinate head on top for coordinate denoising."""

    def __init__(self, config: AtomformerConfig):
        super().__init__(config)
        self.config = config
        self.encoder = AtomformerEncoder(config)
        self.coords_head = nn.Linear(config.dim, 3)

    def forward(
        self,
        input_ids: torch.Tensor,
        coords: torch.Tensor,
        labels_coords: Optional[torch.Tensor] = None,
        fixed: Optional[torch.Tensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
    ) -> Tuple[Optional[torch.Tensor], torch.Tensor]:
        """Forward function call for the coordinate atom modeling model."""
        hidden_states = self.encoder(input_ids, coords, attention_mask)
        coords_pred = self.coords_head(hidden_states)

        loss = None
        if labels_coords is not None:
            labels_coords = labels_coords.to(coords_pred.device)
            loss_fct = nn.L1Loss()
            loss = loss_fct(coords_pred, labels_coords)

        return loss, coords_pred


class InitialStructure2RelaxedStructure(AtomformerPreTrainedModel):
    """Atomformer with an coordinate head on top for relaxed structure prediction."""

    def __init__(self, config: AtomformerConfig):
        super().__init__(config)
        self.config = config
        self.encoder = AtomformerEncoder(config)
        self.coords_head = nn.Linear(config.dim, 3)

    def forward(
        self,
        input_ids: torch.Tensor,
        coords: torch.Tensor,
        labels_coords: Optional[torch.Tensor] = None,
        fixed: Optional[torch.Tensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
    ) -> Tuple[Optional[torch.Tensor], torch.Tensor]:
        """Forward function call.

        Initial structure to relaxed structure model.
        """
        hidden_states = self.encoder(input_ids, coords, attention_mask)
        coords_pred = self.coords_head(hidden_states)

        loss = None
        if labels_coords is not None:
            labels_coords = labels_coords.to(coords_pred.device)
            loss_fct = nn.L1Loss()
            loss = loss_fct(coords_pred, labels_coords)

        return loss, coords_pred


class InitialStructure2RelaxedEnergy(AtomformerPreTrainedModel):
    """Atomformer with an energy head on top for relaxed energy prediction."""

    def __init__(self, config: AtomformerConfig):
        super().__init__(config)
        self.config = config
        self.encoder = AtomformerEncoder(config)
        self.energy_norm = nn.LayerNorm(config.dim)
        self.energy_head = nn.Linear(config.dim, 1, bias=False)

    def forward(
        self,
        input_ids: torch.Tensor,
        coords: torch.Tensor,
        labels_energy: Optional[torch.Tensor] = None,
        fixed: Optional[torch.Tensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
    ) -> Tuple[Optional[torch.Tensor], torch.Tensor]:
        """Forward function call for the relaxed energy prediction model."""
        hidden_states = self.encoder(input_ids, coords, attention_mask)
        energy = self.energy_head(self.energy_norm(hidden_states[:, 0])).squeeze(-1)

        loss = None
        if labels_energy is not None:
            loss_fct = nn.L1Loss()
            loss = loss_fct(energy, labels_energy)

        return loss, energy


class InitialStructure2RelaxedStructureAndEnergy(AtomformerPreTrainedModel):
    """Atomformer with an coordinate and energy head."""

    def __init__(self, config: AtomformerConfig):
        super().__init__(config)
        self.config = config
        self.encoder = AtomformerEncoder(config)
        self.energy_norm = nn.LayerNorm(config.dim)
        self.energy_head = nn.Linear(config.dim, 1, bias=False)
        self.coords_head = nn.Linear(config.dim, 3)

    def forward(
        self,
        input_ids: torch.Tensor,
        coords: torch.Tensor,
        labels_coords: Optional[torch.Tensor] = None,
        forces: Optional[torch.Tensor] = None,
        total_energy: Optional[torch.Tensor] = None,
        formation_energy: Optional[torch.Tensor] = None,
        has_formation_energy: Optional[torch.Tensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
    ) -> Tuple[torch.Tensor, Tuple[torch.Tensor, torch.Tensor]]:
        """Forward function call for the relaxed structure and energy model."""
        atom_hidden_states, pos_hidden_states = self.encoder(
            input_ids, coords, attention_mask
        )

        formation_energy_pred = self.formation_energy_head(
            self.energy_norm(atom_hidden_states[:, 0])
        ).squeeze(-1)
        loss_formation_energy = None
        if formation_energy is not None:
            loss_fct = nn.L1Loss()
            loss_formation_energy = loss_fct(
                formation_energy_pred[has_formation_energy],
                formation_energy[has_formation_energy],
            )
        coords_pred = self.coords_head(atom_hidden_states[:, 1:])
        loss_coords = None
        if labels_coords is not None:
            loss_fct = nn.L1Loss()
            loss_coords = loss_fct(coords_pred, labels_coords)

        loss = torch.Tensor(0).to(coords.device)
        loss = (
            loss + loss_formation_energy if loss_formation_energy is not None else loss
        )
        loss = loss + loss_coords if loss_coords is not None else loss

        return loss, (formation_energy_pred, coords_pred)


class Structure2Energy(AtomformerPreTrainedModel):
    """Atomformer with an atom modeling head on top for masked atom modeling."""

    def __init__(self, config: AtomformerConfig):
        super().__init__(config)
        self.config = config
        self.encoder = AtomformerEncoder(config)
        self.energy_norm = nn.LayerNorm(config.dim)
        self.formation_energy_head = nn.Linear(config.dim, 1, bias=False)

    def forward(
        self,
        input_ids: torch.Tensor,
        coords: torch.Tensor,
        forces: Optional[torch.Tensor] = None,
        total_energy: Optional[torch.Tensor] = None,
        formation_energy: Optional[torch.Tensor] = None,
        has_formation_energy: Optional[torch.Tensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
    ) -> Tuple[Optional[torch.Tensor], Tuple[torch.Tensor, Optional[torch.Tensor]]]:
        """Forward function call for the structure to energy model."""
        atom_hidden_states, pos_hidden_states = self.encoder(
            input_ids, coords, attention_mask
        )

        formation_energy_pred: torch.Tensor = self.formation_energy_head(
            self.energy_norm(atom_hidden_states[:, 0])
        ).squeeze(-1)
        loss = torch.Tensor(0).to(coords.device)
        if formation_energy is not None:
            loss_fct = nn.L1Loss()
            loss = loss_fct(
                formation_energy_pred[has_formation_energy],
                formation_energy[has_formation_energy],
            )

        return loss, (
            formation_energy_pred,
            attention_mask.bool() if attention_mask is not None else None,
        )


class Structure2Forces(AtomformerPreTrainedModel):
    """Atomformer with a forces head on top for forces prediction."""

    def __init__(self, config: AtomformerConfig):
        super().__init__(config)
        self.config = config
        self.encoder = AtomformerEncoder(config)
        self.force_norm = nn.LayerNorm(config.dim)
        self.force_head = nn.Linear(config.dim, 3)
        self.energy_norm = nn.LayerNorm(config.dim)
        self.formation_energy_head = nn.Linear(config.dim, 1, bias=False)

    def forward(
        self,
        input_ids: torch.Tensor,
        coords: torch.Tensor,
        forces: Optional[torch.Tensor] = None,
        total_energy: Optional[torch.Tensor] = None,
        formation_energy: Optional[torch.Tensor] = None,
        has_formation_energy: Optional[torch.Tensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
    ) -> Tuple[torch.Tensor, Tuple[torch.Tensor, Optional[torch.Tensor]]]:
        """Forward function call for the structure to forces model."""
        atom_hidden_states, pos_hidden_states = self.encoder(
            input_ids, coords, attention_mask
        )
        attention_mask = attention_mask.bool() if attention_mask is not None else None

        forces_pred: torch.Tensor = self.force_head(
            self.force_norm(atom_hidden_states[:, 1:])
        )
        loss = torch.Tensor(0).to(coords.device)
        if forces is not None:
            loss_fct = nn.L1Loss()
            loss = loss_fct(forces_pred[attention_mask], forces[attention_mask])

        return loss, (
            forces_pred,
            attention_mask if attention_mask is not None else None,
        )


class Structure2EnergyAndForces(AtomformerPreTrainedModel):
    """Atomformer with an energy and forces head for energy and forces prediction."""

    def __init__(self, config: AtomformerConfig):
        super().__init__(config)
        self.config = config
        self.encoder = AtomformerEncoder(config)
        self.force_norm = nn.LayerNorm(config.dim)
        self.force_head = nn.Linear(config.dim, 3)
        self.energy_norm = nn.LayerNorm(config.dim)
        self.formation_energy_head = nn.Linear(config.dim, 1, bias=False)

    def forward(
        self,
        input_ids: torch.Tensor,
        coords: torch.Tensor,
        forces: Optional[torch.Tensor] = None,
        total_energy: Optional[torch.Tensor] = None,
        formation_energy: Optional[torch.Tensor] = None,
        has_formation_energy: Optional[torch.Tensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
    ) -> Tuple[torch.Tensor, Tuple[torch.Tensor, torch.Tensor, Optional[torch.Tensor]]]:
        """Forward function call for the structure to energy and forces model."""
        atom_hidden_states, pos_hidden_states = self.encoder(
            input_ids, coords, attention_mask
        )

        formation_energy_pred: torch.Tensor = self.formation_energy_head(
            self.energy_norm(atom_hidden_states[:, 0])
        ).squeeze(-1)
        loss_formation_energy = None
        if formation_energy is not None:
            loss_fct = nn.L1Loss()
            loss_formation_energy = loss_fct(
                formation_energy_pred[has_formation_energy],
                formation_energy[has_formation_energy],
            )
        attention_mask = attention_mask.bool() if attention_mask is not None else None
        forces_pred: torch.Tensor = self.force_head(
            self.force_norm(atom_hidden_states[:, 1:])
        )
        loss_forces = None
        if forces is not None:
            loss_fct = nn.L1Loss()
            loss_forces = loss_fct(forces_pred[attention_mask], forces[attention_mask])

        loss = torch.Tensor(0).to(coords.device)
        loss = (
            loss + loss_formation_energy if loss_formation_energy is not None else loss
        )
        loss = loss + loss_forces if loss_forces is not None else loss

        return loss, (formation_energy_pred, forces_pred, attention_mask)