From 0318a293007744ec12f342adfd0246494aa4b1d9 Mon Sep 17 00:00:00 2001 From: Misko Date: Thu, 12 Sep 2024 23:32:10 +0000 Subject: [PATCH 1/6] move escn to deprecated --- src/fairchem/core/models/escn/escn.py | 211 +---- .../core/models/escn/escn_deprecated.py | 838 ++++++++++++++++++ 2 files changed, 848 insertions(+), 201 deletions(-) create mode 100644 src/fairchem/core/models/escn/escn_deprecated.py diff --git a/src/fairchem/core/models/escn/escn.py b/src/fairchem/core/models/escn/escn.py index 0b17e34ea..91069afbc 100644 --- a/src/fairchem/core/models/escn/escn.py +++ b/src/fairchem/core/models/escn/escn.py @@ -39,8 +39,8 @@ from e3nn import o3 -@registry.register_model("escn") -class eSCN(nn.Module, GraphModelMixin): +@registry.register_model("escn_backbone") +class eSCNBackbone(eSCN, BackboneInterface): """Equivariant Spherical Channel Network Paper: Reducing SO(3) Convolutions to SO(2) for Efficient Equivariant GNNs @@ -227,203 +227,6 @@ def __init__( ) self.sphharm_weights = nn.ParameterList(sphharm_weights) - @conditional_grad(torch.enable_grad()) - def forward(self, data): - device = data.pos.device - self.batch_size = len(data.natoms) - self.dtype = data.pos.dtype - - start_time = time.time() - atomic_numbers = data.atomic_numbers.long() - assert ( - atomic_numbers.max().item() < self.max_num_elements - ), "Atomic number exceeds that given in model config" - num_atoms = len(atomic_numbers) - graph = self.generate_graph(data) - - ############################################################### - # Initialize data structures - ############################################################### - - # Compute 3x3 rotation matrix per edge - edge_rot_mat = self._init_edge_rot_mat( - data, graph.edge_index, graph.edge_distance_vec - ) - - # Initialize the WignerD matrices and other values for spherical harmonic calculations - self.SO3_edge_rot = nn.ModuleList() - for i in range(self.num_resolutions): - self.SO3_edge_rot.append(SO3_Rotation(edge_rot_mat, self.lmax_list[i])) - - ############################################################### - # Initialize node embeddings - ############################################################### - - # Init per node representations using an atomic number based embedding - offset = 0 - x = SO3_Embedding( - num_atoms, - self.lmax_list, - self.sphere_channels, - device, - self.dtype, - ) - - offset_res = 0 - offset = 0 - # Initialize the l=0,m=0 coefficients for each resolution - for i in range(self.num_resolutions): - x.embedding[:, offset_res, :] = self.sphere_embedding(atomic_numbers)[ - :, offset : offset + self.sphere_channels - ] - offset = offset + self.sphere_channels - offset_res = offset_res + int((self.lmax_list[i] + 1) ** 2) - - # This can be expensive to compute (not implemented efficiently), so only do it once and pass it along to each layer - mappingReduced = CoefficientMapping(self.lmax_list, self.mmax_list, device) - - ############################################################### - # Update spherical node embeddings - ############################################################### - - for i in range(self.num_layers): - if i > 0: - x_message = self.layer_blocks[i]( - x, - atomic_numbers, - graph.edge_distance, - graph.edge_index, - self.SO3_edge_rot, - mappingReduced, - ) - - # Residual layer for all layers past the first - x.embedding = x.embedding + x_message.embedding - - else: - # No residual for the first layer - x = self.layer_blocks[i]( - x, - atomic_numbers, - graph.edge_distance, - graph.edge_index, - self.SO3_edge_rot, - mappingReduced, - ) - - # Sample the spherical channels (node embeddings) at evenly distributed points on the sphere. - # These values are fed into the output blocks. - x_pt = torch.tensor([], device=device) - offset = 0 - # Compute the embedding values at every sampled point on the sphere - for i in range(self.num_resolutions): - num_coefficients = int((x.lmax_list[i] + 1) ** 2) - x_pt = torch.cat( - [ - x_pt, - torch.einsum( - "abc, pb->apc", - x.embedding[:, offset : offset + num_coefficients], - self.sphharm_weights[i], - ).contiguous(), - ], - dim=2, - ) - offset = offset + num_coefficients - - x_pt = x_pt.view(-1, self.sphere_channels_all) - - ############################################################### - # Energy estimation - ############################################################### - node_energy = self.energy_block(x_pt) - energy = torch.zeros(len(data.natoms), device=device) - energy.index_add_(0, data.batch, node_energy.view(-1)) - # Scale energy to help balance numerical precision w.r.t. forces - energy = energy * 0.001 - - outputs = {"energy": energy} - ############################################################### - # Force estimation - ############################################################### - if self.regress_forces: - forces = self.force_block(x_pt, self.sphere_points) - outputs["forces"] = forces - - if self.show_timing_info is True: - torch.cuda.synchronize() - logging.info( - f"{self.counter} Time: {time.time() - start_time}\tMemory: {len(data.pos)}\t{torch.cuda.max_memory_allocated() / 1000000}" - ) - - self.counter = self.counter + 1 - - return outputs - - # Initialize the edge rotation matrics - def _init_edge_rot_mat(self, data, edge_index, edge_distance_vec): - edge_vec_0 = edge_distance_vec - edge_vec_0_distance = torch.sqrt(torch.sum(edge_vec_0**2, dim=1)) - - # Make sure the atoms are far enough apart - if torch.min(edge_vec_0_distance) < 0.0001: - logging.error( - f"Error edge_vec_0_distance: {torch.min(edge_vec_0_distance)}" - ) - (minval, minidx) = torch.min(edge_vec_0_distance, 0) - logging.error( - f"Error edge_vec_0_distance: {minidx} {edge_index[0, minidx]} {edge_index[1, minidx]} {data.pos[edge_index[0, minidx]]} {data.pos[edge_index[1, minidx]]}" - ) - - norm_x = edge_vec_0 / (edge_vec_0_distance.view(-1, 1)) - - edge_vec_2 = torch.rand_like(edge_vec_0) - 0.5 - edge_vec_2 = edge_vec_2 / ( - torch.sqrt(torch.sum(edge_vec_2**2, dim=1)).view(-1, 1) - ) - # Create two rotated copys of the random vectors in case the random vector is aligned with norm_x - # With two 90 degree rotated vectors, at least one should not be aligned with norm_x - edge_vec_2b = edge_vec_2.clone() - edge_vec_2b[:, 0] = -edge_vec_2[:, 1] - edge_vec_2b[:, 1] = edge_vec_2[:, 0] - edge_vec_2c = edge_vec_2.clone() - edge_vec_2c[:, 1] = -edge_vec_2[:, 2] - edge_vec_2c[:, 2] = edge_vec_2[:, 1] - vec_dot_b = torch.abs(torch.sum(edge_vec_2b * norm_x, dim=1)).view(-1, 1) - vec_dot_c = torch.abs(torch.sum(edge_vec_2c * norm_x, dim=1)).view(-1, 1) - - vec_dot = torch.abs(torch.sum(edge_vec_2 * norm_x, dim=1)).view(-1, 1) - edge_vec_2 = torch.where(torch.gt(vec_dot, vec_dot_b), edge_vec_2b, edge_vec_2) - vec_dot = torch.abs(torch.sum(edge_vec_2 * norm_x, dim=1)).view(-1, 1) - edge_vec_2 = torch.where(torch.gt(vec_dot, vec_dot_c), edge_vec_2c, edge_vec_2) - - vec_dot = torch.abs(torch.sum(edge_vec_2 * norm_x, dim=1)) - # Check the vectors aren't aligned - assert torch.max(vec_dot) < 0.99 - - norm_z = torch.cross(norm_x, edge_vec_2, dim=1) - norm_z = norm_z / (torch.sqrt(torch.sum(norm_z**2, dim=1, keepdim=True))) - norm_z = norm_z / (torch.sqrt(torch.sum(norm_z**2, dim=1)).view(-1, 1)) - norm_y = torch.cross(norm_x, norm_z, dim=1) - norm_y = norm_y / (torch.sqrt(torch.sum(norm_y**2, dim=1, keepdim=True))) - - # Construct the 3D rotation matrix - norm_x = norm_x.view(-1, 3, 1) - norm_y = -norm_y.view(-1, 3, 1) - norm_z = norm_z.view(-1, 3, 1) - - edge_rot_mat_inv = torch.cat([norm_z, norm_x, norm_y], dim=2) - edge_rot_mat = torch.transpose(edge_rot_mat_inv, 1, 2) - - return edge_rot_mat.detach() - - @property - def num_params(self) -> int: - return sum(p.numel() for p in self.parameters()) - - -@registry.register_model("escn_backbone") -class eSCNBackbone(eSCN, BackboneInterface): @conditional_grad(torch.enable_grad()) def forward(self, data: Batch) -> dict[str, torch.Tensor]: device = data.pos.device @@ -534,10 +337,14 @@ def forward(self, data: Batch) -> dict[str, torch.Tensor]: "graph": graph, } + @property + def num_params(self) -> int: + return sum(p.numel() for p in self.parameters()) + @registry.register_model("escn_energy_head") class eSCNEnergyHead(nn.Module, HeadInterface): - def __init__(self, backbone, reduce = "sum"): + def __init__(self, backbone, reduce="sum"): super().__init__() backbone.energy_block = None self.reduce = reduce @@ -558,7 +365,9 @@ def forward( elif self.reduce == "mean": return {"energy": energy / data.natoms} else: - raise ValueError(f"reduce can only be sum or mean, user provided: {self.reduce}") + raise ValueError( + f"reduce can only be sum or mean, user provided: {self.reduce}" + ) @registry.register_model("escn_force_head") diff --git a/src/fairchem/core/models/escn/escn_deprecated.py b/src/fairchem/core/models/escn/escn_deprecated.py new file mode 100644 index 000000000..d175c59b5 --- /dev/null +++ b/src/fairchem/core/models/escn/escn_deprecated.py @@ -0,0 +1,838 @@ +""" +Copyright (c) Meta, Inc. and its affiliates. + +This source code is licensed under the MIT license found in the +LICENSE file in the root directory of this source tree. +""" + +from __future__ import annotations + +import contextlib +import logging +import time +import typing + +import torch +import torch.nn as nn + +if typing.TYPE_CHECKING: + from torch_geometric.data.batch import Batch + +from fairchem.core.common.registry import registry +from fairchem.core.common.utils import conditional_grad +from fairchem.core.models.base import BackboneInterface, GraphModelMixin, HeadInterface +from fairchem.core.models.escn.so3 import ( + CoefficientMapping, + SO3_Embedding, + SO3_Grid, + SO3_Rotation, +) +from fairchem.core.models.scn.sampling import CalcSpherePoints +from fairchem.core.models.scn.smearing import ( + GaussianSmearing, + LinearSigmoidSmearing, + SigmoidSmearing, + SiLUSmearing, +) + +with contextlib.suppress(ImportError): + from e3nn import o3 + + +@registry.register_model("escn") +class eSCN(nn.Module, GraphModelMixin): + """Equivariant Spherical Channel Network + Paper: Reducing SO(3) Convolutions to SO(2) for Efficient Equivariant GNNs + + + Args: + use_pbc (bool): Use periodic boundary conditions + use_pbc_single (bool): Process batch PBC graphs one at a time + regress_forces (bool): Compute forces + otf_graph (bool): Compute graph On The Fly (OTF) + max_neighbors (int): Maximum number of neighbors per atom + cutoff (float): Maximum distance between nieghboring atoms in Angstroms + max_num_elements (int): Maximum atomic number + + num_layers (int): Number of layers in the GNN + lmax_list (int): List of maximum degree of the spherical harmonics (1 to 10) + mmax_list (int): List of maximum order of the spherical harmonics (0 to lmax) + sphere_channels (int): Number of spherical channels (one set per resolution) + hidden_channels (int): Number of hidden units in message passing + num_sphere_samples (int): Number of samples used to approximate the integration of the sphere in the output blocks + edge_channels (int): Number of channels for the edge invariant features + distance_function ("gaussian", "sigmoid", "linearsigmoid", "silu"): Basis function used for distances + basis_width_scalar (float): Width of distance basis function + distance_resolution (float): Distance between distance basis functions in Angstroms + show_timing_info (bool): Show timing and memory info + """ + + def __init__( + self, + use_pbc: bool = True, + use_pbc_single: bool = False, + regress_forces: bool = True, + otf_graph: bool = False, + max_neighbors: int = 40, + cutoff: float = 8.0, + max_num_elements: int = 90, + num_layers: int = 8, + lmax_list: list[int] | None = None, + mmax_list: list[int] | None = None, + sphere_channels: int = 128, + hidden_channels: int = 256, + edge_channels: int = 128, + num_sphere_samples: int = 128, + distance_function: str = "gaussian", + basis_width_scalar: float = 1.0, + distance_resolution: float = 0.02, + show_timing_info: bool = False, + resolution: int | None = None, + ) -> None: + if mmax_list is None: + mmax_list = [2] + if lmax_list is None: + lmax_list = [6] + super().__init__() + + import sys + + if "e3nn" not in sys.modules: + logging.error("You need to install the e3nn library to use the SCN model") + raise ImportError + + self.regress_forces = regress_forces + self.use_pbc = use_pbc + self.use_pbc_single = use_pbc_single + self.cutoff = cutoff + self.otf_graph = otf_graph + self.show_timing_info = show_timing_info + self.max_num_elements = max_num_elements + self.hidden_channels = hidden_channels + self.num_layers = num_layers + self.num_atoms = 0 + self.num_sphere_samples = num_sphere_samples + self.sphere_channels = sphere_channels + self.max_neighbors = max_neighbors + self.edge_channels = edge_channels + self.distance_resolution = distance_resolution + self.grad_forces = False + self.lmax_list = lmax_list + self.mmax_list = mmax_list + self.num_resolutions: int = len(self.lmax_list) + self.sphere_channels_all: int = self.num_resolutions * self.sphere_channels + self.basis_width_scalar = basis_width_scalar + self.distance_function = distance_function + + # variables used for display purposes + self.counter = 0 + + # non-linear activation function used throughout the network + self.act = nn.SiLU() + + # Weights for message initialization + self.sphere_embedding = nn.Embedding( + self.max_num_elements, self.sphere_channels_all + ) + + # Initialize the function used to measure the distances between atoms + assert self.distance_function in [ + "gaussian", + "sigmoid", + "linearsigmoid", + "silu", + ] + self.num_gaussians = int(cutoff / self.distance_resolution) + if self.distance_function == "gaussian": + self.distance_expansion = GaussianSmearing( + 0.0, + cutoff, + self.num_gaussians, + basis_width_scalar, + ) + if self.distance_function == "sigmoid": + self.distance_expansion = SigmoidSmearing( + 0.0, + cutoff, + self.num_gaussians, + basis_width_scalar, + ) + if self.distance_function == "linearsigmoid": + self.distance_expansion = LinearSigmoidSmearing( + 0.0, + cutoff, + self.num_gaussians, + basis_width_scalar, + ) + if self.distance_function == "silu": + self.distance_expansion = SiLUSmearing( + 0.0, + cutoff, + self.num_gaussians, + basis_width_scalar, + ) + + # Initialize the transformations between spherical and grid representations + self.SO3_grid = nn.ModuleList() + for lval in range(max(self.lmax_list) + 1): + SO3_m_grid = nn.ModuleList() + for m in range(max(self.lmax_list) + 1): + SO3_m_grid.append(SO3_Grid(lval, m, resolution=resolution)) + + self.SO3_grid.append(SO3_m_grid) + + # Initialize the blocks for each layer of the GNN + self.layer_blocks = nn.ModuleList() + for i in range(self.num_layers): + block = LayerBlock( + i, + self.sphere_channels, + self.hidden_channels, + self.edge_channels, + self.lmax_list, + self.mmax_list, + self.distance_expansion, + self.max_num_elements, + self.SO3_grid, + self.act, + ) + self.layer_blocks.append(block) + + # Output blocks for energy and forces + self.energy_block = EnergyBlock( + self.sphere_channels_all, self.num_sphere_samples, self.act + ) + if self.regress_forces: + self.force_block = ForceBlock( + self.sphere_channels_all, self.num_sphere_samples, self.act + ) + + # Create a roughly evenly distributed point sampling of the sphere for the output blocks + self.sphere_points = nn.Parameter( + CalcSpherePoints(self.num_sphere_samples), requires_grad=False + ) + + # For each spherical point, compute the spherical harmonic coefficient weights + sphharm_weights: list[nn.Parameter] = [] + for i in range(self.num_resolutions): + sphharm_weights.append( + nn.Parameter( + o3.spherical_harmonics( + torch.arange(0, self.lmax_list[i] + 1).tolist(), + self.sphere_points, + False, + ), + requires_grad=False, + ) + ) + self.sphharm_weights = nn.ParameterList(sphharm_weights) + + @conditional_grad(torch.enable_grad()) + def forward(self, data): + device = data.pos.device + self.batch_size = len(data.natoms) + self.dtype = data.pos.dtype + + start_time = time.time() + atomic_numbers = data.atomic_numbers.long() + assert ( + atomic_numbers.max().item() < self.max_num_elements + ), "Atomic number exceeds that given in model config" + num_atoms = len(atomic_numbers) + graph = self.generate_graph(data) + + ############################################################### + # Initialize data structures + ############################################################### + + # Compute 3x3 rotation matrix per edge + edge_rot_mat = self._init_edge_rot_mat( + data, graph.edge_index, graph.edge_distance_vec + ) + + # Initialize the WignerD matrices and other values for spherical harmonic calculations + self.SO3_edge_rot = nn.ModuleList() + for i in range(self.num_resolutions): + self.SO3_edge_rot.append(SO3_Rotation(edge_rot_mat, self.lmax_list[i])) + + ############################################################### + # Initialize node embeddings + ############################################################### + + # Init per node representations using an atomic number based embedding + offset = 0 + x = SO3_Embedding( + num_atoms, + self.lmax_list, + self.sphere_channels, + device, + self.dtype, + ) + + offset_res = 0 + offset = 0 + # Initialize the l=0,m=0 coefficients for each resolution + for i in range(self.num_resolutions): + x.embedding[:, offset_res, :] = self.sphere_embedding(atomic_numbers)[ + :, offset : offset + self.sphere_channels + ] + offset = offset + self.sphere_channels + offset_res = offset_res + int((self.lmax_list[i] + 1) ** 2) + + # This can be expensive to compute (not implemented efficiently), so only do it once and pass it along to each layer + mappingReduced = CoefficientMapping(self.lmax_list, self.mmax_list, device) + + ############################################################### + # Update spherical node embeddings + ############################################################### + + for i in range(self.num_layers): + if i > 0: + x_message = self.layer_blocks[i]( + x, + atomic_numbers, + graph.edge_distance, + graph.edge_index, + self.SO3_edge_rot, + mappingReduced, + ) + + # Residual layer for all layers past the first + x.embedding = x.embedding + x_message.embedding + + else: + # No residual for the first layer + x = self.layer_blocks[i]( + x, + atomic_numbers, + graph.edge_distance, + graph.edge_index, + self.SO3_edge_rot, + mappingReduced, + ) + + # Sample the spherical channels (node embeddings) at evenly distributed points on the sphere. + # These values are fed into the output blocks. + x_pt = torch.tensor([], device=device) + offset = 0 + # Compute the embedding values at every sampled point on the sphere + for i in range(self.num_resolutions): + num_coefficients = int((x.lmax_list[i] + 1) ** 2) + x_pt = torch.cat( + [ + x_pt, + torch.einsum( + "abc, pb->apc", + x.embedding[:, offset : offset + num_coefficients], + self.sphharm_weights[i], + ).contiguous(), + ], + dim=2, + ) + offset = offset + num_coefficients + + x_pt = x_pt.view(-1, self.sphere_channels_all) + + ############################################################### + # Energy estimation + ############################################################### + node_energy = self.energy_block(x_pt) + energy = torch.zeros(len(data.natoms), device=device) + energy.index_add_(0, data.batch, node_energy.view(-1)) + # Scale energy to help balance numerical precision w.r.t. forces + energy = energy * 0.001 + + outputs = {"energy": energy} + ############################################################### + # Force estimation + ############################################################### + if self.regress_forces: + forces = self.force_block(x_pt, self.sphere_points) + outputs["forces"] = forces + + if self.show_timing_info is True: + torch.cuda.synchronize() + logging.info( + f"{self.counter} Time: {time.time() - start_time}\tMemory: {len(data.pos)}\t{torch.cuda.max_memory_allocated() / 1000000}" + ) + + self.counter = self.counter + 1 + + return outputs + + # Initialize the edge rotation matrics + def _init_edge_rot_mat(self, data, edge_index, edge_distance_vec): + edge_vec_0 = edge_distance_vec + edge_vec_0_distance = torch.sqrt(torch.sum(edge_vec_0**2, dim=1)) + + # Make sure the atoms are far enough apart + if torch.min(edge_vec_0_distance) < 0.0001: + logging.error( + f"Error edge_vec_0_distance: {torch.min(edge_vec_0_distance)}" + ) + (minval, minidx) = torch.min(edge_vec_0_distance, 0) + logging.error( + f"Error edge_vec_0_distance: {minidx} {edge_index[0, minidx]} {edge_index[1, minidx]} {data.pos[edge_index[0, minidx]]} {data.pos[edge_index[1, minidx]]}" + ) + + norm_x = edge_vec_0 / (edge_vec_0_distance.view(-1, 1)) + + edge_vec_2 = torch.rand_like(edge_vec_0) - 0.5 + edge_vec_2 = edge_vec_2 / ( + torch.sqrt(torch.sum(edge_vec_2**2, dim=1)).view(-1, 1) + ) + # Create two rotated copys of the random vectors in case the random vector is aligned with norm_x + # With two 90 degree rotated vectors, at least one should not be aligned with norm_x + edge_vec_2b = edge_vec_2.clone() + edge_vec_2b[:, 0] = -edge_vec_2[:, 1] + edge_vec_2b[:, 1] = edge_vec_2[:, 0] + edge_vec_2c = edge_vec_2.clone() + edge_vec_2c[:, 1] = -edge_vec_2[:, 2] + edge_vec_2c[:, 2] = edge_vec_2[:, 1] + vec_dot_b = torch.abs(torch.sum(edge_vec_2b * norm_x, dim=1)).view(-1, 1) + vec_dot_c = torch.abs(torch.sum(edge_vec_2c * norm_x, dim=1)).view(-1, 1) + + vec_dot = torch.abs(torch.sum(edge_vec_2 * norm_x, dim=1)).view(-1, 1) + edge_vec_2 = torch.where(torch.gt(vec_dot, vec_dot_b), edge_vec_2b, edge_vec_2) + vec_dot = torch.abs(torch.sum(edge_vec_2 * norm_x, dim=1)).view(-1, 1) + edge_vec_2 = torch.where(torch.gt(vec_dot, vec_dot_c), edge_vec_2c, edge_vec_2) + + vec_dot = torch.abs(torch.sum(edge_vec_2 * norm_x, dim=1)) + # Check the vectors aren't aligned + assert torch.max(vec_dot) < 0.99 + + norm_z = torch.cross(norm_x, edge_vec_2, dim=1) + norm_z = norm_z / (torch.sqrt(torch.sum(norm_z**2, dim=1, keepdim=True))) + norm_z = norm_z / (torch.sqrt(torch.sum(norm_z**2, dim=1)).view(-1, 1)) + norm_y = torch.cross(norm_x, norm_z, dim=1) + norm_y = norm_y / (torch.sqrt(torch.sum(norm_y**2, dim=1, keepdim=True))) + + # Construct the 3D rotation matrix + norm_x = norm_x.view(-1, 3, 1) + norm_y = -norm_y.view(-1, 3, 1) + norm_z = norm_z.view(-1, 3, 1) + + edge_rot_mat_inv = torch.cat([norm_z, norm_x, norm_y], dim=2) + edge_rot_mat = torch.transpose(edge_rot_mat_inv, 1, 2) + + return edge_rot_mat.detach() + + @property + def num_params(self) -> int: + return sum(p.numel() for p in self.parameters()) + + +class MessageBlock(torch.nn.Module): + """ + Message block: Perform message passing + + Args: + layer_idx (int): Layer number + sphere_channels (int): Number of spherical channels + hidden_channels (int): Number of hidden channels used during the SO(2) conv + edge_channels (int): Size of invariant edge embedding + lmax_list (list:int): List of degrees (l) for each resolution + mmax_list (list:int): List of orders (m) for each resolution + distance_expansion (func): Function used to compute distance embedding + max_num_elements (int): Maximum number of atomic numbers + SO3_grid (SO3_grid): Class used to convert from grid the spherical harmonic representations + act (function): Non-linear activation function + """ + + def __init__( + self, + layer_idx: int, + sphere_channels: int, + hidden_channels: int, + edge_channels: int, + lmax_list: list[int], + mmax_list: list[int], + distance_expansion, + max_num_elements: int, + SO3_grid: SO3_Grid, + act, + ) -> None: + super().__init__() + self.layer_idx = layer_idx + self.act = act + self.hidden_channels = hidden_channels + self.sphere_channels = sphere_channels + self.SO3_grid = SO3_grid + self.num_resolutions = len(lmax_list) + self.lmax_list = lmax_list + self.mmax_list = mmax_list + self.edge_channels = edge_channels + + # Create edge scalar (invariant to rotations) features + self.edge_block = EdgeBlock( + self.edge_channels, + distance_expansion, + max_num_elements, + self.act, + ) + + # Create SO(2) convolution blocks + self.so2_block_source = SO2Block( + self.sphere_channels, + self.hidden_channels, + self.edge_channels, + self.lmax_list, + self.mmax_list, + self.act, + ) + self.so2_block_target = SO2Block( + self.sphere_channels, + self.hidden_channels, + self.edge_channels, + self.lmax_list, + self.mmax_list, + self.act, + ) + + def forward( + self, + x, + atomic_numbers, + edge_distance, + edge_index, + SO3_edge_rot, + mappingReduced, + ): + ############################################################### + # Compute messages + ############################################################### + + # Compute edge scalar features (invariant to rotations) + # Uses atomic numbers and edge distance as inputs + x_edge = self.edge_block( + edge_distance, + atomic_numbers[edge_index[0]], # Source atom atomic number + atomic_numbers[edge_index[1]], # Target atom atomic number + ) + + # Copy embeddings for each edge's source and target nodes + x_source = x.clone() + x_target = x.clone() + x_source._expand_edge(edge_index[0, :]) + x_target._expand_edge(edge_index[1, :]) + + # Rotate the irreps to align with the edge + x_source._rotate(SO3_edge_rot, self.lmax_list, self.mmax_list) + x_target._rotate(SO3_edge_rot, self.lmax_list, self.mmax_list) + + # Compute messages + x_source = self.so2_block_source(x_source, x_edge, mappingReduced) + x_target = self.so2_block_target(x_target, x_edge, mappingReduced) + + # Add together the source and target results + x_target.embedding = x_source.embedding + x_target.embedding + + # Point-wise spherical non-linearity + x_target._grid_act(self.SO3_grid, self.act, mappingReduced) + + # Rotate back the irreps + x_target._rotate_inv(SO3_edge_rot, mappingReduced) + + # Compute the sum of the incoming neighboring messages for each target node + x_target._reduce_edge(edge_index[1], len(x.embedding)) + + return x_target + + +class SO2Block(torch.nn.Module): + """ + SO(2) Block: Perform SO(2) convolutions for all m (orders) + + Args: + sphere_channels (int): Number of spherical channels + hidden_channels (int): Number of hidden channels used during the SO(2) conv + edge_channels (int): Size of invariant edge embedding + lmax_list (list:int): List of degrees (l) for each resolution + mmax_list (list:int): List of orders (m) for each resolution + act (function): Non-linear activation function + """ + + def __init__( + self, + sphere_channels: int, + hidden_channels: int, + edge_channels: int, + lmax_list: list[int], + mmax_list: list[int], + act, + ) -> None: + super().__init__() + self.sphere_channels = sphere_channels + self.hidden_channels = hidden_channels + self.lmax_list = lmax_list + self.mmax_list = mmax_list + self.num_resolutions: int = len(lmax_list) + self.act = act + + num_channels_m0 = 0 + for i in range(self.num_resolutions): + num_coefficents = self.lmax_list[i] + 1 + num_channels_m0 = num_channels_m0 + num_coefficents * self.sphere_channels + + # SO(2) convolution for m=0 + self.fc1_dist0 = nn.Linear(edge_channels, self.hidden_channels) + self.fc1_m0 = nn.Linear(num_channels_m0, self.hidden_channels, bias=False) + self.fc2_m0 = nn.Linear(self.hidden_channels, num_channels_m0, bias=False) + + # SO(2) convolution for non-zero m + self.so2_conv = nn.ModuleList() + for m in range(1, max(self.mmax_list) + 1): + so2_conv = SO2Conv( + m, + self.sphere_channels, + self.hidden_channels, + edge_channels, + self.lmax_list, + self.mmax_list, + self.act, + ) + self.so2_conv.append(so2_conv) + + def forward( + self, + x, + x_edge, + mappingReduced, + ): + num_edges = len(x_edge) + + # Reshape the spherical harmonics based on m (order) + x._m_primary(mappingReduced) + + # Compute m=0 coefficients separately since they only have real values (no imaginary) + + # Compute edge scalar features for m=0 + x_edge_0 = self.act(self.fc1_dist0(x_edge)) + + x_0 = x.embedding[:, 0 : mappingReduced.m_size[0]].contiguous() + x_0 = x_0.view(num_edges, -1) + + x_0 = self.fc1_m0(x_0) + x_0 = x_0 * x_edge_0 + x_0 = self.fc2_m0(x_0) + x_0 = x_0.view(num_edges, -1, x.num_channels) + + # Update the m=0 coefficients + x.embedding[:, 0 : mappingReduced.m_size[0]] = x_0 + + # Compute the values for the m > 0 coefficients + offset = mappingReduced.m_size[0] + for m in range(1, max(self.mmax_list) + 1): + # Get the m order coefficients + x_m = x.embedding[ + :, offset : offset + 2 * mappingReduced.m_size[m] + ].contiguous() + x_m = x_m.view(num_edges, 2, -1) + # Perform SO(2) convolution + x_m = self.so2_conv[m - 1](x_m, x_edge) + x_m = x_m.view(num_edges, -1, x.num_channels) + x.embedding[:, offset : offset + 2 * mappingReduced.m_size[m]] = x_m + + offset = offset + 2 * mappingReduced.m_size[m] + + # Reshape the spherical harmonics based on l (degree) + x._l_primary(mappingReduced) + + return x + + +class SO2Conv(torch.nn.Module): + """ + SO(2) Conv: Perform an SO(2) convolution + + Args: + m (int): Order of the spherical harmonic coefficients + sphere_channels (int): Number of spherical channels + hidden_channels (int): Number of hidden channels used during the SO(2) conv + edge_channels (int): Size of invariant edge embedding + lmax_list (list:int): List of degrees (l) for each resolution + mmax_list (list:int): List of orders (m) for each resolution + act (function): Non-linear activation function + """ + + def __init__( + self, + m: int, + sphere_channels: int, + hidden_channels: int, + edge_channels: int, + lmax_list: list[int], + mmax_list: list[int], + act, + ) -> None: + super().__init__() + self.hidden_channels = hidden_channels + self.lmax_list = lmax_list + self.mmax_list = mmax_list + self.sphere_channels = sphere_channels + self.num_resolutions: int = len(self.lmax_list) + self.m = m + self.act = act + + num_channels = 0 + for i in range(self.num_resolutions): + num_coefficents = 0 + if self.mmax_list[i] >= m: + num_coefficents = self.lmax_list[i] - m + 1 + + num_channels = num_channels + num_coefficents * self.sphere_channels + + assert num_channels > 0 + + # Embedding function of the distance + self.fc1_dist = nn.Linear(edge_channels, 2 * self.hidden_channels) + + # Real weights of SO(2) convolution + self.fc1_r = nn.Linear(num_channels, self.hidden_channels, bias=False) + self.fc2_r = nn.Linear(self.hidden_channels, num_channels, bias=False) + + # Imaginary weights of SO(2) convolution + self.fc1_i = nn.Linear(num_channels, self.hidden_channels, bias=False) + self.fc2_i = nn.Linear(self.hidden_channels, num_channels, bias=False) + + def forward(self, x_m, x_edge) -> torch.Tensor: + # Compute edge scalar features + x_edge = self.act(self.fc1_dist(x_edge)) + x_edge = x_edge.view(-1, 2, self.hidden_channels) + + # Perform the complex weight multiplication + x_r = self.fc1_r(x_m) + x_r = x_r * x_edge[:, 0:1, :] + x_r = self.fc2_r(x_r) + + x_i = self.fc1_i(x_m) + x_i = x_i * x_edge[:, 1:2, :] + x_i = self.fc2_i(x_i) + + x_m_r = x_r[:, 0] - x_i[:, 1] + x_m_i = x_r[:, 1] + x_i[:, 0] + + return torch.stack((x_m_r, x_m_i), dim=1).contiguous() + + +class EdgeBlock(torch.nn.Module): + """ + Edge Block: Compute invariant edge representation from edge diatances and atomic numbers + + Args: + edge_channels (int): Size of invariant edge embedding + distance_expansion (func): Function used to compute distance embedding + max_num_elements (int): Maximum number of atomic numbers + act (function): Non-linear activation function + """ + + def __init__( + self, + edge_channels, + distance_expansion, + max_num_elements, + act, + ) -> None: + super().__init__() + self.in_channels = distance_expansion.num_output + self.distance_expansion = distance_expansion + self.act = act + self.edge_channels = edge_channels + self.max_num_elements = max_num_elements + + # Embedding function of the distance + self.fc1_dist = nn.Linear(self.in_channels, self.edge_channels) + + # Embedding function of the atomic numbers + self.source_embedding = nn.Embedding(self.max_num_elements, self.edge_channels) + self.target_embedding = nn.Embedding(self.max_num_elements, self.edge_channels) + nn.init.uniform_(self.source_embedding.weight.data, -0.001, 0.001) + nn.init.uniform_(self.target_embedding.weight.data, -0.001, 0.001) + + # Embedding function of the edge + self.fc1_edge_attr = nn.Linear( + self.edge_channels, + self.edge_channels, + ) + + def forward(self, edge_distance, source_element, target_element): + # Compute distance embedding + x_dist = self.distance_expansion(edge_distance) + x_dist = self.fc1_dist(x_dist) + + # Compute atomic number embeddings + source_embedding = self.source_embedding(source_element) + target_embedding = self.target_embedding(target_element) + + # Compute invariant edge embedding + x_edge = self.act(source_embedding + target_embedding + x_dist) + return self.act(self.fc1_edge_attr(x_edge)) + + +class EnergyBlock(torch.nn.Module): + """ + Energy Block: Output block computing the energy + + Args: + num_channels (int): Number of channels + num_sphere_samples (int): Number of samples used to approximate the integral on the sphere + act (function): Non-linear activation function + """ + + def __init__( + self, + num_channels: int, + num_sphere_samples: int, + act, + ) -> None: + super().__init__() + self.num_channels = num_channels + self.num_sphere_samples = num_sphere_samples + self.act = act + + self.fc1 = nn.Linear(self.num_channels, self.num_channels) + self.fc2 = nn.Linear(self.num_channels, self.num_channels) + self.fc3 = nn.Linear(self.num_channels, 1, bias=False) + + def forward(self, x_pt) -> torch.Tensor: + # x_pt are the values of the channels sampled at different points on the sphere + x_pt = self.act(self.fc1(x_pt)) + x_pt = self.act(self.fc2(x_pt)) + x_pt = self.fc3(x_pt) + x_pt = x_pt.view(-1, self.num_sphere_samples, 1) + return torch.sum(x_pt, dim=1) / self.num_sphere_samples + + +class ForceBlock(torch.nn.Module): + """ + Force Block: Output block computing the per atom forces + + Args: + num_channels (int): Number of channels + num_sphere_samples (int): Number of samples used to approximate the integral on the sphere + act (function): Non-linear activation function + """ + + def __init__( + self, + num_channels: int, + num_sphere_samples: int, + act, + ) -> None: + super().__init__() + self.num_channels = num_channels + self.num_sphere_samples = num_sphere_samples + self.act = act + + self.fc1 = nn.Linear(self.num_channels, self.num_channels) + self.fc2 = nn.Linear(self.num_channels, self.num_channels) + self.fc3 = nn.Linear(self.num_channels, 1, bias=False) + + def forward(self, x_pt, sphere_points) -> torch.Tensor: + # x_pt are the values of the channels sampled at different points on the sphere + x_pt = self.act(self.fc1(x_pt)) + x_pt = self.act(self.fc2(x_pt)) + x_pt = self.fc3(x_pt) + x_pt = x_pt.view(-1, self.num_sphere_samples, 1) + forces = x_pt * sphere_points.view(1, self.num_sphere_samples, 3) + return torch.sum(forces, dim=1) / self.num_sphere_samples From 2f0ccf79da4176c88d77af6f3304750a532d1bdf Mon Sep 17 00:00:00 2001 From: Misko Date: Thu, 12 Sep 2024 23:49:14 +0000 Subject: [PATCH 2/6] lint and patch --- src/fairchem/core/models/escn/escn.py | 5 +- .../core/models/escn/escn_deprecated.py | 112 +++++++++++++++++- .../core/models/escn/escn_exportable.py | 48 +++++--- 3 files changed, 139 insertions(+), 26 deletions(-) diff --git a/src/fairchem/core/models/escn/escn.py b/src/fairchem/core/models/escn/escn.py index 91069afbc..35772d768 100644 --- a/src/fairchem/core/models/escn/escn.py +++ b/src/fairchem/core/models/escn/escn.py @@ -9,7 +9,6 @@ import contextlib import logging -import time import typing import torch @@ -20,7 +19,7 @@ from fairchem.core.common.registry import registry from fairchem.core.common.utils import conditional_grad -from fairchem.core.models.base import BackboneInterface, GraphModelMixin, HeadInterface +from fairchem.core.models.base import BackboneInterface, HeadInterface from fairchem.core.models.escn.so3 import ( CoefficientMapping, SO3_Embedding, @@ -40,7 +39,7 @@ @registry.register_model("escn_backbone") -class eSCNBackbone(eSCN, BackboneInterface): +class eSCNBackbone(BackboneInterface): """Equivariant Spherical Channel Network Paper: Reducing SO(3) Convolutions to SO(2) for Efficient Equivariant GNNs diff --git a/src/fairchem/core/models/escn/escn_deprecated.py b/src/fairchem/core/models/escn/escn_deprecated.py index d175c59b5..f96f34a18 100644 --- a/src/fairchem/core/models/escn/escn_deprecated.py +++ b/src/fairchem/core/models/escn/escn_deprecated.py @@ -10,17 +10,13 @@ import contextlib import logging import time -import typing import torch import torch.nn as nn -if typing.TYPE_CHECKING: - from torch_geometric.data.batch import Batch - from fairchem.core.common.registry import registry from fairchem.core.common.utils import conditional_grad -from fairchem.core.models.base import BackboneInterface, GraphModelMixin, HeadInterface +from fairchem.core.models.base import GraphModelMixin from fairchem.core.models.escn.so3 import ( CoefficientMapping, SO3_Embedding, @@ -836,3 +832,109 @@ def forward(self, x_pt, sphere_points) -> torch.Tensor: x_pt = x_pt.view(-1, self.num_sphere_samples, 1) forces = x_pt * sphere_points.view(1, self.num_sphere_samples, 3) return torch.sum(forces, dim=1) / self.num_sphere_samples + + +class LayerBlock(torch.nn.Module): + """ + Layer block: Perform one layer (message passing and aggregation) of the GNN + + Args: + layer_idx (int): Layer number + sphere_channels (int): Number of spherical channels + hidden_channels (int): Number of hidden channels used during the SO(2) conv + edge_channels (int): Size of invariant edge embedding + lmax_list (list:int): List of degrees (l) for each resolution + mmax_list (list:int): List of orders (m) for each resolution + distance_expansion (func): Function used to compute distance embedding + max_num_elements (int): Maximum number of atomic numbers + SO3_grid (SO3_grid): Class used to convert from grid the spherical harmonic representations + act (function): Non-linear activation function + """ + + def __init__( + self, + layer_idx: int, + sphere_channels: int, + hidden_channels: int, + edge_channels: int, + lmax_list: list[int], + mmax_list: list[int], + distance_expansion, + max_num_elements: int, + SO3_grid: SO3_Grid, + act, + ) -> None: + super().__init__() + self.layer_idx = layer_idx + self.act = act + self.lmax_list = lmax_list + self.mmax_list = mmax_list + self.num_resolutions = len(lmax_list) + self.sphere_channels = sphere_channels + self.sphere_channels_all = self.num_resolutions * self.sphere_channels + self.SO3_grid = SO3_grid + + # Message block + self.message_block = MessageBlock( + self.layer_idx, + self.sphere_channels, + hidden_channels, + edge_channels, + self.lmax_list, + self.mmax_list, + distance_expansion, + max_num_elements, + self.SO3_grid, + self.act, + ) + + # Non-linear point-wise comvolution for the aggregated messages + self.fc1_sphere = nn.Linear( + 2 * self.sphere_channels_all, self.sphere_channels_all, bias=False + ) + + self.fc2_sphere = nn.Linear( + self.sphere_channels_all, self.sphere_channels_all, bias=False + ) + + self.fc3_sphere = nn.Linear( + self.sphere_channels_all, self.sphere_channels_all, bias=False + ) + + def forward( + self, + x, + atomic_numbers, + edge_distance, + edge_index, + SO3_edge_rot, + mappingReduced, + ): + # Compute messages by performing message block + x_message = self.message_block( + x, + atomic_numbers, + edge_distance, + edge_index, + SO3_edge_rot, + mappingReduced, + ) + + # Compute point-wise spherical non-linearity on aggregated messages + max_lmax = max(self.lmax_list) + + # Project to grid + x_grid_message = x_message.to_grid(self.SO3_grid, lmax=max_lmax) + x_grid = x.to_grid(self.SO3_grid, lmax=max_lmax) + x_grid = torch.cat([x_grid, x_grid_message], dim=3) + + # Perform point-wise convolution + x_grid = self.act(self.fc1_sphere(x_grid)) + x_grid = self.act(self.fc2_sphere(x_grid)) + x_grid = self.fc3_sphere(x_grid) + + # Project back to spherical harmonic coefficients + x_message._from_grid(x_grid, self.SO3_grid, lmax=max_lmax) + + # Return aggregated messages + return x_message diff --git a/src/fairchem/core/models/escn/escn_exportable.py b/src/fairchem/core/models/escn/escn_exportable.py index c1a40ff59..d60b24a84 100644 --- a/src/fairchem/core/models/escn/escn_exportable.py +++ b/src/fairchem/core/models/escn/escn_exportable.py @@ -139,8 +139,12 @@ def __init__( # Initialize the transformations between spherical and grid representations self.SO3_grid = nn.ModuleDict() - self.SO3_grid["lmax_lmax"] = SO3_Grid(self.lmax, self.lmax, resolution=resolution) - self.SO3_grid["lmax_mmax"] = SO3_Grid(self.lmax, self.mmax, resolution=resolution) + self.SO3_grid["lmax_lmax"] = SO3_Grid( + self.lmax, self.lmax, resolution=resolution + ) + self.SO3_grid["lmax_mmax"] = SO3_Grid( + self.lmax, self.mmax, resolution=resolution + ) self.mappingReduced = CoefficientMapping([self.lmax], [self.mmax]) # Initialize the blocks for each layer of the GNN @@ -157,7 +161,7 @@ def __init__( self.max_num_elements, self.SO3_grid, self.act, - self.mappingReduced + self.mappingReduced, ) self.layer_blocks.append(block) @@ -185,7 +189,6 @@ def __init__( requires_grad=False, ) - def forward(self, data: dict[str, torch.Tensor]) -> dict[str, torch.Tensor]: pos: torch.Tensor = data["pos"] batch_idx: torch.Tensor = data["batch"] @@ -207,9 +210,7 @@ def forward(self, data: dict[str, torch.Tensor]) -> dict[str, torch.Tensor]: ############################################################### # Compute 3x3 rotation matrix per edge - edge_rot_mat = self._init_edge_rot_mat( - edge_index, edge_distance_vec - ) + edge_rot_mat = self._init_edge_rot_mat(edge_index, edge_distance_vec) wigner = rotation_to_wigner(edge_rot_mat, 0, self.lmax).detach() ############################################################### @@ -252,7 +253,9 @@ def forward(self, data: dict[str, torch.Tensor]) -> dict[str, torch.Tensor]: # Sample the spherical channels (node embeddings) at evenly distributed points on the sphere. # These values are fed into the output blocks. - x_pt = torch.einsum("abc, pb->apc", x_message, self.sphharm_weights).contiguous() + x_pt = torch.einsum( + "abc, pb->apc", x_message, self.sphharm_weights + ).contiguous() ############################################################### # Energy estimation @@ -335,6 +338,7 @@ def _init_edge_rot_mat(self, edge_index, edge_distance_vec): def num_params(self) -> int: return sum(p.numel() for p in self.parameters()) + class LayerBlock(torch.nn.Module): """ Layer block: Perform one layer (message passing and aggregation) of the GNN @@ -387,7 +391,7 @@ def __init__( max_num_elements, self.SO3_grid, self.act, - self.mappingReduced + self.mappingReduced, ) # Non-linear point-wise comvolution for the aggregated messages @@ -422,7 +426,11 @@ def forward( # Compute point-wise spherical non-linearity on aggregated messages # Project to grid - to_grid_mat = self.SO3_grid["lmax_lmax"].to_grid_mat[:, :, self.SO3_grid["lmax_lmax"].mapping.coefficient_idx(self.lmax, self.lmax)] + to_grid_mat = self.SO3_grid["lmax_lmax"].to_grid_mat[ + :, + :, + self.SO3_grid["lmax_lmax"].mapping.coefficient_idx(self.lmax, self.lmax), + ] x_grid_message = torch.einsum("bai,zic->zbac", to_grid_mat, x_message) # x_grid = x.to_grid(self.SO3_grid["lmax_lmax"]) @@ -435,7 +443,11 @@ def forward( x_grid = self.fc3_sphere(x_grid) # Project back to spherical harmonic coefficients - from_grid_mat = self.SO3_grid["lmax_lmax"].from_grid_mat[:, :, self.SO3_grid["lmax_lmax"].mapping.coefficient_idx(self.lmax, self.lmax)] + from_grid_mat = self.SO3_grid["lmax_lmax"].from_grid_mat[ + :, + :, + self.SO3_grid["lmax_lmax"].mapping.coefficient_idx(self.lmax, self.lmax), + ] return torch.einsum("bai,zbac->zic", from_grid_mat, x_grid) @@ -498,7 +510,7 @@ def __init__( self.lmax, self.mmax, self.act, - self.mappingReduced + self.mappingReduced, ) self.so2_block_target = SO2Block( self.sphere_channels, @@ -507,7 +519,7 @@ def __init__( self.lmax, self.mmax, self.act, - self.mappingReduced + self.mappingReduced, ) def forward( @@ -558,7 +570,9 @@ def forward( x_target = torch.bmm(wigner_inv[:, :, self.out_mask], x_target) # Compute the sum of the incoming neighboring messages for each target node - new_embedding = torch.zeros(x.shape, dtype=x_target.dtype, device=x_target.device) + new_embedding = torch.zeros( + x.shape, dtype=x_target.dtype, device=x_target.device + ) new_embedding.index_add_(0, edge_index[1], x_target) return new_embedding @@ -585,7 +599,7 @@ def __init__( lmax: int, mmax: int, act, - mappingReduced + mappingReduced, ) -> None: super().__init__() self.sphere_channels = sphere_channels @@ -646,9 +660,7 @@ def forward( offset = self.mappingReduced.m_size[0] for m in range(1, self.mmax + 1): # Get the m order coefficients - x_m = x[ - :, offset : offset + 2 * self.mappingReduced.m_size[m] - ].contiguous() + x_m = x[:, offset : offset + 2 * self.mappingReduced.m_size[m]].contiguous() x_m = x_m.view(num_edges, 2, -1) # Perform SO(2) convolution x_m = self.so2_conv[m - 1](x_m, x_edge) From ae8664e7630b4c990a4507096275ecae311996ab Mon Sep 17 00:00:00 2001 From: Misko Date: Thu, 12 Sep 2024 23:57:07 +0000 Subject: [PATCH 3/6] fix import --- src/fairchem/core/models/escn/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fairchem/core/models/escn/__init__.py b/src/fairchem/core/models/escn/__init__.py index 11555c32f..10ee517a6 100644 --- a/src/fairchem/core/models/escn/__init__.py +++ b/src/fairchem/core/models/escn/__init__.py @@ -1,5 +1,5 @@ from __future__ import annotations -from .escn import eSCN +from .escn_deprecated import eSCN __all__ = ["eSCN"] From f30bead3e4eed46ec81bf6dcbc5d6c35ce06a37d Mon Sep 17 00:00:00 2001 From: Misko Date: Fri, 13 Sep 2024 16:26:13 +0000 Subject: [PATCH 4/6] add nnmodule --- src/fairchem/core/models/escn/escn.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fairchem/core/models/escn/escn.py b/src/fairchem/core/models/escn/escn.py index 35772d768..d0bf697ed 100644 --- a/src/fairchem/core/models/escn/escn.py +++ b/src/fairchem/core/models/escn/escn.py @@ -39,7 +39,7 @@ @registry.register_model("escn_backbone") -class eSCNBackbone(BackboneInterface): +class eSCNBackbone(nn.Module, BackboneInterface): """Equivariant Spherical Channel Network Paper: Reducing SO(3) Convolutions to SO(2) for Efficient Equivariant GNNs From a7e6d1d87ed47aa07ce0ea1e4e883dcdff262aba Mon Sep 17 00:00:00 2001 From: Misko Date: Fri, 13 Sep 2024 17:08:58 +0000 Subject: [PATCH 5/6] add graph model mixin --- src/fairchem/core/models/escn/escn.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/fairchem/core/models/escn/escn.py b/src/fairchem/core/models/escn/escn.py index d0bf697ed..7e321436e 100644 --- a/src/fairchem/core/models/escn/escn.py +++ b/src/fairchem/core/models/escn/escn.py @@ -19,7 +19,7 @@ from fairchem.core.common.registry import registry from fairchem.core.common.utils import conditional_grad -from fairchem.core.models.base import BackboneInterface, HeadInterface +from fairchem.core.models.base import BackboneInterface, GraphModelMixin, HeadInterface from fairchem.core.models.escn.so3 import ( CoefficientMapping, SO3_Embedding, @@ -39,7 +39,7 @@ @registry.register_model("escn_backbone") -class eSCNBackbone(nn.Module, BackboneInterface): +class eSCNBackbone(nn.Module, BackboneInterface, GraphModelMixin): """Equivariant Spherical Channel Network Paper: Reducing SO(3) Convolutions to SO(2) for Efficient Equivariant GNNs From 926ba1f76ec8e1b2cf5442bc9ca9dccb9a23dd0e Mon Sep 17 00:00:00 2001 From: Misko Date: Fri, 13 Sep 2024 17:31:49 +0000 Subject: [PATCH 6/6] forgot to add edge rot mat --- src/fairchem/core/models/escn/escn.py | 57 +++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/src/fairchem/core/models/escn/escn.py b/src/fairchem/core/models/escn/escn.py index 7e321436e..36c90dbc3 100644 --- a/src/fairchem/core/models/escn/escn.py +++ b/src/fairchem/core/models/escn/escn.py @@ -336,6 +336,63 @@ def forward(self, data: Batch) -> dict[str, torch.Tensor]: "graph": graph, } + # Initialize the edge rotation matrics + def _init_edge_rot_mat(self, data, edge_index, edge_distance_vec): + edge_vec_0 = edge_distance_vec + edge_vec_0_distance = torch.sqrt(torch.sum(edge_vec_0**2, dim=1)) + + # Make sure the atoms are far enough apart + if torch.min(edge_vec_0_distance) < 0.0001: + logging.error( + f"Error edge_vec_0_distance: {torch.min(edge_vec_0_distance)}" + ) + (minval, minidx) = torch.min(edge_vec_0_distance, 0) + logging.error( + f"Error edge_vec_0_distance: {minidx} {edge_index[0, minidx]} {edge_index[1, minidx]} {data.pos[edge_index[0, minidx]]} {data.pos[edge_index[1, minidx]]}" + ) + + norm_x = edge_vec_0 / (edge_vec_0_distance.view(-1, 1)) + + edge_vec_2 = torch.rand_like(edge_vec_0) - 0.5 + edge_vec_2 = edge_vec_2 / ( + torch.sqrt(torch.sum(edge_vec_2**2, dim=1)).view(-1, 1) + ) + # Create two rotated copys of the random vectors in case the random vector is aligned with norm_x + # With two 90 degree rotated vectors, at least one should not be aligned with norm_x + edge_vec_2b = edge_vec_2.clone() + edge_vec_2b[:, 0] = -edge_vec_2[:, 1] + edge_vec_2b[:, 1] = edge_vec_2[:, 0] + edge_vec_2c = edge_vec_2.clone() + edge_vec_2c[:, 1] = -edge_vec_2[:, 2] + edge_vec_2c[:, 2] = edge_vec_2[:, 1] + vec_dot_b = torch.abs(torch.sum(edge_vec_2b * norm_x, dim=1)).view(-1, 1) + vec_dot_c = torch.abs(torch.sum(edge_vec_2c * norm_x, dim=1)).view(-1, 1) + + vec_dot = torch.abs(torch.sum(edge_vec_2 * norm_x, dim=1)).view(-1, 1) + edge_vec_2 = torch.where(torch.gt(vec_dot, vec_dot_b), edge_vec_2b, edge_vec_2) + vec_dot = torch.abs(torch.sum(edge_vec_2 * norm_x, dim=1)).view(-1, 1) + edge_vec_2 = torch.where(torch.gt(vec_dot, vec_dot_c), edge_vec_2c, edge_vec_2) + + vec_dot = torch.abs(torch.sum(edge_vec_2 * norm_x, dim=1)) + # Check the vectors aren't aligned + assert torch.max(vec_dot) < 0.99 + + norm_z = torch.cross(norm_x, edge_vec_2, dim=1) + norm_z = norm_z / (torch.sqrt(torch.sum(norm_z**2, dim=1, keepdim=True))) + norm_z = norm_z / (torch.sqrt(torch.sum(norm_z**2, dim=1)).view(-1, 1)) + norm_y = torch.cross(norm_x, norm_z, dim=1) + norm_y = norm_y / (torch.sqrt(torch.sum(norm_y**2, dim=1, keepdim=True))) + + # Construct the 3D rotation matrix + norm_x = norm_x.view(-1, 3, 1) + norm_y = -norm_y.view(-1, 3, 1) + norm_z = norm_z.view(-1, 3, 1) + + edge_rot_mat_inv = torch.cat([norm_z, norm_x, norm_y], dim=2) + edge_rot_mat = torch.transpose(edge_rot_mat_inv, 1, 2) + + return edge_rot_mat.detach() + @property def num_params(self) -> int: return sum(p.numel() for p in self.parameters())