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config.yaml
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gpu: 'cuda:0'
log_every_n_steps: 50
lr: 2e-4
min_lr: 1e-7
weight_decay: 0.0
epochs: 10
warmup_epochs: 0.3
patience_epochs: 0.7
load_model: None
# Load the pretrained GNN model
# load_model: ckpt/schnet # pre-trained SchNet
# load_model: ckpt/se3transformer # pre-trained SE(3)-Transformer
# load_model: ckpt/egnn # pre-trained EGNN
# load_model: ckpt/torchmdnet # pre-trained TorchMD-Net
# Select the GNN model. Supported models:
# - SchNet: K. T. Schütt et al., https://aip.scitation.org/doi/10.1063/1.5019779
# - SE(3)-Transformer: F. B. Fuchs et al., https://arxiv.org/abs/2006.10503
# - EGNN: V. G. Satorras et al., https://arxiv.org/abs/2102.09844
# - TorchMD-Net: P. Thölke et al., https://arxiv.org/abs/2202.02541
# The defualt settings are listed below.
model:
# name: "SchNet"
# num_atoms: 28
# bond_feat_dim: 1
# num_targets: 1
# hidden_channels: 256
# num_filters: 256
# num_interactions: 5
# num_gaussians: 32
# cutoff: 5.0
# max_num_neighbors: 32
# readout: 'add'
# name: 'SE3Transformer'
# num_layers: 3
# atom_feature_size: 28
# num_channels: 8
# num_degrees: 4
# edge_dim: 4
# div: 4
# pooling: 'avg'
# n_heads: 2
# cutoff: 5.0
# max_num_neighbors: 32
name: "EGNN"
hidden_channels: 256
in_edge_nf: 0
n_layers: 5
residual: True
attention: True
normalize: True
tanh: False
cutoff: 5.0
max_atom_type: 28
max_chirality_type: 5
max_num_neighbors: 32
# name: "TorchMD-Net"
# hidden_channels: 256
# num_layers: 6
# num_rbf: 32
# rbf_type: "expnorm"
# trainable_rbf: True
# activation: "silu"
# attn_activation: "silu"
# neighbor_embedding: True
# num_heads: 8
# distance_influence: "both"
# cutoff_lower: 0.0
# cutoff_upper: 5.0
# max_atom_type: 28
# max_chirality_type: 5
# max_num_neighbors: 32
# Select the dataset. Supported datasets:
# - ANI-1: J. S. Smith et al., https://www.nature.com/articles/sdata2017193
# - ANI-1x: J. S. Smith et al., https://www.nature.com/articles/s41597-020-0473-z
# - ISO17: K. T. Schütt et al., https://arxiv.org/abs/1706.08566
# - MD22: S. Chmiela et al., https://www.science.org/doi/10.1126/sciadv.adf0873
# - SPICE: P. Eastman et al., https://www.nature.com/articles/s41597-022-01882-6
dataset:
batch_size: 256
num_workers: 8
valid_size: 0.1
test_size: 0.1
data_dir: './ANI-1'
# data_dir: './ANI-1x'
# data_dir: './iso17'
# data_dir: './MD22/md22_Ac-Ala3-NHMe.xyz'
# data_dir: './MD22/md22_DHA.xyz'
# data_dir: './MD22/md22_stachyose.xyz'
# data_dir: './MD22/md22_AT-AT.xyz'
# data_dir: './MD22/md22_AT-AT-CG-CG.xyz'
# data_dir: './MD22/md22_buckyball-catcher.xyz'
# data_dir: './MD22/md22_double-walled_nanotube.xyz'
# data_dir: './SPICE'
seed: 666