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Merge branch 'main' into patch-5
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‎configs/allscaip/backbone/md_NeNo.yaml‎

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model: fairchem.core.models.allscaip.AllScAIP.AllScAIPBackbone
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# Global Configs
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num_layers: 10
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hidden_size: 640
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direct_forces: ${direct_forces}
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regress_forces: True
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regress_stress: ${regress_stress}
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use_compile: ${use_compile}
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use_padding: ${direct_forces}
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dataset_list: ${dataset_list}
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use_node_path: True
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use_freq_mask: False
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use_sincx_mask: False
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# Molecular Graph Configs
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max_num_elements: 110
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max_batch_size: 96 # this is set to be the max number of batch that could be sampled by the sampler
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max_atoms: ${max_atoms}
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max_radius: ${cutoff_radius}
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use_pbc: ${use_pbc}
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knn_k: ${max_neighbors}
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knn_soft: true
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knn_sigmoid_scale: 0.2
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knn_lse_scale: 0.1
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knn_use_low_mem: true
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knn_pad_size: ${max_neighbors_pad_size}
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# Graph Neural Networks Configs
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atten_name: memory_efficient
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atten_num_heads: 10
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# Regularization Configs
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# atten_dropout: 0.1
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# mlp_dropout: 0.05
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# node_ffn_dropout: 0.05
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# edge_ffn_dropout: 0.05
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# scalar_output_dropout: 0.05
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# vector_output_dropout: 0.05

‎configs/allscaip/backbone/sm_NeAnNoSi.yaml‎

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model: fairchem.core.models.allscaip.AllScAIP.AllScAIPBackbone
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# Global Configs
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num_layers: 6
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hidden_size: 512
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direct_forces: ${direct_forces}
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regress_forces: True
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regress_stress: ${regress_stress}
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use_compile: ${use_compile}
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use_padding: ${direct_forces}
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dataset_list: ${dataset_list}
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use_node_path: True
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use_freq_mask: True
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use_sincx_mask: True
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# Molecular Graph Configs
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max_num_elements: 110
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max_batch_size: 96 # this is set to be the max number of batch that could be sampled by the sampler
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max_atoms: ${max_atoms}
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max_radius: ${cutoff_radius}
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use_pbc: ${use_pbc}
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knn_k: ${max_neighbors}
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knn_soft: true
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knn_sigmoid_scale: 0.2
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knn_lse_scale: 0.1
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knn_use_low_mem: true
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knn_pad_size: ${max_neighbors_pad_size}
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# Graph Neural Networks Configs
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atten_name: memory_efficient
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atten_num_heads: 8
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# Regularization Configs
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# atten_dropout: 0.1
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# mlp_dropout: 0.05
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# node_ffn_dropout: 0.05
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# edge_ffn_dropout: 0.05
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# scalar_output_dropout: 0.05
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# vector_output_dropout: 0.05

‎configs/allscaip/cluster/local.yaml‎

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run_dir: /data/ericqu/rundir
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mode: LOCAL
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device: CUDA
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ranks_per_node: 1
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dataloader_workers: 0
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timeout_hr: 12
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debug: True
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mem_gb: 64
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cpus_per_task: 9
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account: null
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qos: gpu
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partition: gpu
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omol_all_path: /data/OMOL/ALL
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omol_4M_train_path: /data/OMOL/4M/train_4M
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data_root_dir: /data/ericqu
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additional_parameters:
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nodelist: germain

‎configs/allscaip/dataset/omol.yaml‎

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omol_train:
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splits:
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train:
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src: ${cluster.omol_all_path}/train
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format: ase_db
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a2g_args:
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molecule_cell_size: 120.0
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r_energy: True
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r_forces: True
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r_data_keys: ['spin', 'charge']
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key_mapping:
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energy: omol_energy
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forces: ${omol_forces_key}
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transforms:
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common_transform:
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dataset_name: omol
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omol_val:
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splits:
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val:
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sample_n: 20000
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src: ${cluster.omol_all_path}/val
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# metal_ligand_ood:
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# sample_n: 20000
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# src: ${cluster.omol_all_path}/metal_ligand_ood
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# elytes_ood:
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# sample_n: 20000
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# src: ${cluster.omol_all_path}/elytes_ood
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val_metal_complexes:
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sample_n: 20000
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src: ${cluster.omol_all_path}/val
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subset_to:
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- op: in
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metadata_key: data_ids
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rhv:
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- metal_complexes
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val_electrolytes:
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sample_n: 20000
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src: ${cluster.omol_all_path}/val
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subset_to:
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- op: in
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metadata_key: data_ids
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rhv:
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- elytes
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val_biomolecules:
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sample_n: 20000
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src: ${cluster.omol_all_path}/val
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subset_to:
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- op: in
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metadata_key: data_ids
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rhv:
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- biomolecules
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val_spice:
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src: ${cluster.omol_all_path}/val
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subset_to:
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- op: in
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metadata_key: data_ids
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rhv:
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- spice
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val_neutralorganics:
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sample_n: 20000
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src: ${cluster.omol_all_path}/val
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subset_to:
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- op: in
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metadata_key: data_ids
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rhv:
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- ani2x
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- orbnet_denali
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- geom_orca6
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- trans1x
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- rgd
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format: ase_db
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a2g_args:
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molecule_cell_size: 120.0
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r_energy: True
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r_forces: True
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r_data_keys: ['spin', 'charge']
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# r_edges: ${cpu_graph}
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# radius: ${cutoff_radius}
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# max_neigh: ${max_neighbors}
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key_mapping:
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energy: omol_energy
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forces: ${omol_forces_key}
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transforms:
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common_transform:
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dataset_name: omol

‎configs/allscaip/dataset/omol_4M.yaml‎

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omol_train:
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splits:
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train:
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src: ${cluster.omol_4M_train_path}
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format: ase_db
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a2g_args:
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molecule_cell_size: 120.0
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r_energy: True
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r_forces: True
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r_data_keys: ['spin', 'charge']
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key_mapping:
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energy: omol_energy
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forces: ${omol_forces_key}
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transforms:
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common_transform:
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dataset_name: omol
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omol_val:
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splits:
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val:
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sample_n: 20000
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src: ${cluster.omol_all_path}/val
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# metal_ligand_ood:
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# sample_n: 20000
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# src: ${cluster.omol_all_path}/metal_ligand_ood
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# elytes_ood:
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# sample_n: 20000
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# src: ${cluster.omol_all_path}/elytes_ood
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val_metal_complexes:
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sample_n: 20000
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src: ${cluster.omol_all_path}/val
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subset_to:
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- op: in
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metadata_key: data_ids
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rhv:
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- metal_complexes
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val_electrolytes:
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sample_n: 20000
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src: ${cluster.omol_all_path}/val
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subset_to:
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- op: in
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metadata_key: data_ids
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rhv:
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- elytes
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val_biomolecules:
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sample_n: 20000
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src: ${cluster.omol_all_path}/val
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subset_to:
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- op: in
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metadata_key: data_ids
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rhv:
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- biomolecules
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val_spice:
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src: ${cluster.omol_all_path}/val
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subset_to:
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- op: in
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metadata_key: data_ids
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rhv:
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- spice
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val_neutralorganics:
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sample_n: 20000
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src: ${cluster.omol_all_path}/val
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subset_to:
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- op: in
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metadata_key: data_ids
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rhv:
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- ani2x
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- orbnet_denali
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- geom_orca6
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- trans1x
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- rgd
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format: ase_db
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a2g_args:
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molecule_cell_size: 120.0
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r_energy: True
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r_forces: True
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r_data_keys: ['spin', 'charge']
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# r_edges: ${cpu_graph}
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# radius: ${cutoff_radius}
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# max_neigh: ${max_neighbors}
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key_mapping:
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energy: omol_energy
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forces: ${omol_forces_key}
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transforms:
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common_transform:
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dataset_name: omol

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