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Merge branch 'main' into optional-pmg
2 parents 9a0114c + abcf16f commit e7b5f9e

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‎configs/uma/benchmark/omol-geom.yaml‎

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defaults:
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- cluster: v100
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- checkpoint: uma_sm
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- _self_
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benchmark_name: geom_conformers
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job:
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run_name: ${checkpoint.model_name}
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run_dir: ${cluster.run_dir}
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device_type: ${cluster.device}
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debug: ${cluster.debug}
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scheduler:
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mode: ${cluster.mode}
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distributed_init_method: FILE
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num_array_jobs: 400
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slurm:
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partition: ${cluster.partition}
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mem_gb: ${cluster.mem_gb}
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timeout_hr: 72
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logger:
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_target_: fairchem.core.common.logger.WandBSingletonLogger.init_wandb
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_partial_: true
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entity: fairchem
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project: uma-benchmarks
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group: ${checkpoint.model_name}
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job_type: ${benchmark_name}
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runner:
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_target_: fairchem.core.components.calculate.omol_runner.OMolRunner
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calculator:
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_target_: fairchem.core.FAIRChemCalculator.from_model_checkpoint
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name_or_path: ${checkpoint.ckpt_path}
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task_name: omol
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input_data: ${cluster.data_root_dir}/conformer_inputs.pkl
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benchmark_name: ${benchmark_name}
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benchmark:
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_target_: fairchem.core.components.calculate.recipes.omol.conformers
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_partial_: True
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reducer:
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_target_: fairchem.core.components.benchmark.omol_reducer.OMolReducer
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benchmark_name: ${benchmark_name}

‎configs/uma/benchmark/omol-ieea.yaml‎

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defaults:
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- cluster: v100
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- checkpoint: uma_sm
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- _self_
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benchmark_name: ie_ea
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job:
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run_name: ${checkpoint.model_name}
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run_dir: ${cluster.run_dir}
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device_type: ${cluster.device}
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debug: ${cluster.debug}
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scheduler:
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mode: ${cluster.mode}
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distributed_init_method: FILE
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num_array_jobs: 10
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slurm:
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partition: ${cluster.partition}
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mem_gb: ${cluster.mem_gb}
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timeout_hr: 72
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logger:
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_target_: fairchem.core.common.logger.WandBSingletonLogger.init_wandb
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_partial_: true
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entity: fairchem
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project: uma-benchmarks
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group: ${checkpoint.model_name}
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job_type: ${benchmark_name}
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runner:
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_target_: fairchem.core.components.calculate.omol_runner.OMolRunner
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calculator:
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_target_: fairchem.core.FAIRChemCalculator.from_model_checkpoint
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name_or_path: ${checkpoint.ckpt_path}
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task_name: omol
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input_data: ${cluster.data_root_dir}/ieea_inputs.pkl
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benchmark_name: ${benchmark_name}
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benchmark:
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_target_: fairchem.core.components.calculate.recipes.omol.ieea
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_partial_: True
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reducer:
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_target_: fairchem.core.components.benchmark.omol_reducer.OMolReducer
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benchmark_name: ${benchmark_name}

‎configs/uma/benchmark/omol-pocket.yaml‎

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defaults:
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- cluster: v100
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- checkpoint: uma_sm
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- _self_
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benchmark_name: ligand_pocket
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job:
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run_name: ${checkpoint.model_name}
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run_dir: ${cluster.run_dir}
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device_type: ${cluster.device}
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debug: ${cluster.debug}
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scheduler:
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mode: ${cluster.mode}
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distributed_init_method: FILE
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num_array_jobs: 1
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slurm:
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partition: ${cluster.partition}
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mem_gb: ${cluster.mem_gb}
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timeout_hr: 72
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logger:
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_target_: fairchem.core.common.logger.WandBSingletonLogger.init_wandb
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_partial_: true
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entity: fairchem
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project: uma-benchmarks
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group: ${checkpoint.model_name}
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job_type: ${benchmark_name}
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runner:
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_target_: fairchem.core.components.calculate.omol_runner.OMolRunner
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calculator:
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_target_: fairchem.core.FAIRChemCalculator.from_model_checkpoint
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name_or_path: ${checkpoint.ckpt_path}
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task_name: omol
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input_data: ${cluster.data_root_dir}/ligand_pocket_inputs.pkl
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benchmark_name: ${benchmark_name}
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benchmark:
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_target_: fairchem.core.components.calculate.recipes.omol.ligand_pocket
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_partial_: True
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reducer:
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_target_: fairchem.core.components.benchmark.omol_reducer.OMolReducer
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benchmark_name: ${benchmark_name}

‎configs/uma/benchmark/omol-prot.yaml‎

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defaults:
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- cluster: v100
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- checkpoint: uma_sm
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- _self_
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benchmark_name: protonation_energies
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job:
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run_name: ${checkpoint.model_name}
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run_dir: ${cluster.run_dir}
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device_type: ${cluster.device}
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debug: ${cluster.debug}
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scheduler:
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mode: ${cluster.mode}
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distributed_init_method: FILE
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num_array_jobs: 400
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slurm:
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partition: ${cluster.partition}
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mem_gb: ${cluster.mem_gb}
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timeout_hr: 72
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logger:
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_target_: fairchem.core.common.logger.WandBSingletonLogger.init_wandb
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_partial_: true
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entity: fairchem
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project: uma-benchmarks
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group: ${checkpoint.model_name}
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job_type: ${benchmark_name}
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runner:
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_target_: fairchem.core.components.calculate.omol_runner.OMolRunner
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calculator:
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_target_: fairchem.core.FAIRChemCalculator.from_model_checkpoint
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name_or_path: ${checkpoint.ckpt_path}
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task_name: omol
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input_data: ${cluster.data_root_dir}/protonation_inputs.pkl
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benchmark_name: ${benchmark_name}
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benchmark:
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_target_: fairchem.core.components.calculate.recipes.omol.protonation
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_partial_: True
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reducer:
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_target_: fairchem.core.components.benchmark.omol_reducer.OMolReducer
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benchmark_name: ${benchmark_name}

‎configs/uma/benchmark/omol-scale.yaml‎

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defaults:
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- cluster: v100
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- checkpoint: uma_sm
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- _self_
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benchmark_name: distance_scaling
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job:
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run_name: ${checkpoint.model_name}
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run_dir: ${cluster.run_dir}
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device_type: ${cluster.device}
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debug: ${cluster.debug}
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scheduler:
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mode: ${cluster.mode}
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distributed_init_method: FILE
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num_array_jobs: 200
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slurm:
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partition: ${cluster.partition}
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mem_gb: ${cluster.mem_gb}
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timeout_hr: 72
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logger:
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_target_: fairchem.core.common.logger.WandBSingletonLogger.init_wandb
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_partial_: true
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entity: fairchem
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project: uma-benchmarks
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group: ${checkpoint.model_name}
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job_type: ${benchmark_name}
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runner:
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_target_: fairchem.core.components.calculate.omol_runner.OMolRunner
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calculator:
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_target_: fairchem.core.FAIRChemCalculator.from_model_checkpoint
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name_or_path: ${checkpoint.ckpt_path}
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task_name: omol
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input_data: ${cluster.data_root_dir}/distance_scaling_inputs.pkl
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benchmark_name: ${benchmark_name}
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benchmark:
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_target_: fairchem.core.components.calculate.recipes.omol.distance_scaling
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_partial_: True
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reducer:
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_target_: fairchem.core.components.benchmark.omol_reducer.OMolReducer
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benchmark_name: ${benchmark_name}

‎configs/uma/benchmark/omol-spin.yaml‎

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defaults:
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- cluster: v100
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- checkpoint: uma_sm
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- _self_
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benchmark_name: spin_gap
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job:
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run_name: ${checkpoint.model_name}
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run_dir: ${cluster.run_dir}
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device_type: ${cluster.device}
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debug: ${cluster.debug}
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scheduler:
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mode: ${cluster.mode}
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distributed_init_method: FILE
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num_array_jobs: 10
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slurm:
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partition: ${cluster.partition}
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mem_gb: ${cluster.mem_gb}
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timeout_hr: 72
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logger:
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_target_: fairchem.core.common.logger.WandBSingletonLogger.init_wandb
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_partial_: true
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entity: fairchem
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project: uma-benchmarks
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group: ${checkpoint.model_name}
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job_type: ${benchmark_name}
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runner:
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_target_: fairchem.core.components.calculate.omol_runner.OMolRunner
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calculator:
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_target_: fairchem.core.FAIRChemCalculator.from_model_checkpoint
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name_or_path: ${checkpoint.ckpt_path}
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task_name: omol
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input_data: ${cluster.data_root_dir}/spingap_inputs.pkl
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benchmark_name: ${benchmark_name}
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benchmark:
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_target_: fairchem.core.components.calculate.recipes.omol.spin_gap
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_partial_: True
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reducer:
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_target_: fairchem.core.components.benchmark.omol_reducer.OMolReducer
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benchmark_name: ${benchmark_name}

‎configs/uma/benchmark/omol-strain.yaml‎

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defaults:
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- cluster: v100
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- checkpoint: uma_sm
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- _self_
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benchmark_name: ligand_strain
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job:
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run_name: ${checkpoint.model_name}
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run_dir: ${cluster.run_dir}
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device_type: ${cluster.device}
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debug: ${cluster.debug}
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scheduler:
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mode: ${cluster.mode}
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distributed_init_method: FILE
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num_array_jobs: 400
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slurm:
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partition: ${cluster.partition}
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mem_gb: ${cluster.mem_gb}
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timeout_hr: 72
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logger:
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_target_: fairchem.core.common.logger.WandBSingletonLogger.init_wandb
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_partial_: true
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entity: fairchem
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project: uma-benchmarks
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group: ${checkpoint.model_name}
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job_type: ${benchmark_name}
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runner:
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_target_: fairchem.core.components.calculate.omol_runner.OMolRunner
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calculator:
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_target_: fairchem.core.FAIRChemCalculator.from_model_checkpoint
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name_or_path: ${checkpoint.ckpt_path}
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task_name: omol
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input_data: ${cluster.data_root_dir}/ligand_strain_inputs.pkl
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benchmark_name: ${benchmark_name}
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benchmark:
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_target_: fairchem.core.components.calculate.recipes.omol.ligand_strain
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_partial_: True
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reducer:
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_target_: fairchem.core.components.benchmark.omol_reducer.OMolReducer
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benchmark_name: ${benchmark_name}

‎docs/_toc.yml‎

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chapters:
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- file: dac/datasets/summary
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sections:
80-
- file: dac/datasets/odac
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- file: dac/datasets/odac25
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- file: dac/datasets/odac23
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- file: dac/models
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- file: dac/examples_tutorials/summary
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sections:

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