diff --git a/README.md b/README.md index 48368a8..496b52f 100644 --- a/README.md +++ b/README.md @@ -119,6 +119,19 @@ To switch to the `5M` version, manually set the `load_path` of `MatterSimCalcula MatterSimCalculator(load_path="MatterSim-v1.0.0-5M.pth", device=device) ``` +## Finetune +> [!TIP] +> MatterSim provides a finetune script to finetune the pre-trained MatterSim model on a custom dataset. +> Please refer to the [MatterSim documentation](https://microsoft.github.io/mattersim/) for more details. + +### A minimal finetune example + +```bash +torchrun --nproc_per_node=1 src/mattersim/training/finetune_mattersim.py --load_model_path mattersim-v1.0.0-1m --train_data_path tests/data/high_level_water.xyz +``` + + + ## Reference diff --git a/docs/index.rst b/docs/index.rst index 8ec9b84..6b0ac55 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -82,4 +82,5 @@ Frequently Asked Questions user_guide/installation user_guide/getting_started + user_guide/finetune examples/examples diff --git a/docs/user_guide/finetune.rst b/docs/user_guide/finetune.rst new file mode 100644 index 0000000..9ef6ad0 --- /dev/null +++ b/docs/user_guide/finetune.rst @@ -0,0 +1,86 @@ + +Finetune MatterSim +================== + +Finetune Script +--------------- + +MatterSim provides a finetune script to +finetune the pre-trained MatterSim model on a custom dataset. +You can find the script in the ``training`` folder or in the +`github link `_. + +Finetune Parameters +-------------------- + +The finetune script accepts several command-line arguments to customize the training process. Below is a list of the available parameters: + +- **run_name**: (str) The name of the run. Default is "example". + +- **train_data_path**: (str) Path to the training data file. Supports various file types readable by ASE (e.g., `.xyz`, `.traj`, `.cif`) and `.pkl` files. Default is "./sample.xyz". + +- **valid_data_path**: (str) Path to the validation data file. Default is None. + +- **load_model_path**: (str) Path to load the pre-trained model. Default is "mattersim-v1.0.0-1m". + +- **save_path**: (str) Path to save the trained model. Default is "./results". + +- **save_checkpoint**: (bool) Whether to save checkpoints during training. Default is False. + +- **ckpt_interval**: (int) Interval (in epochs) to save checkpoints. Default is 10. + +- **device**: (str) Device to use for training, either "cuda" or "cpu". Default is "cuda". + +- **cutoff**: (float) Cutoff radius for interactions. Default is 5.0. + +- **threebody_cutoff**: (float) Cutoff radius for three-body interactions, should be smaller than the two-body cutoff. Default is 4.0. + +- **epochs**: (int) Number of training epochs. Default is 1000. + +- **batch_size**: (int) Batch size for training. Default is 16. + +- **lr**: (float) Learning rate for the optimizer. Default is 2e-4. + +- **step_size**: (int) Step size for the learning rate scheduler. Default is 10. + +- **include_forces**: (bool) Whether to include forces in the training. Default is True. + +- **include_stresses**: (bool) Whether to include stresses in the training. Default is False. + +- **force_loss_ratio**: (float) Ratio of force loss in the total loss. Default is 1.0. + +- **stress_loss_ratio**: (float) Ratio of stress loss in the total loss. Default is 0.1. + +- **early_stop_patience**: (int) Patience for early stopping. Default is 10. + +- **seed**: (int) Random seed for reproducibility. Default is 42. + +- **re_normalize**: (bool) Whether to re-normalize energy and forces according to new data. Default is False. + +- **scale_key**: (str) Key for scaling forces. Only used when ``re_normalize`` is True. Default is "per_species_forces_rms". + +- **shift_key**: (str) Key for shifting energy. Only used when ``re_normalize`` is True. Default is "per_species_energy_mean_linear_reg". + +- **init_scale**: (float) Initial scale value. Only used when ``re_normalize`` is True. Default is None. + +- **init_shift**: (float) Initial shift value. Only used when ``re_normalize`` is True. Default is None. + +- **trainable_scale**: (bool) Whether the scale is trainable. Only used when ``re_normalize`` is True. Default is False. + +- **trainable_shift**: (bool) Whether the shift is trainable. Only used when ``re_normalize`` is True. Default is False. + +- **wandb**: (bool) Whether to use Weights & Biases for logging. Default is False. + +- **wandb_api_key**: (str) API key for Weights & Biases. Default is None. + +- **wandb_project**: (str) Project name for Weights & Biases. Default is "wandb_test". + +These parameters allow you to customize the finetuning process to suit your specific dataset and computational resources. + +Finetune Example +---------------- +You can replace the data path with your own data path. + +.. code-block:: bash + + torchrun --nproc_per_node=1 src/mattersim/training/finetune_mattersim.py --load_model_path mattersim-v1.0.0-1m --train_data_path xyz_files/train.xyz --valid_data_path xyz_files/valid.xyz --batch_size 16 --lr 2e-4 --step_size 20 --epochs 200 --save_path ./finetune_result --save_checkpoint --ckpt_interval 20 --include_stresses --include_forces diff --git a/tests/data/high_level_water.xyz b/tests/data/high_level_water.xyz new file mode 100644 index 0000000..95fe107 --- /dev/null +++ b/tests/data/high_level_water.xyz @@ -0,0 +1,1940 @@ +192 +Lattice="13.7044938 0.0 0.0 -5.3e-07 13.7044938 0.0 -5.3e-07 -5.3e-07 13.7044938" Properties=species:S:1:pos:R:3:forces:R:3 energy=-30011.49340274 cutoff=-1.0 nneightol=1.2 pbc="T T T" 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