Merge pull request #13 from wengroup/devel

Add training script for atomic tensor

scripts/configs/atomic_tensor.yaml

@@ -0,0 +1,117 @@
+## Config files for atomic tensor (i.e. a tensor value for each atom)
+
+seed_everything: 35
+log_level: info
+
+data:
+  tensor_target_name: nmr_tensor
+  atom_selector: atom_selector
+  tensor_target_formula: ij=ji
+  root: .
+  trainset_filename: /Users/mjwen.admin/Documents/Dataset/NMR_tensor/si_nmr_data_small.json
+  valset_filename: /Users/mjwen.admin/Documents/Dataset/NMR_tensor/si_nmr_data_small.json
+  testset_filename: /Users/mjwen.admin/Documents/Dataset/NMR_tensor/si_nmr_data_small.json
+  r_cut: 5.0
+  reuse: false
+  loader_kwargs:
+    batch_size: 2
+    shuffle: true
+
+model:
+  ##########
+  # embedding
+  ##########
+
+  # atom species embedding
+  species_embedding_dim: 16
+
+  # spherical harmonics embedding of edge direction
+  irreps_edge_sh: 0e + 1o + 2e
+
+  # radial edge distance embedding
+  radial_basis_type: bessel
+  num_radial_basis: 8
+  radial_basis_start: 0.
+  radial_basis_end: 5.
+
+  ##########
+  # message passing conv layers
+  ##########
+  num_layers: 3
+
+  # radial network
+  invariant_layers: 2 # number of radial layers
+  invariant_neurons: 32 # number of hidden neurons in radial function
+
+  # Average number of neighbors used for normalization. Options:
+  # 1. `auto` to determine it automatically, by setting it to average number
+  #    of neighbors of the training set
+  # 2. float or int provided here.
+  # 3. `null` to not use it
+  average_num_neighbors: auto
+
+  # point convolution
+  conv_layer_irreps: 32x0o+32x0e + 16x1o+16x1e + 4x2o+4x2e
+  nonlinearity_type: gate
+  normalization: batch
+  resnet: true
+
+  ##########
+  # output
+  ##########
+
+  # output_format and output_formula should be used together.
+  # - output_format (can be `irreps` or `cartesian`) determines what the loss
+  #   function will be on (either on the irreps space or the cartesian space).
+  # - output_formula gives what the cartesian formula of the tensor is.
+  #   For example, ijkl=jikl=klij specifies a forth-rank elasticity tensor.
+  output_format: irreps
+  output_formula: ij=ji
+
+  # pooling node feats to graph feats
+  reduce: mean
+
+trainer:
+  max_epochs: 10 # number of maximum training epochs
+  num_nodes: 1
+  accelerator: cpu
+  devices: 1
+
+  callbacks:
+    - class_path: pytorch_lightning.callbacks.ModelCheckpoint
+      init_args:
+        monitor: val/score
+        mode: min
+        save_top_k: 3
+        save_last: true
+        verbose: false
+    - class_path: pytorch_lightning.callbacks.EarlyStopping
+      init_args:
+        monitor: val/score
+        mode: min
+        patience: 150
+        min_delta: 0
+        verbose: true
+    - class_path: pytorch_lightning.callbacks.ModelSummary
+      init_args:
+        max_depth: -1
+
+  #logger:
+  #  class_path: pytorch_lightning.loggers.wandb.WandbLogger
+  #  init_args:
+  #    save_dir: matten_logs
+  #    project: matten_proj
+
+optimizer:
+  class_path: torch.optim.Adam
+  init_args:
+    lr: 0.01
+    weight_decay: 0.00001
+
+lr_scheduler:
+  class_path: torch.optim.lr_scheduler.ReduceLROnPlateau
+  init_args:
+    mode: min
+    factor: 0.5
+    patience: 50
+    verbose: true

scripts/configs/materials_tensor.yaml

@@ -3,6 +3,7 @@ log_level: info
 
 data:
   root: ../datasets/
+  tensor_target_name: elastic_tensor_full
   trainset_filename: example_crystal_elasticity_tensor_n100.json
   valset_filename: example_crystal_elasticity_tensor_n100.json
   testset_filename: example_crystal_elasticity_tensor_n100.json

scripts/train_atomic_tensor.py

@@ -0,0 +1,81 @@
+"""Script to train the materials tensor model."""
+
+from pathlib import Path
+from typing import Dict, List, Union
+
+import yaml
+from loguru import logger
+from pytorch_lightning import Trainer, seed_everything
+from pytorch_lightning.cli import instantiate_class as lit_instantiate_class
+
+from matten.dataset.structure_scalar_tensor import TensorDataModule
+from matten.log import set_logger
+from matten.model_factory.task import TensorRegressionTask
+from matten.model_factory.tfn_atomic_tensor import AtomicTensorModel
+
+
+def instantiate_class(d: Union[Dict, List]):
+    args = tuple()  # no positional args
+    if isinstance(d, dict):
+        return lit_instantiate_class(args, d)
+    elif isinstance(d, list):
+        return [lit_instantiate_class(args, x) for x in d]
+    else:
+        raise ValueError(f"Cannot instantiate class from {d}")
+
+
+def get_args(path: Path):
+    """Get the arguments from the config file."""
+    with open(path, "r") as f:
+        config = yaml.safe_load(f)
+    return config
+
+
+def main(config: Dict):
+    dm = TensorDataModule(**config["data"])
+    dm.prepare_data()
+    dm.setup()
+
+    model = AtomicTensorModel(
+        tasks=TensorRegressionTask(name=config["data"]["tensor_target_name"]),
+        backbone_hparams=config["model"],
+        dataset_hparams=dm.get_to_model_info(),
+        optimizer_hparams=config["optimizer"],
+        lr_scheduler_hparams=config["lr_scheduler"],
+    )
+
+    try:
+        callbacks = instantiate_class(config["trainer"].pop("callbacks"))
+        lit_logger = instantiate_class(config["trainer"].pop("logger"))
+    except KeyError:
+        callbacks = None
+        lit_logger = None
+
+    trainer = Trainer(
+        callbacks=callbacks,
+        logger=lit_logger,
+        **config["trainer"],
+    )
+
+    logger.info("Start training!")
+    trainer.fit(model, datamodule=dm)
+
+    # test
+    logger.info("Start testing!")
+    trainer.test(ckpt_path="best", datamodule=dm)
+
+    # print path of best checkpoint
+    logger.info(f"Best checkpoint path: {trainer.checkpoint_callback.best_model_path}")
+
+
+if __name__ == "__main__":
+    config_file = Path(__file__).parent / "configs" / "atomic_tensor.yaml"
+    config = get_args(config_file)
+
+    seed = config.get("seed_everything", 1)
+    seed_everything(seed)
+
+    log_level = config.get("log_level", "INFO")
+    set_logger(log_level)
+
+    main(config)

scripts/train_materials_tensor.py

@@ -37,7 +37,7 @@ def main(config: Dict):
     dm.setup()
 
     model = ScalarTensorModel(
-        tasks=TensorRegressionTask(name="elastic_tensor_full"),
+        tasks=TensorRegressionTask(name=config["data"]["tensor_target_name"]),
         backbone_hparams=config["model"],
         dataset_hparams=dm.get_to_model_info(),
         optimizer_hparams=config["optimizer"],

src/matten/dataset/structure_scalar_tensor.py

@@ -50,6 +50,8 @@ class TensorDataset(InMemoryDataset):
             10.0, 0:1.0}}, then for data points with minLC less than 0, it will have
             a weight of 10, and for those with minLC larger than 0, it will have a
             weight of 1. By default `None` means all data points has a weight of 1.
+        atom_selector: a list of bools to indicate which atoms to use in the structure
+            to compute the target. If `None`, all atoms are used.
         global_featurizer: featurizer to compute global features.
         normalize_global_features: whether to normalize the global feature.
         atom_featuruzer:  featurizer to compute atom features.
@@ -79,6 +81,7 @@ def __init__(
         log_scalar_targets: List[bool] = None,
         normalize_scalar_targets: List[bool] = None,
         tensor_target_weight: Dict[str, Dict[str, float]] = None,
+        atom_selector: List[bool] = None,
         global_featurizer: None = None,
         normalize_global_features: bool = False,
         atom_featurizer: None = None,
@@ -97,6 +100,7 @@ def __init__(
         self.normalize_tensor_target = normalize_tensor_target
 
         self.tensor_target_weight = tensor_target_weight
+        self.atom_selector = atom_selector
 
         self.scalar_target_names = (
             [] if scalar_target_names is None else scalar_target_names
@@ -259,7 +263,7 @@ def _get_crystals(self, df):
                 # TODO, convert to irreps tensor, assuming all input tensor is Cartesian
                 converter = CartesianTensorWrapper(formula=self.tensor_target_formula)
                 df[self.tensor_target_name] = df[self.tensor_target_name].apply(
-                    lambda x: converter.from_cartesian(x).reshape(1, -1)
+                    lambda x: torch.atleast_2d(converter.from_cartesian(x))
                 )
             elif self.tensor_target_format == "cartesian":
                 df[self.tensor_target_name] = df[self.tensor_target_name].apply(
@@ -303,6 +307,10 @@ def _get_crystals(self, df):
                         y[self.tensor_target_name] * self.tensor_target_scale
                     )
 
+                # atom selector
+                if self.atom_selector is not None:
+                    y["atom_selector"] = torch.as_tensor(row[self.atom_selector])
+
                 x = None
                 if self.global_featurizer:
                     # feats
@@ -414,6 +422,7 @@ def __init__(
         tensor_target_scale: float = 1.0,
         normalize_tensor_target: bool = False,
         tensor_target_weight: Dict[str, Dict[str, float]] = None,
+        atom_selector: List[bool] = None,
         scalar_target_names: List[str] = None,
         log_scalar_targets: List[bool] = None,
         normalize_scalar_targets: List[bool] = None,
@@ -457,6 +466,7 @@ def __init__(
         self.tensor_target_scale = tensor_target_scale
         self.normalize_tensor_target = normalize_tensor_target
         self.tensor_target_weight = tensor_target_weight
+        self.atom_selector = atom_selector
 
         self.scalar_target_names = scalar_target_names
         self.log_scalar_targets = log_scalar_targets
@@ -563,6 +573,7 @@ def setup(self, stage: Optional[str] = None):
             log_scalar_targets=self.log_scalar_targets,
             normalize_scalar_targets=self.normalize_scalar_targets,
             tensor_target_weight=self.tensor_target_weight,
+            atom_selector=self.atom_selector,
             global_featurizer=gf,
             normalize_global_features=self.normalize_global_features,
             atom_featurizer=af,
@@ -584,6 +595,7 @@ def setup(self, stage: Optional[str] = None):
             log_scalar_targets=self.log_scalar_targets,
             normalize_scalar_targets=self.normalize_scalar_targets,
             tensor_target_weight=self.tensor_target_weight,
+            atom_selector=self.atom_selector,
             global_featurizer=gf,
             normalize_global_features=self.normalize_global_features,
             atom_featurizer=af,
@@ -605,6 +617,7 @@ def setup(self, stage: Optional[str] = None):
             log_scalar_targets=self.log_scalar_targets,
             normalize_scalar_targets=self.normalize_scalar_targets,
             tensor_target_weight=self.tensor_target_weight,
+            atom_selector=self.atom_selector,
             global_featurizer=gf,
             normalize_global_features=self.normalize_global_features,
             atom_featurizer=af,

src/matten/model/model.py

@@ -338,6 +338,11 @@ def shared_step(self, batch, mode: str):
         # ========== compute predictions ==========
         preds = self.decode(graphs)
 
+        # select atoms
+        if "atom_selector" in labels:
+            selector = labels["atom_selector"]
+            preds = {k: v[selector] for k, v in preds.items()}
+
         # ========== compute losses ==========
         target_weight = graphs.get("target_weight", None)
         individual_loss, total_loss = self.compute_loss(
@@ -504,6 +509,8 @@ def preprocess_batch(self, batch: DataPoint) -> Tuple[DataPoint, Dict[str, Tenso
 
         # task labels
         labels = {name: graphs.y[name] for name in self.tasks}
+        if "atom_selector" in graphs.y:
+            labels["atom_selector"] = graphs.y["atom_selector"]
 
         # convert graphs to a dict to use NequIP stuff
         graphs = graphs.tensor_property_to_dict()