Prediction for atomic tensor

notebooks/predict_atomic.py

@@ -0,0 +1,29 @@
+"""
+An example script make predictions of any tensor.
+"""
+
+from pymatgen.core import Structure
+
+from matten.predict import predict
+
+
+def get_structure():
+    a = 5.46
+    lattice = [[0, a / 2, a / 2], [a / 2, 0, a / 2], [a / 2, a / 2, 0]]
+    basis = [[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]]
+    Si = Structure(lattice, ["Si", "Si"], basis)
+
+    return Si
+
+
+if __name__ == "__main__":
+    structure = get_structure()
+
+    # predict for one structure
+    tensors = predict(
+        structure,
+        model_identifier="/Users/mjwen.admin/Downloads/trained",
+        checkpoint="epoch=9-step=100.ckpt",
+        is_atomic_tensor=True,
+    )
+    print("value:", tensors)

src/matten/predict.py

@@ -13,6 +13,7 @@
 
 from matten.dataset.structure_scalar_tensor import TensorDatasetPrediction
 from matten.log import set_logger
+from matten.model_factory.tfn_atomic_tensor import AtomicTensorModel
 from matten.model_factory.tfn_scalar_tensor import ScalarTensorModel
 from matten.utils import CartesianTensorWrapper, yaml_load
 
@@ -31,9 +32,11 @@ def get_pretrained_model_dir(identifier: str) -> Path:
         return Path(__file__).parent.parent.parent / "pretrained" / identifier
 
 
-def get_pretrained_model(identifier: str, checkpoint: str = "model_final.ckpt"):
+def get_pretrained_model(
+    identifier: str, checkpoint: str = "model_final.ckpt", model_class=ScalarTensorModel
+):
     directory = get_pretrained_model_dir(identifier)
-    model = ScalarTensorModel.load_from_checkpoint(
+    model = model_class.load_from_checkpoint(
         checkpoint_path=directory.joinpath(checkpoint).as_posix(),
         map_location="cpu",
     )
@@ -62,6 +65,7 @@ def get_data_loader(
         "valset_filename",
         "testset_filename",
         "compute_dataset_statistics",
+        "atom_selector",
     ]:
         try:
             config.pop(k)
@@ -151,6 +155,7 @@ def predict(
     batch_size: int = 200,
     logger_level: str = "ERROR",
     is_elasticity_tensor: bool = True,
+    is_atomic_tensor: bool = False,
 ) -> Union[ElasticTensor, List[ElasticTensor]]:
     f"""
     Predict the property of a structure or a list of structures.
@@ -174,6 +179,8 @@ def predict(
         is_elasticity_tensor: whether the target property is an elasticity tensor. If
             `True`, the returned value will be a pymargen `ElasticTensor` object.
             Otherwise, it will be numpy array.
+        is_atomic_tensor: whether the target property is an atomic tensor. If `True`,
+            we predict a tensor value for each atom in the structure.
 
     Returns:
         Predicted tensor(s). `None` if the model cannot make prediction for a structure.
@@ -186,7 +193,16 @@ def predict(
     else:
         single_struct = False
 
-    model = get_pretrained_model(identifier=model_identifier, checkpoint=checkpoint)
+    if is_atomic_tensor:
+        model_class = AtomicTensorModel
+        is_elasticity_tensor = False
+    else:
+        model_class = ScalarTensorModel
+    model = get_pretrained_model(
+        identifier=model_identifier,
+        checkpoint=checkpoint,
+        model_class=model_class,
+    )
     check_species(model, structure)
     loader = get_data_loader(structure, model_identifier, batch_size=batch_size)
 
@@ -223,10 +239,10 @@ def predict(
     else:
         pred_tensors = predictions
 
-    if single_struct:
+    if single_struct and not is_atomic_tensor:
         return pred_tensors[0]
-    else:
-        return pred_tensors
+
+    return pred_tensors
 
 
 if __name__ == "__main__":