Merge branch 'main' of https://github.com/ulissigroup/finetuna into main

Author: jmusiel

README.md

@@ -28,6 +28,6 @@ You are all set! Now in your VASP input folder, run the calculation by: `finetun
 
 ### Usage
 
-If you have an ASE atoms object, see example [1](https://github.com/ulissigroup/finetuna/blob/main/examples/online_al_example.py) and [2](https://github.com/ulissigroup/finetuna/blob/main/examples/online_al_beef_example.py).
+If you have an ASE atoms object, see example [1](https://github.com/ulissigroup/finetuna/blob/main/examples/online_al/online_al_example.py) and [2](https://github.com/ulissigroup/finetuna/blob/main/examples/beef/online_al_beef_example.py).
 
 If you have VASP input files (INCAR, KPOINTS, POTCAR, and POSCAR), see example [3](https://github.com/ulissigroup/finetuna/tree/main/finetuna/vasp_wrapper).

examples/N2H_Ag111_dissociation/N2H_Ag111.py

@@ -7,7 +7,6 @@
 from finetuna.utils import calculate_surface_k_points
 
 if __name__ == "__main__":
-
     traj = Trajectory("N2H_Ag111.traj")  # change this path to your trajectory file
 
     ml_potential = FinetunerCalc(

examples/beef/online_al_beef_example.py

@@ -71,7 +71,6 @@
     vasp_inputs["ibrion"] = -1
 
     with VaspInteractive(**vasp_inputs) as parent_calc:
-
         learner = OnlineLearner(
             learner_params={
                 "query_every_n_steps": 100,

examples/online_al/online_al_example.py

@@ -7,7 +7,6 @@
 from finetuna.utils import calculate_surface_k_points
 
 if __name__ == "__main__":
-
     traj = Trajectory("random1447590.traj")  # change this path to your trajectory file
 
     ml_potential = FinetunerCalc(

examples/quantum_espresso/qe_gpu_online_al_example.py

@@ -15,7 +15,6 @@
 import os
 
 if __name__ == "__main__":
-
     traj = Trajectory("ch3_cu_final.traj")  # change this path to your trajectory file
 
     ml_potential = FinetunerCalc(

finetuna/atomistic_methods.py

@@ -23,7 +23,8 @@ def __init__(self, starting_images, intermediate_samples=3):
         ----------
         starting_images: list. Initial and final images to be used for the NEB.
 
-        intermediate_samples: int. Number of intermediate samples to be used in constructing the NEB"""
+        intermediate_samples: int. Number of intermediate samples to be used in constructing the NEB
+        """
 
         self.starting_images = copy.deepcopy(starting_images)
         self.intermediate_samples = intermediate_samples

finetuna/finetuner_utils/utils.py

@@ -26,6 +26,7 @@ def close_db(self):
 from ocpmodels.common.registry import registry
 from ocpmodels.models.gemnet.gemnet import GemNetT
 
+
 # imported in __init__.py
 @registry.register_model("gemnet_t_uncertainty")
 class GemNetTUncertainty(GemNetT):

finetuna/ml_potentials/finetuner_ensemble_calc.py

@@ -48,7 +48,6 @@ def __init__(
         checkpoint_paths: "list[str]",
         mlp_params: dict = {},
     ) -> None:
-
         # self.model_classes = model_classes
         # self.model_paths = model_paths
         self.checkpoint_paths = checkpoint_paths

finetuna/mongo.py

@@ -200,7 +200,6 @@ def _make_results_dict(atoms):
     # Results. This may duplicate information in the calculator,
     # but we have no control on what the calculator does.
     if calculator:
-
         if not calculator.calculation_required(atoms, ["energy"]):
             results_dict["energy"] = atoms.get_potential_energy(apply_constraint=False)
 

finetuna/ocp_models/gemnet_t/int_descriptor_gemnet_t.py

@@ -21,7 +21,6 @@ def __init__(
         checkpoint_path,
         cpu=True,
     ):
-
         if cpu:
             map_location = torch.device("cpu")
         else:

finetuna/tests/cases/online_ft_gemnet_oc_CuNP_test.py

@@ -31,6 +31,6 @@ def get_al_config(cls) -> dict:
             },
         }
         al_config["ocp"] = {
-            "checkpoint_path": "/home/jovyan/shared-scratch/ocp_checkpoints/for_finetuna/public_checkpoints/scaling_attached/gemnet_oc_base_oc20_oc22_attscale.pt",
+            "checkpoint_path": "/home/jovyan/shared-scratch/ocp_checkpoints/for_finetuna/new_public_checkpoints/gnoc_finetune_all_s2ef.pt",
         }
         return al_config