add file output xyz file including final atoms object to ase and forcefield jobs (#1206)

* add file output to ase and forcefield jobs

* remove useless file

Author: JaGeo

src/atomate2/ase/utils.py

@@ -16,6 +16,7 @@
 from ase.constraints import FixSymmetry
 from ase.filters import FrechetCellFilter
 from ase.io import Trajectory as AseTrajectory
+from ase.io import write
 from ase.optimize import BFGS, FIRE, LBFGS, BFGSLineSearch, LBFGSLineSearch, MDMin
 from ase.optimize.sciopt import SciPyFminBFGS, SciPyFminCG
 from monty.serialization import dumpfn
@@ -328,6 +329,7 @@ def relax(
         fmax: float = 0.1,
         steps: int = 500,
         traj_file: str = None,
+        final_atoms_object_file: str = "final_atoms_object.xyz",
         interval: int = 1,
         verbose: bool = False,
         cell_filter: Filter = FrechetCellFilter,
@@ -346,6 +348,8 @@ def relax(
             Max number of steps for relaxation.
         traj_file : str
             The trajectory file for saving.
+        final_atoms_object_file: str
+            The final atoms object file for saving.
         interval : int
             The step interval for saving the trajectories.
         verbose : bool
@@ -389,6 +393,9 @@ def relax(
             np.linalg.norm(traj.frame_properties[-1]["forces"][idx]) < abs(fmax)
             for idx in range(len(struct))
         )
+        if final_atoms_object_file is not None:
+            write(final_atoms_object_file, atoms, format="extxyz", append=True)
+
         return AseResult(
             final_mol_or_struct=struct,
             trajectory=traj,

tests/forcefields/test_jobs.py

@@ -193,7 +193,7 @@ def test_m3gnet_relax_maker(si_structure):
 
 
 @mace_paths
-def test_mace_static_maker(si_structure: Structure, test_dir: Path, model):
+def test_mace_static_maker(si_structure: Structure, clean_dir, model):
     # generate job
     # NOTE the test model is not trained on Si, so the energy is not accurate
     job = ForceFieldStaticMaker(
@@ -212,6 +212,8 @@ def test_mace_static_maker(si_structure: Structure, test_dir: Path, model):
     assert output1.output.n_steps == 1
     assert output1.forcefield_version == get_imported_version("mace-torch")
 
+    assert Path("final_atoms_object.xyz").exists()
+
     with pytest.warns(FutureWarning):
         MACEStaticMaker()