improve ASE traj (#633)

add functions to convert from others formats to ASE traj format

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Enhanced system and labeled system handling with new parameters and
functionalities.
  - Improved stress calculations by modifying method parameters.

- **Bug Fixes**
- Corrected return types for several methods to ensure consistency and
reliability.

- **Tests**
- Added new test cases to validate system setups and trajectory file
operations.

- **Chores**
- Updated Python version matrix in workflow to include only version
3.11.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <[email protected]>
Signed-off-by: C. Thang Nguyen <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Jinzhe Zeng <[email protected]>

dpdata/plugins/ase.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING
+import os
+from typing import TYPE_CHECKING, Generator
 
 import numpy as np
 
@@ -94,7 +95,7 @@ def from_labeled_system(self, atoms: ase.Atoms, **kwargs) -> dict:
             "forces": np.array([forces]),
         }
         try:
-            stress = atoms.get_stress(False)
+            stress = atoms.get_stress(voigt=False)
         except PropertyNotImplementedError:
             pass
         else:
@@ -110,7 +111,7 @@ def from_multi_systems(
         step: int | None = None,
         ase_fmt: str | None = None,
         **kwargs,
-    ) -> ase.Atoms:
+    ) -> Generator[ase.Atoms, None, None]:
         """Convert a ASE supported file to ASE Atoms.
 
         It will finally be converted to MultiSystems.
@@ -140,7 +141,7 @@ def from_multi_systems(
         frames = ase.io.read(file_name, format=ase_fmt, index=slice(begin, end, step))
         yield from frames
 
-    def to_system(self, data, **kwargs):
+    def to_system(self, data, **kwargs) -> list[ase.Atoms]:
         """Convert System to ASE Atom obj."""
         from ase import Atoms
 
@@ -158,7 +159,7 @@ def to_system(self, data, **kwargs):
 
         return structures
 
-    def to_labeled_system(self, data, *args, **kwargs):
+    def to_labeled_system(self, data, *args, **kwargs) -> list[ase.Atoms]:
         """Convert System to ASE Atoms object."""
         from ase import Atoms
         from ase.calculators.singlepoint import SinglePointCalculator
@@ -300,6 +301,46 @@ def from_labeled_system(
 
         return dict_frames
 
+    def to_system(self, data, file_name: str = "confs.traj", **kwargs) -> None:
+        """Convert System to ASE Atoms object.
+
+        Parameters
+        ----------
+        file_name : str
+            path to file
+        """
+        from ase.io import Trajectory
+
+        if os.path.isfile(file_name):
+            os.remove(file_name)
+
+        list_atoms = ASEStructureFormat().to_system(data, **kwargs)
+        traj = Trajectory(file_name, "a")
+        _ = [traj.write(atom) for atom in list_atoms]
+        traj.close()
+        return
+
+    def to_labeled_system(
+        self, data, file_name: str = "labeled_confs.traj", *args, **kwargs
+    ) -> None:
+        """Convert System to ASE Atoms object.
+
+        Parameters
+        ----------
+        file_name : str
+            path to file
+        """
+        from ase.io import Trajectory
+
+        if os.path.isfile(file_name):
+            os.remove(file_name)
+
+        list_atoms = ASEStructureFormat().to_labeled_system(data, *args, **kwargs)
+        traj = Trajectory(file_name, "a")
+        _ = [traj.write(atom) for atom in list_atoms]
+        traj.close()
+        return
+
 
 @Driver.register("ase")
 class ASEDriver(Driver):

tests/test_ase_traj.py

@@ -67,5 +67,29 @@ def setUp(self):
         self.v_places = 4
 
 
+@unittest.skipIf(skip_ase, "skip ase related test. install ase to fix")
+class TestASEtraj4(unittest.TestCase, CompSys, IsPBC):
+    def setUp(self):
+        self.system_1 = dpdata.System("ase_traj/MoS2", fmt="deepmd")
+        self.system_1.to(file_name="ase_traj/tmp.traj", fmt="ase/traj")
+        self.system_2 = dpdata.System("ase_traj/tmp.traj", fmt="ase/traj")
+        self.places = 6
+        self.e_places = 6
+        self.f_places = 6
+        self.v_places = 4
+
+
+@unittest.skipIf(skip_ase, "skip ase related test. install ase to fix")
+class TestASEtraj4Labeled(unittest.TestCase, CompLabeledSys, IsPBC):
+    def setUp(self):
+        self.system_1 = dpdata.LabeledSystem("ase_traj/MoS2", fmt="deepmd")
+        self.system_1.to(file_name="ase_traj/tmp1.traj", fmt="ase/traj")
+        self.system_2 = dpdata.LabeledSystem("ase_traj/tmp1.traj", fmt="ase/traj")
+        self.places = 6
+        self.e_places = 6
+        self.f_places = 6
+        self.v_places = 4
+
+
 if __name__ == "__main__":
     unittest.main()