Add functionality to read ASE *.traj file in Trajectory class method from_file() #3422
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exenGT
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janosh
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Oct 25, 2023
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…ile tests/files/LiMnO2_test_relax.traj.
Signed-off-by: Jingyang Wang <[email protected]>
pymatgen/core/trajectory.py
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| constant_lattice=constant_lattice, | ||
| **kwargs, | ||
| ) | ||
| if not is_mol: |
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You should do if is_mol (return from_molecules) and then else (return from_structures). Makes more sense to start with a positive logic statement rather than a negative.
janosh
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Nov 8, 2023
tests/core/test_trajectory.py
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| @@ -471,3 +471,7 @@ def test_xdatcar_write(self): | |||
| written_traj = Trajectory.from_file("traj_test_XDATCAR") | |||
| self._check_traj_equality(self.traj, written_traj) | |||
| os.remove("traj_test_XDATCAR") | |||
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| def test_read_file(self): | |||
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best match the method name in the test name: i.e. test_from_file. Also, maybe check the traj length and composition of the 1st frame for extra safety.
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Signed-off-by: Janosh Riebesell <[email protected]>
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…from_file() (materialsproject#3422) * Add functionality to read ASE *.traj files in Trajectory.from_file(). * fix Trajectory.from_file turning abs path into file name --------- Signed-off-by: Jingyang Wang <[email protected]> Signed-off-by: Janosh Riebesell <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>
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Summary:
Add functionality to read ASE *.traj file in Trajectory class method from_file(), located in core/trajectory.py.
Purpose:
As ASE *.traj file is a standard format for generating and storing relaxation / MD trajectories, it would be nice to have a method which can read a Pymatgen Trajectory instance from an ASE *.traj file.