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PhononMaker add options to calculate_pdos and save force constants to file #1008

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merged 13 commits into from
Nov 14, 2024
Merged

PhononMaker add options to calculate_pdos and save force constants to file #1008

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443261a
add calculate_pdos and make force constance can be save
Oct 6, 2024
8c9d72c
add calculate_pdos and make force constance can be save
Oct 6, 2024
fed3be7
Update phonons.py
chouyoudou Oct 7, 2024
101e276
Apply pre-commit hooks for code formatting and linting
Oct 7, 2024
0467419
Merge pull request #1 from materialsproject/main
chouyoudou Oct 7, 2024
17139d9
Fix issues found by pre-commit hooks
Oct 7, 2024
5ea3757
Merge branch 'main' into main
chouyoudou Oct 18, 2024
c62b1ac
add force_constants2file parameter
Oct 19, 2024
ebc7938
- Renamed "force_constants2file" to "force_constants_filename"
Oct 21, 2024
061139d
Merge branch 'main' into main
chouyoudou Oct 21, 2024
cdb55f4
fix doc string placement
janosh Nov 14, 2024
fb4fa29
refactor from_forces_born handling create_force_constants_file
janosh Nov 14, 2024
f041efb
fix typo
janosh Nov 14, 2024
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4 changes: 4 additions & 0 deletions src/atomate2/common/flows/phonons.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,8 @@ class BasePhononMaker(Maker, ABC):
determines the dft or force field code.
store_force_constants: bool
if True, force constants will be stored
calculate_pdos: bool
if True, the projected phonon density of states will be calculated
socket: bool
If True, use the socket for the calculation
"""
Expand Down Expand Up @@ -150,6 +152,7 @@ class BasePhononMaker(Maker, ABC):
kpath_scheme: str = "seekpath"
code: str = None
store_force_constants: bool = True
calculate_pdos: bool = False
socket: bool = False

def make(
Expand Down Expand Up @@ -355,6 +358,7 @@ def make(
optimization_run_uuid=optimization_run_uuid,
create_thermal_displacements=self.create_thermal_displacements,
store_force_constants=self.store_force_constants,
calculate_pdos=self.calculate_pdos,
**self.generate_frequencies_eigenvectors_kwargs,
)

Expand Down
12 changes: 11 additions & 1 deletion src/atomate2/common/schemas/phonons.py
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Expand Up @@ -350,7 +350,7 @@ def from_forces_born(
# kwargs["filename_phonopy_yaml"] = "phonopy.yaml"

# with phonopy.load("phonopy.yaml") the phonopy API can be used
phonon.save(filename_phonopy_yaml)
phonon.save(filename_phonopy_yaml, settings={'force_constants': kwargs.get("store_force_constants", True)})

# get phonon band structure
kpath_dict, kpath_concrete = PhononBSDOSDoc.get_kpath(
Expand Down Expand Up @@ -406,6 +406,16 @@ def from_forces_born(
kppa=kpoint_density_dos,
force_gamma=True,
)
# projected dos
if kwargs.get("calculate_pdos", False):
phonon.run_mesh(kpoint.kpts[0], with_eigenvectors=True, is_mesh_symmetry=False)
phonon_dos_sigma = kwargs.get("phonon_dos_sigma", None)
dos_use_tetrahedron_method = kwargs.get("dos_use_tetrahedron_method", True)
phonon.run_projected_dos(
sigma=phonon_dos_sigma, use_tetrahedron_method=dos_use_tetrahedron_method
)
phonon.write_projected_dos()

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Does it make sense to also add an automatic plot here? Likely a bit more work. I am fine with just adding this for now.

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This directly relates to the next question: do you want the option to save it in the schema? If so, you would need to develop a parser.

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Does it make sense to also add an automatic plot here? Likely a bit more work. I am fine with just adding this for now.

I think it could be useful to provide summed PDOS, for example by element type or symmetry-equivalent atoms. However, user needs in this area are often quite diverse, making it challenging to implement something that meets all needs as straightforwardly as the TDOS plot.

This directly relates to the next question: do you want the option to save it in the schema? If so, you would need to develop a parser.

The current approach saves the PDOS in an external file, similar to the TDOS format. I believe a simple adjustment to the default filename to match the style of atomate2 (e.g., phonon_pdos.yaml instead of the default projected_dos.dat in phonopy) would suffice.

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I am fine with this for now. But is it really a yaml? If not, rather keep the dat

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Actually, it is not a yaml; it was just renamed with a .yaml extension in atomate2 for TDOS.

phonon.run_mesh(kpoint.kpts[0])
phonon_dos_sigma = kwargs.get("phonon_dos_sigma", None)
dos_use_tetrahedron_method = kwargs.get("dos_use_tetrahedron_method", True)
Expand Down
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