New factories for phonons workflow in atomate2

[emarazzi]

The PR introduces 2 new factories to handle inputs generation for:

• wfq_nscf_from_gsinput
• phononpert_from_gsinput for a phonon calculation on a single perturbation, along with the corresponding method in abio.inputs.

[Copilot]

Pull request overview

This PR introduces two new factory functions for generating Abinit inputs for phonon-related calculations in atomate2 workflows. The changes add capabilities to create inputs for NSCF calculations on K+Q grids and for single phonon perturbation calculations, along with the underlying input generation method.

Changes:

• Added make_phpert_input method in AbinitInput class to generate inputs for phonon perturbation calculations
• Added wfq_nscf_from_gsinput factory function to create NSCF inputs on K+Q grids
• Added phononpert_from_gsinput factory function to create single phonon perturbation inputs
• Modified scf_for_phonons to make nbdbuf a configurable parameter and improve smearing handling logic

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 9 comments.

File	Description
abipy/abio/inputs.py	Adds make_phpert_input method to generate Abinit input for a single phonon perturbation using DFPT
abipy/abio/factories.py	Adds wfq_nscf_from_gsinput factory for K+Q grid NSCF calculations and phononpert_from_gsinput factory for single phonon perturbation inputs; updates scf_for_phonons to allow configurable nbdbuf and improved smearing condition

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[Copilot]

The docstring is missing documentation for the phonon_tol parameter. Similar functions like ddepert_from_gsinput (line 1448) properly document all parameters including the tolerance parameter. The docstring should include documentation for phonon_tol explaining it's a dictionary with a single key defining the type of tolerance and its value, with a default of {"tolvrs": 1.0e-10}.

Suggested change

	Returns an |AbinitInput| to perform a BEC calculations for a specific perturbation based on a ground state |AbinitInput|.
	Args:
	gs_input: an |AbinitInput| representing a ground state calculation, likely the SCF performed to get the WFK.
	phonon_pert: dict with the Abinit variables defining the perturbation
	Example: {'idir': 1, 'ipert': 4, 'qpt': [0.0, 0.0, 0.0]},
	Returns an |AbinitInput| to perform a phonon (DFPT) calculation for a specific perturbation based on a ground
	state |AbinitInput|.
	Args:
	gs_input: an |AbinitInput| representing a ground state calculation, likely the SCF performed to get the WFK.
	phonon_pert: dict with the Abinit variables defining the perturbation
	Example: {'idir': 1, 'ipert': 4, 'qpt': [0.0, 0.0, 0.0]},
	phonon_tol: dict specifying the DFPT convergence tolerance. It should contain a single key defining the
	type of tolerance (e.g., "tolvrs") and its numerical value. If None, a default of {"tolvrs": 1.0e-10}
	is used.

[Copilot]

The prepgkk parameter is defined but never used in the function body. Unlike the similar make_ph_inputs_qpoint method which passes prepgkk to abiget_irred_phperts, this method doesn't use it anywhere. Either this parameter should be removed from the signature, or it should be passed to the appropriate location if it's needed.

[Copilot]

The parameter spacing around = doesn't match the codebase convention. Throughout factories.py, parameters use parameter=None (no spaces) rather than parameter = None (with spaces). This applies to nband in this function signature.

[gmatteo]

Thanks