From 17f56c97fd18213811feed9c91c99106349cb346 Mon Sep 17 00:00:00 2001 From: Jiongzhi ZHENG Date: Thu, 29 Aug 2024 13:30:24 -0400 Subject: [PATCH] Update phonons.py --- src/atomate2/common/flows/phonons.py | 142 +++++++++++++-------------- 1 file changed, 71 insertions(+), 71 deletions(-) diff --git a/src/atomate2/common/flows/phonons.py b/src/atomate2/common/flows/phonons.py index 71654143bd..1b4b02e8c6 100644 --- a/src/atomate2/common/flows/phonons.py +++ b/src/atomate2/common/flows/phonons.py @@ -365,79 +365,79 @@ def make( jobs.append(phonon_collect) - # add the new structure and displacement data to the flow - - #new_structure=add_structure(structure, phonon_maker=self.phonon_displacement_maker) - new_displacement = add_new_structure(structure=structure, - supercell_matrix=supercell_matrix, - displacement=self.displacement, - sym_reduce=self.sym_reduce, - symprec=self.symprec, - use_symmetrized_structure=self.use_symmetrized_structure, - kpath_scheme=self.kpath_scheme, - code=self.code,) - jobs.append(new_displacement) - - #jobs.append(new_structure) - new_displacement_calcs = run_phonon_displacements( - displacements=new_displacement.output, - structure=structure, - supercell_matrix=supercell_matrix, - phonon_maker=self.phonon_displacement_maker, - socket=self.socket, - prev_dir_argname=self.prev_calc_dir_argname, - prev_dir=prev_dir, - ) - jobs.append(new_displacement_calcs) - - updated_displacements=add_displacement_data(displacement_calcs.output, new_displacement_calcs.output) - - jobs.append(updated_displacements) - - # now use your updated displacements with the additional displacement - phonon_collect2=generate_frequencies_eigenvectors(supercell_matrix=supercell_matrix, - displacement=self.displacement, - sym_reduce=self.sym_reduce, - symprec=self.symprec, - use_symmetrized_structure=self.use_symmetrized_structure, - kpath_scheme=self.kpath_scheme, - code=self.code, - mp_id=self.mp_id, - structure=structure, - displacement_data=updated_displacements.output, - epsilon_static=epsilon_static, - born=born, - total_dft_energy=total_dft_energy, - static_run_job_dir=static_run_job_dir, - static_run_uuid=static_run_uuid, - born_run_job_dir=born_run_job_dir, - born_run_uuid=born_run_uuid, - optimization_run_job_dir=optimization_run_job_dir, - optimization_run_uuid=optimization_run_uuid, - create_thermal_displacements=self.create_thermal_displacements, - store_force_constants=self.store_force_constants, - **self.generate_frequencies_eigenvectors_kwargs) + # # add the new structure and displacement data to the flow + + # #new_structure=add_structure(structure, phonon_maker=self.phonon_displacement_maker) + # new_displacement = add_new_structure(structure=structure, + # supercell_matrix=supercell_matrix, + # displacement=self.displacement, + # sym_reduce=self.sym_reduce, + # symprec=self.symprec, + # use_symmetrized_structure=self.use_symmetrized_structure, + # kpath_scheme=self.kpath_scheme, + # code=self.code,) + # jobs.append(new_displacement) + + # #jobs.append(new_structure) + # new_displacement_calcs = run_phonon_displacements( + # displacements=new_displacement.output, + # structure=structure, + # supercell_matrix=supercell_matrix, + # phonon_maker=self.phonon_displacement_maker, + # socket=self.socket, + # prev_dir_argname=self.prev_calc_dir_argname, + # prev_dir=prev_dir, + # ) + # jobs.append(new_displacement_calcs) + + # updated_displacements=add_displacement_data(displacement_calcs.output, new_displacement_calcs.output) + + # jobs.append(updated_displacements) + + # # now use your updated displacements with the additional displacement + # phonon_collect2=generate_frequencies_eigenvectors(supercell_matrix=supercell_matrix, + # displacement=self.displacement, + # sym_reduce=self.sym_reduce, + # symprec=self.symprec, + # use_symmetrized_structure=self.use_symmetrized_structure, + # kpath_scheme=self.kpath_scheme, + # code=self.code, + # mp_id=self.mp_id, + # structure=structure, + # displacement_data=updated_displacements.output, + # epsilon_static=epsilon_static, + # born=born, + # total_dft_energy=total_dft_energy, + # static_run_job_dir=static_run_job_dir, + # static_run_uuid=static_run_uuid, + # born_run_job_dir=born_run_job_dir, + # born_run_uuid=born_run_uuid, + # optimization_run_job_dir=optimization_run_job_dir, + # optimization_run_uuid=optimization_run_uuid, + # create_thermal_displacements=self.create_thermal_displacements, + # store_force_constants=self.store_force_constants, + # **self.generate_frequencies_eigenvectors_kwargs) - jobs.append(phonon_collect2) - - check_convergenced = check_convergence(phonon_collect.phonon_bandstructure, - phonon_collect2.phonon_bandstructure, - supercell_matrix=supercell_matrix, - displacement=self.displacement, - sym_reduce=self.sym_reduce, - symprec=self.symprec, - use_symmetrized_structure=self.use_symmetrized_structure, - kpath_scheme=self.kpath_scheme, - code=self.code, - mp_id=self.mp_id, - structure=structure, - displacement_data=updated_displacements.output, - epsilon_static=epsilon_static, - born=born, - total_dft_energy=total_dft_energy, - **self.generate_frequencies_eigenvectors_kwargs) + # jobs.append(phonon_collect2) + + # check_convergenced = check_convergence(phonon_collect.phonon_bandstructure, + # phonon_collect2.phonon_bandstructure, + # supercell_matrix=supercell_matrix, + # displacement=self.displacement, + # sym_reduce=self.sym_reduce, + # symprec=self.symprec, + # use_symmetrized_structure=self.use_symmetrized_structure, + # kpath_scheme=self.kpath_scheme, + # code=self.code, + # mp_id=self.mp_id, + # structure=structure, + # displacement_data=updated_displacements.output, + # epsilon_static=epsilon_static, + # born=born, + # total_dft_energy=total_dft_energy, + # **self.generate_frequencies_eigenvectors_kwargs) - jobs.append(check_convergenced) + # jobs.append(check_convergenced) # create a flow including all jobs for a phonon computation return Flow(jobs, phonon_collect.output)