Update phonons.py

leslie-zheng · Aug 29, 2024 · 17f56c9 · 17f56c9
1 parent a592e44
commit 17f56c9
Showing 1 changed file with 71 additions and 71 deletions.
diff --git 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)