Add pre optimization steps to phonon workflow

src/autoplex/auto/phonons/flows.py

@@ -73,6 +73,9 @@ class CompleteDFTvsMLBenchmarkWorkflow(Maker):
         The total number of randomly displaced structures to be generated.
     displacement_maker: BaseVaspMaker
         Maker used for a static calculation for a supercell.
+    pre_relax_maker: BaseVaspMaker
+        Maker used for the bulk relax unit cell calculation
+        before the phonon_relax_maker or rattled_relax_maker.
     phonon_bulk_relax_maker: BaseVaspMaker
         Maker used for the bulk relax unit cell calculation.
     rattled_bulk_relax_maker: BaseVaspMaker
@@ -181,7 +184,7 @@ class CompleteDFTvsMLBenchmarkWorkflow(Maker):
     add_dft_rattled_struct: bool = True
     add_rss_struct: bool = False
     displacement_maker: BaseVaspMaker = None
-    phonon_bulk_relax_maker: BaseVaspMaker | None = field(
+    pre_relax_maker: BaseVaspMaker | None = field(
         default_factory=lambda: DoubleRelaxMaker.from_relax_maker(
             TightRelaxMaker(
                 name="dft tight relax",
@@ -210,32 +213,9 @@ class CompleteDFTvsMLBenchmarkWorkflow(Maker):
             )
         )
     )
+    phonon_bulk_relax_maker: BaseVaspMaker | None = None
     phonon_static_energy_maker: BaseVaspMaker | None = None
-
-    rattled_bulk_relax_maker: BaseVaspMaker | None = field(
-        default_factory=lambda: TightRelaxMaker(
-            run_vasp_kwargs={"handlers": {}},
-            input_set_generator=TightRelaxSetGenerator(
-                user_incar_settings={
-                    "ALGO": "Normal",
-                    "ISPIN": 1,
-                    "LAECHG": False,
-                    "ISYM": 0,  # to be changed
-                    "ISMEAR": 0,
-                    "SIGMA": 0.05,  # to be changed back
-                    "LCHARG": False,  # Do not write the CHGCAR file
-                    "LWAVE": False,  # Do not write the WAVECAR file
-                    "LVTOT": False,  # Do not write LOCPOT file
-                    "LORBIT": None,  # No output of projected or partial DOS in EIGENVAL, PROCAR and DOSCAR
-                    "LOPTICS": False,  # No PCDAT file
-                    "NSW": 200,
-                    "NELM": 500,
-                    # to be removed
-                    "NPAR": 4,
-                }
-            ),
-        )
-    )
+    rattled_bulk_relax_maker: BaseVaspMaker | None = None
     isolated_atom_maker: IsoAtomStaticMaker | None = None
     n_structures: int = 10
     displacements: list[float] = field(default_factory=lambda: [0.01])
@@ -342,16 +322,22 @@ def make(
             ),
             default_hyperparameters["GAP"]["soap"],
         )
-        # add an optional pre-optimization step here
 
         for structure, mp_id in zip(structure_list, mp_ids):
+            if self.pre_relax_maker is not None:
+                pre_relax_job = self.pre_relax_maker.make(structure)
+                flows.append(pre_relax_job)
+                new_structure = pre_relax_job.output.structure
+                pre_relax_job.name = "dft tight relax"
+            else:
+                new_structure = structure
             self.supercell_settings.setdefault(mp_id, {})
             logging.warning(
                 "Currently, "
                 "the same supercell settings for single-atom displaced and rattled supercells are used."
             )
             supercell_matrix_job = reduce_supercell_size_job(
-                structure=structure,
+                structure=new_structure,
                 min_length=self.supercell_settings.get("min_length", 15),
                 max_length=self.supercell_settings.get("max_length", 20),
                 fallback_min_length=self.supercell_settings.get(
@@ -371,7 +357,7 @@ def make(
 
             if self.add_dft_rattled_struct:
                 add_dft_ratt = self.add_dft_rattled(
-                    structure=structure,
+                    structure=new_structure,
                     mp_id=mp_id,
                     displacement_maker=self.displacement_maker,
                     rattled_bulk_relax_maker=self.rattled_bulk_relax_maker,
@@ -399,7 +385,7 @@ def make(
                 fit_input.update({mp_id: add_dft_ratt.output})
             if self.add_dft_phonon_struct:
                 add_dft_phon = self.add_dft_phonons(
-                    structure=structure,
+                    structure=new_structure,
                     mp_id=mp_id,
                     displacements=self.displacements,
                     symprec=self.symprec,
@@ -465,6 +451,13 @@ def make(
                 for ibenchmark_structure, benchmark_structure in enumerate(
                     benchmark_structures
                 ):
+                    # To make sure that the structure is optimized
+                    if (
+                        self.pre_relax_maker is not None
+                        and self.phonon_bulk_relax_maker is None
+                    ):
+                        self.phonon_bulk_relax_maker = self.pre_relax_maker
+
                     # hard coded at the moment as other displacements
                     # are not treated correctly in benchmark part
                     complete_bm = complete_benchmark(