Merge pull request #29 from JaGeo/fix_inconsistent_settings_bulk_static

Fix inconsistent settings bulk relax runs  (ISMEAR=0)

Author: JaGeo

autoplex/auto/flows.py

@@ -11,7 +11,6 @@
     from emmet.core.math import Matrix3D
     from pymatgen.core.structure import Structure
 
-from atomate2.vasp.flows.phonons import PhononMaker as DFTPhononMaker
 from jobflow import Flow, Maker
 
 from autoplex.auto.jobs import (
@@ -22,7 +21,7 @@
 )
 from autoplex.benchmark.flows import PhononBenchmarkMaker
 from autoplex.benchmark.jobs import write_benchmark_metrics
-from autoplex.data.flows import TightDFTStaticMaker
+from autoplex.data.flows import DFTPhononMaker, TightDFTStaticMaker
 from autoplex.fitting.flows import MLIPFitMaker
 
 __all__ = [

autoplex/data/flows.py

@@ -14,8 +14,10 @@
     PhononDisplacementMaker,
     run_phonon_displacements,
 )
-from atomate2.vasp.jobs.core import StaticMaker
-from atomate2.vasp.sets.core import StaticSetGenerator
+from atomate2.vasp.flows.core import DoubleRelaxMaker
+from atomate2.vasp.flows.phonons import PhononMaker
+from atomate2.vasp.jobs.core import StaticMaker, TightRelaxMaker
+from atomate2.vasp.sets.core import StaticSetGenerator, TightRelaxSetGenerator
 from jobflow import Flow, Maker
 from phonopy.structure.cells import get_supercell
 from pymatgen.core import Molecule, Site
@@ -24,6 +26,7 @@
 from autoplex.data.jobs import generate_randomized_structures
 
 __all__ = [
+    "DFTPhononMaker",
     "IsoAtomMaker",
     "IsoAtomStaticMaker",
     "RandomStructuresDataGenerator",
@@ -83,6 +86,117 @@ class TightDFTStaticMaker(PhononDisplacementMaker):
     )
 
 
+@dataclass
+class DFTPhononMaker(PhononMaker):
+    """
+    Adapted PhononMaker to calculate harmonic phonons with VASP and Phonopy.
+
+    The input set used is same as PhononMaker from atomate2.
+    Only difference is Spin polarization is switched off and Gaussian smearing is used
+
+    Parameters
+    ----------
+    name : str = "phonon"
+        Name of the flows produced by this maker.
+    sym_reduce : bool = True
+        Whether to reduce the number of deformations using symmetry.
+    symprec : float = 1e-4
+        Symmetry precision to use in the
+        reduction of symmetry to find the primitive/conventional cell
+        (use_primitive_standard_structure, use_conventional_standard_structure)
+        and to handle all symmetry-related tasks in phonopy
+    displacement: float = 0.01
+        displacement distance for phonons
+    min_length: float = 20.0
+        min length of the supercell that will be built
+    prefer_90_degrees: bool = True
+        if set to True, supercell algorithm will first try to find a supercell
+        with 3 90 degree angles
+    get_supercell_size_kwargs: dict = {}
+        kwargs that will be passed to get_supercell_size to determine supercell size
+    use_symmetrized_structure: str or None = None
+        allowed strings: "primitive", "conventional", None
+
+        - "primitive" will enforce to start the phonon computation
+          from the primitive standard structure
+          according to Setyawan, W., & Curtarolo, S. (2010).
+          High-throughput electronic band structure calculations:
+          Challenges and tools. Computational Materials Science,
+          49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010.
+          This makes it possible to use certain k-path definitions
+          with this workflow. Otherwise, we must rely on seekpath
+        - "conventional" will enforce to start the phonon computation
+          from the conventional standard structure
+          according to Setyawan, W., & Curtarolo, S. (2010).
+          High-throughput electronic band structure calculations:
+          Challenges and tools. Computational Materials Science,
+          49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010.
+          We will however use seekpath and primitive structures
+          as determined by from phonopy to compute the phonon band structure
+    bulk_relax_maker : .BaseVaspMaker or None
+        A maker to perform a tight relaxation on the bulk.
+        Set to ``None`` to skip the
+        bulk relaxation
+    static_energy_maker : .BaseVaspMaker or None
+        A maker to perform the computation of the DFT energy on the bulk.
+        Set to ``None`` to skip the
+        static energy computation
+    born_maker: .BaseVaspMaker or None
+        Maker to compute the BORN charges.
+    phonon_displacement_maker : .BaseVaspMaker or None
+        Maker used to compute the forces for a supercell.
+    generate_frequencies_eigenvectors_kwargs : dict
+        Keyword arguments passed to :obj:`generate_frequencies_eigenvectors`.
+    create_thermal_displacements: bool
+        Arg that determines if thermal_displacement_matrices are computed
+    kpath_scheme: str = "seekpath"
+        scheme to generate kpoints. Please be aware that
+        you can only use seekpath with any kind of cell
+        Otherwise, please use the standard primitive structure
+        Available schemes are:
+        "seekpath", "hinuma", "setyawan_curtarolo", "latimer_munro".
+        "seekpath" and "hinuma" are the same definition but
+        seekpath can be used with any kind of unit cell as
+        it relies on phonopy to handle the relationship
+        to the primitive cell and not pymatgen
+    code: str = "vasp"
+        determines the DFT code. currently only vasp is implemented.
+        This keyword might enable the implementation of other codes
+        in the future
+    store_force_constants: bool
+        if True, force constants will be stored
+    """
+
+    name: str = "phonon"
+    sym_reduce: bool = True
+    symprec: float = 1e-4
+    displacement: float = 0.01
+    min_length: float | None = 20.0
+    prefer_90_degrees: bool = True
+    get_supercell_size_kwargs: dict = field(default_factory=dict)
+    use_symmetrized_structure: str | None = None
+    bulk_relax_maker: BaseVaspMaker | None = field(
+        default_factory=lambda: DoubleRelaxMaker.from_relax_maker(
+            TightRelaxMaker(
+                input_set_generator=TightRelaxSetGenerator(
+                    user_incar_settings={"ISPIN": 1, "LAECHG": False, "ISMEAR": 0}
+                )
+            )
+        ),
+    )
+    static_energy_maker: BaseVaspMaker | None = field(
+        default_factory=lambda: StaticMaker(
+            input_set_generator=StaticSetGenerator(
+                auto_ispin=False,
+                user_incar_settings={"ISPIN": 1, "LAECHG": False, "ISMEAR": 0},
+            )
+        )
+    )
+    phonon_displacement_maker: BaseVaspMaker = field(
+        default_factory=TightDFTStaticMaker
+    )
+
+
 @dataclass
 class IsoAtomStaticMaker(StaticMaker):
     """

tests/auto/test_auto_flows.py

@@ -85,8 +85,8 @@ def test_complete_dft_vs_ml_benchmark_workflow(
     }
 
     fake_run_vasp_kwargs = {
-        "tight relax 1": {"incar_settings": ["NSW"]},
-        "tight relax 2": {"incar_settings": ["NSW"]},
+        "tight relax 1": {"incar_settings": ["NSW", "ISMEAR"]},
+        "tight relax 2": {"incar_settings": ["NSW", "ISMEAR"]},
         "phonon static 1/2": {"incar_settings": ["NSW", "ISMEAR"]},
         "phonon static 2/2": {"incar_settings": ["NSW", "ISMEAR"]},
         "phonon static 1/3": {
@@ -356,10 +356,10 @@ def test_phonon_dft_ml_data_generation_flow(
     }
 
     fake_run_vasp_kwargs = {
-        "tight relax 1": {"incar_settings": ["NSW"]},
-        "tight relax 2": {"incar_settings": ["NSW"]},
+        "tight relax 1": {"incar_settings": ["NSW", "ISMEAR"]},
+        "tight relax 2": {"incar_settings": ["NSW", "ISMEAR"]},
         "phonon static 1/2": {"incar_settings": ["NSW", "ISMEAR"]},
-        "phonon static 2/2": {"incar_settings": ["NSW"]},
+        "phonon static 2/2": {"incar_settings": ["NSW", "ISMEAR"]},
         "phonon static 1/3": {
             "incar_settings": ["NSW", "ISMEAR"],
             "check_inputs": ["incar", "kpoints", "potcar"],