add adapted makers

autoplex/auto/jobs.py

@@ -1,10 +1,16 @@
 """General AutoPLEX automation jobs."""
 from __future__ import annotations
 
+from dataclasses import dataclass, field
 from typing import TYPE_CHECKING
 
 from atomate2.forcefields.flows.phonons import PhononMaker
-from atomate2.forcefields.jobs import GAPRelaxMaker, GAPStaticMaker
+from atomate2.forcefields.jobs import (
+    ForceFieldRelaxMaker,
+    ForceFieldStaticMaker,
+    GAPRelaxMaker,
+    GAPStaticMaker,
+)
 from atomate2.vasp.flows.phonons import PhononMaker as DFTPhononMaker
 from atomate2.vasp.powerups import (
     update_user_incar_settings,
@@ -17,7 +23,124 @@
 
 from autoplex.data.flows import IsoAtomMaker, RandomStructuresDataGenerator
 
-# This should be a maker rather than a job in a job
+
+@dataclass
+class MLPhononMaker(PhononMaker):
+    """
+    Maker to calculate harmonic phonons with a force field.
+
+    Calculate the harmonic phonons of a material. Initially, a tight structural
+    relaxation is performed to obtain a structure without forces on the atoms.
+    Subsequently, supercells with one displaced atom are generated and accurate
+    forces are computed for these structures. With the help of phonopy, these
+    forces are then converted into a dynamical matrix. To correct for polarization
+    effects, a correction of the dynamical matrix based on BORN charges can
+    be performed. The BORN charges can be supplied manually.
+    Finally, phonon densities of states, phonon band structures
+    and thermodynamic properties are computed.
+
+    .. Note::
+        It is heavily recommended to symmetrize the structure before passing it to
+        this flow. Otherwise, a different space group might be detected and too
+        many displacement calculations will be generated.
+        It is recommended to check the convergence parameters here and
+        adjust them if necessary. The default might not be strict enough
+        for your specific case.
+
+    Parameters
+    ----------
+    name : str
+        Name of the flows produced by this maker.
+    sym_reduce : bool
+        Whether to reduce the number of deformations using symmetry.
+    symprec : float
+        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
+        displacement distance for phonons
+    min_length: float
+        min length of the supercell that will be built
+    prefer_90_degrees: bool
+        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
+        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 : .ForceFieldRelaxMaker or None
+        A maker to perform a tight relaxation on the bulk.
+        Set to ``None`` to skip the
+        bulk relaxation
+    static_energy_maker : .ForceFieldStaticMaker
+        A maker to perform the computation of the DFT energy on the bulk.
+        Set to ``None`` to skip the
+        static energy computation
+    phonon_displacement_maker : .ForceFieldStaticMaker 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
+        Bool that determines if thermal_displacement_matrices are computed
+    kpath_scheme: str
+        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
+        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
+    """
+
+    ml_dir: str = "gapfit.xml"
+    min_length: float | None = 20.0
+    bulk_relax_maker: ForceFieldRelaxMaker | None = (
+        field(
+            default=GAPRelaxMaker(
+                potential_param_file_name=ml_dir,
+                relax_cell=True,
+                relax_kwargs={"interval": 500},
+            )
+        ),
+    )
+    phonon_displacement_maker: ForceFieldStaticMaker | None = (
+        field(default=GAPStaticMaker(potential_param_file_name=ml_dir)),
+    )
+    static_energy_maker: ForceFieldStaticMaker = (
+        field(default=GAPStaticMaker(potential_param_file_name=ml_dir)),
+    )
+    store_force_constants: bool = False
+    generate_frequencies_eigenvectors_kwargs: dict = field(
+        default_factory=lambda: {"units": "THz"}
+    )
+
+
 @job
 def get_phonon_ml_calculation_jobs(
     ml_dir: str,

autoplex/benchmark/jobs.py

@@ -54,7 +54,6 @@ def compute_bandstructure_benchmark_metrics(
         ml_bs=ml_phonon_bs,
         dft_bs=dft_phonon_bs,
         file_name=file_name,
-        img_format="eps",
     )
 
     return Response(output=overall_rmse)  # TODO TaskDoc

autoplex/benchmark/utils.py

@@ -92,8 +92,7 @@ def rmse_kdep_plot(
 def compare_plot(
     ml_bs: PhononBandStructureSymmLine,
     dft_bs: PhononBandStructureSymmLine,
-    file_name="band_comparison.eps",
-    img_format="eps",
+    file_name: str = "band_comparison.eps",
 ):
     """
     Save DFT and ML phonon band-structure overlay plot for visual comparison.
@@ -106,8 +105,6 @@ def compare_plot(
         DFT generated pymatgen phonon band-structure object
     file_name: str.
         Name of the saved plot
-    img_format: str
-        File extension of plot to be saved, default is eps
 
     Returns
     -------
@@ -117,6 +114,6 @@ def compare_plot(
     plotter = PhononBSPlotter(bs=ml_bs)
     plotter2 = PhononBSPlotter(bs=dft_bs)
     new_plotter = plotter.plot_compare(plotter2)
-    new_plotter.figure.savefig(file_name, format=img_format)
+    new_plotter.figure.savefig(file_name)
 
     return new_plotter.figure

autoplex/data/flows.py

@@ -7,6 +7,7 @@
 
 if TYPE_CHECKING:
     from atomate2.vasp.jobs.base import BaseVaspMaker
+    from atomate2.vasp.sets.base import VaspInputGenerator
     from emmet.core.math import Matrix3D
     from pymatgen.core.structure import Species, Structure
 from atomate2.common.jobs.phonons import (
@@ -28,6 +29,100 @@
 __all__ = ["RandomStructuresDataGenerator", "IsoAtomMaker"]
 
 
+@dataclass
+class TightDFTStaticMaker(PhononDisplacementMaker):
+    """Adapted phonon displacement maker for static calculation.
+
+    The input set used is same as PhononDisplacementMaker.
+    Only difference is Spin polarization is switched off and Gaussian smearing is used
+
+    Parameters
+    ----------
+    name : str
+        The job name.
+    input_set_generator : .VaspInputGenerator
+        A generator used to make the input set.
+    write_input_set_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
+    copy_vasp_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
+    run_vasp_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.run_vasp`.
+    task_document_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
+    stop_children_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.should_stop_children`.
+    write_additional_data : dict
+        Additional data to write to the current directory. Given as a dict of
+        {filename: data}. Note that if using FireWorks, dictionary keys cannot contain
+        the "." character which is typically used to denote file extensions. To avoid
+        this, use the ":" character, which will automatically be converted to ".". E.g.
+        ``{"my_file:txt": "contents of the file"}``.
+    """
+
+    input_set_generator: VaspInputGenerator = field(
+        default_factory=lambda: StaticSetGenerator(
+            user_kpoints_settings={"reciprocal_density": 100},
+            user_incar_settings={
+                "IBRION": 2,
+                "ISPIN": 1,
+                "ISMEAR": 0,
+                "ISIF": 3,
+                "ENCUT": 700,
+                "EDIFF": 1e-7,
+                "LAECHG": False,
+                "LREAL": False,
+                "ALGO": "Normal",
+                "NSW": 0,
+                "LCHARG": False,
+            },
+            auto_ispin=False,
+        )
+    )
+
+
+@dataclass
+class IsoAtomStaticMaker(StaticMaker):
+    """
+    Maker to create Isolated atoms static jobs.
+
+    Parameters
+    ----------
+    name : str
+        The job name.
+    input_set_generator : .VaspInputGenerator
+        A generator used to make the input set.
+    write_input_set_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
+    copy_vasp_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
+    run_vasp_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.run_vasp`.
+    task_document_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
+    stop_children_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.should_stop_children`.
+    write_additional_data : dict
+        Additional data to write to the current directory. Given as a dict of
+        {filename: data}. Note that if using FireWorks, dictionary keys cannot contain
+        the "." character which is typically used to denote file extensions. To avoid
+        this, use the ":" character, which will automatically be converted to ".". E.g.
+        ``{"my_file:txt": "contents of the file"}``.
+    """
+
+    name: str = "static"
+    input_set_generator: VaspInputGenerator = field(
+        default_factory=lambda: StaticSetGenerator(
+            user_kpoints_settings={"reciprocal_density": 1},
+            user_incar_settings={
+                "ISPIN": 1,
+                "LAECHG": False,
+                "ISMEAR": 0,
+            },
+        )
+    )
+
+
 @dataclass
 class RandomStructuresDataGenerator(Maker):
     """
@@ -163,6 +258,7 @@ def make(self, all_species: list[Species]):
                     user_kpoints_settings={"grid_density": 1},
                 ),
             ).make(iso_atom)
+
             isoatom_calcs = update_user_incar_settings(
                 isoatom_calcs,
                 {"NPAR": 4, "ISPIN": 1, "LAECHG": False, "ISMEAR": 0},

tests/auto/debug.py

@@ -2,31 +2,31 @@
 PLEASE IGNORE ANY FILES CONCERNING DEBUGGING
 """
 
-#from pathlib import Path
-#from pymatgen.core.structure import Structure
-#from dataclasses import dataclass, field
-#from jobflow import Flow, Maker, OutputReference, job
-#from autoplex.auto.jobs import PhononMLCalculationJob
-
-#__all__ = ["debugger"]
-
-
-#@dataclass
-#class debugger(Maker):
-   # name: str = "debug"
-
-   # def make(self, structure_list: list[Structure], **fit_kwargs):
-      #  jobs = []
-
-        #for struc in structure_list:
-            #debug = PhononMLCalculationJob(
-            #    structure=struc,
-            #    displacements=[0.1],
-             #   min_length=20,
-             #   ml_dir="/home/certural/Calc/testAtomateTwo/YuxingPot/gap.xml",
-           # )
-            # debug = PhononMLCalculationJob(structure=struc, displacements=[0.1], min_length=20, ml_dir="/home/certural/Calc/block_2023-09-24-23-23-10-568937/launcher_2023-09-25-08-43-25-183334/gap.xml")
-          #  jobs.append(debug)
-
-        #flow = Flow(jobs)
-        #return flow
+# from pathlib import Path
+# from pymatgen.core.structure import Structure
+# from dataclasses import dataclass, field
+# from jobflow import Flow, Maker, OutputReference, job
+# from autoplex.auto.jobs import PhononMLCalculationJob
+#
+# __all__ = ["debugger"]
+#
+#
+# @dataclass
+# class debugger(Maker):
+#    name: str = "debug"
+#
+#    def make(self, structure_list: list[Structure], **fit_kwargs):
+#        jobs = []
+#
+#         for struc in structure_list:
+#             debug = PhononMLCalculationJob(
+#                structure=struc,
+#                displacements=[0.1],
+#                min_length=20,
+#                ml_dir="/home/certural/Calc/testAtomateTwo/YuxingPot/gap.xml",
+#            )
+#             debug = PhononMLCalculationJob(structure=struc, displacements=[0.1], min_length=20, ml_dir="/home/certural/Calc/block_2023-09-24-23-23-10-568937/launcher_2023-09-25-08-43-25-183334/gap.xml")
+#            jobs.append(debug)
+#
+#         flow = Flow(jobs)
+#         return flow