VASP Defect Code

pyproject.toml

@@ -40,7 +40,7 @@ amset = ["amset>=0.4.15", "pydash"]
 cclib = ["cclib"]
 mp = ["mp-api>=0.27.5"]
 phonons = ["phonopy>=1.10.8", "seekpath"]
-defects = ["pymatgen-analysis-defects>=2022.11.21", "dscribe>=1.2.0"]
+defects = ["pymatgen-analysis-defects>=2022.11.30", "dscribe>=1.2.0"]
 docs = [
     "numpydoc==1.5.0",
     "ipython==8.8.0",
@@ -53,7 +53,7 @@ dev = ["pre-commit>=2.12.1"]
 tests = ["pytest==7.2.1", "pytest-cov==4.0.0", "FireWorks==2.0.3"]
 strict = [
     "pydantic==1.10.4",
-    "pymatgen==2023.1.20",
+    "pymatgen==2023.1.30",
     "custodian==2022.5.26",
     "monty==2022.9.9",
     "jobflow==0.1.9",
@@ -65,7 +65,7 @@ strict = [
     "numpy",
     "mp-api==0.30.8",
     "dscribe==1.2.1",
-    "pymatgen-analysis-defects==2022.11.21",
+    "pymatgen-analysis-defects==2023.1.30",
 ]
 
 [project.scripts]

src/atomate2/common/analysis/defects/flows.py

@@ -3,14 +3,21 @@
 from __future__ import annotations
 
 import logging
+from abc import ABC, abstractmethod
 from dataclasses import dataclass
+from pathlib import Path
 
+import numpy.typing as npt
 from jobflow import Flow, Job, Maker, OutputReference
+from pymatgen.analysis.defects.core import Defect
 from pymatgen.core.structure import Structure
 
 from atomate2.common.analysis.defects.jobs import (
+    bulk_supercell_calculation,
     get_ccd_documents,
     get_charged_structures,
+    get_supercell_from_prv_calc,
+    spawn_defect_calcs,
     spawn_energy_curve_calcs,
 )
 
@@ -27,10 +34,10 @@ class ConfigurationCoordinateMaker(Maker):
     ----------
     name: str
         The name of the flow created by this maker.
-    relax_maker: .BaseVaspMaker or None
+    relax_maker: Maker
         A maker to perform a atomic-position-only relaxation on the defect charge
         states.
-    static_maker: .BaseVaspMaker or None
+    static_maker: Maker
         A maker to perform the single-shot static calculation of the distorted
         structures.
     distortions: tuple[float, ...]
@@ -138,3 +145,163 @@ def make(
             output=ccd_job.output,
             name=name,
         )
+
+
+@dataclass
+class FormationEnergyMaker(Maker, ABC):
+    """Maker class to help calculate of the formation energy diagram.
+
+    Maker class to calculate formation energy diagrams. The main settings for
+    this maker is the `relax_maker` which contains the settings for the atomic
+    relaxations that each defect supercell will undergo. The `relax_maker`
+    uses a `ChargeStateRelaxSetGenerator` by default but more complex makers
+    like the `HSEDoubleRelaxMaker` can be used for more accurate (but expensive)
+    calculations.
+    If the `validate_maker` is set to True, the maker will check for some basic
+    settings in the `relax_maker` to make sure the calculations are done correctly.
+
+    Attributes
+    ----------
+    relax_maker: Maker
+        A maker to perform a atomic-position-only relaxation on the defect charge
+        states. Since these calculations are expensive and the settings might get
+        messy, it is recommended for each implementation of this maker to check
+        some of the most important settings in the `relax_maker`.  Please see
+        `FormationEnergyMaker.validate_maker` for more details.
+    name: str
+        The name of the flow created by this maker.
+    """
+
+    relax_maker: Maker
+    name: str = "formation energy"
+
+    def __post_init__(self):
+        self.validate_maker()
+
+    def make(
+        self,
+        defect: Defect,
+        bulk_supercell_dir: str | Path | None = None,
+        supercell_matrix: npt.NDArray | None = None,
+        defect_index: int | str = "",
+    ):
+        """Make a flow to calculate the formation energy diagram.
+
+        Start a series of charged supercell relaxations from a single defect
+        structure. Since the standard finite size correction (Freysoldt) requires
+        a bulk supercell calculation (to obtain the pristine electrostatic potentia),
+        this maker will either perform a bulk supercell calculation or use a existing
+        one if provided.
+        If a value for the dielectric constant is provided, the Freysoldt correction
+        will be applied to the formation energy.
+
+        Parameters
+        ----------
+        defects: Defect
+            List of defects objects to calculate the formation energy diagram for.
+        bulk_supercell_dir: str | Path | None
+            If provided, the bulk supercell calculation will be skipped.
+        supercell_matrix: NDArray | None
+            The supercell transformation matrix. If None, the supercell matrix
+            will be computed automatically.  If `bulk_supercell_dir` is provided,
+            this parameter will be ignored.
+        defect_index : int | str
+            Additional index to give unique names to the defect calculations.
+            Useful for external bookkeeping of symmetry distinct defects.
+
+        Returns
+        -------
+        flow: Flow
+            The workflow to calculate the formation energy diagram.
+        """
+        jobs = []
+        if bulk_supercell_dir is None:
+            get_sc_job = bulk_supercell_calculation(
+                uc_structure=defect.structure,
+                relax_maker=self.relax_maker,
+                sc_mat=supercell_matrix,
+                update_bulk_maker=self.update_bulk_maker,
+            )
+            sc_mat = get_sc_job.output["sc_mat"]
+            lattice = get_sc_job.output["sc_struct"].lattice
+            bulk_supercell_dir = get_sc_job.output["dir_name"]
+        else:
+            # all additional reader functions need to be in this job
+            # b/c they might receive Response objects instead of data.
+            get_sc_job = get_supercell_from_prv_calc(
+                uc_structure=defect.structure,
+                prv_calc_dir=bulk_supercell_dir,
+                sc_mat_ref=supercell_matrix,
+                structure_from_prv=self.structure_from_prv,
+            )
+            sc_mat = get_sc_job.output["sc_mat"]
+            lattice = get_sc_job.output["lattice"]
+
+        spawn_output = spawn_defect_calcs(
+            defect=defect,
+            sc_mat=sc_mat,
+            relax_maker=self.relax_maker,
+            relaxed_sc_lattice=lattice,
+            defect_index=defect_index,
+            add_info={
+                "bulk_supercell_dir": bulk_supercell_dir,
+                "bulk_supercell_matrix": sc_mat,
+                "bulk_supercell_uuid": get_sc_job.uuid,
+            },
+        )
+        jobs.extend([get_sc_job, spawn_output])
+
+        return Flow(
+            jobs=jobs,
+            name=self.name,
+        )
+
+    @abstractmethod
+    def update_bulk_maker(self, relax_maker: Maker):
+        """Update the maker for the bulk job.
+
+        Common usage case:
+        While almost all of the settings for the bulk relaxation and defect
+        relaxation should be the same, it is usually desirable to allow lattice
+        relaxation for the bulk job only.
+        Assuming the `relax_maker` is only allows atomic relaxations, this method
+        will update the bulk job to allow lattice relaxations.
+
+        Parameters
+        ----------
+        relax_maker: Maker
+            The maker used to create the defect job.
+
+        Returns:
+        --------
+        Maker:
+            The updated maker.
+        """
+        raise NotImplementedError("This method is not implemented yet.")
+
+    @abstractmethod
+    def structure_from_prv(self, previous_dir: str) -> Structure:
+        """Copy the output structure from previous directory.
+
+        Parameters
+        ----------
+        previous_dir: str
+            The directory to copy from.
+
+        Returns
+        -------
+        structure: Structure
+        """
+
+    @abstractmethod
+    def validate_maker(self):
+        """Check some key settings in the relax maker.
+
+        Since this workflow is pretty complex but allows you to use any
+        relax maker, it can be easy to make mistakes in the settings.
+        This method should check the most important settings and raise
+        an error if something is wrong.
+
+        Example:  For VASP, the relax maker should have:
+            `ISIF = 2` and `use_structure_charge = True`
+        """