pymatgen.entries.compatibility — pymatgen 2020.7.3 documentation

# Source code for pymatgen.entries.compatibility

    # coding: utf-8
    # Copyright (c) Pymatgen Development Team.
    # Distributed under the terms of the MIT License.
    """
    This module implements Compatibility corrections for mixing runs of different
    functionals.
    """

    import os
    import abc
    import warnings

    from collections import defaultdict
    from typing import Sequence, Union, Optional
    from monty.design_patterns import cached_class
    from monty.serialization import loadfn
    from monty.json import MSONable

    from pymatgen.io.vasp.sets import MITRelaxSet, MPRelaxSet
    from pymatgen.core.periodic_table import Element
    from pymatgen.analysis.structure_analyzer import oxide_type, sulfide_type
    from pymatgen.entries.computed_entries import ComputedEntry, \
        ConstantEnergyAdjustment, CompositionEnergyAdjustment, TemperatureEnergyAdjustment

    MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
    MU_H2O = -2.4583  # Free energy of formation of water, eV/H2O, used by MaterialsProjectAqueousCompatibility

    __author__ = "Ryan Kingsbury, Shyue Ping Ong, Anubhav Jain, Stephen Dacek, Sai Jayaraman"
    __copyright__ = "Copyright 2012-2020, The Materials Project"
    __version__ = "1.0"
    __maintainer__ = "Shyue Ping Ong"
    __email__ = "shyuep@gmail.com"
    __date__ = "April 2020"

    class CompatibilityError(Exception):
        """
        Exception class for Compatibility. Raised by attempting correction
        on incompatible calculation
        """
        pass

    class Correction(metaclass=abc.ABCMeta):
        """
        A Correction class is a pre-defined scheme for correction a computed
        entry based on the type and chemistry of the structure and the
        calculation parameters. All Correction classes must implement a
        correct_entry method.
        """

        @abc.abstractmethod
        def get_correction(self, entry):
            """
            Returns correction for a single entry.

            Args:
                entry: A ComputedEntry object.

            Returns:
                The energy correction to be applied.

            Raises:
                CompatibilityError if entry is not compatible.
            """
            return

        def correct_entry(self, entry):
            """
            Corrects a single entry.

            Args:
                entry: A ComputedEntry object.

            Returns:
                An processed entry.

            Raises:
                CompatibilityError if entry is not compatible.
            """
            entry.correction += self.get_correction(entry)
            return entry

    class PotcarCorrection(Correction):
        """
        Checks that POTCARs are valid within a pre-defined input set. This
        ensures that calculations performed using different InputSets are not
        compared against each other.

        Entry.parameters must contain a "potcar_symbols" key that is a list of
        all POTCARs used in the run. Again, using the example of an Fe2O3 run
        using Materials Project parameters, this would look like
        entry.parameters["potcar_symbols"] = ['PAW_PBE Fe_pv 06Sep2000',
        'PAW_PBE O 08Apr2002'].
        """

        def __init__(self, input_set, check_hash=False):
            """
            Args:
                input_set: InputSet object used to generate the runs (used to check
                    for correct potcar symbols)

                check_hash (bool): If true, uses the potcar hash to check for valid
                    potcars. If false, uses the potcar symbol (Less reliable).
                    Defaults to True

            Raises:
                ValueError if entry do not contain "potcar_symbols" key.
                CombatibilityError if wrong potcar symbols
            """
            potcar_settings = input_set.CONFIG["POTCAR"]
            if isinstance(list(potcar_settings.values())[-1],
                          dict):
                if check_hash:
                    self.valid_potcars = {k: d["hash"] for k, d in
                                          potcar_settings.items()}
                else:
                    self.valid_potcars = {k: d["symbol"] for k, d in
                                          potcar_settings.items()}
            else:
                if check_hash:
                    raise ValueError('Cannot check hashes of potcars,'
                                     ' hashes are not set')
                else:
                    self.valid_potcars = {k: d for k, d in
                                          potcar_settings.items()}

            self.input_set = input_set
            self.check_hash = check_hash

        def get_correction(self, entry) -> float:
            """
            :param entry: A ComputedEntry/ComputedStructureEntry
            :return: Correction.
            """
            if self.check_hash:
                if entry.parameters.get("potcar_spec"):
                    psp_settings = set([d.get("hash")
                                        for d in entry.parameters[
                                            "potcar_spec"] if d])
                else:
                    raise ValueError('Cannot check hash '
                                     'without potcar_spec field')
            else:
                if entry.parameters.get("potcar_spec"):
                    psp_settings = set([d.get("titel").split()[1]
                                        for d in entry.parameters[
                                            "potcar_spec"] if d])
                else:
                    psp_settings = set([sym.split()[1]
                                        for sym in entry.parameters[
                                            "potcar_symbols"] if sym])

            if {self.valid_potcars.get(str(el))
                    for el in entry.composition.elements} != psp_settings:
                raise CompatibilityError('Incompatible potcar')
            return 0

        def __str__(self):
            return "{} Potcar Correction".format(self.input_set.__name__)

    @cached_class
    class GasCorrection(Correction):
        """
        Correct gas energies to obtain the right formation energies. Note that
        this depends on calculations being run within the same input set.
        """

        def __init__(self, config_file):
            """
            Args:
                config_file: Path to the selected compatibility.yaml config file.
            """
            c = loadfn(config_file)
            self.name = c['Name']
            self.cpd_energies = c['Advanced']['CompoundEnergies']

        def get_correction(self, entry) -> float:
            """
            :param entry: A ComputedEntry/ComputedStructureEntry
            :return: Correction.
            """
            comp = entry.composition

            rform = entry.composition.reduced_formula
            if rform in self.cpd_energies:
                return self.cpd_energies[rform] * comp.num_atoms \
                       - entry.uncorrected_energy

            return 0

        def __str__(self):
            return "{} Gas Correction".format(self.name)

    @cached_class
    class AnionCorrection(Correction):
        """
        Correct anion energies to obtain the right formation energies. Note that
        this depends on calculations being run within the same input set.
        """

        def __init__(self, config_file, correct_peroxide=True):
            """
            Args:
                config_file: Path to the selected compatibility.yaml config file.
                correct_peroxide: Specify whether peroxide/superoxide/ozonide
                    corrections are to be applied or not.
            """
            c = loadfn(config_file)
            self.oxide_correction = c['OxideCorrections']
            self.sulfide_correction = c.get('SulfideCorrections', defaultdict(
                float))
            self.name = c['Name']
            self.correct_peroxide = correct_peroxide

        def get_correction(self, entry) -> float:
            """
            :param entry: A ComputedEntry/ComputedStructureEntry
            :return: Correction.
            """
            comp = entry.composition
            if len(comp) == 1:  # Skip element entry
                return 0

            correction = 0
            # Check for sulfide corrections
            if Element("S") in comp:
                sf_type = "sulfide"
                if entry.data.get("sulfide_type"):
                    sf_type = entry.data["sulfide_type"]
                elif hasattr(entry, "structure"):
                    sf_type = sulfide_type(entry.structure)
                if sf_type in self.sulfide_correction:
                    correction += self.sulfide_correction[sf_type] * comp["S"]

            # Check for oxide, peroxide, superoxide, and ozonide corrections.
            if Element("O") in comp:
                if self.correct_peroxide:
                    if entry.data.get("oxide_type"):
                        if entry.data["oxide_type"] in self.oxide_correction:
                            ox_corr = self.oxide_correction[
                                entry.data["oxide_type"]]
                            correction += ox_corr * comp["O"]
                        if entry.data["oxide_type"] == "hydroxide":
                            ox_corr = self.oxide_correction["oxide"]
                            correction += ox_corr * comp["O"]

                    elif hasattr(entry, "structure"):
                        ox_type, nbonds = oxide_type(entry.structure, 1.05,
                                                     return_nbonds=True)
                        if ox_type in self.oxide_correction:
                            correction += self.oxide_correction[ox_type] * \
                                          nbonds
                        elif ox_type == "hydroxide":
                            correction += self.oxide_correction["oxide"] * \
                                          comp["O"]
                    else:
                        warnings.warn(
                            "No structure or oxide_type parameter present. Note "
                            "that peroxide/superoxide corrections are not as "
                            "reliable and relies only on detection of special"
                            "formulas, e.g., Li2O2.")
                        rform = entry.composition.reduced_formula
                        if rform in UCorrection.common_peroxides:
                            correction += self.oxide_correction["peroxide"] * \
                                          comp["O"]
                        elif rform in UCorrection.common_superoxides:
                            correction += self.oxide_correction["superoxide"] * \
                                          comp["O"]
                        elif rform in UCorrection.ozonides:
                            correction += self.oxide_correction["ozonide"] * \
                                          comp["O"]
                        elif Element("O") in comp.elements and len(comp.elements) \
                                > 1:
                            correction += self.oxide_correction['oxide'] * \
                                          comp["O"]
                else:
                    correction += self.oxide_correction['oxide'] * comp["O"]

            return correction

        def __str__(self):
            return "{} Anion Correction".format(self.name)

    @cached_class
    class AqueousCorrection(Correction):
        """
        This class implements aqueous phase compound corrections for elements
        and H2O.
        """

        def __init__(self, config_file):
            """
            Args:
                config_file: Path to the selected compatibility.yaml config file.
            """
            c = loadfn(config_file)
            self.cpd_energies = c['AqueousCompoundEnergies']
            self.name = c["Name"]

        def get_correction(self, entry) -> float:
            """
            :param entry: A ComputedEntry/ComputedStructureEntry
            :return: Correction.
            """
            comp = entry.composition
            rform = comp.reduced_formula
            cpdenergies = self.cpd_energies
            correction = 0
            if rform in cpdenergies:
                if rform in ["H2", "H2O"]:
                    correction = cpdenergies[rform] * comp.num_atoms \
                                 - entry.uncorrected_energy - entry.correction
                else:
                    correction += cpdenergies[rform] * comp.num_atoms
            if not rform == "H2O":
                correction += 0.5 * 2.46 * min(comp["H"] / 2.0, comp["O"])
            return correction

        def __str__(self):
            return "{} Aqueous Correction".format(self.name)

    @cached_class
    class UCorrection(Correction):
        """
        This class implements the GGA/GGA+U mixing scheme, which allows mixing of
        entries. Entry.parameters must contain a "hubbards" key which is a dict
        of all non-zero Hubbard U values used in the calculation. For example,
        if you ran a Fe2O3 calculation with Materials Project parameters,
        this would look like entry.parameters["hubbards"] = {"Fe": 5.3}
        If the "hubbards" key is missing, a GGA run is assumed.

        It should be noted that ComputedEntries assimilated using the
        pymatgen.apps.borg package and obtained via the MaterialsProject REST
        interface using the pymatgen.matproj.rest package will automatically have
        these fields populated.
        """
        common_peroxides = ["Li2O2", "Na2O2", "K2O2", "Cs2O2", "Rb2O2", "BeO2",
                            "MgO2", "CaO2", "SrO2", "BaO2"]
        common_superoxides = ["LiO2", "NaO2", "KO2", "RbO2", "CsO2"]
        ozonides = ["LiO3", "NaO3", "KO3", "NaO5"]

        def __init__(self, config_file, input_set, compat_type):
            """
            Args:
                config_file: Path to the selected compatibility.yaml config file.
                input_set: InputSet object (to check for the +U settings)
                compat_type: Two options, GGA or Advanced.  GGA means all GGA+U
                    entries are excluded.  Advanced means mixing scheme is
                    implemented to make entries compatible with each other,
                    but entries which are supposed to be done in GGA+U will have the
                    equivalent GGA entries excluded. For example, Fe oxides should
                    have a U value under the Advanced scheme. A GGA Fe oxide run
                    will therefore be excluded under the scheme.
            """
            if compat_type not in ['GGA', 'Advanced']:
                raise CompatibilityError("Invalid compat_type {}"
                                         .format(compat_type))

            c = loadfn(config_file)

            self.input_set = input_set
            if compat_type == 'Advanced':
                self.u_settings = self.input_set.CONFIG["INCAR"]["LDAUU"]
                self.u_corrections = c["Advanced"]["UCorrections"]
            else:
                self.u_settings = {}
                self.u_corrections = {}

            self.name = c["Name"]
            self.compat_type = compat_type

        def get_correction(self, entry) -> float:
            """
            :param entry: A ComputedEntry/ComputedStructureEntry
            :return: Correction.
            """
            if entry.parameters.get("run_type") not in ["GGA", "GGA+U"]:
                raise CompatibilityError('Entry {} has invalid run type {}. Discarding.'
                                         .format(entry.entry_id,
                                                 entry.parameters.get("run_type")))

            calc_u = entry.parameters.get("hubbards", None)
            calc_u = defaultdict(int) if calc_u is None else calc_u
            comp = entry.composition

            elements = sorted([el for el in comp.elements if comp[el] > 0],
                              key=lambda el: el.X)
            most_electroneg = elements[-1].symbol
            correction = 0
            ucorr = self.u_corrections.get(most_electroneg, {})
            usettings = self.u_settings.get(most_electroneg, {})

            for el in comp.elements:
                sym = el.symbol
                # Check for bad U values
                if calc_u.get(sym, 0) != usettings.get(sym, 0):
                    raise CompatibilityError('Invalid U value of %s on %s' %
                                             (calc_u.get(sym, 0), sym))
                if sym in ucorr:
                    correction += float(ucorr[sym]) * comp[el]

            return correction

        def __str__(self):
            return "{} {} Correction".format(self.name, self.compat_type)

    class Compatibility(MSONable, metaclass=abc.ABCMeta):
        """
        Abstract Compatibility class, not intended for direct use.
        Compatibility classes are used to correct the energies of an entry or a set
        of entries. All Compatibility classes must implement .get_adjustments method.
        """
        @abc.abstractmethod
        def get_adjustments(self, entry: ComputedEntry):
            """
            Get the energy adjustments for a ComputedEntry.

            This method must generate a list of EnergyAdjustment objects
            of the appropriate type (constant, composition-based, or temperature-based)
            to be applied to the ComputedEntry, and must raise a CompatibilityError
            if the entry is not compatible.

            Args:
                entry: A ComputedEntry object.

            Returns:
                [EnergyAdjustment]: A list of EnergyAdjustment to be applied to the
                    Entry.

            Raises:
                CompatibilityError if the entry is not compatible
            """
            return

        def process_entry(self, entry):
            """
            Process a single entry with the chosen Corrections.

            Args:
                entry: A ComputedEntry object.
            Returns:
                An adjusted entry if entry is compatible, otherwise None is
                returned.
            """
            if self.process_entries(entry):
                return self.process_entries(entry)[0]
            else:
                return None

        def process_entries(self, entries: Union[ComputedEntry, list], clean: bool = False):
            """
            Process a sequence of entries with the chosen Compatibility scheme.

            Args:
                entries: ComputedEntry or [ComputedEntry]
                clean: bool, whether to remove any previously-applied energy adjustments.
                    If True, all EnergyAdjustment are removed prior to processing the Entry.
                    Default is False.

            Returns:
                A list of adjusted entries.  Entries in the original list which
                are not compatible are excluded.
            """
            # convert input arg to a list if not already
            if isinstance(entries, ComputedEntry):
                entries = [entries]

            processed_entry_list = []

            for entry in entries:
                ignore_entry = False
                # if clean is True, remove all previous adjustments, other than Manual adjustments, from the entry
                if clean:
                    for ea in entry.energy_adjustments:
                        entry.energy_adjustments.remove(ea)

                # get the energy adjustments
                try:
                    adjustments = self.get_adjustments(entry)
                except CompatibilityError as exc:
                    ignore_entry = True
                    print(exc)
                    continue

                for ea in adjustments:
                    # Has this correction already been applied?
                    if (ea.name, ea.cls, ea.value) in [(ea.name, ea.cls, ea.value) for ea in entry.energy_adjustments]:
                        # we already applied this exact correction. Do nothing.
                        pass
                    elif (ea.name, ea.cls) in [(ea.name, ea.cls) for ea in entry.energy_adjustments]:
                        # we already applied a correction with the same name
                        # but a different value. Something is wrong.
                        ignore_entry = True
                        warnings.warn("Entry {} already has an energy adjustment called {}, but its "
                                      "value differs from the value of {:.3f} calculated here. This "
                                      "Entry will be discarded."
                                      .format(entry.entry_id,
                                              ea.name,
                                              ea.value
                                              )
                                      )
                    else:
                        # Add the correction to the energy_adjustments list
                        entry.energy_adjustments.append(ea)

                if not ignore_entry:
                    processed_entry_list.append(entry)

            return processed_entry_list

        def explain(self, entry):
            """
            Prints an explanation of the energy adjustments applied by the
            Compatibility class. Inspired by the "explain" methods in many database
            methodologies.

            Args:
                entry: A ComputedEntry.
            """
            print("The uncorrected energy of {} is {:.3f} eV ({:.3f} eV/atom).".format(
                    entry.composition,
                    entry.uncorrected_energy,
                    entry.uncorrected_energy / entry.composition.num_atoms)
                  )

            if len(entry.energy_adjustments) > 0:
                print("The following energy adjustments have been applied to this entry:")
                for e in entry.energy_adjustments:
                    print("\t\t{}: {:.3f} eV ({:.3f} eV/atom)".format(e.name,
                                                                      e.value,
                                                                      e.value / entry.composition.num_atoms)
                          )
            elif entry.correction == 0:
                print("No energy adjustments have been applied to this entry.")

            print("The final energy after adjustments is {:.3f} eV ({:.3f} eV/atom).".format(
                    entry.energy,
                    entry.energy_per_atom)
                  )

    class CorrectionsList(Compatibility):
        """
        The CorrectionsList class combines a list of corrections to be applied to
        an entry or a set of entries. Note that some of the Corrections have
        interdependencies. For example, PotcarCorrection must always be used
        before any other compatibility. Also, GasCorrection("MP") must be used
        with PotcarCorrection("MP") (similarly with "MIT"). Typically,
        you should use the specific MaterialsProjectCompatibility and
        MITCompatibility subclasses instead.
        """

        def __init__(self, corrections: Sequence):
            """
            Args:
                corrections: List of corrections to apply.
            """
            self.corrections = corrections
            super().__init__()

        def get_adjustments(self, entry):
            """
            Get the list of energy adjustments to be applied to an entry.
            """
            adjustment_list = []
            # try:
            corrections = self.get_corrections_dict(entry)
            for k, v in corrections.items():
                adjustment_list.append(ConstantEnergyAdjustment(v,
                                                                name=k,
                                                                cls=self.as_dict(),
                                                                )
                                       )

            return adjustment_list

        def get_corrections_dict(self, entry):
            """
            Returns the corrections applied to a particular entry.

            Args:
                entry: A ComputedEntry object.

            Returns:
                ({correction_name: value})
            """
            corrections = {}
            for c in self.corrections:
                val = c.get_correction(entry)
                corrections[str(c)] = val
            return corrections

        def get_explanation_dict(self, entry):
            """
            Provides an explanation dict of the corrections that are being applied
            for a given compatibility scheme. Inspired by the "explain" methods
            in many database methodologies.

            Args:
                entry: A ComputedEntry.

            Returns:
                (dict) of the form
                {"Compatibility": "string",
                "Uncorrected_energy": float,
                "Corrected_energy": float,
                "Corrections": [{"Name of Correction": {
                "Value": float, "Explanation": "string"}]}
            """
            centry = self.process_entry(entry)
            if centry is None:
                uncorrected_energy = entry.uncorrected_energy
                corrected_energy = None
            else:
                uncorrected_energy = centry.uncorrected_energy
                corrected_energy = centry.energy
            d = {"compatibility": self.__class__.__name__,
                 "uncorrected_energy": uncorrected_energy,
                 "corrected_energy": corrected_energy}
            corrections = []
            corr_dict = self.get_corrections_dict(entry)
            for c in self.corrections:
                cd = {"name": str(c),
                      "description": c.__doc__.split("Args")[0].strip(),
                      "value": corr_dict.get(str(c), 0)}
                corrections.append(cd)
            d["corrections"] = corrections
            return d

        def explain(self, entry):
            """
            Prints an explanation of the corrections that are being applied for a
            given compatibility scheme. Inspired by the "explain" methods in many
            database methodologies.

            Args:
                entry: A ComputedEntry.
            """
            d = self.get_explanation_dict(entry)
            print("The uncorrected value of the energy of %s is %f eV" %
                  (entry.composition, d["uncorrected_energy"]))
            print("The following corrections / screening are applied for %s:\n" %
                  d["compatibility"])
            for c in d["corrections"]:
                print("%s correction: %s\n" % (c["name"],
                                               c["description"]))
                print("For the entry, this correction has the value %f eV." % c[
                    "value"])
                print("-" * 30)

            print("The final energy after corrections is %f" % d[
                "corrected_energy"])

    class MaterialsProjectCompatibility(CorrectionsList):
        """
        This class implements the GGA/GGA+U mixing scheme, which allows mixing of
        entries. Note that this should only be used for VASP calculations using the
        MaterialsProject parameters (see pymatgen.io.vaspio_set.MPVaspInputSet).
        Using this compatibility scheme on runs with different parameters is not
        valid.
        """

        def __init__(self, compat_type="Advanced", correct_peroxide=True,
                     check_potcar_hash=False):
            """
            Args:
                compat_type: Two options, GGA or Advanced.  GGA means all GGA+U
                    entries are excluded.  Advanced means mixing scheme is
                    implemented to make entries compatible with each other,
                    but entries which are supposed to be done in GGA+U will have the
                    equivalent GGA entries excluded. For example, Fe oxides should
                    have a U value under the Advanced scheme. A GGA Fe oxide run
                    will therefore be excluded under the scheme.
                correct_peroxide: Specify whether peroxide/superoxide/ozonide
                    corrections are to be applied or not.
                check_potcar_hash (bool): Use potcar hash to verify potcars are correct.
            """
            self.compat_type = compat_type
            self.correct_peroxide = correct_peroxide
            self.check_potcar_hash = check_potcar_hash
            fp = os.path.join(MODULE_DIR, "MPCompatibility.yaml")
            super().__init__(
                [PotcarCorrection(MPRelaxSet, check_hash=check_potcar_hash),
                 GasCorrection(fp),
                 AnionCorrection(fp, correct_peroxide=correct_peroxide),
                 UCorrection(fp, MPRelaxSet, compat_type)])

    class MITCompatibility(CorrectionsList):
        """
        This class implements the GGA/GGA+U mixing scheme, which allows mixing of
        entries. Note that this should only be used for VASP calculations using the
        MIT parameters (see pymatgen.io.vaspio_set MITVaspInputSet). Using
        this compatibility scheme on runs with different parameters is not valid.
        """

        def __init__(self, compat_type="Advanced", correct_peroxide=True,
                     check_potcar_hash=False):
            """
            Args:
                compat_type: Two options, GGA or Advanced.  GGA means all GGA+U
                    entries are excluded.  Advanced means mixing scheme is
                    implemented to make entries compatible with each other,
                    but entries which are supposed to be done in GGA+U will have the
                    equivalent GGA entries excluded. For example, Fe oxides should
                    have a U value under the Advanced scheme. A GGA Fe oxide run
                    will therefore be excluded under the scheme.
                correct_peroxide: Specify whether peroxide/superoxide/ozonide
                    corrections are to be applied or not.
                check_potcar_hash (bool): Use potcar hash to verify potcars are correct.
            """
            self.compat_type = compat_type
            self.correct_peroxide = correct_peroxide
            self.check_potcar_hash = check_potcar_hash
            fp = os.path.join(MODULE_DIR, "MITCompatibility.yaml")
            super().__init__(
                [PotcarCorrection(MITRelaxSet, check_hash=check_potcar_hash),
                 GasCorrection(fp),
                 AnionCorrection(fp, correct_peroxide=correct_peroxide),
                 UCorrection(fp, MITRelaxSet, compat_type)])

    class MITAqueousCompatibility(CorrectionsList):
        """
        This class implements the GGA/GGA+U mixing scheme, which allows mixing of
        entries. Note that this should only be used for VASP calculations using the
        MIT parameters (see pymatgen.io.vaspio_set MITVaspInputSet). Using
        this compatibility scheme on runs with different parameters is not valid.
        """

        def __init__(self, compat_type="Advanced", correct_peroxide=True,
                     check_potcar_hash=False):
            """
            Args:
                compat_type: Two options, GGA or Advanced.  GGA means all GGA+U
                    entries are excluded.  Advanced means mixing scheme is
                    implemented to make entries compatible with each other,
                    but entries which are supposed to be done in GGA+U will have the
                    equivalent GGA entries excluded. For example, Fe oxides should
                    have a U value under the Advanced scheme. A GGA Fe oxide run
                    will therefore be excluded under the scheme.
                correct_peroxide: Specify whether peroxide/superoxide/ozonide
                    corrections are to be applied or not.
                check_potcar_hash (bool): Use potcar hash to verify potcars are correct.
            """
            self.compat_type = compat_type
            self.correct_peroxide = correct_peroxide
            self.check_potcar_hash = check_potcar_hash
            fp = os.path.join(MODULE_DIR, "MITCompatibility.yaml")
            super().__init__(
                [PotcarCorrection(MITRelaxSet, check_hash=check_potcar_hash),
                 GasCorrection(fp),
                 AnionCorrection(fp, correct_peroxide=correct_peroxide),
                 UCorrection(fp, MITRelaxSet, compat_type), AqueousCorrection(fp)])

    class MaterialsProjectAqueousCompatibility(Compatibility):
        """
        This class implements the Aqueous energy referencing scheme for constructing
        Pourbaix diagrams from DFT energies, as described in Persson et al.

        This scheme applies various energy adjustments to convert DFT energies into
        Gibbs free energies of formation at 298 K and to guarantee that the experimental
        formation free energy of H2O is reproduced. Briefly, the steps are:

            1. Beginning with the DFT energy of O2, adjust the energy of H2 so that
               the experimental reaction energy of -2.458 eV/H2O is reproduced.
            2. Add entropy to the DFT energy of any compounds that are liquid or
               gaseous at room temperature
            3. Adjust the energy of H2O for consistency with the adjusted H2 energy.
            4. Adjust the DFT energies of solid hydrate compounds (compounds that
               contain water, e.g. FeO.nH2O) such that the energies of the embedded
               H2O molecules are equal to the experimental free energy

        The above energy adjustments are computed dynamically based on the input
        Entries.

        References:
            K.A. Persson, B. Waldwick, P. Lazic, G. Ceder, Prediction of solid-aqueous
            equilibria: Scheme to combine first-principles calculations of solids with
            experimental aqueous states, Phys. Rev. B - Condens. Matter Mater. Phys.
            85 (2012) 1–12. doi:10.1103/PhysRevB.85.235438.
        """

        def __init__(self,
                     solid_compat: Optional[Compatibility] = None,
                     o2_energy: Optional[float] = None,
                     h2o_energy: Optional[float] = None,
                     h2o_adjustments: Optional[float] = None):
            """
            Initialize the MaterialsProjectAqueousCompatibility class.

            Note that this class requires as inputs the ground-state DFT energies of O2 and H2O, plus the value of any
            energy adjustments applied to an H2O molecule. If these parameters are not provided in __init__, they can
            be automatically populated by included ComputedEntry for the ground state of O2 and H2O in a list of entries
            passed to process_entries. process_entries will fail if one or the other is not provided.

            Args:
                solid_compat: Compatiblity scheme used to pre-process solid DFT energies prior to applying aqueous
                    energy adjustments. Default: MaterialsProjectCompatibility.
                o2_energy: The ground-state DFT energy of oxygen gas, including any adjustments or corrections, in eV/atom.
                    If not set, this value will be determined from any O2 entries passed to process_entries.
                    Default: None
                h2o_energy: The ground-state DFT energy of water, including any adjstments or corrections, in eV/atom.
                    If not set, this value will be determined from any H2O entries passed to process_entries.
                    Default: None
                h2o_adjustments: Total energy adjustments applied to one water molecule, in eV/atom.
                    If not set, this value will be determined from any H2O entries passed to process_entries.
                    Default: None
            """
            self.solid_compat = solid_compat
            self.o2_energy = o2_energy
            self.h2o_energy = h2o_energy
            self.h2o_adjustments = h2o_adjustments

            if not all([self.o2_energy, self.h2o_energy, self.h2o_adjustments]):
                warnings.warn("You did not provide the required O2 and H2O energies. {} "
                              "needs these energies in order to compute the appropriate energy adjustments. It will try "
                              "to determine the values from ComputedEntry for O2 and H2O passed to process_entries, but "
                              "will fail if these entries are not provided.".format(type(self).__name__))

            # Standard state entropy of molecular-like compounds at 298K (-T delta S)
            # from Kubaschewski Tables (eV/atom)
            self.cpd_entropies = {"O2": 0.316731,
                                  "N2": 0.295729,
                                  "F2": 0.313025,
                                  "Cl2": 0.344373,
                                  "Br": 0.235039,
                                  "Hg": 0.234421,
                                  "H2O": 0.071963,  # 0.215891 eV/H2O
                                  }
            self.name = "MP Aqueous free energy adjustment"
            super().__init__()

        def get_adjustments(self, entry: ComputedEntry):
            """
            Returns the corrections applied to a particular entry.

            Args:
                entry: A ComputedEntry object.

            Returns:
                [EnergyAdjustment]: Energy adjustments to be applied to entry.

            Raises:
                CompatibilityError if the required O2 and H2O energies have not been provided to
                MaterialsProjectAqueousCompatibility during init or in the list of entries passed to process_entries.
            """
            adjustments = []
            if self.o2_energy is None or self.h2o_energy is None or self.h2o_adjustments is None:
                raise CompatibilityError("You did not provide the required O2 and H2O energies. "
                                         "{} needs these energies in order to compute "
                                         "the appropriate energy adjustments. Either specify the energies as arguments "
                                         "to {}.__init__ or run process_entries on a list that includes ComputedEntry for "
                                         "the ground state of O2 and H2O.".format(type(self).__name__, type(self).__name__))

            # compute the free energies of H2 and H2O (eV/atom) to guarantee that the
            # formationfree energy of H2O is equal to -2.4583 eV/H2O from experiments
            # (MU_H2O from pourbaix module)

            # Free energy of H2 in eV/atom, fitted using Eq. 40 of Persson et al. PRB 2012 85(23)
            # for this calculation ONLY, we need the (corrected) DFT energy of water
            self.h2_energy = round(
                0.5 * (3 * (self.h2o_energy - self.cpd_entropies["H2O"]) -
                       (self.o2_energy - self.cpd_entropies["O2"]) -
                       MU_H2O
                       ), 6
            )

            # Free energy of H2O, fitted for consistency with the O2 and H2 energies.
            self.fit_h2o_energy = round((2 * self.h2_energy +
                                        (self.o2_energy - self.cpd_entropies["O2"]) +
                                        MU_H2O
                                         ) / 3,
                                        6
                                        )

            comp = entry.composition
            rform = comp.reduced_formula

            # pin the energy of all H2 entries to h2_energy
            if rform == "H2":
                adjustments.append(
                    ConstantEnergyAdjustment(self.h2_energy * comp.num_atoms - entry.energy,
                                             name="MP Aqueous H2 / H2O referencing",
                                             cls=self.as_dict(),
                                             description="Adjusts the H2 and H2O energy to reproduce the experimental "
                                                         "Gibbs formation free energy of H2O, based on the DFT energy "
                                                         "of Oxygen"
                                             ))

            # pin the energy of all H2O entries to fit_h2o_energy
            elif rform == "H2O":
                adjustments.append(
                    ConstantEnergyAdjustment(self.fit_h2o_energy * comp.num_atoms - entry.energy,
                                             name="MP Aqueous H2 / H2O referencing",
                                             cls=self.as_dict(),
                                             description="Adjusts the H2 and H2O energy to reproduce the experimental "
                                                         "Gibbs formation free energy of H2O, based on the DFT energy "
                                                         "of Oxygen"
                                             ))

            # add minus T delta S to the DFT energy (enthalpy) of compounds that are
            # molecular-like at room temperature
            elif rform in self.cpd_entropies and rform != "H2O":
                adjustments.append(
                    TemperatureEnergyAdjustment(-1 * self.cpd_entropies[rform] / 298, 298,
                                                comp.num_atoms,
                                                name="Compound entropy at room temperature",
                                                cls=self.as_dict(),
                                                description="Adds the entropy (T delta S) to energies of compounds that "
                                                            "are gaseous or liquid at standard state"
                                                ))

            # TODO - detection of embedded water molecules is not very sophisticated
            # Should be replaced with some kind of actual structure detection

            # For any compound except water, check to see if it is a hydrate (contains)
            # H2O in its structure. If so, adjust the energy to remove MU_H2O ev per
            # embedded water molecule.
            # in other words, we assume that the DFT energy of such a compound is really
            # a superposition of the "real" solid DFT energy (FeO in this case) and the free
            # energy of some water molecules
            # e.g. that E_FeO.nH2O = E_FeO + n * g_H2O
            # so, to get the most accurate gibbs free energy, we want to replace
            # g_FeO.nH2O = E_FeO.nH2O + dE_Fe + (n+1) * dE_O + 2n dE_H
            # with
            # g_FeO = E_FeO.nH2O + dE_Fe + dE_O + n g_H2O
            # where E is DFT energy, dE is an energy correction, and g is gibbs free energy
            # This means we have to 1) remove energy corrections associated with H and O in water
            # and then 2) remove the free energy of the water molecules
            if not rform == "H2O":
                # count the number of whole water molecules in the composition
                nH2O = int(min(comp["H"] / 2.0, comp["O"]))
                if nH2O > 0:
                    # first, remove any H or O corrections already applied to H2O in the
                    # formation energy so that we don't double count them
                    # next, remove MU_H2O for each water molecule present
                    hydrate_adjustment = -1 * (self.h2o_adjustments * 3 + MU_H2O)

                    adjustments.append(
                        CompositionEnergyAdjustment(
                            hydrate_adjustment,
                            nH2O,
                            name="MP Aqueous hydrate",
                            cls=self.as_dict(),
                            description="Adjust the energy of solid hydrate compounds (compounds "
                                        "containing H2O molecules in their structure) so that the "
                                        "free energies of embedded H2O molecules match the experimental"
                                        " value enforced by the MP Aqueous energy referencing scheme."
                            )
                    )

            return adjustments

        def process_entries(self, entries: Union[ComputedEntry, list], clean: bool = False):
            """
            Process a sequence of entries with the chosen Compatibility scheme.

            Args:
                entries: ComputedEntry or [ComputedEntry]
                clean: bool, whether to remove any previously-applied energy adjustments.
                    If True, all EnergyAdjustment are removed prior to processing the Entry.
                    Default is False.

            Returns:
                A list of adjusted entries.  Entries in the original list which
                are not compatible are excluded.
            """
            # convert input arg to a list if not already
            if isinstance(entries, ComputedEntry):
                entries = [entries]

            # pre-process entries with the given solid compatibility class
            if self.solid_compat:
                entries = self.solid_compat.process_entries(entries, clean=True)

            # extract the DFT energies of oxygen and water from the list of entries, if present
            if not self.o2_energy:
                o2_entries = [e for e in entries if e.composition.reduced_formula == 'O2']
                if o2_entries:
                    self.o2_energy = min(e.energy_per_atom for e in o2_entries)

            if not self.h2o_energy and not self.h2o_adjustments:
                h2o_entries = [e for e in entries if e.composition.reduced_formula == 'H2O']
                if h2o_entries:
                    h2o_entries = sorted(h2o_entries, key=lambda e: e.energy_per_atom)
                    self.h2o_energy = h2o_entries[0].energy_per_atom
                    self.h2o_adjustments = h2o_entries[0].correction / h2o_entries[0].composition.num_atoms

            return super().process_entries(entries)