pymatgen.entries.compatibility module

This module implements Compatibility corrections for mixing runs of different functionals.

class AnionCorrection(*args, **kwargs)[source]

Bases: pymatgen.entries.compatibility.AnionCorrection

Correct anion energies to obtain the right formation energies. Note that this depends on calculations being run within the same input set.

Pass through… :param args: :param kwargs: :return:

class AqueousCorrection(*args, **kwargs)[source]

Bases: pymatgen.entries.compatibility.AqueousCorrection

This class implements aqueous phase compound corrections for elements and H2O.

Pass through… :param args: :param kwargs: :return:

class Compatibility(corrections: Sequence)[source]

Bases: monty.json.MSONable

The Compatibility 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.

Parameters

corrections – List of corrections to apply.

explain(entry)[source]

Prints an explanation of the corrections that are being applied for a given compatibility scheme. Inspired by the “explain” methods in many database methodologies.

Parameters

entry – A ComputedEntry.

get_corrections_dict(entry)[source]

Returns the corrections applied to a particular entry.

Parameters

entry – A ComputedEntry object.

Returns

value})

Return type

({correction_name

get_explanation_dict(entry)[source]

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.

Parameters

entry – A ComputedEntry.

Returns

(dict) of the form {“Compatibility”: “string”, “Uncorrected_energy”: float, “Corrected_energy”: float, “Corrections”: [{“Name of Correction”: { “Value”: float, “Explanation”: “string”}]}

process_entries(entries)[source]

Process a sequence of entries with the chosen Compatibility scheme.

Parameters

entries – A sequence of entries.

Returns

An list of adjusted entries. Entries in the original list which are not compatible are excluded.

process_entry(entry)[source]

Process a single entry with the chosen Corrections.

Parameters

entry – A ComputedEntry object.

Returns

An adjusted entry if entry is compatible, otherwise None is returned.

exception CompatibilityError[source]

Bases: Exception

Exception class for Compatibility. Raised by attempting correction on incompatible calculation

class Correction[source]

Bases: object

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.

correct_entry(entry)[source]

Corrects a single entry.

Parameters

entry – A ComputedEntry object.

Returns

An processed entry.

Raises

CompatibilityError if entry is not compatible. –

abstract get_correction(entry)[source]

Returns correction for a single entry.

Parameters

entry – A ComputedEntry object.

Returns

The energy correction to be applied.

Raises

CompatibilityError if entry is not compatible. –

class GasCorrection(*args, **kwargs)[source]

Bases: pymatgen.entries.compatibility.GasCorrection

Correct gas energies to obtain the right formation energies. Note that this depends on calculations being run within the same input set.

Pass through… :param args: :param kwargs: :return:

class MITAqueousCompatibility(compat_type='Advanced', correct_peroxide=True, check_potcar_hash=False)[source]

Bases: pymatgen.entries.compatibility.Compatibility

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.

Parameters

  • 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.

class MITCompatibility(compat_type='Advanced', correct_peroxide=True, check_potcar_hash=False)[source]

Bases: pymatgen.entries.compatibility.Compatibility

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.

Parameters

  • 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.

class MaterialsProjectAqueousCompatibility(compat_type='Advanced', correct_peroxide=True, check_potcar_hash=False)[source]

Bases: pymatgen.entries.compatibility.Compatibility

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.

Parameters

  • 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.

class MaterialsProjectCompatibility(compat_type='Advanced', correct_peroxide=True, check_potcar_hash=False)[source]

Bases: pymatgen.entries.compatibility.Compatibility

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.

Parameters

  • 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.

class PotcarCorrection(input_set, check_hash=False)[source]

Bases: pymatgen.entries.compatibility.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’].

Parameters

  • 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 –

get_correction(entry) → float[source]
Parameters

entry – A ComputedEntry/ComputedStructureEntry

Returns

Correction.

class UCorrection(*args, **kwargs)[source]

Bases: pymatgen.entries.compatibility.UCorrection

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.

Pass through… :param args: :param kwargs: :return: