DBClasses module

class DBClasses.MDAbadParameters(*args, **kwargs)

Bases: HttkObject

Auxiliary geometric parameters for post-processing and filtering.

Stores additional values computed from relaxed structures that are used in downstream analysis (e.g., defect depth and expansion filtering).

key

Defect key linking these parameters to a defect entry.

Type:

int

depth

Defect depth metric (typically along the surface normal / z-direction).

Type:

float

expansion_factor

Relative expansion measure used to detect unstable/”exploded” runs.

Type:

float

defect_index

Index of the defect atom in the atom list used for depth calculations.

Type:

int

lattice_constant

Lattice constant metric used for later analysis.

Type:

float

Notes

The httk_typed_init schema in the decorator should include lattice_constant if it is intended to be stored in the database.

class DBClasses.MDDefectCell(*args, **kwargs)

Bases: HttkObject

Database object for a relaxed defect structure.

Stores the relaxed defect cell structure associated with a host material and a defect name/key.

host_name

Name/identifier of the host material (often includes method tags like “_PBE”).

Type:

str

defect_structure

Relaxed structure stored in HTTK format.

Type:

httk.atomistic.Structure

defect_name

Defect identifier (often includes dopant and configuration label).

Type:

str

key

Unique defect key used to join against other tables/results.

Type:

int

class DBClasses.MDDefectInfos(*args, **kwargs)

Bases: HttkObject

Metadata container for defect classification and search.

Stores human- and workflow-friendly defect metadata such as defect type, configuration identifier, and boolean flags (vacancy/substitutional/interstitial). Intended primarily for searching and filtering defects in the database.

key

Unique identifier for the defect entry.

Type:

int

host_name

Name/identifier of the host material.

Type:

str

defect_name

Name/identifier of the defect (often includes dopant and site/type).

Type:

str

defect_type

High-level defect category label.

Type:

str

configuration

Configuration label (e.g., site index or symmetry-derived tag).

Type:

str

vacancy

True if the defect is a vacancy type.

Type:

bool

substitutional

True if the defect is substitutional.

Type:

bool

interstitial

True if the defect is interstitial.

Type:

bool

class DBClasses.MDDelta(*args, **kwargs)

Bases: HttkObject

Store stability delta between interstitial and adatom configurations.

The delta is defined as:

delta = E_interstitial_min - E_adatom_min

Interpretation

• delta < 0: interstitial is more stable

• delta > 0: adatom is more stable

host

Host material identifier.

Type:

str

dopant

Dopant identifier.

Type:

str

defect

Defect name corresponding to the chosen minimum-energy configuration.

Type:

str

key

Defect key corresponding to defect.

Type:

int

delta

Energy difference in eV (as defined above).

Type:

float

class DBClasses.MDScreenResult(*args, **kwargs)

Bases: Result

Store stability delta between interstitial and adatom configurations.

The delta is defined as:

delta = E_interstitial_min - E_adatom_min

Interpretation

• delta < 0: interstitial is more stable

• delta > 0: adatom is more stable

host

Host material identifier.

Type:

str

dopant

Dopant identifier.

Type:

str

defect

Defect name corresponding to the chosen minimum-energy configuration.

Type:

str

key

Defect key corresponding to defect.

Type:

int

delta

Energy difference in eV (as defined above).

Type:

float