Structure Database Module

Implements StructureDB: a minimalist SQLite database for storing SmactStructure-compatible POSCAR files.

Tools for database interfacing for high throughput IO.

class smact.structure_prediction.database.StructureDB(db: str)[source]

Bases: object

SQLite Structure Database interface.

Acts as a context manager for database interfacing and wraps several useful SQLite commands within methods.

db: The database name.

conn: The database connection. Only open when used as a context manager.

cur: The database connection cursor. Only usable when class implemented as context manager.

Examples

Connecting to a database in memory:

>>> DB = StructureDB(':memory:')
>>> with DB as c:
...     _ = c.execute("CREATE TABLE test (id, val)")
...     c.execute("SELECT * FROM test").fetchall()
[]
>>> DB.cur.execute("SELECT * FROM test").fetchall()
Traceback (most recent call last):
    ...
sqlite3.ProgrammingError: Cannot operate on a closed database.

add_mp_icsd()[source]

Add a table populated with Materials Project-hosted ICSD structures.

Note

This is very computationally expensive for large datasets and will not likely run on a laptop. If possible, download a pre-constructed database.

Parameters

table (str) – The name of the table to add.
mp_data – The Materials Project data to parse. If this is None, data will be downloaded. Downloading data needs mp_api_key to be set.
mp_api_key (str) – A Materials Project API key. Only needed if mp_data is None.

Returns

The number of structs added.

add_struct(struct: SmactStructure, table: str)[source]

Add a SmactStructure to a table.

Parameters

struct – The SmactStructure to add.
table – The name of the table to add the structure to.

add_structs(structs: Sequence[SmactStructure], table: str, commit_after_each: Optional[bool] = False) → int[source]

Add several SmactStructures to a table.

Parameters

structs – Iterable of SmactStructure s to add to table.
table – The name of the table to add the structs to.
commit_after_each (bool, optional) – Whether to commit the addition after each structure is added. This is useful when adding a large number of structures over a long timeframe, as it ensures some structures are added, even if the program terminates before completion. Defaults to False.

Returns

The number of structures added.

add_table(table: str)[source]

Add a table to the database.

Parameters: table – The name of the table to add

get_structs(composition: str, table: str) → List[SmactStructure][source]

Get SmactStructures for a given composition.

Parameters

composition – The composition to search for. See SmactStructure.composition().
table – The name of the table in which to search.

Returns

A list of SmactStructure s.

get_with_species(species: List[Tuple[str, int]], table: str) → List[SmactStructure][source]

Get SmactStructures containing given species.

Parameters

species – A list of species as tuples, in (element, charge) format.
table – The name of the table from which to get the species.

Returns

A list of SmactStructure s in the table that contain the species.

smact.structure_prediction.database.parse_mprest()[source]

Parse MPRester query data to generate structures.

Parameters

data – A dictionary containing the keys ‘structure’ and ‘material_id’, with the associated values.
determine_oxi (str) – The method to determine the assignments oxidation states in the structure. Options are ‘BV’, ‘comp_ICSD’,’both’ for determining the oxidation states by bond valence, ICSD statistics or trial both sequentially, respectively.

Returns

An oxidation-state-decorated SmactStructure.