structure

The crystal structure to be used for the analysis. The input can be anything compatible with the Structure toolkit class. Accepted inputs include:

a filename (cif or poscar) (recommended)

yamltomlpython

structure: NaCl.cif

structure = NaCl.cif

structure="NaCl.cif"

a dictionary that points to a database entry.

yamltomlpython

# example 1
structure:
    database_table: MatprojStructure
    database_id: mp-123

# example 2
structure:
    database_table: StaticEnergy
    database_id: 50

# example 3
structure:
    database_table: Relaxation
    database_id: 50
    structure_field: structure_final

# example 1
[structure]
database_table: MatprojStructure
database_id: mp-123

# example 2
[structure]
database_table: StaticEnergy
database_id: 50

# example 3
[structure]
database_table: Relaxation
database_id: 50
structure_field: structure_final

# example 1
structure={
    "database_table": "MatprojStructure",
    "database_id": "mp-123",
}

# example 2
structure={
    "database_table": "StaticEnergy",
    "database_id": 50,
}

# example 3
structure={
    "database_table": "Relaxation",
    "database_id": 50,
    "structure_field": "structure_final",
}

Note

instead of database_id, you can also use the run_id or directory to indicate which entry to load. Further, if the database table is linked to multiple structures (e.g. relaxations have a structure_start and structure_final), then you can also add the structure_field to specify which to choose.

a Structure object (best for advanced logic)

python

from simmate.toolkit import Structure

structure = Structure(
    lattice=[
        [2.846, 2.846, 0.000],
        [2.846, 0.000, 2.846],
        [0.000, 2.846, 2.846],
    ],
    species=["Na", "Cl"],
    coords=[
        [0.5, 0.5, 0.5],
        [0.0, 0.0, 0.0],
    ],
    coords_are_cartesian=False,
)

a Structure database object

python

structure = ExampleTable.objects.get(id=123)

json/dictionary serialization from pymatgen