How to setup structures

There are two ways to feed your initial structure to aiida-supercell, i.e. CIF as SinglefileData and structure stored as StructureData object. Below, you can find cons and pros for each of options.


We normally access to the structure of disordered solids via CIF where partial occupancy of each site is provided. It also can contain the formal charges for each site. The most straightfoward way to use aiida-supercell is storing the CIF as SinglefileData and then use it for the calculations:

from aiida.orm import DataFactory
SinglefileData = DataFactory('singlefile')
singlefileobject = SinglefileData(file=absolute_path/to/CIF)

If this step is done detached from submission script, the created AiiDA object needs to stored and the pk or uuid needs to be recorded for actual calculations:

<SinglefileData: uuid: 10419a5f-dd70-4659-bb13-e33544d2724f (unstored)>
singlefileobject = SinglefileData(path=path/to/CIF).store()

Providing formal charges

In case you would like to provide the formal charges within the CIF, charges are needed to be defined as:

Ca1  +2
AlT1 +3
AlT2 +3
SiT2 +4
O1   -2
O2   -2
O3   -2

while _atom_type_symbol has to be same as _atom_site_label as below:

Ca1   0.33750 0.16250 0.51100 1.00000
AlT1  0.00000 0.00000 0.00000 1.00000
AlT2  0.14310 0.35690 0.95280 0.50000
SiT2  0.14310 0.35690 0.95280 0.50000
O1    0.50000 0.00000 0.18840 1.00000
O2    0.14180 0.35820 0.28320 1.00000
O3    0.08720 0.17060 0.80330 1.00000


The other way to provide structure, is reading the structure and then storing it as StructureData. It needs to be carefully checked by user whether the partial occupancies are read and written correctly.

from pymatgen.core import Structure
from aiida.orm import DataFactory

StructureData = DataFactory('structure')
strc_pmg = Structure.from_file('path/to/CIF')
structure = StructureData(pymatgen_structure=strc_pmg)

Providing formal charges

In this case, providing formal charges should be done through charges input parameter.