Exporting structures to TCOD¶
Export of
StructureData
and
CifData
(or any other data type,
which can be converted to them) to the
Theoretical Crystallography Open Database (TCOD) can be divided into
following workflow steps:
No. | Description | Input | Output | Type | Implemented? |
---|---|---|---|---|---|
0 | Conversion of the StructureData to CifData | StructureData |
CifData |
Inline | + |
1 | Detection of the symmetry and reduction to the unit cell | CifData |
CifData |
Inline | + |
2 | Niggli reduction of the unit cell | CifData |
CifData |
Inline | — |
3 | Addition of structure properties (total energy, residual forces) | CifData ,
ParameterData |
CifData |
Inline | PW and CP |
4 | Addition of the metadata for reproduction of the results | CifData |
CifData |
Inline | ~ |
5 | Depostition to the TCOD | CifData |
ParameterData |
Job | + |
Type of each step’s calculation
(InlineCalculation
or JobCalculation
)
defined in column Type. Each step is described in more detail below:
- Conversion of the StructureData to CifData
Conversion between the
StructureData
andCifData
is done via ASE atoms object.
- Detection of the symmetry and reduction to the unit cell
Detection of the symmetry and reduction to the unit cell is performed using pyspglib.spglib.refine_cell() function.
- Niggli reduction of the unit cell
Reduction of the unit cell to Niggli cell is a nice to have feature, as it would allow to represent structure as an unambiguously selected unit cell.
- Addition of structure properties (energy, remaining forces)
The structure properties from the calculations, such as total energy and residual forces can be extracted from
ParameterData
nodes and put into related TCOD CIF dictionaries tags using calculation-specific parameter translator, derived fromBaseTcodtranslator
.
- Addition of the metadata for reproduction of the results
Current metadata, added for reproducibility, includes scripts for re-running of calculations, outputs from the calculations and exported subset of AiiDA database. It’s not quite clear what/how to record the metadata for calculations of type
InlineCalculation
.
- Depostition to the TCOD
Deposition of the final
CifData
to the TCOD is performed using cif_cod_deposit script from cod-tools package.