Exporting structures to TCOD¶
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:
|0||Conversion of the StructureData to CifData||
|1||Detection of the symmetry and reduction to the unit cell||
|2||Niggli reduction of the unit cell||
|3||Addition of structure properties (total energy, residual forces)||
||Inline||PW and CP|
|4||Addition of the metadata for reproduction of the results||
|5||Depostition to the TCOD||
Type of each step’s calculation
defined in column Type. Each step is described in more detail below:
- Conversion of the StructureData to CifData
- Conversion between the
CifDatais 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 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
ParameterDatanodes and put into related TCOD CIF dictionaries tags using calculation-specific parameter translator, derived from
- 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
- Depostition to the TCOD
- Deposition of the final
CifDatato the TCOD is performed using cif_cod_deposit script from the codtools plugin.