Structure¶
A structure describes a crystalline phase used to calculate diffraction. It combines a symmetry setting, unit-cell geometry and atom sites. It can be imported from a structural CIF or assembled from crystallographic information.
Symmetry and setting¶
The space group and its setting determine which positions and cell parameters are independent. Check that the chosen setting matches the coordinate system of the structural data you are using.
A symmetry-related value is not an additional independent fitting direction. A table can display several coordinates or cell dimensions even when symmetry relates or fixes them. Symmetry is one of several reasons a fit cannot vary a value; see free and fixed.
Unit cell¶
Cell lengths and angles define the repeating geometry. Their units and allowed relationships depend on the crystallographic setting. Inspect the starting calculated reflection positions before fitting the cell: an instrumental calibration error can also move peaks.
Atom sites¶
| Quantity | Meaning | What to inspect |
|---|---|---|
| Site label and element | Identify the site and its scattering species | Consistency with the intended composition |
| Fractional coordinates | Locate the representative site in the unit cell | Coordinate setting, symmetry and plausible geometry |
| Occupancy | Describes occupation of the site | Composition and relationships between species sharing a site |
| Displacement parameters | Describe displacement around the average position | Isotropic/anisotropic convention, units and physically meaningful values |
| Wyckoff position | Describes the site's symmetry position | Restrictions on coordinates and site multiplicity |
Keep the displacement convention used by the source structure; quantities expressed with different conventions should not be compared by name alone. Use parameters for free/fixed values, uncertainty and constraints.
A structure file¶
A structure is saved as one .edi data block. The example below is structures/lif.edi from the LiF project: the symmetry, unit cell and atom sites described above map directly onto its keys.
data_lif
_edi.schema_version 3
_cell.length_a 4.0267
_cell.length_b 4.0267
_cell.length_c 4.0267
_cell.angle_alpha 90.
_cell.angle_beta 90.
_cell.angle_gamma 90.
_space_group.name_h_m "F m -3 m"
_space_group.coord_system_code 1
loop_
_atom_site.id
_atom_site.type_symbol
_atom_site.fract_x
_atom_site.fract_y
_atom_site.fract_z
_atom_site.wyckoff_letter
_atom_site.occupancy
_atom_site.adp_iso
_atom_site.adp_type
Li1 Li 0. 0. 0. a 1. 1.2 Biso
F1 F 0.5 0.5 0.5 b 1. 0.8 BisoA structure imported from a CIF uses the same layout. See data formats for how .edi relates to CIF.
Phases and experiment links¶
A project may contain several structures. An experiment links the structures that contribute to its calculated pattern, with a scale for each link. Adding a structure to the project does not by itself establish that it contributes to every measurement.
Check which phases should contribute and whether their links are enabled. Structural quantities describe the sample; background and peak-profile terms belong to the experiment even though they also affect the calculated pattern.
Edit structures in the or , then calculate the saved model from Command line.