Section 3.3.10. Other pdCIF applications

It is common to simulate a diffraction pattern from a known or hypothetical structural model. The structural model is recorded in CIF using core data items, such as _atom_site_label, _atom_site_fract_x, _atom_site_fract_y, _atom_site_fract_z, _atom_site_U_iso_or_equiv and _atom_site_occupancy, as well as the unit cell in _cell_length_* and _cell_angle_*. Calculated reflection intensities can be recorded using _refln_index_* and _refln_F_squared_calc, as described in Section 3.3.5.4. The simulated pattern can be recorded using _pd_calc_* data items, as described in Section 3.3.5.2.

The simulated diffraction pattern will be determined not only by the structural parameters, but also by the type of experiment that is being simulated. For example, it is good practice to define data items to specify the type of radiation in _diffrn_radiation_probe, the wavelength in _diffrn_radiation_wavelength and the profile in _pd_proc_ls_profile_function.

For phase identification, a CIF will include unprocessed measurements, as described in Section 3.3.8. Sample characterization information, for example chemical analysis information, can often aid phase determination. Characterization information is described in Section 3.3.4.1. Similarly, sample preparation information can also be quite valuable (see Section 3.3.4.1). Since preferred orientation or other artifacts of the measurement can make phase identification more difficult, it is a good idea to include specimen preparation and mounting information, as described in Section 3.3.4.2.

Peaks will be located and documented in the peak table, as discussed in Section 3.3.5.3. In this case, it can be very helpful to specify _pd_peak_wavelength_id for peaks that are clearly a Kα₂ component. Similarly, recording a peak width can also be helpful for some autoindexing programs.

To identify peaks by phase in the case where at least one phase in a material is known but other peaks remain unidentified requires the use of a reflection table and a phase table, as shown in Example 3.3.10.1. This example shows a diffraction pattern with eight peaks, of which five have been identified as arising from a phase where the unit cell has not yet been determined. The peaks labelled B1, B2 and B3 are referenced in the peak table, but are not defined in the reflection loop. This implies that they arise from an unknown phase or phases. The remaining peaks A1 to A5 are referenced in the peak table. Note that the reflection table must include the _refln_index_* data items, even though no reflection indices are assigned. This is because CIF rules require that the _refln_index_* data items be present in this loop, as noted in the pdCIF dictionary definitions for _pd_refln_peak_id and _pd_refln_phase_id. The place holder ? is used to indicate that the reflection indices are not yet known.