International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 3.3, pp. 126-128

Section 3.3.8. pdCIF for storing unprocessed measurements

B. H. Tobya*

aNIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562, USA
Correspondence e-mail: brian.toby@nist.gov

3.3.8. pdCIF for storing unprocessed measurements

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While many researchers prepare a CIF only when a project is complete, there are good reasons for preparing a pdCIF when the diffraction data are measured, as this is the best time to document how the measurement was performed. Much of the instrumental information will remain unchanged for all pdCIFs from a given diffraction instrument, so it is a good idea to prepare a file that describes each of the common settings for an instrument. This file will probably contain some of the following data items and their associated values:

(i) The _pd_instr_* items, such as the instrument type in _pd_instr_geometry, the size of the instrument and the collimation in _pd_instr_dist_* and _pd_instr_divg_*, and monochromatization in _pd_instr_monochr_* (see Section 3.3.4.3[link])

(ii) Depending on how the calibration is performed, it may be appropriate to include _pd_calib_* items.

(iii) Information about the radiation source should be specified using the _diffrn_radiation_* and _diffrn_source_* data items.

(iv) Detector information should be specified using _diffrn_detector_* items, for example, the detector type in _diffrn_detector_type and perhaps calibration values such as the deadtime (in _diffrn_detector_dtime).

A second section of the pdCIF will contain information specific to the experiment, such as the diffraction conditions (i.e. pressure and temperature) recorded using the _diffrn_ambient_* data items. Sample and specimen information will appear in the _pd_prep_*, _pd_spec_* and _pd_char_* data items.

A third section of the pdCIF contains the observations. The data items used to specify the unprocessed observations will vary with the type of instrument used, as described in Sections 3.3.8.1[link] to 3.3.8.10 below.

3.3.8.1. Single pulse-counting detectors

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In the most common measurement method, where a single pulse-counting detector is scanned over a range of [2\theta], the _pd_meas_* entries (see Section 3.3.4.4[link]) will be of the form shown in Example 3.3.8.1[link]. If the data were scanned using a variable step size, the observations might be given as shown in Example 3.3.8.2[link]. Note that when _pd_meas_counts_* is used, the values given must be counts, so that the standard uncertainty will be the square root of the intensity values. This means that the intensity values must not be scaled, for example if the values were counts per second; otherwise the statistical uncertainty estimates will be incorrect.

Example 3.3.8.1. Measurements from a single pulse-counting detector with constant-step scan.

[Scheme scheme27]

Example 3.3.8.2. Measurements from a single pulse-counting detector with variable-step scan.

[Scheme scheme28]

3.3.8.2. Detectors that do not count pulses

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When the method used to detect intensities does not count individual quanta as they hit the detector, for example, the digitization of intensities recorded on film or on an imaging plate, or even with data recorded using a detector having a built-in deadtime correction, the standard-uncertainty values are not the square root of the intensities. [Note that when the actual deadtime correction is known, it is best to incorporate this scaling into the monitor value (see _pd_meas_counts_monitor in Section 3.3.4.4[link]) or else save the uncorrected measurements and create a second set of corrected intensity values as _pd_proc_intensity_net (see Section 3.3.5.1[link]).] The _pd_meas entries for an experiment using non-pulse-counting detection will look like the examples given in Section 3.3.8.1[link], except that the data loop will be in the form [Scheme scheme29] or [Scheme scheme30] If standard uncertainties for the intensity values are known, they can be given using the conventional notation [Scheme scheme31] Note that when _pd_meas_intensity_* is used, it is best to specify _pd_meas_units_of_intensity as well.

3.3.8.3. Multiple detectors

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At present, CIF does not offer the ability to construct true multi-dimen­sional data structures. However, many instruments with multiple detectors produce reasonably tractable numbers of data points. For such instruments, it is possible to include an additional data item, _pd_meas_detector_id, in the loop with the data to indicate the detector that made the observation.

In Example 3.3.8.3[link], four detectors placed 20° apart are referenced with arbitrarily chosen labels A, B, C and D. Note that the detector characteristics will typically be specified in a separate calibration loop containing terms such as _pd_calib_detector_id, _pd_calib_detector_response and _pd_calib_2theta_offset. The labels given for _pd_calib_detector_id should match those in _pd_meas_detector_id.

Example 3.3.8.3. Identifying intensities from multiple detectors.

[Scheme scheme32]

3.3.8.4. Energy-dispersive X-ray detection

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For energy-dispersive X-ray diffraction, an X-ray detector is placed at a fixed value of [2\theta] and a diffractogram is measured on a multichannel analyser. The channel number is then calibrated to yield photon energies. From the energy and [2\theta] angle, a d-spacing or Q value [(Q = 4 \pi\sin\theta/\lambda)] is calculated for each diffraction point. Note that energy, d spacing or Q are not the experimental independent variable. Rather, they result from processing, since calibration information is required. The calibration equation should be described in _pd_calibration_conversion_eqn.

In Example 3.3.8.4[link], the nominal [2\theta] setting is 6.5°, but the actual position (determined by prior calibration) is 6.6071°, so the difference is indicated using a _pd_calib_2theta_offset value (see Section 3.3.4.3[link]).

Example 3.3.8.4. Measurements from an energy-dispersive X-ray diffraction experiment.

[Scheme scheme33]

3.3.8.5. Neutron time-of-flight detection

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Neutron time-of-flight (TOF) detection in theory should be no different from energy-dispersive X-ray detection, but TOF instruments record complex three-dimensional data structures, where diffraction intensities are recorded as a function of time for as many as several hundred detectors. For some instruments, both the position along the detector and the time of flight are recorded, so there may be effectively thousands of detectors. To add even further complexity, the data may be binned in different time steps for detectors at different [2\theta] values. CIF is likely to be cumbersome for the storage of unprocessed measurements from TOF instruments, owing to the one-dimensional nature of CIF, but it could be useful to translate files from one binary format to another using CIF as a common intermediate. To do this, a single loop is used for all data points, where each detector (or detector section, in the case of a position-sensitive detector) is assigned a detector ID. In a second loop, the detector ID values are defined. In addition to [2\theta], _pd_meas_angle_omega and _pd_meas_angle_chi are defined where needed (Example 3.3.8.5[link]).

Example 3.3.8.5. Measurements from a neutron time-of-flight diffraction experiment.

[Scheme scheme34]

TOF data are usually reduced to a small number of `banks' consisting of intensity as a function of d space or Q, where multiple detectors are summed. Data in this form can be recorded using a loop containing _pd_proc_d_spacing and _pd_proc_intensity_net. A data block is needed for each bank.

3.3.8.6. Digitized film and image plates

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To record intensities from digitized X-ray film or from image plates properly requires the storing of two-dimensional data structures, which in some cases can be accommodated through imgCIF (see Chapters 2.3[link] and 3.7[link] ). However, it is possible to record a one-dimensional scan using _pd_meas_position and _pd_meas_intensity_total (not _pd_meas_counts_total!). _pd_proc_2theta_corrected values can then be assigned using calibration information, and they can then be included in the same loop, as in Section 3.3.8.4[link].

3.3.8.7. Direct background measurements

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For some diffraction experiments, particularly for the determination of radial distribution functions, measurements are made for background scattering from the diffraction instrument and from the sample container. When this is done, the values can be included in a single loop using _pd_meas_counts_background, _pd_meas_counts_container and _pd_meas_counts_total.

3.3.8.8. Noting sample orientation

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For texture measurements, intensity measurements can be made as a function of different sample setting angles. These setting angles can be specified using _pd_meas_angle_chi, _pd_meas_angle_omega and _pd_meas_angle_phi. The change in these values may be specified by including these data items in the loop with the diffraction intensities. In some cases, it may be more convenient to separate measurements with different setting angles into different blocks. In this case, the values for the setting angle(s) that are invariant will be set outside of a loop.

It is common in powder diffraction to reduce preferred orientation and improve crystallite averaging by rocking or rotating the sample. This is indicated by specifying the axis used for rocking, usually [\varphi] for capillary specimens or [\chi] for flat-plate specimens, as _pd_meas_rocking_axis. The data item _pd_meas_rocking_angle is used to record the angular range through which the sample is rocked, where 360 indicates that one complete revolution occurs during each counting period. Numbers greater than 360 are possible.

3.3.8.9. Use of an incident-intensity monitor

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For radiation sources for which the intensity may vary, such as synchrotron-radiation sources, the intensity of the incident radiation is measured using an incident-intensity monitor. This value may be specified for every data point using _pd_meas_counts_monitor (or _pd_meas_intensity_monitor) by including this data item in the loop with the diffraction intensities. For some instruments, counting times are set so that the same number of monitor counts are measured for each data point. If this is the case, _pd_meas_counts_monitor will be the same for every data point and need not be included in the loop.

3.3.8.10. Recording detector livetime

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The detector deadtime is often more a function of the counting electronics than of the intrinsic properties of the detector. In these circumstances, the counting circuit may provide a gating signal that indicates when the electronics are processing an event versus when the circuit is idle and waiting for an event to process. From this gating signal, a detector livetime signal can be generated. Livetime is a better way to correct intensities than applying a deadtime correction, because if appreciable numbers of events are processed but are not counted (for example, counts due to fluor­escence), the actual deadtime can be quite high, even though the recorded number of counts can be quite low. To use the livetime signal, the count time can be multiplied by the livetime or the livetime can be treated as a monitor (see Section 3.3.8.9[link]). If an incident-intensity monitor and a livetime are both available, the _pd_meas_intensity_monitor value can contain the incident intensity times the livetime.








































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