UB Tools with Natrolite Data#

This tutorial demonstrates how to use the UB tools in NeuXtalViz to process CORELLI Natrolite data (chemical formula \(\mathrm{Na_2Al_2Si_3O_{10}\cdot 2H_2O}\)).

Step 1: Convert to Q#

In the Convert to Q tab:

Set the instrument to CORELLI.
Enter the IPTS and run numbers for the Natrolite dataset.
Set the wavelength range and select the appropriate calibration file.
Click Convert to Q to load the data and build the Q volume.

../_images/Natrolite_UB_convert_Q.png — Convert Natrolite data to Q for CORELLI.#

Step 2: Add reference peaks#

In the Inspect / Verify tab:

Use the horizontal, vertical, and diffraction controls to define a region of interest in the detector view.
Set the coordinates for the first reference reflection and click Add Peak to record it.

../_images/Natrolite_UB_first_peak.png — First reference peak for Natrolite on CORELLI.#

Adjust the ROI and diffraction coordinate for a second reflection and click Add Peak again.

../_images/Natrolite_UB_second_peak.png — Second reference peak for Natrolite on CORELLI.#

Step 3: Set initial UB from unit cell#

Back in the UB tools interface:

Enter approximate lattice parameters for Natrolite (a, b, c and angles \(\alpha\), \(\beta\), \(\gamma\)).
Click Set UB to construct an initial UB matrix from these lattice parameters and the reference peaks.

../_images/Natrolite_UB_set.png — Initial UB matrix based on the Natrolite unit cell.#

Step 4: Hand index reference peaks#

In the Peaks tab:

Select the first reference peak in the table.
Enter its expected (h, k, l) values in the hand-indexing fields.
Use the helper controls to copy the integer indices and calculate the predicted peak position.

../_images/Natrolite_UB_index_first_peak.png — Hand indexing the first Natrolite peak.#

Select the second reference peak and repeat the hand-indexing procedure for its (h, k, l) values.

../_images/Natrolite_UB_index_second_peak.png — Hand indexing the second Natrolite peak.#

Step 5: Refine UB matrix (constrained)#

Back in the UB tab:

Choose an optimization mode such as Constrained that reflects the expected symmetry.
Click Refine UB to refine the UB matrix using the indexed reference peaks.

../_images/Natrolite_UB_calculate_UB.png — Refined UB matrix for Natrolite on CORELLI (constrained).#

Step 6: Index peaks#

In the Peaks tab:

Switch to the indexing sub-tab if needed.
Click Index Peaks to apply the refined UB matrix to the peak list and assign Miller indices.

../_images/Natrolite_UB_index_peaks.png — Automatic indexing of Natrolite peaks.#

Step 7: Predict, integrate, and filter peaks#

In the Analyze Peaks workflow:

Use the Predict Peaks controls to propose additional peaks based on the current UB matrix and centering.

../_images/Natrolite_UB_predict_peaks.png — Predicted Natrolite peaks based on the refined UB.#

Enable adaptive and centroid options as needed and click Integrate Peaks to integrate the predicted peaks.

../_images/Natrolite_UB_integrate_peaks.png — Integrated Natrolite peaks.#

Apply a filter on peak intensity or signal-to-noise using the Filter Peaks controls to refine the working peak list.

../_images/Natrolite_UB_filter_peaks.png — Filtered Natrolite peak list.#

Step 8: Refine UB matrix (orthorhombic)#

Return to the UB tab:

Change the optimization mode to Orthorhombic (or another appropriate symmetry).
Click Refine UB again to update the UB matrix using the filtered, integrated peaks.

../_images/Si_UB_refine_UB.png — Final UB refinement for Natrolite on CORELLI.#

Step 9: View indexed peaks#

In the Peaks tab:

Select a peak from the table to highlight it in the Q-space view.
Inspect the indexing, Q position, and fit quality for the selected reflection.

../_images/Natrolite_UB_view_peak.png — View and inspect an indexed Natrolite peak.#

Step 10: Slice view#

In the Convert to HKL tab:

Choose a slice direction and coordinate.
Click Convert to HKL to generate a reciprocal-space slice based on the refined UB matrix.

../_images/Natrolite_UB_slice_view.png — HKL slice view for the refined Natrolite UB.#

Step 11: Save UB#

Back in the Convert to Q tab:

Click Save UB to write the refined UB matrix to disk for use in subsequent CORELLI Natrolite analysis.

../_images/Natrolite_UB_save_UB.png — Save the refined UB matrix for Natrolite.#