UB Tools with Scolecite Data#

This tutorial demonstrates how to use the UB tools in NeuXtalViz to process TOPAZ Scolecite data (chemical formula \(\mathrm{CaAl_2Si_3O_{10}\cdot 3H_2O}\)).

Step 1: Convert to Q#

In the Convert to Q tab:

  • Select the TOPAZ instrument.

  • Enter the IPTS and run numbers for the Scolecite dataset.

  • (Optionally) set wavelength and calibration options as needed.

  • Click Convert to Q to load the data and build the Q volume.

../_images/Scolecite_UB_convert_Q.png

Convert Scolecite data to Q for TOPAZ.#

Step 2: Find peaks#

Still in the Convert to Q tab:

  • Adjust the peak-finding parameters (maximum number of peaks, density threshold, minimum distance).

  • Click Find Peaks to locate Bragg peaks in the Q volume.

../_images/Scolecite_UB_find_peaks.png

Find Bragg peaks in the Scolecite Q volume.#

Step 3: Primitive cell#

In the UB tab:

  • Set tolerances and cell-parameter bounds for the Niggli reduction.

  • Click Primitive Cell (Niggli) to search for a primitive cell consistent with the peak list.

../_images/Scolecite_UB_primitive_cell.png

Primitive cell solutions for Scolecite.#

Step 4: Conventional cell#

From the list of candidate cells:

  • Select the row corresponding to the desired conventional cell.

  • Click Select to adopt it as the working unit cell.

../_images/Scolecite_UB_conventional_cell.png

Select a conventional cell for Scolecite on TOPAZ.#

Step 5: Refine UB matrix#

With the conventional cell selected:

  • Choose an optimization mode (for example, Monoclinic).

  • Click Refine UB to refine the UB matrix against the peak list.

../_images/Scolecite_UB_refine_UB.png

Refined UB matrix for Scolecite.#

Step 6: View indexed peaks#

In the Peaks tab:

  • Select a peak in the table to highlight it in the Q-space view.

  • Inspect the indexing and fit quality.

../_images/Scolecite_UB_view_peak.png

View and inspect an indexed peak.#

Step 7: HKL slice view#

In the Convert to HKL tab:

  • Choose a slice direction and coordinate.

  • Click Convert to HKL to generate a reciprocal-space slice.

../_images/Scolecite_UB_slice_view.png

HKL slice view for the refined UB.#

Step 8: Save UB#

Back in the Convert to Q tab:

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

../_images/Scolecite_UB_save_UB.png

Save the refined UB matrix for Scolecite.#