User Guidance

Single-Crystal Diffractometer

TOPAZ | BL-12 | SNS

TOPAZ is a neutron wavelength-resolved time-of-flight (TOF) Laue single-crystal diffractometer at the Spallation Neutron Source (SNS). This guide focuses on the steps most users need to get started: determine the UB matrix, plan sample orientations, reduce TOPAZ data to an HKL file, and continue to nuclear, magnetic, or diffuse-scattering analysis.

Start Here

TOPAZ Introduction
NDIP Single Crystal Diffraction - launch TOPAZ Data Reduction, JANA2020, Olex2, ShelXle, DISCUS, and NeuXtalViz.
NeuXtalViz TOPAZ Tutorials - determine/refine the UB matrix, plan the experiment, and inspect reciprocal space.
Single-Crystal Diffraction Documentation - common ORNL workflows, software resources, and examples.
SNS Remote Analysis Service - access TOPAZ experiment files and analysis systems in a web browser.

TOPAZ workflow:
UB matrix → experiment plan → data collection → TOPAZ Data Reduction (ReductionGUI) → HKL → nuclear or magnetic structure refinement.

Diffuse-scattering workflow:
UB matrix → GARNET → normalized 3D reciprocal-space data → 3D-ΔPDF and/or diffuse-scattering modeling.

Access TOPAZ Data and Software

TOPAZ experiment data are stored under:

/SNS/TOPAZ/IPTS-#####/

where IPTS-##### is the experiment proposal number. Use the experiment shared area for analysis products and files used with the TOPAZ team:

/SNS/TOPAZ/IPTS-#####/shared/

NDIP Single Crystal Diffraction - launch the main single-crystal applications without installing software locally.
SNS Remote Analysis Service - work directly with IPTS files and Mantid-based workflows.
ONCat - find run numbers, sample conditions, acquisition times, and experiment metadata.

The NDIP application page should be treated as the authoritative source for the currently deployed software versions.

1. Find and Refine the UB Matrix

A reliable orientation matrix (UB) is required for experiment planning, indexing, and integrated-intensity reduction. Use NeuXtalViz UB Tools with one or more initial TOPAZ runs.

Load TOPAZ data. Enter the IPTS and representative run numbers containing clear Bragg peaks.
Find peaks and convert to reciprocal space.
Determine the unit cell. Inspect candidate primitive and conventional cells and select the crystallographically appropriate cell.
Index and refine. Refine the UB matrix using the appropriate lattice constraints and review the indexing statistics.
Verify visually. Overlay indexed peaks on the reciprocal-space data and inspect systematic unindexed intensity before saving the UB matrix.

Tutorials:

Most strong Bragg peaks should be indexed by the selected cell and UB matrix. Systematic unindexed peaks can indicate a second domain, twinning, a superstructure, modulation, or magnetic scattering.

If satellite reflections are present, use the NeuXtalViz Modulation Tools to identify candidate modulation vectors before final integration.

2. Plan the Experiment

After obtaining a stable UB matrix, use the NeuXtalViz Experiment Planner to choose sample orientations that provide the reciprocal-space coverage required for the experiment.

Load the refined UB matrix.
Define the crystallographic cell and the reciprocal-space region or reflection set of interest.
Simulate detector coverage for a candidate sample orientation.
Add orientations to fill missing reciprocal-space regions and improve completeness and redundancy.
Save the orientation plan and revise it if the measured diffraction differs from expectation.

See Experiment Plan with Silicon Data for a step-by-step TOPAZ example.

During data collection, inspect representative peaks and reciprocal-space slices before committing to the full orientation series. Check the UB matrix, peak shapes and mosaicity, unindexed peaks, satellites, and the reciprocal-space regions being measured.

3. Run TOPAZ Data Reduction (ReductionGUI)

For standard Bragg diffraction, the immediate reduction goal is a corrected, integrated HKL reflection file for nuclear or magnetic structure analysis. Open NDIP Single Crystal Diffraction and start TOPAZ Data Reduction.

For experiments using the shared analysis directories, reduction and calibration files are normally kept under:

/SNS/TOPAZ/IPTS-#####/shared/ReductionGUI/
/SNS/TOPAZ/IPTS-#####/shared/calibration/

Before running the final reduction, confirm:

IPTS number and run list;
the refined UB matrix for the mounted crystal;
integration settings appropriate for the measured peak shape and mosaicity;
sample information required for wavelength-dependent absorption correction; and
any special handling required for multiple domains, satellite reflections, or magnetic peaks.

The TOPAZ reduction workflow indexes and integrates reflections and applies the instrument- and sample-dependent corrections required to place observations on a consistent intensity scale. These include incident-spectrum, detector-response, Lorentz, and wavelength-dependent sample-absorption corrections. Extinction is normally handled during structure refinement when required.

Primary output: TOPAZ integrated reflections can be exported in SHELX HKLF 2 TOF-Laue format. Each observation retains the Miller indices, integrated intensity and uncertainty, batch identifier, and neutron wavelength.

Before proceeding to refinement, inspect representative strong, medium, and weak reflections. Check integration, background, detector-edge cases, overlapping peaks, and any wavelength- or run-dependent anomalies.

4. Nuclear and Magnetic Structure Analysis on NDIP

After ReductionGUI produces the HKL file, continue directly on the NDIP Single Crystal Diffraction platform.

JANA2020 - nuclear and magnetic structures, twinning, multiple domains, commensurate or incommensurate modulation, and superspace refinement.
Olex2 - conventional small-molecule and inorganic structure solution and refinement.
ShelXle - graphical interface for standard SHELX refinement workflows using TOPAZ HKL data.
NeuXtalViz - reciprocal-space and crystal-structure visualization before and alongside refinement.

For magnetic diffraction, first establish which reflections or satellites are magnetic, determine the propagation vector when applicable, and use magnetic symmetry or representation analysis before refinement. JANA2020 is the preferred NDIP environment for combined nuclear/magnetic refinement, multiple propagation vectors, modulation, or complex symmetry.

Additional software and refinement resources are available on the Single-Crystal Diffraction Software Resources page.

5. Diffuse Scattering: GARNET and 3D-ΔPDF

Diffuse-scattering experiments follow a different analysis path from Bragg-only structure refinement. For TOPAZ, use GARNET for reciprocal-space reconstruction and normalization, followed by 3D-ΔPDF and/or model-based diffuse-scattering analysis.

Determine a reliable UB matrix.
Reconstruct and normalize with GARNET. Combine the selected orientations into an HKL reciprocal-space volume using the appropriate normalization and corrections.
Inspect the 3D diffuse intensity. Use slices and cuts to distinguish structured diffuse scattering from Bragg tails, background, and artifacts.
Calculate the 3D-ΔPDF when appropriate. Use Mantid DeltaPDF3D or NeuXtalViz to transform diffuse intensity into real-space pair correlations.
Model the disorder. Use DISCUS on NDIP or other specialized software when quantitative atomistic or defect modeling is required.

See NeuXtalViz 3D-ΔPDF with Tb₅Ru₆Sn₁₈ Data for step-by-step TOPAZ example.

See the Single-Crystal Diffraction Software Resources page for additional diffuse-scattering tools.

Useful Links for TOPAZ Users

Publications and Acknowledgment

Publications containing TOPAZ data should include the required facility acknowledgment:

This research [or, A portion of this research] used resources at the Spallation Neutron Source, a DOE Office of Science User Facility operated by the Oak Ridge National Laboratory.

Instrument reference: Coates L., Cao H.B., Chakoumakos B.C., Frontzek M., Hoffmann C., Kovalevsky A., Liu Y., Meilleur F., dos Santos A.M., Myles D.A., Wang X.P., Ye F., "A suite-level review of the neutron single-crystal diffraction instruments at Oak Ridge National Laboratory", Review of Scientific Instruments, 89, 092802 (2018).

Please submit publications, theses, patents, and other research products to PuSH (Publications of SNS and HFIR).

Need Help?

Contact the TOPAZ Instrument Team for experiment-specific questions about UB determination, experiment planning, integration, absorption, twinning, modulation, magnetic diffraction, or diffuse scattering. For computing and data-access problems, use the support information on the Single-Crystal Diffraction Documentation and Data Management pages.