SRS mail-in

The Structural Sciences group now has official mail-in total scattering [PDF] (11-ID-B) and rapid acquisition powder diffraction [XRD] (17-BM) programs. Total scattering data (11-ID-B) OR powder diffraction data (17-BM) can be acquired for up to 40 samples per proposal. Currently, we only offer these services for solid/powder samples at ambient conditions. Previous experience handling 2-D image data from area detectors and extracting PDFs is strongly recommended. Rapid access mail-in proposals can be submitted to the APS proposal system.

Frequently asked questions

General

How do I get mail-in PDF/XRD for my samples?

1. Submit a rapid access mail-in proposal [NOT regular rapid access] to 11-ID-B (PDF) or 17-BM (XRD).
2. Request sample cartridges (link included in automated email)
3. Receive mail-in kit with supplies and detailed instructions on sample preparation and registration.
4. Register samples, then ship back to 11-ID-B or 17-BM.
5. After receiving notification, download data from Globus.

Can I get XRD and PDF on the same samples?

Currently, we are only offering mail-in PDF at 11-ID-B. 17-BM offers mail-in rapid acquisition XRD. Separate rapid access mail-in proposals must be submitted to 11-ID-B and 17-BM.

How many samples can be run under each proposal?

Each sample cartridge holds up to 20 sample capillaries. A maximum of 2 cartridges can be requested per mail-in proposal.

What type of samples can be run?

Samples must be solid/powder and fit into a 1.1 mm OD capillary. Pre-cut kapton capillaries of the appropriate size will be provided with the mail-in kit. Samples will be run on a rolling basis as time permits during the run. We CANNOT guarantee that samples will be run immediately after receipt. Samples that cannot be stored at ambient conditions for weeks should not be submitted to the mail-in program.

What equipment/materials do I need to prepare my samples?

The mail-in kit contains either 1 or 2 pre-labelled 20-capillary holders, 20 or 40 pre-cut kapton (polyimide) capillaries, rubber bands, bubble wrap, an address label, and printed instructions. We do not provide any other type of capillaries in the mail-in kit. You will need to provide your own epoxy/clay/etc. to seal both ends of your samples.

How do I prepare my sample capillaries?

Detailed instructions will be included in your mail-in kit.

1. Use clay or epoxy (preferred) to plug one end of the capillary. The length of the plug should be no larger than 2 mm. We discourage the use of wax to seal capillaries.
2. Load sample powder from the other end. The filling length should be no less than 7 mm. When the loaded capillary is placed into the cassette, the powder should fill the entire gap in the holder. No clay or empty capillary should be present in the gap region.
3. Plug the other end with clay or epoxy. Be sure there is no clay or epoxy left on the outside surface of the capillary, or the capillary may not be able to fit into the hole of the cassette holder. Do not place labels or tape on the outside of the capillary.

How should I load the sample cartridges?

1. Load your first sample into position 1. Attention: position 1 is actually the SECOND hole from the left. Leave the hole to the left to position 1 open. Beamline staff will place a CeO2 standard in the leftmost hole (position 0).
2. Continue until you load all your samples, or you reach positon 20. Leave the open hole after position 20 empty. For total scattering/PDF, you must include an empty capillary as one of your 20 samples.
3. Submit sample registration information using the link provided in the proposal approval email. You must provide position number and the corresponding chemical name for every sample. Any empty capillary should be registered as “empty polyimide tubing” (if kapton). For total scattering/PDF, you should provide the stoichiometry in addition to the chemical name. Chemical formulas, broad categories, or sample codes alone are NOT acceptable.

The rubber bands are difficult to handle. Any tips?

Tweezers help a lot if you have short nails, fake nails (tested by beamline staff!), or are working in a glovebox. A spare set of rubber bands has been included in your mail-in kit in the bag of capillaries.

I broke, lost, or ran out of <X>. Where can I get replacement parts and/or extra materials?

Cartridges: Sample cartridges are 3-D printed at the APS. Contact 11-ID-B staff if you need a replacement cartridge. Due to differences in the resolution of various 3-D printers and materials used, it is not currently a viable option to have users print their own replacements.

Capillaries: Additional capillaries can be purchased from Cole-Parmer at the link below. You will need to cut the capillaries into 17.5 mm lengths. https://www.coleparmer.com/i/cole-parmer-polyimide-tubing-0-0395-id-x-0-0435-od-five-12-l-pack/9582009

Rubber bands: Small poly bands (hair elastics) can be purchased at any pharmacy or beauty supply store.

Clay: Modelling clay can be purchased at any arts and crafts store.

Epoxy: 5 minute epoxy can be purchased at any hardware store.

When can I ship my samples to the beamline?

You must complete your sample registration AND confirmation before beamline staff will approve your ESAF. Do not ship your samples until you receive notification that your ESAF has been approved.

How can I access my data?

TIFs containing 2-D diffraction data of your samples and an appropriate calibrant will be uploaded to Globus into the aps#data collection at /gdata/dm/11IDB/GUP-<mailin proposal number>/ . To retrieve your data, follow the steps below:

1. Using a web browser, navigate to https://www.globus.org/
2. Create a Globus account if you do not already have one and sign in with your Globus username.
3. Choose "aps#data" endpoint (collection) and click "Continue" in order to authenticate.
4. Authenticate with your DM username (typically "d<badge number>"). Use the same password that you use to access APS Beamline User Portal.
5. Navigate to experiment folder (path) /gdata/dm/11IDB/GUP-<mailin proposal number>/
6. Click “Transfer or Sync to..” and select the Globus endpoint you wish to transfer your data to. If using your local computer as an endpoint, you will need to install Globus Personal Connect.

Additional instructions on transferring files to your local computer in Globus are available at https://docs.globus.org/how-to/get-started/

Globus Connect Personal is available at https://www.globus.org/globus-connect-personal

What data is provided?

Powder diffraction data is collected on area detectors and saved as TIFs. This 2-D data must be masked and reduced to 1-D diffraction data by the end user before PDFs can be extracted. The following files will be provided for each experiment:

<cartridge_barcode>_<samplenumber>.tif: TIFF image containing 2-D diffraction data for sample <samplenumber>.

<cartridge_barcode>_<samplenumber>.tif.metadata: text file (human-readable) containing the wavelength, detector distance, and numerous other parameters for sample <samplenumber>. This file enables GSAS-II to automatically detect the wavelength and nominal detector distance.

<cartridge_barcode>_0.tif: TIFF image containing 2-D diffraction data of CeO2 (11-ID-B) or LaB6 (17-BM). This should be used to determine appropriate calibration parameters.

What do I do with these TIFs?

Diffraction data are acquired as images on a large flat panel detector. You will need to mask and reduce these 2-D diffraction images to 1-D diffraction patterns before extracting pair distribution functions (total scattering data only) or any sort of modelling (diffraction or total scattering). Masking, data reduction and PDF extraction are the responsibility of the user. A number of software packages for reduction of images to diffraction patterns are freely available, including GSAS-II, FIT2D and pyFAI. Tutorials for data reduction in GSAS-II (calibration and integration) are available at https://subversion.xray.aps.anl.gov/pyGSAS/trunk/help/Tutorials.html .

11-ID-B/PDF specific

How soon will I get my data?

Samples will be run on a rolling basis as time permits during the run. We CANNOT guarantee that samples will be run immediately after receipt. Samples that cannot be stored at ambient conditions for weeks should not be submitted to the mail-in program. Samples received during the last two weeks of the run or during shutdowns may not be run until the following cycle (~6 weeks). You will be notified by email when your data is available.

What control samples, calibrants, etc do I need for PDF as compared with powder diffraction?

In addition to your samples of interest, it is your responsibility to include an empty capillary of each type in your sample cartridge. If you are only using the 1.1 mm OD capillaries included in your mail-in kit, you will need to include 1 empty kapton capillary. If you choose to load some samples in quartz capillaries and some in kapton, you will need to include an empty kapton capillary AND an empty quartz capillary. For diffraction images collected on an area detector, you will need a calibrant to determine the appropriate integration parameters. Beamline staff will insert a CeO2 standard into position 0 of your cartridge after it is shipped back to the beamline.

My samples contain heavy (high Z) elements. Should I dilute them, and what should I use to dilute them? Will they fluoresce?

For PDF, we strongly recommend that you NOT dilute your samples with anything. Anything mixed in your samples will contribute additional atomic correlations to the extracted PDF. If you choose to dilute your samples, it is your responsibility to include a control sample containing just your diluent. Currently, we have been running mail-in PDF at 58.6 keV by default. For samples containing elements between Ag and Er, significant fluorescence will be evident in your data if samples are run at 58.6 keV. Samples containing elements between Tm and Tl will fluoresce if run at 87 keV. Samples containing elements from Pb and above should not fluoresce at either energy. Readily available PDF extraction packages including pdfgetX2 and xPDFsuite include corrections for fluorescence. The fluorescence correction in pdfgetX2 generally is a constant value vs Q (i.e. flat line) correction and can be implemented in other software packages.

Why is the kapton background is much higher than my sample background?

11-ID-B uses attenuators as needed to prevent saturation of the detector. The following filter settings are recorded in each metadata file (as of February 2020): Filter=0 (no attenuation), Filter=1 (~1.5 fold attenuation), Filter=2 (~3 fold attenuation), and Filter=3 (~5 fold attenuation). A good starting point for the background scaling should account for the attenuation and the relative value of i00 (also in metadata).

What PDF extraction software packages are available?

An incomplete list of software packages for PDF extraction includes PDFgetX2, PDFgetX3/xPDFsuite, GSAS-II, and GudrunX.

17-BM specific

How soon will I get my data?

Samples will be run on selected dates during each run. Contact 17-BM staff for exact dates.

How does this differ from the mail-in program at 11-BM?

17-BM offers medium resolution diffraction data on up to 40 samples per proposal; 11-BM offers high resolution data for up to 8 samples. We encourage users to make use of both services for their diffraction needs.