SRS mail-in

From SRS_mail-in
(Redirected from Main Page)
Jump to: navigation, search

Overview

The Structural Sciences group now has official mail-in total scattering [PDF] (11-ID-B) and rapid acquisition powder diffraction [XRD] (17-BM) programs in addition to the long-standing high resolution powder diffraction mail-in program at 11-BM. 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 (11-ID-B and 17-BM) and extracting PDFs (11-ID-B) is strongly recommended. Rapid access mail-in proposals can be submitted to the APS proposal system.

Announcements

Current operations (September 14-26, 2020)

We are currently able to receive mail-in samples. Please register and ship your samples when you are ready.

Currently, the APS is in limited operations, with no external users on site. We are able to run standard mail-in measurements, which are conducted at ambient conditions for powder/solid samples that can be loaded into 1.1 mm kapton capillaries. We are also able to run non-capillary samples at ambient conditions and a limited selection of simple in situ experiments for remote users.

For standard mail-in measurements only, please submit a rapid access mail-in proposal as described here. Mail-in proposals can be submitted at any time.

For non-capillary samples or simple in situ experiments, please contact beamline staff, who will advise you as to whether your experiment lies within the scope of our current operations. Some general guidelines for feasible experiments include use of standard beamline-provided sample environments, limited on-site (APS) staff time required, and no on-site (APS) wet chemistry lab use required. Beamline staff may advise you to submit either a rapid access proposal (no deadline) or a regular general user proposal (3 submission deadlines/year) as appropriate.

For all other experiments, please submit a regular general user proposal. We recommend contacting beamline staff regarding feasibility of the proposed experiments before submission.


Contents

Previous announcements

Maintenance period (August 13-September 13, 2020)

The APS maintenance period begins at 12:00 August 13 and runs until September 13. No X-ray measurements can be performed during this time period. We expect to resume standard mail-in measurements after the maintenance period. Please note that standard mail-in measurements are performed on powder/solid samples loaded into 1.1 mm kapton capillaries at ambient conditions only. For all other experiments, please contact beamline staff.

Mail-in samples can now be shipped to the beamline, and will be run sometime after the beam comes back up (September 14th or later).

11-ID-B only: Please wait until September 6th before shipping standard mail-in samples unless otherwise instructed by beamline staff.

For 17-BM, 11-BM, and all other measurements at 11-ID-B, please contact beamline staff.


Current operations (August 4, 2020)

Currently, the APS is in limited operations, with no external users on site. We are able to run standard mail-in measurements, which are conducted at ambient conditions for powder/solid samples that can be loaded into 1.1 mm kapton capillaries. We are also able to run non-capillary samples at ambient conditions and a limited selection of simple in situ experiments for remote users.

For standard mail-in measurements only, please submit a rapid access mail-in proposal as described here. Mail-in proposals can be submitted at any time.

For non-capillary samples or simple in situ experiments, please contact beamline staff, who will advise you as to whether your experiment lies within the scope of our current operations. Some general guidelines for feasible experiments include use of standard beamline-provided sample environments, limited on-site (APS) staff time required, and no on-site (APS) wet chemistry lab use required. Beamline staff may advise you to submit either a rapid access proposal (no deadline) or a regular general user proposal (3 submission deadlines/year) as appropriate.

For all other experiments, please submit a regular general user proposal. We recommend contacting beamline staff regarding feasibility of the proposed experiments before submission.

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.

How do I submit a proposal to the mail-in PDF or XRD programs?

The proposal submission process is similar to that for 11-BM:

  1. Log into the beamtime proposal system.
  2. Under "Create a new proposal," click "General User Proposal." This will launch a pop-up window entitled "Select Your General User Proposal Type."
  3. Select "Rapid Access Mail-in Powder Diffraction or PDF (11-BM,11-ID,17-BM) Proposal," then choose 11-ID-B (PDF) or 17-BM (XRD) as the beamline.
  4. Write an abstract. Make sure to address the recommended points.
  5. Submit proposal.

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.

Under what conditions can samples be run?

Currently, we are only offering room temperature measurements at 11-ID-B and 17-BM.

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 sample registration has been approved.

What address should I ship my samples to?

For 11-ID-B proposals, samples should be shipped to:

 Beamline 11-ID-B Staff
 9700 S. Cass Ave, Bldg. 433/B003
 Argonne National Laboratory
 Lemont, IL 60439

For 17-BM proposals, samples should be shipped to:

 Beamline 17-BM Staff
 9700 S. Cass Ave, Bldg. 433/D003
 Argonne National Laboratory
 Lemont, IL 60439

Do NOT ship samples to the APS until beamline staff approves your sample registration!

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>/ (11-ID-B data) or /gdata/dm/17BM/GUP-<mailin proposal number>/ (17-BM data). 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 at ambient conditions only; 11-BM offers high resolution diffraction data for up to 8 samples, with the possibility of collecting data at temperatures between 100 and 400 K. We encourage users to make use of both services for their diffraction needs. For additional information regarding the 11-BM mail-in program please consult the 11-BM website

Detailed instructions for mail-in powder diffraction (17-BM) and total scattering (11-ID-B)

A hard copy of the instructions below will be provided with your mail-in kit.

Please read the instructions below regarding sample preparation, registration, and shipment carefully. Failure to comply with these directions may result in your samples not being processed.

You should receive either one or two capillary cassettes as shown in Figure 1. The cassettes are plastic and can be damaged if dropped on a hard surface. Please handle with care. The top cover of the cassette has a barcode and a QR code. It is tied to the holder by rubber bands at both ends (rubber bands not shown in Figure 1). When you return the cassette, the cover must be tied to the holder in the same way you receive it. The front side of the cover is labelled "Front"; the front of the holder is labelled "APS Mail-in". The words should be on the same side when the cover is placed on the holder.

Figure1.jpg

Figure 1

You should also receive one or two bags of capillaries with two additional rubber bands and a return shipping label. The capillaries are pre-cut to a length of 17.5 mm and fit into the cassette holder with the cover on. You are provided with 20 capillaries for each cartridge you receive. If you run out of capillaries during sample preparation, you can purchase and cut capillaries yourself. The provided capillaries are Cole-Parmer Polyimide tubing, 0.0395"ID x 0.0435"OD. The capillaries can be purchased at the following link: https://www.coleparmer.com/i/cole-parmer-polyimide-tubing-0-0395-id-x-0-0435-od-five-12-l-pack/9582009

Loading powder samples into capillaries

  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. In most cases, you should be able to pick up the powder by dipping the open end of the capillary into the powder due to capillary force. Then turn the capillary over, gravity will let the powder drop to the close end. You may need to gently rub or rotate the capillary to help the fall of the powder. If none of these work, find a needle, wire, or solid tubing smaller than the capillary size (1.0 mm or below), and push the powder to the closed end. Make sure not to overpressurize the powder. 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 (Figure 2). 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.

Loading capillaries into cassette holder

  1. Remove the rubber bands and take off the cover. You may need to use tweezers to remove the rubber bands.
  2. Load your first sample into position 1. Attention: position 1 is actually the SECOND hole from the left. The capillary in Figure 2 is at position 1. Leave the hole to the left to position 1 open. Beamline staff will place either a LaB6 (17-BM) or CeO2 (11-ID-B) standard in the leftmost hole (position 0).

Figure2.png

Figure 2

  1. Load the next sample into position 2, which is immediately to the right of position 1. Continue until you load all your samples, or you reach position 20. Leave the open hole after position 20 empty. For total scattering/PDF, you must include an empty capillary as one of your samples. We recommend that you place your empty capillary in position 1. Take notes as you load the capillaries to insure you know which sample is which. In the unlikely event that a hole is misshapen to the point where a capillary cannot be inserted, skip it and use the next position. Be sure it is not the plugging material outside the capillary causing the problem.
  2. Put the cover back on and secure it with rubber bands.

Registering your samples

Before samples are returned to the beamline, they must be registered and approved by beamline staff. Submit sample registration information using the link provided in the proposal approval email. You must provide position number and the corresponding chemical name. 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. For example, "MOF-123" is NOT acceptable. “Nickel oxide mixed with sodium aluminum silicate” is acceptable. Only register your samples after you load them into the cassette. Do not modify the sample order in the cassette after you register them.

Return shipping

  1. A label with the return address will be provided to you in your kit. Otherwise, after beamline staff have approved your ESAF, samples can be shipped to:
    Beamline 11-ID-B Staff
    9700 S. Cass Ave, Bldg. 433/B003
    Argonne National Laboratory
    Lemont, IL 60439
    OR
    Beamline 17-BM Staff
    9700 S. Cass Ave, Bldg. 433/D002
    Argonne National Laboratory
    Lemont, IL 60439
  2. Wrap the sample cassettes in bubble wrap to keep your samples and cassettes intact during shipment. Note that it is your responsibility to make sure the cassette returned in good condition and is ready to be measured.

Getting your data

Your data will be uploaded to Globus into the aps#data collection at one of the paths below:

(11-ID-B): /gdata/dm/11IDB/GUP-<mailin proposal number>/

(17-BM): /gdata/dm/17BM/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>/ OR /gdata/dm/17BM/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 .

Processing your data

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). 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 .

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 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 either LaB6 (17-BM) or CeO2 (11-ID-B). This should be used to determine appropriate calibration parameters.