Difference between revisions of "SRS mail-in"
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==Acknowledgement statement== | ==Acknowledgement statement== | ||
Please use the acknowledgement statement below for publications utilizing data from the 11-ID-B and/or 17-BM mail-in programs: | Please use the acknowledgement statement below for publications utilizing data from the 11-ID-B and/or 17-BM and/or 11-BM mail-in programs: | ||
When only the mail-in program is used: | |||
''This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. The mail-in program at Beamline 11-ID-B (and/or 17-BM, 11-BM) contributed to the data.'' | |||
When both normal GUPs at 17-BM/11-ID-B/11-BM and the mail-in program are used: | |||
''This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. The Beamline 11-ID-B (or 17-BM, 11-BM) and its mail-in program contributed to the data.'' | |||
When normal GUPs at other beamlines and the mail-in program are used: | |||
''This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. The beamlines XXX, YYY and the mail-in program at 11-ID-B (and/or 17-BM, 11-BM) contributed to the data.'' | |||
=Announcements= | |||
<span style="color:red"><u>'''Course materials from the X-ray Powder Diffraction and Pair Distribution Function Data Analysis Course now available!'''</u></span> | |||
<span style="color:red">Recordings from the XRD-PDF course offered by the Structural Sciences group in 2020, which include background material in addition to instructions handling your data in GSAS-II, are available [https://anl.box.com/s/l3lgklgbaeoxgn1v3h52acb4nn7m4gvt here].</span> | |||
<u>'''Maintenance period (August 3-September 12, 2022)'''</u> | |||
We have resumed standard mail-in measurements after the maintenance period ended on September 13, 2022. | |||
<u>'''Current operations (May 31-August 2, 2022)'''</u> | |||
The 2022-2 second session began on Sept 13, and will be connected with the 2022-3 run cycle starting on Oct 3rd and ending on Dec 19th. We are currently able to receive mail-in samples. Please register and ship your samples when you are ready.''' | |||
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. | |||
For '''standard mail-in measurements only''', please submit a '''rapid access mail-in proposal''' as described [https://wiki-ext.aps.anl.gov/srsmailin/index.php/SRS_mail-in#How_do_I_submit_a_proposal_to_the_mail-in_PDF_or_XRD_programs.3F here.] Mail-in proposals can be submitted at any time. | For '''standard mail-in measurements only''', please submit a '''rapid access mail-in proposal''' as described [https://wiki-ext.aps.anl.gov/srsmailin/index.php/SRS_mail-in#How_do_I_submit_a_proposal_to_the_mail-in_PDF_or_XRD_programs.3F here.] Mail-in proposals can be submitted at any time. | ||
For | For all other experiments (non-standard ''ex situ'' and all ''in situ'' measuremements), please submit either a '''rapid access proposal''' for the 2022-2 cycle (no deadline) or a '''regular general user proposal''' (3 submission deadlines/year) as appropriate. If you are planning to submit a rapid access proposal, please first contact beamline staff regarding feasibility of the proposed experiments. Besides, reserved rapid access time may run out way before the run cycle ends. | ||
Previous announcements are archived [[previous_announcements|here]]. | |||
__TOC__ | |||
=Frequently asked questions= | =Frequently asked questions= | ||
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For 11-ID-B proposals, samples should be shipped to: | For 11-ID-B proposals, samples should be shipped to: | ||
Beamline 11-ID-B Staff | Beamline 11-ID-B Staff | ||
9700 S. Cass Ave, Bldg. 433/ | ATTN: Wenqian Xu | ||
9700 S. Cass Ave, Bldg. 433/D008 | |||
Argonne National Laboratory | Argonne National Laboratory | ||
Lemont, IL 60439 | Lemont, IL 60439 | ||
| Line 178: | Line 121: | ||
For 17-BM proposals, samples should be shipped to: | For 17-BM proposals, samples should be shipped to: | ||
Beamline 17-BM Staff | Beamline 17-BM Staff | ||
9700 S. Cass Ave, Bldg. 433/ | ATTN: Wenqian Xu | ||
9700 S. Cass Ave, Bldg. 433/D008 | |||
Argonne National Laboratory | Argonne National Laboratory | ||
Lemont, IL 60439 | Lemont, IL 60439 | ||
'''Do NOT ship samples to the APS until beamline staff approves your sample registration!''' | '''Do NOT ship samples to the APS until beamline staff approves your sample registration!''' | ||
===How soon will I get my data?=== | |||
'''11-ID-B/total scattering/PDF''': 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) ([https://www.aps.anl.gov/Machine-Status/APS-Long-Range-Operations-Schedule see APS long range schedule here]). You will be notified by email when your data is available. | |||
'''17-BM/rapid acquisition XRD''': Samples will be run on selected dates during each run. Contact 17-BM staff for exact dates. | |||
===How can I access my data?=== | ===How can I access my data?=== | ||
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===What do I do with these TIFs?=== | ===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. | 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. | ||
A variety of resources are available to aid you in processing your data: | |||
# Tutorials for data reduction in GSAS-II (calibration and integration) are available at https://subversion.xray.aps.anl.gov/pyGSAS/trunk/help/Tutorials.html . | |||
# A demo for reduction of data from the 11-ID-B mail-in program using GSAS-II is available [https://anl.box.com/s/qu9uujgdt9emf36x8vepsu7su6ebysp6 here.]'' | |||
# <span style="color:gray">'''Recordings from the XRD-PDF course offered by the Structural Sciences group last year, which include background material in addition to instructions handling your data in GSAS-II, are available [https://anl.box.com/s/l3lgklgbaeoxgn1v3h52acb4nn7m4gvt here].'''</span> | |||
==11-ID-B/PDF specific== | ==11-ID-B/PDF specific== | ||
===How soon will I get my data?=== | ===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). | 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) ([https://www.aps.anl.gov/Machine-Status/APS-Long-Range-Operations-Schedule see APS long range schedule here]). 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?=== | ===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. | 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. | 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. <span style="color:red"><u>'''Important notes: (1) one or more positions from 0 to 20 should be your background capillary, e.g. an empty Kapton tubing. You must put it in before shipping to us; (2) position 0 is for standard material, leave it open, we will fill in this position before measurement.'''</u></span> | ||
===My samples contain heavy (high Z) elements. Should I dilute them, and what should I use to dilute them? Will they fluoresce?=== | ===My samples contain heavy (high Z) elements. Should I dilute them, and what should I use to dilute them? Will they fluoresce?=== | ||
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===Why is the kapton background is much higher than my sample background?=== | ===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 ( | 11-ID-B uses attenuators as needed to prevent saturation of the detector. A good starting point for the background scaling should account for the attenuation and the relative value of i00 (also in metadata). | ||
'''For data collected January 2021 and later:''' The following filter settings are recorded in each metadata file: Filter=0 (no attenuation), Filter=1 to Filter=5 (1.888388229^(filternumber) attenuation @ 0.2115 Angstroms, 2.771303927^(filternumber) attenuation @ 0.1432 Angstroms) | |||
'''For data collected December 2020 and earlier:''' The following filter settings are recorded in each metadata file: Filter=0 (no attenuation), Filter=1 (~1.5 fold attenuation), Filter=2 (~3 fold attenuation), and Filter=3 (~5 fold attenuation). | |||
===What PDF extraction software packages are available?=== | ===What PDF extraction software packages are available?=== | ||
An incomplete list of software packages for PDF extraction includes PDFgetX2, PDFgetX3/xPDFsuite, GSAS-II, and GudrunX. | An incomplete list of software packages for PDF extraction includes PDFgetX2, PDFgetX3 (command line)/xPDFsuite (GUI), GSAS-II, and GudrunX. | ||
===What are appropriate instrument parameters for use in PDFgui?=== | ===What are appropriate instrument parameters for use in PDFgui?=== | ||
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===How does this differ from the mail-in program at 11-BM?=== | ===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 [https://11bm.xray.aps.anl.gov/users_instruct01.html the 11-BM website] | 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 [https://11bm.xray.aps.anl.gov/users_instruct01.html the 11-BM website] | ||
===What instrument parameters should I use in my Rietveld refinement software?=== | |||
Instrument parameter files (formatted for GSAS-II) can be downloaded [https://anl.box.com/s/gnae4dicpd0dokjaqrmjjvl3g08811bc here.] Parameters are available for 27 and 51 keV. The nominal distances are in the file names (i.e. d300 is collected at a nominal position of 300 mm). | |||
=Detailed instructions for mail-in powder diffraction (17-BM) and total scattering (11-ID-B)= | =Detailed instructions for mail-in powder diffraction (17-BM) and total scattering (11-ID-B)= | ||
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. | '''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 cartridges as shown in Figure 1. The cartridges are plastic and '''can be damaged if dropped on a hard surface. Please handle with care.''' The top cover of the cartridge 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 cartridge, 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. | You should receive either one or two capillary cartridges as shown in Figure 1. The cartridges are plastic and '''can be damaged if dropped on a hard surface. Please handle with care.''' The top cover of the cartridge 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 cartridge, 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. | ||
| Line 282: | Line 240: | ||
# 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: | # 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 | #:Beamline 11-ID-B Staff | ||
#:9700 S. Cass Ave, Bldg. 433/ | #:ATTN: Wenqian Xu | ||
#:9700 S. Cass Ave, Bldg. 433/D008 | |||
#:Argonne National Laboratory | #:Argonne National Laboratory | ||
#:Lemont, IL 60439 | #:Lemont, IL 60439 | ||
| Line 288: | Line 247: | ||
#:'''OR''' | #:'''OR''' | ||
#:Beamline 17-BM Staff | #:Beamline 17-BM Staff | ||
#:9700 S. Cass Ave, Bldg. 433/ | #:ATTN: Wenqian Xu | ||
#:9700 S. Cass Ave, Bldg. 433/D008 | |||
#:Argonne National Laboratory | #:Argonne National Laboratory | ||
#:Lemont, IL 60439 | #:Lemont, IL 60439 | ||
| Line 314: | Line 274: | ||
==Processing your data== | ==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. | 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. | ||
A variety of resources are available to aid you in processing your data: | |||
# Tutorials for data reduction in GSAS-II (calibration and integration) are available at https://subversion.xray.aps.anl.gov/pyGSAS/trunk/help/Tutorials.html . | |||
# A demo for reduction of data from the 11-ID-B mail-in program using GSAS-II is available [https://anl.box.com/s/qu9uujgdt9emf36x8vepsu7su6ebysp6 here.]'' | |||
# <span style="color:gray">'''Recordings from the XRD-PDF course offered by the Structural Sciences group last year, which include background material in addition to instructions handling your data in GSAS-II, are available [https://anl.box.com/s/l3lgklgbaeoxgn1v3h52acb4nn7m4gvt here].'''</span> | |||
The following files will be provided for each experiment: | 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: 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 LaB<sub>6</sub> (17-BM) or CeO<sub>2</sub> (11-ID-B). This should be used to determine appropriate calibration parameters. | |||
Instrument parameters files (17-BM) and data suitable for extraction of instrument parameters (11-ID-B) are available on Box: | |||
*11-ID-B (PDF): Nickel data suitable for determining instrument parameters in PDFgui (Qdamp and Qbroad) are available [https://anl.box.com/s/7f7cofqic9rvxveduz5fn2yr4uqighpa here.] Note that the naming scheme for the files is: _00 files are kapton, _25 are nickel, and _-01 are CeO2. The nominal distances are in the file names (so d0170 was collected at a nominal position of 170 mm). | |||
*17-BM (XRD): Instrument parameter files (formatted for GSAS-II) can be downloaded [https://anl.box.com/s/gnae4dicpd0dokjaqrmjjvl3g08811bc here.] Parameters are available for 27 and 51 keV. The nominal distances are in the file names (i.e. d300 is collected at a nominal position of 300 mm). | |||
Latest revision as of 20:53, 27 September 2022
Please note that this wiki contains information regarding the mail-in programs at beamlines 11-ID-B (total scattering/pair distribution function) and 17-BM (rapid acquisition/medium resolution powder diffraction) only. For information regarding the mail-in program at 11-BM (high resolution powder diffraction), please consult the 11-BM website.
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.
Acknowledgement statement
Please use the acknowledgement statement below for publications utilizing data from the 11-ID-B and/or 17-BM and/or 11-BM mail-in programs:
When only the mail-in program is used:
This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. The mail-in program at Beamline 11-ID-B (and/or 17-BM, 11-BM) contributed to the data.
When both normal GUPs at 17-BM/11-ID-B/11-BM and the mail-in program are used:
This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. The Beamline 11-ID-B (or 17-BM, 11-BM) and its mail-in program contributed to the data.
When normal GUPs at other beamlines and the mail-in program are used:
This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. The beamlines XXX, YYY and the mail-in program at 11-ID-B (and/or 17-BM, 11-BM) contributed to the data.
Announcements
Course materials from the X-ray Powder Diffraction and Pair Distribution Function Data Analysis Course now available!
Recordings from the XRD-PDF course offered by the Structural Sciences group in 2020, which include background material in addition to instructions handling your data in GSAS-II, are available here.
Maintenance period (August 3-September 12, 2022)
We have resumed standard mail-in measurements after the maintenance period ended on September 13, 2022.
Current operations (May 31-August 2, 2022)
The 2022-2 second session began on Sept 13, and will be connected with the 2022-3 run cycle starting on Oct 3rd and ending on Dec 19th. We are currently able to receive mail-in samples. Please register and ship your samples when you are ready.
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.
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 all other experiments (non-standard ex situ and all in situ measuremements), please submit either a rapid access proposal for the 2022-2 cycle (no deadline) or a regular general user proposal (3 submission deadlines/year) as appropriate. If you are planning to submit a rapid access proposal, please first contact beamline staff regarding feasibility of the proposed experiments. Besides, reserved rapid access time may run out way before the run cycle ends.
Previous announcements are archived here.
Frequently asked questions
General
How do I get mail-in PDF/XRD for my samples?
- Submit a rapid access mail-in proposal [NOT regular rapid access] to 11-ID-B (PDF) or 17-BM (XRD).
- Request sample cartridges (link included in automated email).
- Receive mail-in kit with supplies and detailed instructions on sample preparation and registration.
- Register samples, then ship back to 11-ID-B or 17-BM.
- 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:
- Log into the proposal system: APS Beam Time Access System
- Under "Create a new proposal," click "General User Proposal." This will launch a pop-up window entitled "Select Your General User Proposal Type."
- 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.
- Write an abstract. Make sure to address the recommended points.
- 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.
- 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.
- 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 cartridge, the powder should fill the entire gap in the holder. No clay or empty capillary should be present in the gap region.
- 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 cartridge holder. Do not place labels or tape on the outside of the capillary.
How should I load the sample cartridges?
- 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).
- 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.
- 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 ATTN: Wenqian Xu 9700 S. Cass Ave, Bldg. 433/D008 Argonne National Laboratory Lemont, IL 60439
For 17-BM proposals, samples should be shipped to:
Beamline 17-BM Staff ATTN: Wenqian Xu 9700 S. Cass Ave, Bldg. 433/D008 Argonne National Laboratory Lemont, IL 60439
Do NOT ship samples to the APS until beamline staff approves your sample registration!
How soon will I get my data?
11-ID-B/total scattering/PDF: 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) (see APS long range schedule here). You will be notified by email when your data is available.
17-BM/rapid acquisition XRD: Samples will be run on selected dates during each run. Contact 17-BM staff for exact dates.
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:
- Using a web browser, navigate to https://www.globus.org/
- Create a Globus account if you do not already have one and sign in with your Globus username.
- Choose "aps#data" endpoint (collection) and click "Continue" in order to authenticate.
- Authenticate with your DM username (typically "d<badge number>"). Use the same password that you use to access APS Beamline User Portal.
- Navigate to experiment folder (path) /gdata/dm/11IDB/GUP-<mailin proposal number>/
- 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 in the APS User Portal and 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.
A variety of resources are available to aid you in processing your data:
- Tutorials for data reduction in GSAS-II (calibration and integration) are available at https://subversion.xray.aps.anl.gov/pyGSAS/trunk/help/Tutorials.html .
- A demo for reduction of data from the 11-ID-B mail-in program using GSAS-II is available here.
- Recordings from the XRD-PDF course offered by the Structural Sciences group last year, which include background material in addition to instructions handling your data in GSAS-II, are available here.
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) (see APS long range schedule here). 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. Important notes: (1) one or more positions from 0 to 20 should be your background capillary, e.g. an empty Kapton tubing. You must put it in before shipping to us; (2) position 0 is for standard material, leave it open, we will fill in this position before measurement.
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. A good starting point for the background scaling should account for the attenuation and the relative value of i00 (also in metadata).
For data collected January 2021 and later: The following filter settings are recorded in each metadata file: Filter=0 (no attenuation), Filter=1 to Filter=5 (1.888388229^(filternumber) attenuation @ 0.2115 Angstroms, 2.771303927^(filternumber) attenuation @ 0.1432 Angstroms)
For data collected December 2020 and earlier: The following filter settings are recorded in each metadata file: Filter=0 (no attenuation), Filter=1 (~1.5 fold attenuation), Filter=2 (~3 fold attenuation), and Filter=3 (~5 fold attenuation).
What PDF extraction software packages are available?
An incomplete list of software packages for PDF extraction includes PDFgetX2, PDFgetX3 (command line)/xPDFsuite (GUI), GSAS-II, and GudrunX.
What are appropriate instrument parameters for use in PDFgui?
We have collected data on nickel that can be used to determine Qdamp and Qbroad. The data is available for download here. The naming scheme for the files is: _00 files are kapton, _25 are nickel, and _-01 are CeO2. The nominal distances are in the file names (so d0170 was collected at a nominal position of 170 mm).
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
What instrument parameters should I use in my Rietveld refinement software?
Instrument parameter files (formatted for GSAS-II) can be downloaded here. Parameters are available for 27 and 51 keV. The nominal distances are in the file names (i.e. d300 is collected at a nominal position of 300 mm).
Detailed instructions for mail-in powder diffraction (17-BM) and total scattering (11-ID-B)
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 cartridges as shown in Figure 1. The cartridges are plastic and can be damaged if dropped on a hard surface. Please handle with care. The top cover of the cartridge 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 cartridge, 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.
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 cartridge 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
- 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.
- 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 cartridge, the powder should fill the entire gap in the holder (Figure 2). No clay or empty capillary should be present in the gap region.
- 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 cartridge holder. Do not place labels or tape on the outside of the capillary.
Loading capillaries into cartridge holder
- Remove the rubber bands and take off the cover. You may need to use tweezers to remove the rubber bands.
- 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).
- 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.
- Put the cover back on and secure it with rubber bands.
Figure 2
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 cartridge. Do not modify the sample order in the cartridge after you register them.
Return shipping
- 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
- ATTN: Wenqian Xu
- 9700 S. Cass Ave, Bldg. 433/D008
- Argonne National Laboratory
- Lemont, IL 60439
- OR
- Beamline 17-BM Staff
- ATTN: Wenqian Xu
- 9700 S. Cass Ave, Bldg. 433/D008
- Argonne National Laboratory
- Lemont, IL 60439
- Wrap the sample cartridges in bubble wrap to keep your samples and cartridges intact during shipment. Note that it is your responsibility to make sure the cartridge 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:
- Using a web browser, navigate to https://www.globus.org/
- Create a Globus account if you do not already have one and sign in with your Globus username.
- Choose "aps#data" endpoint (collection) and click "Continue" in order to authenticate.
- Authenticate with your DM username (typically "d<badge number>"). Use the same password that you use to access APS Beamline User Portal.
- Navigate to experiment folder (path) /gdata/dm/11IDB/GUP-<mailin proposal number>/ OR /gdata/dm/17BM/GUP-<mailin proposal number>/
- 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 in the APS User Portal and 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.
A variety of resources are available to aid you in processing your data:
- Tutorials for data reduction in GSAS-II (calibration and integration) are available at https://subversion.xray.aps.anl.gov/pyGSAS/trunk/help/Tutorials.html .
- A demo for reduction of data from the 11-ID-B mail-in program using GSAS-II is available here.
- Recordings from the XRD-PDF course offered by the Structural Sciences group last year, which include background material in addition to instructions handling your data in GSAS-II, are available here.
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.
Instrument parameters files (17-BM) and data suitable for extraction of instrument parameters (11-ID-B) are available on Box:
- 11-ID-B (PDF): Nickel data suitable for determining instrument parameters in PDFgui (Qdamp and Qbroad) are available here. Note that the naming scheme for the files is: _00 files are kapton, _25 are nickel, and _-01 are CeO2. The nominal distances are in the file names (so d0170 was collected at a nominal position of 170 mm).
- 17-BM (XRD): Instrument parameter files (formatted for GSAS-II) can be downloaded here. Parameters are available for 27 and 51 keV. The nominal distances are in the file names (i.e. d300 is collected at a nominal position of 300 mm).
