Sample Alignment Quick Reference

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This reference is intended for staff or advanced users - steps are outlined with a minimum of detail
Prior to this section make sure beamline alignment has been performed (Beamline Alignment Quick Reference)

1) Verify optic alignment
Perform CCD changeover to Coolsnap
Drive focusing optic into beam, adjust OSAX and OSAY so outgoing focused beam is not clipped and remnant central parallel beam intensity is minimized
Close NES slits to 0.1x0.1, adjust FOMX and FOMY to center optic on beam axis - outgoing wavefront as clipped by slits should look symmetric around the edges
Record this as your "optic in" position, move FOMX so parallel beam is unobstructed with NES slits at 1x1 (should be ~+4000 relative move) - record this as your "parallel beam" position

NOTES:
i) Central stop may be offset from the center of optic - do not simply put image of central stop in the center of the beam footprint when aligning optic
ii) Focal length in mm = (zp diameter in um)*(outermost zone width in nm)*(energy in keV)/1239.842

2) Mount and visually inspect sample
Move Objective Y to 0.0, rotate Sample Theta to 90 degrees, vent chamber
Remove old sample, slide new sample stick into machined slot, verify sample is flush with bottom of slot
Pump down chamber
View sample from top camera, roughly adjust SAMZ to put surface on marked focal plane
View sample from upstream camera, roughly adjust SAMY to put intended scanning region level with marked focal spot

NOTES:
i) Camera positions will not be accurate until chamber is pumped down

3) Flatten sample with x-rays
If phi alignment is necessary, move SAMX so a reference edge of the sample is visible in downstream parallel beam image
Observe edge position under SAMY motion of +/-1000, adjust Sample Phi until visible edge is parallel to this motion
Move Sample Theta to 0.0 degrees, during this motion watch upstream sample edge and adjust OSAZ and SAMZ as needed to avoid collision
Move SAMX so the front face of the sample is visible as an edge in the downstream parallel beam image
Adjust Sample Theta to find crossover between leading edge and trailing edge obstructing beam, set this to be user Theta=0.0
Observe surface edge position under SAMY motion of +/-1000, adjust Sample Chi until visible edge is parallel to this motion

NOTES:
i) Stop coarse motors frequently during these steps
ii) Make sure SAMY ends back up at coarse height found above at the end of this section

4) Parallel beam diffraction alignment
Mark NES slit center in Coolsnap image with crosshair
Calculate substrate scattering condition using Bragg law calculator, drive Sample Theta and detector Two Theta to these values (keep surface on focal plane with SAMZ)
Position fluorescent screen in front of Coolsnap viewable by outboard camera, find and coarsely optimize reflection using Sample Theta, remove screen
Close NES vertical slits to 0.1, adjust Sample Chi to align streak vertically with marked slit center
Open NES vertical slits, fine scan Sample Theta to maximize integrated ROI signal
Close NES horizontal slits to 0.1, adjust detector Two theta to center reflection on marked slit center
Re-open NES slits to 1x1, if any contrast is visible center intended scanning area in beam footprint using SAMX and SAMY (keep on focal plane with SAMZ)
Calculate the difference between the film scattering condition and the substrate scattering condition using Bragg law calculator
Make a two positioner theta/two theta scan relative to the current position encompassing both the substrate peak and the film peak
Drive to the film peak, if any contrast is visible center intended scanning area in beam footprint using SAMX and SAMY (keep on focal plane with SAMZ)

NOTES:
i) Stop coarse motors frequently during these steps
ii) Increase counting time substantially relative to substrate peak and view th/tth scan in log scale to find the film peak
iii) When centering using diffraction topography crosshair position runs out from beam axis unless SAMX and SAMZ are correctly moved together, check this by closing NES slits

5) Focused beam alignment
Drive FOMX and FOMY to "optic in" position from step 1
At film peak two theta perform CCD changeover to either PI-LCX or PIXIS-XF
Move in outboard fluorescent detector and add as a detector trigger
Scan SAMX and SAMY to coarsely find intended scanning region or object using diffractive and fluorescent contrast
Once something is coarsely located (to within ~100um2), adjust SAMZ to bring sample surface to focal plane then stop all sample motor motion
Activate hybrid optic motion by entering the current HybridX/HybridY readback values into the HybridX/HybridY command fields
Find some local contrast - any diffraction or fluorescence signal that shows variation over a ~5um linear scan - and use this to focus
Typical initial coarse focal scan correcting for known runout:

Outer loop positioners	Scan width(#pts)	Inner loop positioner	Scan width(#pts)
FOMZ	400um (10pts)	Hybrid Y	5um (50 pts)
Hybrid X	-2.0um (10pts)	-	-
Hybrid Y	-1.2um (10pts)	-	-

Once coarse focus is obtained, reduce all outer loop positioners by a factor of four and re-scan to find fine focus

NOTES:
i) Do not expose PI detectors or outboard fluorescent detector when in "parallel beam" condition
ii) Once enabled the Hybrid motion MUST be de-activated prior to any activation of X/Y coarse motors, and then re-enabled in the new readback position
iii) Instrument temperature equilibration will be causing position drift during the focal scans, monitor object position with linear X/Y scans
iv) After focusing, remove extra positioners and add reasonable soft limits around any motions likely to be scanned (to prevent "move to zero" crashes)