Generate runfile

The next step is to align each sample and generate a script that will be used to collect data. It is recommended to use the provided prsoxr_script_gen.py to assist in generating a runfile. This section will outline how to use this script and automate the data collection process. It only requires numpy and pandas to be installed.

Initial sample information

The first step to generating a runfile is to fill out the “Setup Parameters” section. This section compiles some basic bookeeping that will later allow you to sort your new data.

Begin with information about the samples mounted on the plate:

"""
Setup Parameters
"""
save_dir = '.../P-RSoXR/' # Location to save script
save_name = 'test_spol' # Scipt name

#Store sample names and energies you want to run
sample_list = {} #Do not change this line
sample_list['Samp_A'] = [270.0, 284.5, 287.3, 288.7]
sample_list['Samp_B'] = [270.0, 284.3, 288.7]
sample_list['Samp_C'] = [250.0, 283.5, 284.8, 285.3]

#External energy calibration
EnergyOffset = 0 # [eV]

You will need to set a directory (save_dir) that you want to save the script and a descriptive name (save_name). The scans you want to run for each sample is stored in the sample_list dictionary. All you need to do is make a new key for each sample and a corresponding list of each energy that you want to run on that sample.

The energies that you pick will want to be the true energies that you want to run. If you wish to apply some external offset, you can set EnergyOffset to some value other than 0. The final script will then run:

energy_run = energy_in_list + EnergyOffset

Note

This script will at no point ask for an input polarization because we recommend running each polarization independently. At beamline 11.0.1.2, changing the polarization state makes the beam intensity semi-unstable for at least 30 minutes. Before any alignment, set the EPU Polarization motor to your desired state.

Once this script has finished running, change the polarization, wait 30 minutes, then run it again.

Sample Positions

Once each sample has been defined, each one requires a series of motor positions based on its location on the sample plate. Each input consists of a list with each element corresponding to a sample, in the order you wish to collect data. We will define the inputs here and describe how you collect them in the following sections:

# Inputs to run sample plate
SampleOrder = ['Samp_A', 'Samp_B', 'Samp_C'] # Order that you want to run samples.
# Motor positions
XPosition = [36.52, 23.36, 0] # 'Sample X' motor position
XOffset = [0.15, 0.15, 0.15] # Offset to translate beam on sample after each energy.
YPosition = [-3.2150, -1.9750, 0] # 'Sample Y' motor position
ZPosition = [-0.27, -0.36, 0] # 'Sample Z' motor position
ZFlipPosition = [0.21, 0.15, 0] # 'Sample Z' motor position when 'Sample Theta' is flipped 180deg
ReverseHolder = [0, 0, 0] #Set to True (1) for a sample that is on the reverse side of the holder
ZDirectBeam = [-2, -2, -1] #'Sample Z' motor positions to access the direct beam
ThetaOffset = [0, -0.55, 0] #'Sample Theta' offset if measuring multiple samples

##
SampleThickness = [250, 250, 250] #Approximate film thickness [A], used to determine dq
LowAngleDensity = [15, 15, 15] #Approximate number of points per fringe at low angles
HighAngleDensity = [9, 9, 9] #Approximate number of points per fringe at high angles
AngleCrossover = [10, 10, 10] #Angle [deg] to cross from low -> high density
##
OverlapPoints = [3, 3, 3] #Number of overlap points upon changing motor. Used for stitching
CheckUncertainty = [3, 3, 3] #Number of points for assessing error at each change in motor conditions. Used for error reduction
HOSBuffer = [2, 2, 2] #Number of points to add upon changing HOS to account for  motor movement.
I0Points = [10, 10, 10] #Number of I0 measureents taken at the start of the scan. Used to calculate direct beam uncertainty
  • Motor Positions:

    1. SampleOrder: This is a list of sample names. They should be in the order that you want to run. Use the same key phrases used in defining your sample dictionary.

    2. XPosition: This is the Sample X motor position at the spot of the sample to be measured.

    3. XOffset: This offset will laterally translate Sample X after each energy. Typically set slightly larger than the size of th beam to measure a fresh spot at each energy. Set to 0 if do not want to move the beam while measuring (not recommended)

    4. YPosition: This is the Sample Y motor position at the spot of the sample to be measured.

    5. ZPosition: This is the Sample Z motor position that cuts the beam in half when Sample Theta = 0

    6. ZFlipPosition: This is the Sample Z motor position that cuts the beam in half when Sample Theta = 180

    7. ReverseHolder: This is a binary option that is set on whether the sample is on the top (0) or bottom (1) of the plate.

    8. ZDirectBeam: This is a Sample Z position that moves the entire plate out of th way enabling a measurement of the direct beam.

    9. ThetaOffset: This is an angle offset to be measured for each sample.

The next settings define the q-spacing. We define this spacing in terms of the number of measurement points we want to collect per fringe. If we assume that the highest frequency fringe spacing will depend on the total film thickness, L = 2*np.pi/thick, the q-spacing is given by dq = L/N where N is the chosen point density.

  • Settings for point density:

    1. SampleThickness: An approximate sample film thickness in [A]. This will be referenced to determine dq

    2. LowAngleDensity: Number of points per fringe at low angles. Nominally high to resolve critical angle, typically on the order of 12-15.

    3. HighAngleDensity: Number of points per fringe at high angles. Lower resolution is often required after the critical angle, typically 8-10.

    4. AngleCrossOver: Angle [deg] to cross from low to high density. We find that 10[deg] is a good location that encompasses the critical angle and at least one full fringe.

The final settings help with measurement statistics and buffers to help delay for motor movements.

  • Settings for Statistics:

    1. OverlapPoints: Number of points to repeat when upstream optics are moved to increase flux. This will be used to stitch the data together.

    2. CheckUncertainty: Number of points to repeat to assess error when changing Higher Order Suppressor or Horizontal Exit Slit Size.

    3. HOSBuffer: Number of points to add, and later discard, to make sure the ‘Higher Order Suppressor`` has reached its new position.

    4. I0Points: Number of times to measure the direct beam measurements at the start of each energy. This value will be averaged and the standard error will then be propogated into measurement uncertainty.

Locate the sample

The following section will outline the process to align the axis of rotation and fill in the reqired motor positions.

Note

Samples mounted on the underside of the sample plate will require slightly different inputs during alignment. Subtract 180 from all Sample Theta positions. If this subtraction causes the angle to be -360, set Sample Theta = 0

  • Locate the sample:

    1. Set Sample Theta = 90

    2. Move Sample X and Sample Y until you reach the position on the sample you wish to measure.

      • Record these motor positions in the script: XPosition and YPosition

      • If you are using an XOffset verify that you have enough space to move across the sample.

    3. Set Sample Theta = 0 and lower Sample Z until the direct beam passes unobstructed. (Typically around (-5 mm) when Sample Theta = 0 or (5 mm) when Sample Theta = -180)

      • Record the Sample Z position in the script: ZDirectBeam

      • Remember to set ZFlipPosition = 1 if the sample is on the bottom of the plate.

Align axis of rotation

This section of the procedure will outline an iterative process. It may take 3 or 4 iterations until the sample is properly aligned.

  1. With CCD Theta = 0 and Sample Theta = 0 run a Sample Z single-motor scan that raises the plate into the beam. We are looking for the motor position that cuts the flux in half.

    • Monitor the total counts as the motor moves. Use the previously calculated I0 as a reference for the full flux.

    • It may be necessary to recalculate the full flux if the intensity has fluctuated.

  2. Set Sample Z to the position that cuts the beam in half and set Sample theta = 4 and CCD Theta = 8. Snap an image.

    Note

    If the beam is properly cut in half, the CCD image will only have signal above the crosshairs.

  • If the beamspot is not within the crosshairs:

    • Run a Sample Theta single-motor scan until the beamspot aligns with the crosshairs. Start with a scan from 3 to 5 degrees. Manually adjust the final position if necessary.

    • If this is the first sample:

      • Set the new Sample Theta == 4

    • Otherwise:

      Calculate the angle offset: AngleOffset = *Sample Theta - 4 * For the remainder of the alignment process, add this to Sample Theta (it can be negative).

    • Return to step 1 and recalculate Sample Z

    Note

    If you calculated your angle offset to be 0.5 deg, when you recalibrate Sample Z, you would start at Sample Theta = 0.5 instead of Sample Theta = 0

  • If the beamspot is within the crosshairs:

    • Set Sample Theta = 10 and CCD Theta = 20 and snap an image.

    • If the beamspot is not within the crosshairs

      • Adjust Sample Theta until it becomes aligned

      • If this is the first sample:

        • Set the new Sample Theta == 10

      • Otherwise:

        • Calculate the angle offset: AngleOffset = Sample Theta - 10

        • For the remainder of the alignment process, add this to Sample Theta (it can be negative).

      • Return to step 1 and recalculate Sample Z

    • If the beamspot does not move (or is acceptable)

      • Record Sample Z in the script: ZPosition

      • Record your angle offset in the script: ThetaOffset

  • Having aligned Sample Theta, set Sample Theta = -180 and CCD Theta = 0.

  • Run a Sample Z single-motor scan that raises the plate into the beam. Find the position that cuts it in half and record it in the script as ZFlipPosition

    Note

    This motor position will typically be the opposite sign of ZPosition and the approximate difference between the two values will be the substrate thickness.

Repeat the last two sections for each sample as needed.

Adjust incident flux

Having aligned each sample, the next step is to setup upstream optics and exposure times to progressively increase flux while the angle is increased. Beamline 11.0.1.2 can achieve up to 7 orders of magnitude by adjusting the following:

  1. Higher Order Suppressor : This is a 4-bounce mirror that is designed to eliminate higher order light. Keep it above 7.5 [deg]

  2. Horizontal Exit Slit Size : This is an upstream beam-shaping slit. At non-resonant energies, this is typically cut down to 150 [mm]. For more flux, it can be increased to 1500 [mm]. This is usually a binary operation.

  3. Exposure : How long do you want to dwell at a single position. It is good practice to never go above 1 [s] exposures. The amount of flux gained beyond that is minimal compared to the increase in beam damage and the overall length of the experiment.

We will manually survey the full theta scan for each sample (at each energy and polarization). Once the flux has dropped by some threshold, we will adjust one of the above motors. This is typically done in the order: Higher Order Suppressor, Exposure, and finally Horizontal Exit Slit Size.

Within prsoxr_script_gen.py, you will want to copy the following block of code for every sample:

"""
COPY THIS BLOCK OF CODE FOR EACH SAMPLE
"""
#########################################
#####            Sample 0           #####
#########################################
DEG = [] # Angles to change settings
HOS = [] # HOS positions
HES = [] # HES positions
EXP = [] # Exposures
#########################################

#########################################
#####           Energy 1            #####
#########################################
DEG.append([1, 4, 10, 15, 20, 25, 30, 40, 75])
HOS.append([12, 11, 10, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5])
HES.append([150, 150, 150, 150, 150, 150, 150, 150, 150])
EXP.append([0.001, 0.001, 0.001, 0.001, 0.1, 0.5, 0.5, 0.5, 0.5])

#########################################
#####           Energy 2            #####
#########################################
DEG.append([1, 4, 6, 10, 12, 15, 20, 25, 30, 40, 60])
HOS.append([12, 11.5,  12, 10, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5])
HES.append([1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500])
EXP.append([0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.1, 0.1, 0.1, 0.1, 0.1])

#########################################
#####           Energy 3            #####
#########################################
DEG.append([1, 4, 6, 10, 12, 15, 20, 25, 30, 40, 60])
HOS.append([12, 11.5,  12, 10, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5])
HES.append([1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500])
EXP.append([0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.1, 0.1, 0.1, 0.1, 0.1])

#########################################
#####           Energy 4            #####
#########################################
DEG.append([1, 4, 6, 10, 12, 15, 20, 25, 30, 40, 60])
HOS.append([12, 11.5,  12, 10, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5])
HES.append([1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500, 1500])
EXP.append([0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.1, 0.1, 0.1, 0.1, 0.1])

#Compile inputs
motors = zip(DEG, HOS, HES, EXP)
temp_list = []
columns = ['Angle', 'HOS', 'HES', 'EXPOSURE']
for deg, hos, hes, exp in motors:
        temp_list.append(pd.DataFrame({'Angle':deg, 'HOS':hos, 'HES':hes, 'EXPOSURE':exp}))
VariableMotors.append(temp_list)
"""
STOP COPYING HERE
"""

The example given is for a sample that will be measured at four energies. Each energy is assigned a list that corresponds to the 3 motors discussed earlier and DEG which corresponds to the Sample Theta. Within these lists we will compile a set of angles, that once reached in our ‘theta-2theta’ scan, will update the upstream optics to increase flux.

  1. Always begin with the following settings: Higher Order Suppressor = 12, Exposure = 0.001, and Horizontal Exit Slit Size = 150 (or Horizontal Exit Slit Size = 1500 if above 285 eV)

  2. Set Sample Theta = 0 , CCD Theta = 0, Sample Z to the direct beam location, and Beamline Energy to the target energy (be sure to include the EnergyOffset). Take a snap of the beam.

    • For any samples with a corresponding AngleOffset, be sure to add it to every Sample Theta used during this alignment step.

    • For samples mounted on the bottom of the plate, be sure to subtract 180 from each Sample Theta

  3. Adjust the Exposure until you maximize counts (or nearly so) without saturating any pixels.

    • Set this value into the first element of the EXP list. In the example, for ‘Energy 1’, this value is 0.001. We recommend to remain at this exposure until the Higher Order Suppressor == 7.5

  4. Set Sample Theta = 4 and CCD Theta = 8 and snap an image with identical settings.

    • The beam should still be visible, and with decent counts. Pixels should be at least hundreds of counts over the background.

    • If the beam is completely gone, or too bright, adjust the Sample Theta position until the beam is at a good intensity to change settings. Remember to update the *DEG list to this new position.

  5. Adjust the Higher Order Suppressor at this new Sample Theta position until you have maximized counts.

    • Set this value into the second element of HOS.

  6. Repeat steps 4 and 5 for Sample Theta = [6, 10, 12, 15, 20, 25, 30, 40, 60]. Remember to set CCD Theta` to double Sample Theta in order to measure the beam.

    • Once Higher Order Suppressor == 7.5, begin increasing Exposure. At Exposure == 1 it is unlikely that any increase will get you better data without going to 10s or higher. It is often not worth collecting this data due to the amount of time it will take.

The provided Sample Theta positions are simply a suggestion. Change them or add more as you see fit for your samples.

Running the script

Once you have filled in all the necessary information, open a python shell and navigate to the directory holding the runfile. Run it with the following line:

>>>python prsoxr_script_gen.py

Two files should be generated in the chosen directory:

  1. A runfile: ‘save_name’.txt

  2. A header file: ‘save_name’_HEADER.txt

The header file keeps information about the samples and the energies that you want to run. This is for sorting the output data once it has been collected. The runfile needs to be transfered onto the beamline computer to run. An example script is provided in PyPXR/example_data for comparison.

Set the acquisition parameters to From File, select the runfile, click Start