Welcome to CHESS <QM>² Sample Alignment¶

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High Dynamic Range Reciprocal Space Mapping (HDRM)

Basic Theory - HDRM¶

High Dynamic Range Mapping (HDRM) is primarily a method for studying single crystal samples, although it can also be effective for studying thin films. HDRM aims is to rapidly study wide regions of reciprocal space, collecting the intense Bragg peaks required to refine crystal structures along with weak features associated with superstructures, and the slowly modulated scattering associated with phonons and short-range order[1].

Single Crytal Alignment

Basic steps for single crystal sample alignment - HDRM

Step 1: Manually stage: center the sample to the beam ¶

        FOURC> umvr samz 0.1 (relative motion of the sample movement up (+) and down (-)) 
        FOURC> umv phi 0
        FOURC> umv phi 180
        Move x and y to make the sample to the cursor
        FOURC> umv phi 90
        FOURC> umv phi 270
        Do it iteratively until the center of the axis match the sample position

Carefully and slowly insert the sample in the top of the sample stage

Step 1: Automated stage: center the sample to the beam ¶

        FOURC> umvr samz 0.1 (relative motion of the sample movement up (+) and down (-)) 
        FOURC> umv phi 0
        FOURC> umvr samx 0.1 (make sure you can see sample is moving towards cross +)
        FOURC> umv phi 180 (check the sample is coming back to cross + )
        Move x and y to make the sample to the cursor
        FOURC> umv phi 90
        FOURC> umvr samy 0.1 (make sure you can see sample is moving towards cross +)
        FOURC> umv phi 270 (check the sample is coming back to cross + )

        Do it iteratively until the center of the axis match the sample position

Step 2 : Create file structure ¶

  a) Create newfile from the SPEC terminal

        Srep 1: You need to provide acurate Element Name (K, Sc etc), special character does not work (.,:" etc)

              FOURC>newfile <samplename>

        # samplename : chemical name of your sample, make sure you created folder in your directory



  Provide all the correct informations for metadata in the server
  # Look the table in the googgle doc

  | Sample name | chemical formula | Crystal Structure | Space group | Space group #| Unit cell parameters | 
  | :----------:| :---------------:| :----------------:| :---------: | :-----------:| :--------------------:
  |   CeO2      |       CeO2       |       Cubic       |   Fm-3m     |    225         |a=5.41, b=5.41, c=5.41, alpha=90, beta=90, gamma=90
  | :----------:| :---------------:| :----------------:| :---------: | :-----------:| :---------------------:


  * sample_chemical_formula -- Provide chemical formula of the sample (e.g AV3Sb5): CeO2
  * crystal_system_rt -- Provide room temperature sample crystal system : cubic
  * sample_space_group -- Provide the sample space group :Fm-3m
  * sample_space_group_number -- Provide the sample space group number : 225
  * sample_unit_cell -- Unit cell dimensions  (units: angstrom) :  a = 5.41, b = 5.41, c = 5.41, alpha = 90, beta = 90, gamma = 90
  * phase_transition -- Will the sample undergo a phase transition during the experiment? If yes,what are the temperature and space group? (default: ):N.A

Step 3: Open HDRMscans.mac script and sort your path (sortmypathout)¶

        i) Go to the folder: /nfs/chess/id4b/<cycle_number>/<proposal_id>  
        ii) Open HDRMscans.mac file in the folder location (this is not from SPEC terminal)
        ii) Change the `_mysample` = <sample_identifier> (#inside the script)
        # _mysample is the sample identifier
        # save the file

check the signals

Step 3: Run HDRMscans.mac script from terminal ¶

    # Any time you have modified .mac files, run the command from the terminal
    FOURC> qdo ./HDRMscans.mac 
    # Notes: HDRMscans.mac contains all the script

Step 4 : If you want to check the best height for the sample (finding smaller sample best position) ¶

    FOURC>heightscan

    a) Data will save at 'tiff' folder (Example : /nfs/chess/id4b/2026-1/sarker-0000-a/tiffs) inside the user folder at id4b
    b) Check the quality of the datasets at nexpy, DONOT Double click the image, the program will crush
    b) Go to the best position of the sample 
        FOURC> umv samz <position of the sample>

Step 5 : Autotune condition (talk to beamline scientist) ¶

  If the autotune is off in the mostab
  a) FOURC> opens (# Open the shutter)
  b) Turn the knob slowly and maximize the counts in IC2
  c) FOURC> closes (# close the shutter)

Step 6: Run three rotation crystal scan ¶

  It will rotate the crystal three times at different chi and theta angle

    FOURC> threextalscan 300 1

    # here parameter 300 is temperature and 1 is sleeping time

    Note: DONOT forget to put the paramters (temerature and sleep time), otherwise, temperature controller will try to go to 0K

    #Notes: In the threextalscan 1st parameter is temperature 300K and the second parameter is waiting time 1 min
        - It will vary chi, theta and phi angle
        - Collect data phi 0-365 with 3650 images (1 degree/frame)
        - You can the change the exposure time (if needed)

    a) Data will save at raw6M in id4b folder (Example : /nfs/chess/id4b/2026-1/sarker-0000-a/raw6M )

Step 7: Check data nexpy ¶

Please look at the Data visualization - Nexpy section

Quick video on 'heightscan' visualization (there is text below as well)¶

Step 2 : Take a look at the priliminary data after data collection¶

Step1 : Go to 'File' tab
Step 2 : Go to 'Import' tab
Step 3: Go to 'Import image stack'
Step 4: Go to desired file location
Step 5: Select the folder (it will not show any images)
Step 6: Select the images (mostly 50-60 images)
Double clicked the stack images
Go to the signal and click log scale
Go to z tab and press forward (it will go through the images)

Quick video on data collection (make sure you read the above instructions before watching the video)¶

Quick video on 'collected data' visualization¶

Step 2 : Take a look at the priliminary data after data collection¶

Step1 : Go to 'File' tab
Step 2 : Go to 'Import' tab
Step 3: Go to 'Import image stack'
Step 4: Go to desired file location
Step 5: Select the folder (it will not show any images)
Step 6: Select the images (mostly 50-60 images)
Double clicked the stack images
Go to the signal and click log scale
Go to z tab and press forward (it will go through the images)

=============================================================================

Temperature modify and collect data

Change temperature from 300K and 90 K- (if you are at Nitrogen atomosphere)¶

    FOURC> te 100
    # note: temperature here is 100 Kelvin

Make sure the temperature is stable before you run script

    FOURC> threextalscan 100 1

Practical guide of the temperature switch between nitrogen and helium

Click the link for details Nitrogen --> Helium and Helium --> Nitrogen

¶

=============================================================================

Thin-film Alignment

Basic steps for single crystal thin-film sample alignment - HDRM. Detector height needs to change because of grazing incidence. Make sure you are able to see the samples (proper light arrangements)

Step 1: Center the sample to the beam

  a) Move chi, phi, and theta positions to their initial setup
        FOURC> umv chi 90   
        FOURC> umv phi 0  
        FOURC> umv th 0

  b) Perform height adjustment
        Check the signal at the diode 
        FOURC> tw samz 0.01
        Move the sample in the Z-directions and cut the beam in half (for example: if the beam size is 300 microns, move 150 microns from the surface when the signal goes down)

  c) Place cursor at center of the sample

              FOURC> umv phi 0
              FOURC> umv phi 180
              FOURC> umv phi 90
              FOURC> umv phi 270

Step 2 : Creating the file structure

  a) Create newfile

        FOURC>newfile samplename


  b) Open HDRMscans.mac script for thin-film
        Change the sample ID

Step 3: Run HDRMscans.mac script from terminal

      FOURC> qdo ./HDRMscans.mac 
      #Notes:HDRMscans.mac contains all the script

Step 3: Check the best height for the sample it will generate tiff file

    FOURC>powderscan 300 1

    a) Check the quality of the data sets at nexpy
    b) Go to the best position of the sample

Step 4: Autotune condition (talk to beamline scientist)

  If the autotune is off in the mostab
  a) FOURC> opens (# Open the shutter)
  b) Turn the knob slowly and maximize the counts in IC2
  c) FOURC> closes (# close the shutter)

Step 5: Run three rotation crystal scan

    FOURC> threxstalscan 300 1 
    #Notes: Parameters: Temperature = 300, Sleep = 1

Step 5: Check data nexpy (please look at the Data visulization - Nexpy section )

Examples of Temperature Dependent Scans¶

300K- 475K at 25K temperature interval¶

Step 1: Follow the instruction of temprature switch 300K-500K and the temperature to stabilize

  def TScans_high_N2 '
  te = 325
  for (loopT=325; loopT<476; loopT=loopT+25){
  eval(sprintf("threextalscan %s 180",loopT))
  }

  '

90K- 300K at 25K temperature interval¶

  def Tscans_low_to_high_N2 '
  for (loopT=90; loopT < 301; loopT=loopT+15){
  eval(sprintf("threextalscan %s 180", loopT))
  }
  '

90K- 100K at 2K temperature interval, 100K-126K at 5K interval and 125K-200K at 25K interval¶

  def HighTScans_different_range '
  for (loopT=90; loopT < 101; loopT=loopT+2){
  eval(sprintf("threextalscan_longexposure %s 180", loopT))
  }

  for (loopT=100; loopT < 126; loopT=loopT+5){
  eval(sprintf("threextalscan_longexposure %s 180", loopT))
  }

  for (loopT=125; loopT < 200; loopT=loopT+25){
  eval(sprintf("threextalscan_longexposure %s 180", loopT))
  }

  '

15K- 90K at 15K temperature interval¶

  def scans_low_to_high_He '
  for (loopT=15; loopT < 91; loopT=loopT+15){
  eval(sprintf("threextalscan %s 180", loopT))
  }
  '

Welcome to CHESS <QM>2 Sample Alignment¶

Basic Theory - HDRM¶

Step 1: Manually stage: center the sample to the beam ¶

Step 1: Automated stage: center the sample to the beam ¶

Step 2 : Create file structure ¶

Step 3: Open HDRMscans.mac script and sort your path (sortmypathout)¶

Step 3: Run HDRMscans.mac script from terminal ¶

Step 4 : If you want to check the best height for the sample (finding smaller sample best position) ¶

Step 5 : Autotune condition (talk to beamline scientist) ¶

Step 6: Run three rotation crystal scan ¶

Step 7: Check data nexpy ¶

Quick video on 'heightscan' visualization (there is text below as well)¶

Step 2 : Take a look at the priliminary data after data collection¶

Quick video on data collection (make sure you read the above instructions before watching the video)¶

Quick video on 'collected data' visualization¶

Step 2 : Take a look at the priliminary data after data collection¶

Change temperature from 300K and 90 K- (if you are at Nitrogen atomosphere)¶

¶

Examples of Temperature Dependent Scans¶

300K- 475K at 25K temperature interval¶

90K- 300K at 25K temperature interval¶

90K- 100K at 2K temperature interval, 100K-126K at 5K interval and 125K-200K at 25K interval¶

15K- 90K at 15K temperature interval¶

Welcome to CHESS <QM>² Sample Alignment¶