Manual_Comix

ComIXS Baffles

Delta=0.02: UP=19.01; DOWN=6.99

Delta=0.2: UP=19.05; DOWN=6.95

Delta=0.3: UP=19.15; DOWN=6.85

ComIXS Energy scale

Below is the content of the *.scl file which was used to calculate the approximate energy scale of N Ka XES spectrum in the first diffraction order.  The values can be adjusted depending on the position of the spectrum at the detector and the position of the CCD (here - CCD_actual_position). Adjusted values are marked with bold. 

[Spectrometer]
CCD_alpha, deg=2.8600
CCD_gamma, deg=7.6000
Zero_order_CCD_position, mm=-53.2000
Zero_order_CCD_pixel, pxl=380
Distance_p_CCD_Grating, mm=430
Groove_density, grooves/mm=1920.0
CCD_actual_position, mm=-25.9900
Number_of_CCD_pixels, pxl=2048.0000
j_factor, micron=0.0135
x_factor, micron=0.0135

The values are considered to be default for the selected beam position settings and for the whole moving range of the ComIXS CCD. This scale is to be used in the ComIXS acquisition and processing software. You can also customize the scale, save it as a text file, load it in the software.

You can use both ComIXS data analyzer software and/or an appropriate macro Igor:Data:Load Wave: Load XES_BACH to perform your own analysis procedure.

ComIXSControlPanelvt-dva.vi

1. Fill the trap with liquid nitrogen. It will last about 5-7 hours (the first time less).

2. Stop the FAN of the ComIXS turbo molecular pump.

3. Run the VI in the continous mode (the button with the two round arrows).

4. CCD: Press Wakeup and cool. The peltier will cool down the CCD to -55 degree Celsius

5.Make sure that the Encoder box is turned on and it is reading a reasonable position (typoically  a number between -20 and -35).

6. In Firefox bookmark toolbar, select the CCD position link and make sure that it is reading the position. If not it will appear a message that the Instrument is not OK.
In that case contact the software BCS group (e.g. Turcinovich, Billè, Chenda..) and ask to "wake up" the Hedeneim encoder position (Central branchline, Left Chamber).

7. Motor. Read the actual position of the CCD. Write the new position and press Write.
NOTE: In order to choose the right energy window you can use ComiX_data_analyse.vi. Typically:
CCD=-33-->energy window=250-1040
CCD=-25-->about 300-800

8. Settings. In the DATA window select the Data and Images that you want to save. Remeber that the images can fill up the memory of the PC very quickly, so, if not necessary, do not select Save Image afterEvery Swipe.
Select the grating in use (e.g. for SG4 select number 3 which is limited to 300-1600 eV).
PLEASE DO NOT change the other parameters!

9. Acquire.
Create and choose the Data file Folder. The scans will be saved with progressive numbers starting from 0.
Choose the exposure time. Choose the time to update the spectrum which is displayed in the window. These intermediate swipes can be saved as .dat or as .img. Choose what files will be saved in the SETTINGS tab.
To measure a single scan select Single.
To measure a series of Energy dependent scans, select Multiple.
MULTIPLE SCAN ACQUISTION:
ENERGY TO FILL.
Photon Energy=initial photon energy
X Factor= energy shift to apply to the calculator in order to have the right gap (max of the harmonic at the selected energy).
Select undulator, Ring Energy, Grating Mono.
Step=energy step in the series
Number of steps=(final energy-initial energy)/step +1
Number of polarizations. 1= only the selected polarization. 2=hor and ver polarization will be acquired at each energy.
Press FILL. ENERGIES to SCAN table will be filled. Check and press Validate. It might be necessary to empty the array before pressing fill.
Select X Und. Gap Optimization.
Select CCD Shutdown (means CCD warmup) after scans or on timer if the acquisition is done overnight. Remember that the N2 trap will not last more than 5-7 hours! It should never be empty with the CCD cold in order to avoid water gettering on the CCD and damage of the CCD.
The Timer_active.vi is a countdown timer which will warmup the CCD and close the FE after the selected time. It need to be startd and activated separately.


NOTE: The acquisition have always a dead time. For example for an acquisition time=10 sec-->real acquisition time=30.45 sec.

The software for the acquisition and analysis of the ComIXS data has been written by Mikhail Yablonskikh using Labview.

ComIXS_data_analyzer.vi

alpha=3.9, gamma=7.6
0-order=-53.2, j_zero_order=540
distance=430, groovedensity=1920
CCD=position(eg -33), pixels=2048
x_factor=0.0135, j_factor=0.0135
-------------------------------------------------
Press CALCULATE. You can see the energy range of the CCD at the actual CCD position.
Select the Data file Folder and press update.
The file .txt will show the parameters (motro positions, etc..) of the scan.
The file  .img will show the CCD in the right window. The vertical lines are the emission.
The lines should cover the full area of the CCD otherwise you need to change the y of the sample. For THIN samples mounted at the center of the sample holder y=27.
The lines should be vertical. If from a zoom you see they are not vertical, rotate the image by an angle (try 0.01). Rotating several times wil add the rotations.
In the scan graph window press PLOT: you will obtain the integrated image after the rotation.
You can slightly adjust the energy scale in order to have the lines at the correct position using two methods:
a) you can change slightly the x_factor and j_factor parameters and then press plot until the elastic peak is at the correct energy.
Or set two A and B cursors on the peaks and calibrate.

Timer_active.vi

Rune the VI and choose the countdown time (e.g. 5 hours). Select the button Shutdown ComIXS and Close FE which will become GREEN.
Press the button REQUEST (otherwise the countdown will not start!)

The software for the acquisition and analysis of the ComIXS data has been written by Mikhail Yablonskikh using Labview.