Tasks to Prepare p2458

1. Homework

Stay healthy.

2. Homework

The aim of the second homework is to familiarize yourself with working on the maxwell cluster. We will also try to establish Slack for communication in the data team so please post questions there.

Try to accomplish the following tasks:

  • Decide which method you want to use for analyzing data:
    • Python or jupyter notebooks
    • MATLAB
    • etc.
  • Access the Maxwell cluster with each of the following methods:
  • Locate the proposal folder and the r522_test.h5 file. The file contains the data I showed in the last session.
  • Open the file and display the different datasets.
  • Calculate the position of the peak in I(q) as a function of the incident X-ray pulse energy.

3. Homework

The Structure of the HDF5-File has changed. A new group has been added containing the XPCS data. More precisely, the train resolved correlation functions, the corresponding delay time values, and the values of the q-bins are saved.

Note

Another convenient way of exploring the HDF5 file is to use the hdfview program on Maxwell.

  • Use a shell on Maxwell, e.g., by using FastX.
  • run module load xray this will make hdfview available.
  • run hdfview file-name to open an HDF5 file.

I have processed a set of runs and saved the results in the datasets folder (see Locations). To make sure that the results are not overwritten, a random number is added to the file name. It does not have any meaning.

The data have been measured with a Vycor sample varying the position of our nanofocus lenses; therefore, the beam size on the sample should vary between the measurements.

This brings us to the 3. Homework:

  • Check the new files and load the data as in the 2. Homework.
  • Characterize the measurements and search for an effect of the varied focal size.
  • Prepare your results in maximum 4 figures for a breakout session on Tuesday.
  • Think about additional data you need in the HDF5-file for our beamtime.

As always, use Slack if you need more information or have questions.

4. Homework

You find new datasets in our scratch folder: measurements of 50nm and 20nm (diameter) Silica spheres in water. In addition to the processed data, I copied the setup-files that were used for the calculation. This makes it more transparent how the data were processed, e.g., which mask was used, etc.

You can now find some Metadata information in the section below. LOTZ is the position of the nanofocus lenses along the beam direction.

If you find the time, try to accompish the following tasks of 4. Homework:

  • As before, analyze the data and compare the datasets with the Vycor measurements.

  • Compare the dynamics of the 50nm and 20nm Silica particles.

  • Prepare your results in maximum 4 figures for breakout sessions during the next meeting.

  • Create a table of your observations and whether or not they fit your expectations:

    expected unexpected
    result 1 result 2
    result 3 result 4
    … …

Metadata

Metadata information on the example datasets.

Vycor Datasets
Run number (900090) LOTZ motor position Sample Transmission (SA2_XTD1_ATT1) # of bunches Pulse energy Remarks
518 32mm No 0.04% 10 0.8mJ background measurement without NAFO
519 32mm No 0.04% 100 0.4mJ background measurement without NAFO
520 32mm No 0.04% 100 0.5mJ background measurement with NAFO
521 32mm Vycor 0.016% 100 0.5mJ Start sample measurement
522 32mm Vycor 0.02% 100 0.4mJ  
523 34mm Vycor 0.02% 100 0.5mJ  
524 36mm Vycor 0.02% 100 0.5mJ  
525 38mm Vycor 0.02% 100 0.5mJ  
526 37mm Vycor 0.02% 100 0.4mJ  
527 35mm Vycor 0.02% 100 0.4mJ  
528 35.5mm Vycor 0.02% 100 0.4mJ  
529 35.25mm Vycor 0.02% 100 0.8mJ Might be Focal point!!!
530 30mm Vycor 0.02% 100 0.7mJ  
531 40.5mm Vycor 0.02% 100 0.8mJ  
Silica Datasets
Run number (900090) LOTZ motor position Sample Transmission (SA2_XTD1_ATT1) # of bunches Pulse energy Remarks
532 35.5mm Si 50nm 1.04% 100.0 0.7mJ Signal is pretty weak. Noisy background can be seen
533 35.5mm   0.0033% 100.0 0.8mJ  
534 35mm   0.0026% 100.0 0.8mJ  
535 35.5mm   0.0026% 100.0 0.8mJ  
536 34mm   0.0026% 100.0 0.75mJ  
537 33mm   0.0026% 100.0 0.8mJ  
538 31mm   0.0026% 100.0 0.8mJ  
539 35.5mm Si 20nm 0.0026% 100.0 0.7mJ  
540 35mm   0.0026% 100.0 0.8mJ  
544 34mm   0.0026% 100.0 0.7mJ  
545 31mm   0.0026% 100.0 0.75mJ  
546 33mm   0.0026% 100.0 0.7mJ  
547 31mm Si 20nm 0.08% 100.0 0.75mJ  
548 33mm   0.08% 100.0 0.75mJ  
549 34mm   0.08% 100.0    
550 35mm   0.08% 100.0 0.75mJ  
551 35.5mm   0.08% 100.0