Virtual Experiment in Oasys

[CFGrote]

Demonstrate the execution of a virtual experiment in Oasys:

Polychromatic x-ray diffraction from lyzozyme crystals at the ESRF

1. The user sets up the beamline and sample-detector geometry in Oasys
2. The user carries out the experiment
3. The data is analysed with appropriate tools.

• [ ] Select appropriate beamline and set it up in Oasys
• [ ] Use a "python script" element in Oasys to feed the data into a GAPD simulation using the SimEx GAPD Calculator and execute the signal generation simulation
• [ ] Analyse the data with appropriate data analysis tools.

[CFGrote]

Select one of these two ESRF beamlines:

• ID30A-3
• ID23-2

[aljosahafner]

Technical specifications:

• ID30A-3 MASSIF: http://www.esrf.eu/home/UsersAndScience/Experiments/MX/About_our_beamlines/id30a-1--massif-1/massif---technical-overview.html OH1 -> OH2 -> EH2 (for MASSIF-3)
• ID23-2: https://journals.iucr.org/s/issues/2010/01/00/hi5601/index.html

For ID23 we will use SRW code and for ID30A we will try with SRW/Wiser code.

[CFGrote]

sounds good. so you want to do both? one would be enough, but as you like...

[CFGrote]

GAPD: needs to run GPU version -> no problem

[JunCEEE]

GAPD Calculator requirements:

• GAPD calculator should be able to output:

  • Pixelized diffraction image according to the detector dimension settings in DiffractorParameters.
  • The photon number obtained in each pixel converted from the calculated scattering intensity.

• GAPD calculator should be able to read:

  • The wavefront output from the propogator calculator (OASIS in this workshop provided by @aljosahafner )
  • The structure trajectory output from the PhotonMatterInteractor (DFT in this workshop provided by @mousumiuk )
  • The geometry parameters from DiffractorParameters

[JunCEEE]

GAPD calculator task breakdown:

• [x] Modify GAPD code to output pixelized diffraction pattern.
• [x] Convert diffraction pattern intensity into photon numbers.
• [ ] Output the diffraction pattern in the singFEL format.
• [ ] Write the GAPDCalculator unittest script in src/simex_platform/Tests/python/unittest/SimExTest/Calculators testing:
  • [ ] Counstruct beam parameters from wavefront data successfully.
  • [ ] Counstruct structure trajectory from trajectory data successfully.
  • [ ] Counstruct geometry parameters from DiffractorParameters data successfully.
  • [ ] Calculate diffraction pattern successfully.

[aljosahafner]

v0.1

• I will go with ID23-2, because it has a paper (these usually offer more details about the properties of optical elements).
• Shadow (ray-tracing) will be used, as it is faster

[JunCEEE]

Documentation related:

• [ ] SimEx installation documentation update

[JunCEEE]

Update at the beginning of this week:

• The prototype of GAPD parameter is committed to https://github.com/PaNOSC-ViNYL/SimEx/blob/gapd/Sources/python/SimEx/Parameters/GAPDPhotonDiffractorParameters.py
• The prototype of GAPD parameter unittest: https://github.com/PaNOSC-ViNYL/SimEx/blob/gapd/Tests/python/unittest/SimExTest/Calculators/GAPDPhotonDiffractorTest.py

ToDO this week: Monday:

• Review the ViNYL API
• [x] The data format from ray-tracing, which one to choose?:
  • SimEx data format
  • openPMD data format (chosen)
• [x] Finish SimEx GAPD calculator unittest

Tuesday:

• [x] Finish GAPD calculator
  • [x] Atomic data format PDB to xyz (via ASE).
  • [x] Finish Monochromatic Beam Test
  • [x] Convert spectrum from Raytracing into plain text for GAPD
  • [x] Finish Polychromatic Beam Test

Wednesday:

• Simulations for 100 diffraction patterns with the beam data from Oasys, using uniform rotation.

Thursday:

• [x] Report writing and presenting

At the end of workshop:

• [ ] Compile new SimEx documentation.
• [ ] SimEx installation documentation update.
• [ ] Remove WPG out of PhotonBeamParameters.