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Script

sim08-make-index-table.py - generates lookup table and a few plots as shown below.

Unit cell

Try to understand crystal symmetry for two unit-cells

Unit cell 1: a=18, b=26, gamma=77

Unit cell 1
# file name: ./v01-sim-lut-cxifsimu-r0123-2017-04-25T09:52:17.txt
# photon energy = 6003.0000 eV
# wavelength = 2.0654 A
# wave number/Evald radius k = 1/lambda = 0.484172 1/A
# sigma_ql = 0.001453 1/A (approximately = k * <pixel size>/
# sigma_qt = 0.000484 1/A (approximately = k * <pixel size>/<sample-to-detector distance> = k*100um/100mm)
# 3*sigma_ql = 0.004358 1/A
# 3*sigma_qt = 0.001453 1/A
# Triclinic crystal cell parameters:
#   a = 18.36 A
#   b = 26.65 A
#   c = 4.81 A
#   alpha = 90.00 deg
#   beta  = 90.00 deg
#   gamma = 77.17 deg

# 3-d space primitive vectors:
#   a1 = ( 18.360000,   0.000000,   0.000000)
#   a2 = (  5.917874,  25.984635,   0.000000)
#   a3 = (  0.000000,   0.000000,   4.810000)
# reciprocal space primitive vectors:
#   b1 = (  0.054466,  -0.012404,   0.000000)
#   b2 = (  0.000000,   0.038484,   0.000000)
#   b3 = (  0.000000,   0.000000,   0.207900)

Unit cell 2: a=26, b=18, gamma=77

Unit cell 2
# file name: ./v01-sim-lut-cxifsimu-r0123-2017-04-25T10:18:21.txt
# photon energy = 6003.0000 eV
# wavelength = 2.0654 A
# wave number/Evald radius k = 1/lambda = 0.484172 1/A
# sigma_ql = 0.001453 1/A (approximately = k * <pixel size>/
# sigma_qt = 0.000484 1/A (approximately = k * <pixel size>/<sample-to-detector distance> = k*100um/100mm)
# 3*sigma_ql = 0.004358 1/A
# 3*sigma_qt = 0.001453 1/A
# Triclinic crystal cell parameters:
#   a = 26.65 A
#   b = 18.36 A
#   c = 4.81 A
#   alpha = 90.00 deg
#   beta  = 90.00 deg
#   gamma = 77.17 deg
# 3-d space primitive vectors:
#   a1 = ( 26.650000,   0.000000,   0.000000)
#   a2 = (  4.077004,  17.901610,   0.000000)
#   a3 = (  0.000000,   0.000000,   4.810000)
# reciprocal space primitive vectors:
#   b1 = (  0.037523,  -0.008546,   0.000000)
#   b2 = (  0.000000,   0.055861,   0.000000)
#   b3 = (  0.000000,   0.000000,   0.207900)

 

Presumably maps (qh vs omega) should be the same up to rotations.

Lookup table and maps

Unit cell 1

beta = 0 and 180

 

Unit cell 2

beta = 0 and 180

Indexing script

./sim09-indexing.py -p

Reconstruct simulated data, plot for hq vs omega

Comparison of look-up table and reconstructed sample

  • All maps are consistent after appropriate rotation
  • almost all lattice nodes can be reconstructed (are included in 2-peak events)

Friquency distributions at indexing

Reconstructed omega vs simulated

Reconstructed lattice

  1. fraser's stripe rotated by omega
  2. use correct transformation for friser's strip and reconstructed angle omega
  3. use correct transformation for friser's strip and simulated angle omega

 

 

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