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Rotation around beta and omega
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Rotation around beta
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, phi and omega
Unit cell
| Code Block | ||||
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AnglesCrystFEL unit cell file version 1.0 lattice_type = triclinic centering = I a = 18.36 A b = 26.65 A c = 4.81 A al = 90.0 deg be = 90.0 deg ga = 102.83 deg |
Detector
| Code Block | ||||
|---|---|---|---|---|
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adu_per_eV = 1.0
; Single panel
0/min_fs = 0
0/max_fs = 1500
0/min_ss = 0
0/max_ss = 1500
0/corner_x = -750.00
0/corner_y = -750.00
0/fs = x
0/ss = y
0/clen = 0.1 ; 10cm
0/res = 9098 ; 109.92 micron pixel size |
pattern_sim
command to generate simulated events:
| Code Block |
|---|
cat quaternion_basis_x90.txt | pattern_sim -g det1500x1500.geom -p cell-fiber.cell -o result_x90 --photon-energy=6003 --spectrum=tophat --beam-bandwidth=1e-6 --min-size=30 --max-size=3 -n 3 -s 1 --no-noise
# output file accumulates events... (bug?)
# OR per event with complete control on names etc.
echo "0.587174 0.803196 0.095372 0.031718" | pattern_sim -g det1500x1500.geom -p cell-fiber.cell -o results_x90 --photon-energy=6003 --spectrum=tophat --beam-bandwidth=1e-6 --min-size=30 --max-size=30 -n 1 -s 1 --no-noise --no-fringes |
Results
Rotation around angles
| Code Block | ||||
|---|---|---|---|---|
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Angles around x,y,z: 90.0 0.0 0.0 quaternion: w,x,y,z: 0.707107 0.707107 0.000000 0.000000around x,y,z: 90.0 0.0 0.0 quaternion: w, x, y, z: 0.707107 0.707107 0.000000 0.000000 Angles around x,y,z: 90.0 0.0 30.0 quaternion: w, x, y, z: 0.683013 0.683013 0.183013 0.183013 Angles around x,y,z: 90.0 0.0 60.0 quaternion: w, x, y, z: 0.612372 0.612372 0.353553 0.353553 Angles around x,y,z: 90.0 0.0 90.0 quaternion: w, x, y, z: 0.500000 0.500000 0.500000 0.500000 Angles around x,y,z: 90.0 0.0 120.0 quaternion: w, x, y, z: 0.353553 0.353553 0.612372 0.612372 Angles around x,y,z: 90.0 0.0 1501.0 quaternion: w, x, y, z: 0.183013707080 0.183013707080 0.683013006171 0.683013 |
Rotation around beta, phi and omega
| Code Block | ||||
|---|---|---|---|---|
| ||||
Angles around x,y,006171 Angles around x,y,z: 7290.0 -30.50 02.0 quaternion: w,x,y,z: 0.808640706999 0.587511706999 -0.024706012341 0.017950012341 Angles around x,y,z: 7290.0 -3 0.50 13.0 quaternion: w,x,y,z: 0.808452706864 0.587704706864 -0.019578018510 0.025006018510 Angles around x,y,z: 7290.0 -3 0.50 24.0 quaternion: w,x,y,z: 0.808203706676 0.587853706676 -0.014449024678 0.032060024678 Angles around x,y,z: 7290.0 -3 0.50 35.0 quaternion: w,x,y,z: 0.807893706434 0.587957706434 -0.009318030844 0.039112030844 Angles around x,y,z: 7290.0 -30.50 46.0 quaternion: w,x,y,z: 0.807521706138 0.588015706138 -0.004187037007 0.037007 ... |
image generated with defailt sample size
images for 30um sample size:
| Code Block | ||||
|---|---|---|---|---|
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Angles around 046160 Angles around x,y,z: 72.0 -3.5 5.0 quaternion: w,x,y,z: 90.0.807087 -3.5 0.5880300 quaternion: w,x,y,z: 0.000944706777 0.053205 |
Unit cell
| Code Block | ||||
|---|---|---|---|---|
| ||||
CrystFEL unit cell file version 1.0
lattice_type = triclinic
centering = I
a = 18.36 A
b = 26.65 A
c = 4.81 A
al = 90.0 deg
be = 90.0 deg
ga = 102.83 deg |
Detector
| Code Block | ||||
|---|---|---|---|---|
| ||||
adu_per_eV = 1.0
; Single panel
0/min_fs = 0
0/max_fs = 1500
0/min_ss = 0
0/max_ss = 1500
0/corner_x = -750.00
0/corner_y = -750.00
0/fs = x
0/ss = y
0/clen = 0.1 ; 10cm
0/res = 9098 ; 109.92 micron pixel size |
pattern_sim
command to generate simulated events:
| Code Block |
|---|
cat quaternion_basis_x90.txt | pattern_sim -g det1500x1500.geom -p cell-fiber.cell -o result_x90 --photon-energy=6003 --spectrum=tophat --beam-bandwidth=1e-6 --min-size=30 --max-size=3 -n 3 -s 1 --no-noise
# output file accumulates events... (bug?)
# OR per event with complete control on names etc.
echo "0.587174 0.803196 0.095372 0.031718" | pattern_sim -g det1500x1500.geom -p cell-fiber.cell -o results_x90 --photon-energy=6003 --spectrum=tophat --beam-bandwidth=1e-6 --min-size=30 --max-size=30 -n 1 -s 1 --no-noise --no-fringes |
Results
Rotation around omega
Angles around x,y,z: 90.0 0 (0,180,1):
image generated with defailt sample size
Angles around x,y,z: 90.0 -3.5 (0,180,1):
...
706777 -0.021594 0.021594
Angles around x,y,z: 90.0 -3.5 1.0 quaternion: w,x,y,z: 0.706562 0.706939 -0.015425 0.027761
Angles around x,y,z: 90.0 -3.5 2.0 quaternion: w,x,y,z: 0.706292 0.707046 -0.009256 0.033926
Angles around x,y,z: 90.0 -3.5 3.0 quaternion: w,x,y,z: 0.705970 0.707100 -0.003085 0.040088
Angles around x,y,z: 90.0 -3.5 4.0 quaternion: w,x,y,z: 0.705593 0.707100 0.003085 0.046247
Angles around x,y,z: 90.0 -3.5 5.0 quaternion: w,x,y,z: 0.705162 0.707046 0.009256 0.052403
... |
| Code Block | ||||
|---|---|---|---|---|
| ||||
Angles around x,y,z: 72.0 -3.5 0.0 quaternion: w,x,y,z: 0.808640 0.587511 -0.024706 0.017950
Angles around x,y,z: 72.0 -3.5 1.0 quaternion: w,x,y,z: 0.808452 0.587704 -0.019578 0.025006
Angles around x,y,z: 72.0 -3.5 2.0 quaternion: w,x,y,z: 0.808203 0.587853 -0.014449 0.032060
Angles around x,y,z: 72.0 -3.5 3.0 quaternion: w,x,y,z: 0.807893 0.587957 -0.009318 0.039112
Angles around x,y,z: 72.0 -3.5 4.0 quaternion: w,x,y,z: 0.807521 0.588015 -0.004187 0.046160
Angles around x,y,z: 72.0 -3.5 5.0 quaternion: w,x,y,z: 0.807087 0.588030 0.000944 0.053205
... |
Summary
- Thomas White did not advice to use
pattern_simdue to potential bugs. - In stead he suggested to use
diffraction. pattern_simhas a few problems in different versionssource /reg/g/cfel/crystfel/crystfel-0.6.2/setup-sh # has problems with peak intensity ~25*e6 ADU, not sensitive to adu_per_eV, etc
- --spectrum=tophat --beam-bandwidth=1e-6 - removes photon energy spread
- --min-size=30 --max-size=30 - changes a size of sample and peak size and intensity
- -n NNN - this option generates accumulated image
- ...
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