[Gate-users] Voxelized phantom material error aborts my computation
Ida Häggström
ida.haggstrom at radfys.umu.se
Fri Oct 11 15:35:59 CEST 2013
Hello gate-users!
I am currently using Gate v5.0.0 to simulate a voxelized phantom consisting
of 9 different materials. When I try to run my main macro I get an error
that I can't figure out:
>> Gate -a "some aliases..." main.mac
!!! GateEbyFComponentCreator::AddToMaterial:
Impossible to add element 'Calcium' with fraction of 0 in material 'Brain'!
Please modify the GateMaterials.db file for this material.
Computation aborted !!!
I don't know if this is truly a problem with my materials or something
else, such as the environment variables on the remote computer I'm using or
something like that. I haven't found any problems with that though, so I
thought I'd ask the forum.
Thanks for any help!
/Ida
My range translator looks like:
-----------------------------------------------------------------
9
0 0 Air false 0.0 0.0 0.0 0.2
1 1 Water false 0.0 0.0 1.0 0.2
2 2 Brain false 0.0 1.0 0.0 0.2
3 3 Adipose false 0.5 0.5 1.0 0.2
4 4 Muscle false 0.5 0.0 0.5 0.2
5 5 Body false 0.5 0.5 0.5 0.2
6 6 Skull false 1.0 1.0 1.0 0.2
7 7 Blood false 1.0 0.0 0.0 0.2
8 8 Body false 0.8 0.8 0.8 0.2
-----------------------------------------------------------------
and my GateMaterials.db (original file):
-----------------------------------------------------------------
[Elements]
Hydrogen: S= H ; Z= 1. ; A= 1.01 g/mole
Helium: S= He ; Z= 2. ; A= 4.003 g/mole
Lithium: S= Li ; Z= 3. ; A= 6.941 g/mole
Beryllium: S= Be ; Z= 4. ; A= 9.012 g/mole
Boron: S= B ; Z= 5. ; A= 10.811 g/mole
Carbon: S= C ; Z= 6. ; A= 12.01 g/mole
Nitrogen: S= N ; Z= 7. ; A= 14.01 g/mole
Oxygen: S= O ; Z= 8. ; A= 16.00 g/mole
Fluorine: S= F ; Z= 9. ; A= 18.998 g/mole
Neon: S= Ne ; Z= 10. ; A= 20.180 g/mole
Sodium: S= Na ; Z= 11. ; A= 22.99 g/mole
Magnesium: S= Mg ; Z= 12. ; A= 24.305 g/mole
Aluminium: S= Al ; Z= 13. ; A= 26.98 g/mole
Silicon: S= Si ; Z= 14. ; A= 28.09 g/mole
Phosphor: S= P ; Z= 15. ; A= 30.97 g/mole
Sulfur: S= S ; Z= 16. ; A= 32.066 g/mole
Chlorine: S= Cl ; Z= 17. ; A= 35.45 g/mole
Argon: S= Ar ; Z= 18. ; A= 39.95 g/mole
Potassium: S= K ; Z= 19. ; A= 39.098 g/mole
Calcium: S= Ca ; Z= 20. ; A= 40.08 g/mole
Scandium: S= Sc ; Z= 21. ; A= 44.956 g/mole
Titanium: S= Ti ; Z= 22. ; A= 47.867 g/mole
Vandium: S= V ; Z= 23. ; A= 50.942 g/mole
Chromium: S= Cr ; Z= 24. ; A= 51.996 g/mole
Manganese: S= Mn ; Z= 25. ; A= 54.938 g/mole
Iron: S= Fe ; Z= 26. ; A= 55.845 g/mole
Cobalt: S= Co ; Z= 27. ; A= 58.933 g/mole
Nickel: S= Ni ; Z= 28. ; A= 58.693 g/mole
Copper: S= Cu ; Z= 29. ; A= 63.39 g/mole
Zinc: S= Zn ; Z= 30. ; A= 65.39 g/mole
Gallium: S= Ga ; Z= 31. ; A= 69.723 g/mole
Germanium: S= Ge ; Z= 32. ; A= 72.61 g/mole
Yttrium: S= Y ; Z= 39. ; A= 88.91 g/mole
Cadmium: S= Cd ; Z= 48. ; A= 112.41 g/mole
Tellurium: S= Te ; Z= 52. ; A= 127.6 g/mole
Iodine: S= I ; Z= 53. ; A= 126.90 g/mole
Cesium: S= Cs ; Z= 55. ; A= 132.905 g/mole
Gadolinium: S= Gd ; Z= 64. ; A= 157.25 g/mole
Lutetium: S= Lu ; Z= 71. ; A= 174.97 g/mole
Tungsten: S= W ; Z= 74. ; A= 183.84 g/mole
Thallium: S= Tl ; Z= 81. ; A= 204.37 g/mole
Lead: S= Pb ; Z= 82. ; A= 207.20 g/mole
Bismuth: S= Bi ; Z= 83. ; A= 208.98 g/mole
Uranium: S= U ; Z= 92. ; A= 238.03 g/mole
[Materials]
Vacuum: d=0.000001 mg/cm3 ; n=1
+el: name=Hydrogen ; n=1
Aluminium: d=2.7 g/cm3 ; n=1 ; state=solid
+el: name=auto ; n=1
Uranium: d=18.90 g/cm3 ; n=1 ; state=solid
+el: name=auto ; n=1
Silicon: d=2.33 g/cm3 ; n=1 ; state=solid
+el: name=auto ; n=1
Germanium: d=5.32 g/cm3 ; n=1 ; state=solid
+el: name=auto ; n=1
Yttrium: d=4.47 g/cm3 ; n=1
+el: name=auto ; n=1
Gadolinium: d=7.9 g/cm3 ; n=1
+el: name=auto ; n=1
Lutetium: d=9.84 g/cm3 ; n=1
+el: name=auto ; n=1
Tungsten: d=19.3 g/cm3 ; n=1 ; state=solid
+el: name=auto ; n=1
Lead: d=11.4 g/cm3 ; n=1 ; state=solid
+el: name=auto ; n=1
Bismuth: d=9.75 g/cm3 ; n=1 ; state=solid
+el: name=auto ; n=1
NaI: d=3.67 g/cm3; n=2; state=solid
+el: name=Sodium ; n=1
+el: name=Iodine ; n=1
PWO: d=8.28 g/cm3; n=3 ; state=Solid
+el: name=Lead; n=1
+el: name=Tungsten; n=1
+el: name=Oxygen; n=4
BGO: d=7.13 g/cm3; n= 3 ; state=solid
+el: name=Bismuth; n=4
+el: name=Germanium; n=3
+el: name=Oxygen; n=12
LSO: d=7.4 g/cm3; n=3 ; state=Solid
+el: name=Lutetium ; n=2
+el: name=Silicon; n=1
+el: name=Oxygen; n=5
GSO: d=6.7 g/cm3; n=3 ; state=Solid
+el: name=Gadolinium ; n=2
+el: name=Silicon; n=1
+el: name=Oxygen; n=5
LuAP: d=8.34 g/cm3; n=3 ; state=Solid
+el: name=Lutetium ; n=1
+el: name=Aluminium; n=1
+el: name=Oxygen; n=3
YAP: d=5.55 g/cm3; n=3 ; state=Solid
+el: name=Yttrium ; n=1
+el: name=Aluminium; n=1
+el: name=Oxygen; n=3
Water: d=1.00 g/cm3; n=2 ; state=liquid
+el: name=Hydrogen ; n=2
+el: name=Oxygen; n=1
Quartz: d=2.2 g/cm3; n=2 ; state=Solid
+el: name=Silicon ; n=1
+el: name=Oxygen ; n=2
Breast: d=1.020 g/cm3 ; n = 8
+el: name=Oxygen; f=0.5270
+el: name=Carbon; f=0.3320
+el: name=Hydrogen ; f=0.1060
+el: name=Nitrogen; f=0.0300
+el: name=Sulfur ; f=0.0020
+el: name=Sodium ; f=0.0010
+el: name=Phosphor; f=0.0010
+el: name=Chlorine ; f=0.0010
Air: d=1.29 mg/cm3 ; n=4 ; state=gas
+el: name=Nitrogen; f=0.755268
+el: name=Oxygen; f=0.231781
+el: name=Argon; f=0.012827
+el: name=Carbon; f=0.000124
Glass: d=2.5 g/cm3; n=4; state=solid
+el: name=Sodium ; f=0.1020
+el: name=Calcium; f=0.0510
+el: name=Silicon; f=0.2480
+el: name=Oxygen; f=0.5990
Plexiglass: d=1.19 g/cm3; n=3; state=solid
+el: name=Hydrogen; f=0.080538
+el: name=Carbon; f=0.599848
+el: name=Oxygen; f=0.319614
Scinti-C9H10: d=1.032 g/cm3 ; n=2
+el: name=Carbon; n=9
+el: name=Hydrogen; n=10
LuYAP-70: d=7.1 g/cm3 ; n=4
+el: name=Lutetium ; n= 7
+el: name=Yttrium ; n= 3
+el: name=Aluminium; n=10
+el: name=Oxygen; n=30
LuYAP-80: d=7.5 g/cm3 ; n=4
+el: name=Lutetium ; n= 8
+el: name=Yttrium ; n= 2
+el: name=Aluminium; n=10
+el: name=Oxygen; n=30
Plastic: d=1.18 g/cm3 ; n=3; state=solid
+el: name=Carbon ; n=5
+el: name=Hydrogen ; n=8
+el: name=Oxygen ; n=2
Paraffine: d=0.8 g/cm3 ; n=3; state=solid
+el: name=Carbon ; n=5
+el: name=Hydrogen ; n=8
+el: name=Oxygen ; n=2
CZT: d=5.68 g/cm3 ; n=3; state=solid
+el: name=Cadmium ; n=9
+el: name=Zinc ; n=1
+el: name=Tellurium ; n=10
Lung: d=0.26 g/cm3 ; n=9
+el: name=Hydrogen ; f=0.103
+el: name=Carbon ; f=0.105
+el: name=Nitrogen ; f=0.031
+el: name=Oxygen ; f=0.749
+el: name=Sodium ; f=0.002
+el: name=Phosphor ; f=0.002
+el: name=Sulfur ; f=0.003
+el: name=Chlorine ; f=0.003
+el: name=Potassium ; f=0.002
Polyethylene: d=0.96 g/cm3 ; n=2
+el: name=Hydrogen ; n=2
+el: name=Carbon ; n=1
PVC: d=1.65 g/cm3 ; n=3 ; state=solid
+el: name=Hydrogen ; n=3
+el: name=Carbon ; n=2
+el: name=Chlorine ; n=1
SS304: d=7.92 g/cm3 ; n=4 ; state=solid
+el: name=Iron ; f=0.695
+el: name=Chromium ; f=0.190
+el: name=Nickel ; f=0.095
+el: name=Manganese ; f=0.020
PTFE: d= 2.18 g/cm3 ; n=2 ; state=solid
+el: name=Carbon ; n=1
+el: name=Fluorine ; n=2
LYSO: d=5.37 g/cm3; n=4 ; state=Solid
+el: name=Lutetium ; f=0.31101534
+el: name=Yttrium ; f=0.368765605
+el: name=Silicon; f=0.083209699
+el: name=Oxygen; f=0.237009356
Body: d=1.00 g/cm3 ; n=2
+el: name=Hydrogen ; f=0.112
+el: name=Oxygen ; f=0.888
Muscle: d=1.05 g/cm3 ; n=9
+el: name=Hydrogen ; f=0.102
+el: name=Carbon ; f=0.143
+el: name=Nitrogen ; f=0.034
+el: name=Oxygen ; f=0.71
+el: name=Sodium ; f=0.001
+el: name=Phosphor ; f=0.002
+el: name=Sulfur ; f=0.003
+el: name=Chlorine ; f=0.001
+el: name=Potassium ; f=0.004
LungMoby: d=0.30 g/cm3 ; n=6
+el: name=Hydrogen ; f=0.099
+el: name=Carbon ; f=0.100
+el: name=Nitrogen ; f=0.028
+el: name=Oxygen ; f=0.740
+el: name=Phosphor ; f=0.001
+el: name=Calcium ; f=0.032
SpineBone: d=1.42 g/cm3 ; n=11
+el: name=Hydrogen ; f=0.063
+el: name=Carbon ; f=0.261
+el: name=Nitrogen ; f=0.039
+el: name=Oxygen ; f=0.436
+el: name=Sodium ; f=0.001
+el: name=Magnesium ; f=0.001
+el: name=Phosphor ; f=0.061
+el: name=Sulfur ; f=0.003
+el: name=Chlorine ; f=0.001
+el: name=Potassium ; f=0.001
+el: name=Calcium ; f=0.133
RibBone: d=1.92 g/cm3 ; n=9
+el: name=Hydrogen ; f=0.034
+el: name=Carbon ; f=0.155
+el: name=Nitrogen ; f=0.042
+el: name=Oxygen ; f=0.435
+el: name=Sodium ; f=0.001
+el: name=Magnesium ; f=0.002
+el: name=Phosphor ; f=0.103
+el: name=Sulfur ; f=0.003
+el: name=Calcium ; f=0.225
Adipose: d=0.92 g/cm3 ; n=6
+el: name=Hydrogen ; f=0.120
+el: name=Carbon ; f=0.640
+el: name=Nitrogen ; f=0.008
+el: name=Oxygen ; f=0.229
+el: name=Phosphor ; f=0.002
+el: name=Calcium ; f=0.001
Blood: d=1.06 g/cm3 ; n=10
+el: name=Hydrogen ; f=0.102
+el: name=Carbon ; f=0.11
+el: name=Nitrogen ; f=0.033
+el: name=Oxygen ; f=0.745
+el: name=Sodium ; f=0.001
+el: name=Phosphor ; f=0.001
+el: name=Sulfur ; f=0.002
+el: name=Chlorine ; f=0.003
+el: name=Potassium ; f=0.002
+el: name=Iron ; f=0.001
Heart: d=1.05 g/cm3 ; n=9
+el: name=Hydrogen ; f=0.104
+el: name=Carbon ; f=0.139
+el: name=Nitrogen ; f=0.029
+el: name=Oxygen ; f=0.718
+el: name=Sodium ; f=0.001
+el: name=Phosphor ; f=0.002
+el: name=Sulfur ; f=0.002
+el: name=Chlorine ; f=0.002
+el: name=Potassium ; f=0.003
Kidney: d=1.05 g/cm3 ; n=10
+el: name=Hydrogen ; f=0.103
+el: name=Carbon ; f=0.132
+el: name=Nitrogen ; f=0.03
+el: name=Oxygen ; f=0.724
+el: name=Sodium ; f=0.002
+el: name=Phosphor ; f=0.002
+el: name=Sulfur ; f=0.002
+el: name=Chlorine ; f=0.002
+el: name=Potassium ; f=0.002
+el: name=Calcium ; f=0.001
Liver: d=1.06 g/cm3 ; n=9
+el: name=Hydrogen ; f=0.102
+el: name=Carbon ; f=0.139
+el: name=Nitrogen ; f=0.03
+el: name=Oxygen ; f=0.716
+el: name=Sodium ; f=0.002
+el: name=Phosphor ; f=0.003
+el: name=Sulfur ; f=0.003
+el: name=Chlorine ; f=0.002
+el: name=Potassium ; f=0.003
Lymph: d=1.03 g/cm3 ; n=7
+el: name=Hydrogen ; f=0.108
+el: name=Carbon ; f=0.041
+el: name=Nitrogen ; f=0.011
+el: name=Oxygen ; f=0.832
+el: name=Sodium ; f=0.003
+el: name=Sulfur ; f=0.001
+el: name=Chlorine ; f=0.004
Pancreas: d=1.04 g/cm3 ; n=9
+el: name=Hydrogen ; f=0.106
+el: name=Carbon ; f=0.169
+el: name=Nitrogen ; f=0.022
+el: name=Oxygen ; f=0.694
+el: name=Sodium ; f=0.002
+el: name=Phosphor ; f=0.002
+el: name=Sulfur ; f=0.001
+el: name=Chlorine ; f=0.002
+el: name=Potassium ; f=0.002
Intestine: d=1.03 g/cm3 ; n=9
+el: name=Hydrogen ; f=0.106
+el: name=Carbon ; f=0.115
+el: name=Nitrogen ; f=0.022
+el: name=Oxygen ; f=0.751
+el: name=Sodium ; f=0.001
+el: name=Phosphor ; f=0.001
+el: name=Sulfur ; f=0.001
+el: name=Chlorine ; f=0.002
+el: name=Potassium ; f=0.001
Skull: d=1.61 g/cm3 ; n=9
+el: name=Hydrogen ; f=0.05
+el: name=Carbon ; f=0.212
+el: name=Nitrogen ; f=0.04
+el: name=Oxygen ; f=0.435
+el: name=Sodium ; f=0.001
+el: name=Magnesium ; f=0.002
+el: name=Phosphor ; f=0.081
+el: name=Sulfur ; f=0.003
+el: name=Calcium ; f=0.176
Cartilage: d=1.10 g/cm3 ; n=8
+el: name=Hydrogen ; f=0.096
+el: name=Carbon ; f=0.099
+el: name=Nitrogen ; f=0.022
+el: name=Oxygen ; f=0.744
+el: name=Sodium ; f=0.005
+el: name=Phosphor ; f=0.022
+el: name=Sulfur ; f=0.009
+el: name=Chlorine ; f=0.003
Brain: d=1.04 g/cm3 ; n=9
+el: name=Hydrogen ; f=0.107
+el: name=Carbon ; f=0.145
+el: name=Nitrogen ; f=0.022
+el: name=Oxygen ; f=0.712
+el: name=Sodium ; f=0.002
+el: name=Phosphor ; f=0.004
+el: name=Sulfur ; f=0.002
+el: name=Chlorine ; f=0.003
+el: name=Potassium ; f=0.003
Spleen: d=1.06 g/cm3 ; n=9
+el: name=Hydrogen ; f=0.103
+el: name=Carbon ; f=0.113
+el: name=Nitrogen ; f=0.032
+el: name=Oxygen ; f=0.741
+el: name=Sodium ; f=0.001
+el: name=Phosphor ; f=0.003
+el: name=Sulfur ; f=0.002
+el: name=Chlorine ; f=0.002
+el: name=Potassium ; f=0.003
-----------------------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20131011/080b778c/attachment-0001.html>
More information about the Gate-users
mailing list