[Gate-users] Possible PhysicsList problem? Full work example included.
Jye Smith
jye.smith at gmail.com
Tue Apr 7 01:08:27 CEST 2015
Thanks Jenny, David and Nicolas for your replies.
I deleted everything in the physics section and replaced it with the below
lines. I tried a few different libraries.
*/gate/physics/addPhysicsList QGSP_BIC_EMY*
*/gate/physics/addProcess RadioactiveDecay*
And got the below error every time.
*### === Deexcitation model UAtomDeexcitation is activated for 3 regions:*
* sphere*
* *** Break *** segmentation violation*
After hunting through the mailing list and a bit of google-fu it looks like
a memory issue. Im currently running vGate with 4G of RAM. Can someone
running more RAM please confirm the macro will run fine. Im in the process
of installing Gate on a server (16G) to try it myself but am running into
proxy issues :(
Cheers
Jye
On Thu, Apr 2, 2015 at 9:45 AM, Jye Smith <jye.smith at gmail.com> wrote:
> Hello GATE,
>
> Im currently using GATE for therapy dosimetry applications and initially
> ran some test macros with 131I, 177Lu, 90Y to validate the results against
> OLINDA. Everything looked great, even when running the macro with mono
> energetic particles and comparing the results against published literature.
>
> Recently I decided to have a look at other diagnostic isotopes 99mTc, 67Ga
> etc and some alpha emitters e.g. 223Ra. I found the marco I was using
> (originally based on the mouse dosimetry example) did not give results
> close OLINDA when I simply changed the ion source. Ive got a feeling Im
> not including all of the required parameters in the Physics and tried the
> PhysicsList option with out luck.
>
> Ive uploaded a working example to http://dropcanvas.com/53wei which is a
> simple ~100gm sphere I can compare to OLINDAs sphere results. The .xls
> file is a summary of the results. You can see that for 18F and 177Lu the
> difference in dose to the sphere is within a few percent. However for
> 67Ga, 99mTc and 223Ra the difference is large. It appear all positron/beta
> emitters I model the results or good. For gamma and alpha emitters the
> results are very different.
>
> I think the correct PhysicsList I need is QGSP_BIC_EMY (e.g.
> /gate/physics/addPhysicsList QGSP_BIC_EMY) and it should allow me to
> simulate gamma, beta and alphas by just changing the ion source. Ive been
> doing this from the command line like below;
>
> Gate -a
> [sourcefile,source.dat][numparticles,1000000][outfilename,1.0M_18F.hdr][AtomicNumber,9][AtomicMass,18][ExcitationEnergy,0]
> main.mac
>
> Any help in correcting the Physics list (or what every else is wrong) is
> greatly appreciated.
>
> Cheers
> Jye
>
> main.mac copied here for convenience and to help anyone searching for
> solutions in the future.
>
> #=====================================================
> # How to run macro
> #=====================================================
>
> #Gate -a
> [sourcefile,source.dat][numparticles,1000000][outfilename,1.0M_18F.hdr][AtomicNumber,9][AtomicMass,18][ExcitationEnergy,0]
> main.mac
> #Gate -a
> [sourcefile,source.dat][numparticles,1000000][outfilename,1.0M_177Lu.hdr][AtomicNumber,71][AtomicMass,177][ExcitationEnergy,0]
> main.mac
> #Gate -a
> [sourcefile,source.dat][numparticles,1000000][outfilename,1.0M_67Ga.hdr][AtomicNumber,31][AtomicMass,67][ExcitationEnergy,0]
> main.mac
> #Gate -a
> [sourcefile,source.dat][numparticles,1000000][outfilename,1.0M_99mTc.hdr][AtomicNumber,43][AtomicMass,99][ExcitationEnergy,142.6833]
> main.mac
> #Gate -a
> [sourcefile,source.dat][numparticles,1000000][outfilename,1.0M_223Ra.hdr][AtomicNumber,88][AtomicMass,223][ExcitationEnergy,0]
> main.mac
>
> #=====================================================
> # GEOMETRY
> #=====================================================
>
> /gate/geometry/setMaterialDatabase GateMaterials.db
>
> # World
> /gate/world/geometry/setXLength 1 m
> /gate/world/geometry/setYLength 1 m
> /gate/world/geometry/setZLength 1 m
> /gate/world/setMaterial Air
>
> # Global Box
> /gate/world/daughters/name sphere
> /gate/world/daughters/insert compressedMatrix
>
> /gate/sphere/geometry/insertReader interfile
> /gate/sphere/interfileReader/insertTranslator range
> /gate/sphere/interfileReader/rangeTranslator/readTable range_geo.dat
>
> /gate/sphere/interfileReader/readFile sphere.iff
>
> #=====================================================
> # PHYSICS
> #=====================================================
>
> /gate/physics/addProcess RadioactiveDecay
>
> /gate/physics/addProcess PhotoElectric
> /gate/physics/processes/PhotoElectric/setModel StandardModel
>
> /gate/physics/addProcess Compton
> /gate/physics/processes/Compton/setModel StandardModel
>
> /gate/physics/addProcess RayleighScattering
> /gate/physics/processes/RayleighScattering/setModel PenelopeModel
>
> /gate/physics/addProcess ElectronIonisation
> /gate/physics/processes/ElectronIonisation/setModel StandardModel e-
> /gate/physics/processes/ElectronIonisation/setModel StandardModel e+
>
> /gate/physics/addProcess Bremsstrahlung e-
> /gate/physics/addProcess Bremsstrahlung e+
> /gate/physics/processes/Bremsstrahlung/setModel StandardModel e-
> /gate/physics/processes/Bremsstrahlung/setModel StandardModel e+
>
> /gate/physics/addProcess PositronAnnihilation e+
>
> /gate/physics/addProcess MultipleScattering e+
> /gate/physics/addProcess MultipleScattering e-
>
> /gate/physics/addProcess GammaConversion
> /gate/physics/processes/GammaConversion/setModel StandardModel
>
> #=====================================================
> # DETECTORS
> #=====================================================
>
> /gate/actor/addActor DoseActor
> doseDistribution
> /gate/actor/doseDistribution/attachTo sphere
> /gate/actor/doseDistribution/stepHitType random
> /gate/actor/doseDistribution/setPosition 0 0 0 cm
>
> /gate/actor/doseDistribution/setResolution 128 128 128
>
> /gate/actor/doseDistribution/enableEdep false
> /gate/actor/doseDistribution/enableUncertaintyEdep false
> /gate/actor/doseDistribution/enableSquaredEdep false
> /gate/actor/doseDistribution/enableDose true
> /gate/actor/doseDistribution/enableUncertaintyDose false
> /gate/actor/doseDistribution/enableSquaredDose false
> /gate/actor/doseDistribution/enableNumberOfHits false
> /gate/actor/doseDistribution/save output/{outfilename}
>
> /gate/actor/addActor SimulationStatisticActor stat
> /gate/actor/stat/save output/{outfilename}-output-stat.txt
>
> #=====================================================
> # INITIALISATION
> #=====================================================
>
> /gate/run/initialize
>
> #=====================================================
> # SOURCE :
> #=====================================================
>
> /gate/source/addSource isotope voxel
>
> /gate/source/isotope/reader/insert interfile
> /gate/source/isotope/interfileReader/translator/insert range
> /gate/source/isotope/interfileReader/rangeTranslator/readTable {sourcefile}
>
> /gate/source/isotope/interfileReader/readFile sphere.iff
>
> /gate/source/isotope/setPosition -64. -64. -64. mm
>
> /gate/source/isotope/gps/particle ion
> /gate/source/isotope/gps/ion {AtomicNumber} {AtomicMass} 0
> {ExcitationEnergy}
>
> /gate/source/isotope/gps/energytype Mono
> /gate/source/isotope/gps/monoenergy 0. keV
>
> /gate/source/isotope/gps/angtype iso
>
> #=====================================================
> # VISUALISATION
> #=====================================================
>
> /vis/disable
>
> #=====================================================
> # RANDOM
> #=====================================================
> /gate/random/setEngineName MersenneTwister
> /gate/random/setEngineSeed auto
>
> #=====================================================
> # START
> #=====================================================
>
> /gate/application/noGlobalOutput
> /gate/application/setTotalNumberOfPrimaries {numparticles}
> /gate/application/start
>
> exit
>
>
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