[Gate-users] Ion source: empty output
Débora Salvado
debbiesal at gmail.com
Fri Jan 16 13:09:47 CET 2015
Thank you, I'll try to run with these modifications.
I have GATE 6.2 running on a virtual machine (vGATE version 2.1).
Regards,
Débora Salvado
2015-01-16 12:03 GMT+00:00 Pietrzyk, Uwe <u.pietrzyk at fz-juelich.de>:
>
> Hi Debora,
>
> since you are not using the physicslist mechanism, you should add this
> following
> statement to stop the ion, i.e. to have it interact:
>
> /gate/physics/addProcess IonIonisation
> /gate/physics/processes/IonIonisation/setStepFunction GenericIon 0.1 0.02
> mm
>
> I also placed the source into a surrounding volume made of water to have
> the ion interact.
> This volume is defined like a normal phantom volume.
>
> -----
> # SOURCE
> # Create the source volume/phantom
>
> /gate/world/daughters/name source_vol
> /gate/world/daughters/insert sphere
> /gate/source_vol/geometry/setRmax 10.0 mm
> /gate/source_vol/geometry/setRmin 0.0 mm
> /gate/source_vol/placement/setTranslation 0. 0. 0. mm
> /gate/source_vol/setMaterial {SourceVolMaterial} <— you habe to change
> this ...
> /gate/source_vol/vis/setColor white
> #/gate/source_vol/vis/forceWireframe
> /gate/source_vol/vis/forceSolid
> /gate/source_vol/vis/setVisible 1
>
> /gate/source_vol/attachPhantomSD
>
> ——
>
> You may also check your system through visualisation and if you see
> *blue* lines, those a ions, which have a *positive* charge
>
> Which version of GATE are you using? With Gate_v7.0 or with a previous
> version
> like 6.2?
>
> Kind regards,
>
> Uwe Pietrzyk
>
>
> /----------------------------------------------------------------------
> Prof. Dr. Uwe Pietrzyk
> Diplom-Physiker
> Institut für Neurowissenschaften und Medizin / INM-4
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> ----------------------------------------------------------------------/
>
> On 16 Jan 2015, at 12:40, Débora Salvado <debbiesal at gmail.com> wrote:
>
> Hi,
> I've attached my main macro, let me know if you have any problems to see
> it.
>
> Débora Salvado
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 16 Jan 2015 12:18:30 +0100
> From: narbor <nicolas.arbor at iphc.cnrs.fr>
> To: D?bora Salvado <debbiesal at gmail.com>
> Cc: Gate Users <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] Ion source: empty output
> Message-ID: <54B8F386.1060407 at iphc.cnrs.fr
> >
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> Hi D?bora,
> Could you send us your main.mac file just to have a look ?
> Thanks.
> Nicolas Arbor
>
> ***********************************************************************
> Nicolas ARBOR
> Ma?tre de Conf?rences
> Universit? de Strasbourg - UFR Physique et Ing?nierie
> Groupe de recherche RaMsEs - Institut Pluridisciplinaire Hubert Curien
> ***********************************************************************
>
> Le 16/01/2015 12:09, D?bora Salvado a ?crit :
> > I increased the verbosity of my simulation to:
> >
> > /event/verbose 1
> >
> > and now when I run my simulation, it keeps giving me this message:
> >
> > =====================================
> > G4EventManager::ProcessOneEvent()
> > =====================================
> > G4PrimaryTransformer::PrimaryVertex (0(mm),0(mm),0(mm),1.51525e+08(nsec))
> > 1 primaries are passed from G4EventTransformer.
> > !!!!!!! Now start processing an event !!!!!!!
> > Track (trackID 1, parentID 0) is processed with stopping code 2
> > Track (trackID 3, parentID 1) is processed with stopping code 2
> > Track (trackID 2, parentID 1) is processed with stopping code 2
> > NULL returned from G4StackManager.
> > Terminate current event processing.
> >
> > I've read that some users solved this problem by adding the
> > RadioactiveDecay process to their physics list. But I have it in my
> > macro... so can someone help me?
> >
> > Thanks,
> > D?bora Salvado
> >
> >
> >
> > 2015-01-15 19:22 GMT+00:00 Marc Chamberland
> > <MarcChamberland at cmail.carleton.ca
> > <mailto:MarcChamberland at cmail.carleton.ca>>:
> >
> > Hmm? I don?t have experience with the sinogram output, so I?d try
> > looking at the Root singles output. Is it also empty?
> >
> > Perhaps also increasing the verbosity might help you diagnose
> > what?s going on. I don?t know which verbosity to increase, though!
> > Perhaps:
> >
> > /event/verbose 1 (or 2 or 3)
> > See if this produces any messages that might point you in the
> > right direction.
> >
> > Marc
> >
> >
> >
> > __________________________
> >
> > Marc Chamberland, MSc
> > PhD candidate
> > Department of Physics
> > Carleton University
> > Ottawa (ON)
> >
> >> On Jan 15, 2015, at 14:04, D?bora Salvado <debbiesal at gmail.com
> >> <mailto:debbiesal at gmail.com>> wrote:
> >>
> >> Thanks Marc,
> >>
> >> I add this line to the physics list:
> >> /gate/physics/addProcess RadioactiveDecay
> >>
> >> and tried to run: again no errors but an empty .sin file at the end.
> >>
> >> Any more suggestions?
> >>
> >> D?bora Salvado
> >>
> >> 2015-01-15 18:36 GMT+00:00 Marc Chamberland
> >> <MarcChamberland at cmail.carleton.ca
> >> <mailto:MarcChamberland at cmail.carleton.ca>>:
> >>
> >> Hi D?bora,
> >>
> >> The first thing I would check is that your physics list has
> >> the radioactive decay process enabled.
> >>
> >> Marc
> >>
> >>
> >>
> >> __________________________
> >>
> >> Marc Chamberland, MSc
> >> PhD candidate
> >> Department of Physics
> >> Carleton University
> >> Ottawa (ON)
> >>
> >>> On Jan 15, 2015, at 13:30, D?bora Salvado
> >>> <debbiesal at gmail.com <mailto:debbiesal at gmail.com>> wrote:
> >>>
> >>> Dear Gate users,
> >>>
> >>> I have my main .mac file parameterized for different sources.
> >>>
> >>> It works for the following definition of source:
> >>>
> >>> /gate/source/addSource source1
> >>> /gate/source/source1/gps/type Point
> >>> /gate/source/source1/gps/centre 0. 0. 0. mm
> >>> /gate/source/source1/gps/particle gamma
> >>> /gate/source/source1/gps/energy 159. keV
> >>> /gate/source/source1/setActivity 3000000. Bq
> >>> /gate/source/source1/gps/angtype iso
> >>>
> >>> However, when I try to run it for an ion source, with this
> >>> definition:
> >>>
> >>> /gate/source/addSource source1
> >>> /gate/source/source1/setActivity 3000000. Bq
> >>> /gate/source/source1/gps/type Point
> >>> /gate/source/source1/gps/centre 0. 0. 0. mm
> >>> /gate/source/source1/gps/particle ion
> >>> /gate/source/source1/gps/ion 53 123 0 0
> >>> /gate/source/source1/setForcedUnstableFlag true
> >>> /gate/source/source1/setForcedHalfLife 47520. s
> >>> /gate/source/source1/gps/energytype Mono
> >>> /gate/source/source1/gps/monoenergy 0. keV
> >>> /gate/source/source1/gps/number 1
> >>> /gate/source/source1/gps/angtype iso
> >>> /gate/source/source1/gps/mintheta 0. deg
> >>> /gate/source/source1/gps/maxtheta 180. deg
> >>> /gate/source/source1/gps/minphi 0. deg
> >>> /gate/source/source1/gps/maxphi 360. deg
> >>>
> >>> It runs but the output projection file .sin is empty...
> >>> When I run with the first source instead, I get a .sin file
> >>> with some data.
> >>> I don't really have an error, it's just that my simulation
> >>> doesn't generate anything. Can someone help me figure out
> >>> what's happening?
> >>>
> >>> Regards,
> >>> D?bora Salvado
> >>> _______________________________________________
> >>> Gate-users mailing list
> >>> Gate-users at lists.opengatecollaboration.org
> >>> <mailto:Gate-users at lists.opengatecollaboration.org>
> >>>
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> >>
> >>
> >
> >
> >
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
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