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<div>Hi Debora,</div>
<div><br>
</div>
<div>since you are not using the physicslist mechanism, you should add this following</div>
<div>statement to stop the ion, i.e. to have it interact:</div>
<div><br>
</div>
<div>/gate/physics/addProcess IonIonisation</div>
<div>/gate/physics/processes/IonIonisation/setStepFunction GenericIon 0.1 0.02 mm</div>
<div><br>
</div>
<div>I also placed the source into a surrounding volume made of water to have the ion interact.</div>
<div>This volume is defined like a normal phantom volume.</div>
<div><br>
</div>
<div>-----</div>
<div>
<div># SOURCE</div>
<div># Create the source volume/phantom</div>
<div><br>
</div>
<div>/gate/world/daughters/name <span class="Apple-tab-span" style="white-space:pre">
</span>source_vol</div>
<div>/gate/world/daughters/insert <span class="Apple-tab-span" style="white-space:pre">
</span>sphere</div>
<div>/gate/source_vol/geometry/setRmax <span class="Apple-tab-span" style="white-space:pre">
</span>10.0 mm</div>
<div>/gate/source_vol/geometry/setRmin <span class="Apple-tab-span" style="white-space:pre">
</span>0.0 mm</div>
<div>/gate/source_vol/placement/setTranslation <span class="Apple-tab-span" style="white-space:pre">
</span>0. 0. 0. mm</div>
<div>/gate/source_vol/setMaterial <span class="Apple-tab-span" style="white-space:pre">
</span>{SourceVolMaterial} <— you habe to change this ...</div>
<div>/gate/source_vol/vis/setColor <span class="Apple-tab-span" style="white-space:pre">
</span>white</div>
<div>#/gate/source_vol/vis/forceWireframe</div>
<div>/gate/source_vol/vis/forceSolid</div>
<div>/gate/source_vol/vis/setVisible<span class="Apple-tab-span" style="white-space:pre">
</span>1</div>
<div><br>
</div>
<div>/gate/source_vol/attachPhantomSD</div>
</div>
<div><br>
</div>
<div>——</div>
<div><br>
</div>
<div>You may also check your system through visualisation and if you see</div>
<div><b>blue</b> lines, those a ions, which have a <b>positive</b> charge</div>
<div><br>
</div>
<div>Which version of GATE are you using? With Gate_v7.0 or with a previous version</div>
<div>like 6.2?</div>
<div><br>
</div>
<div>Kind regards,</div>
<div><br>
</div>
<div>Uwe Pietrzyk</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div><span style="orphans: 2; widows: 2;">/----------------------------------------------------------------------</span></div>
<div style="orphans: 2; widows: 2;">Prof. Dr. Uwe Pietrzyk<br>
Diplom-Physiker<br>
Institut für Neurowissenschaften und Medizin / INM-4<br>
Forschungszentrum Jülich GmbH<br>
52425 Jülich<br>
Tel: +49-2461-61 4763<br>
Fax: +49-2461-61 2820<br>
Mobil: +49-162-103-4871<br>
eMail: <a href="mailto:U.Pietrzyk@fz-juelich.de">U.Pietrzyk@fz-juelich.de</a><br>
<a href="http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html">http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html</a><br>
&<br>
Bergische Universität Wuppertal<br>
Fachbereich C - Physik / D.08.01<br>
Gaußstr. 20<br>
42097 Wuppertal<br>
Tel: +49-(0)202-439-3523<br>
Fax: +49-(0)202-439-2811<br>
eMail: <a href="mailto:Uwe.Pietrzyk@physik.uni-wuppertal.de">Uwe.Pietrzyk@physik.uni-wuppertal.de</a><br>
<a href="http://www.medizinphysik.uni-wuppertal.de/">http://www.medizinphysik.uni-wuppertal.de</a><br>
----------------------------------------------------------------------/</div>
</div>
<br>
<div>
<div>On 16 Jan 2015, at 12:40, Débora Salvado <<a href="mailto:debbiesal@gmail.com">debbiesal@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr">Hi,<br>
I've attached my main macro, let me know if you have any problems to see it.<br>
<br clear="all">
<div>
<div>
<div class="gmail_signature">Débora Salvado<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Fri, 16 Jan 2015 12:18:30 +0100<br>
From: narbor <<a href="mailto:nicolas.arbor@iphc.cnrs.fr">nicolas.arbor@iphc.cnrs.fr</a>><br>
To: D?bora Salvado <<a href="mailto:debbiesal@gmail.com">debbiesal@gmail.com</a>><br>
Cc: Gate Users <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>><br>
Subject: Re: [Gate-users] Ion source: empty output<br>
Message-ID: <<a href="mailto:54B8F386.1060407@iphc.cnrs.fr">54B8F386.1060407@iphc.cnrs.fr</a>
<div id=":1vj" class="">><br>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
<br>
Hi D?bora,<br>
Could you send us your main.mac file just to have a look ?<br>
Thanks.<br>
Nicolas Arbor<br>
<br>
***********************************************************************<br>
Nicolas ARBOR<br>
Ma?tre de Conf?rences<br>
Universit? de Strasbourg - UFR Physique et Ing?nierie<br>
Groupe de recherche RaMsEs - Institut Pluridisciplinaire Hubert Curien<br>
***********************************************************************<br>
<br>
Le 16/01/2015 12:09, D?bora Salvado a ?crit :<br>
> I increased the verbosity of my simulation to:<br>
><br>
> /event/verbose 1<br>
><br>
> and now when I run my simulation, it keeps giving me this message:<br>
><br>
> =====================================<br>
> G4EventManager::ProcessOneEvent()<br>
> =====================================<br>
> G4PrimaryTransformer::PrimaryVertex (0(mm),0(mm),0(mm),1.51525e+08(nsec))<br>
> 1 primaries are passed from G4EventTransformer.<br>
> !!!!!!! Now start processing an event !!!!!!!<br>
> Track (trackID 1, parentID 0) is processed with stopping code 2<br>
> Track (trackID 3, parentID 1) is processed with stopping code 2<br>
> Track (trackID 2, parentID 1) is processed with stopping code 2<br>
> NULL returned from G4StackManager.<br>
> Terminate current event processing.<br>
><br>
> I've read that some users solved this problem by adding the<br>
> RadioactiveDecay process to their physics list. But I have it in my<br>
> macro... so can someone help me?<br>
><br>
> Thanks,<br>
> D?bora Salvado<br>
><br>
><br>
><br>
> 2015-01-15 19:22 GMT+00:00 Marc Chamberland<br>
> <<a href="mailto:MarcChamberland@cmail.carleton.ca">MarcChamberland@cmail.carleton.ca</a><br>
> <mailto:<a href="mailto:MarcChamberland@cmail.carleton.ca">MarcChamberland@cmail.carleton.ca</a>>>:<br>
><br>
> Hmm? I don?t have experience with the sinogram output, so I?d try<br>
> looking at the Root singles output. Is it also empty?<br>
><br>
> Perhaps also increasing the verbosity might help you diagnose<br>
> what?s going on. I don?t know which verbosity to increase, though!<br>
> Perhaps:<br>
><br>
> /event/verbose 1 (or 2 or 3)<br>
> See if this produces any messages that might point you in the<br>
> right direction.<br>
><br>
> Marc<br>
><br>
><br>
><br>
> __________________________<br>
><br>
> Marc Chamberland, MSc<br>
> PhD candidate<br>
> Department of Physics<br>
> Carleton University<br>
> Ottawa (ON)<br>
><br>
>> On Jan 15, 2015, at 14:04, D?bora Salvado <<a href="mailto:debbiesal@gmail.com">debbiesal@gmail.com</a><br>
>> <mailto:<a href="mailto:debbiesal@gmail.com">debbiesal@gmail.com</a>>> wrote:<br>
>><br>
>> Thanks Marc,<br>
>><br>
>> I add this line to the physics list:<br>
>> /gate/physics/addProcess RadioactiveDecay<br>
>><br>
>> and tried to run: again no errors but an empty .sin file at the end.<br>
>><br>
>> Any more suggestions?<br>
>><br>
>> D?bora Salvado<br>
>><br>
>> 2015-01-15 18:36 GMT+00:00 Marc Chamberland<br>
>> <<a href="mailto:MarcChamberland@cmail.carleton.ca">MarcChamberland@cmail.carleton.ca</a><br>
>> <mailto:<a href="mailto:MarcChamberland@cmail.carleton.ca">MarcChamberland@cmail.carleton.ca</a>>>:<br>
>><br>
>> Hi D?bora,<br>
>><br>
>> The first thing I would check is that your physics list has<br>
>> the radioactive decay process enabled.<br>
>><br>
>> Marc<br>
>><br>
>><br>
>><br>
>> __________________________<br>
>><br>
>> Marc Chamberland, MSc<br>
>> PhD candidate<br>
>> Department of Physics<br>
>> Carleton University<br>
>> Ottawa (ON)<br>
>><br>
>>> On Jan 15, 2015, at 13:30, D?bora Salvado<br>
>>> <<a href="mailto:debbiesal@gmail.com">debbiesal@gmail.com</a> <mailto:<a href="mailto:debbiesal@gmail.com">debbiesal@gmail.com</a>>> wrote:<br>
>>><br>
>>> Dear Gate users,<br>
>>><br>
>>> I have my main .mac file parameterized for different sources.<br>
>>><br>
>>> It works for the following definition of source:<br>
>>><br>
>>> /gate/source/addSource source1<br>
>>> /gate/source/source1/gps/type Point<br>
>>> /gate/source/source1/gps/centre 0. 0. 0. mm<br>
>>> /gate/source/source1/gps/particle gamma<br>
>>> /gate/source/source1/gps/energy 159. keV<br>
>>> /gate/source/source1/setActivity 3000000. Bq<br>
>>> /gate/source/source1/gps/angtype iso<br>
>>><br>
>>> However, when I try to run it for an ion source, with this<br>
>>> definition:<br>
>>><br>
>>> /gate/source/addSource source1<br>
>>> /gate/source/source1/setActivity 3000000. Bq<br>
>>> /gate/source/source1/gps/type Point<br>
>>> /gate/source/source1/gps/centre 0. 0. 0. mm<br>
>>> /gate/source/source1/gps/particle ion<br>
>>> /gate/source/source1/gps/ion 53 123 0 0<br>
>>> /gate/source/source1/setForcedUnstableFlag true<br>
>>> /gate/source/source1/setForcedHalfLife 47520. s<br>
>>> /gate/source/source1/gps/energytype Mono<br>
>>> /gate/source/source1/gps/monoenergy 0. keV<br>
>>> /gate/source/source1/gps/number 1<br>
>>> /gate/source/source1/gps/angtype iso<br>
>>> /gate/source/source1/gps/mintheta 0. deg<br>
>>> /gate/source/source1/gps/maxtheta 180. deg<br>
>>> /gate/source/source1/gps/minphi 0. deg<br>
>>> /gate/source/source1/gps/maxphi 360. deg<br>
>>><br>
>>> It runs but the output projection file .sin is empty...<br>
>>> When I run with the first source instead, I get a .sin file<br>
>>> with some data.<br>
>>> I don't really have an error, it's just that my simulation<br>
>>> doesn't generate anything. Can someone help me figure out<br>
>>> what's happening?<br>
>>><br>
>>> Regards,<br>
>>> D?bora Salvado<br>
>>> _______________________________________________<br>
>>> Gate-users mailing list<br>
>>> <a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a><br>
>>> <mailto:<a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a>><br>
>>> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>
>><br>
>><br>
><br>
><br>
><br>
><br>
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