<html> <head> <meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"> </head> <body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"> <div><br> </div> <div><br> </div> Hi Andrea, <div><br> </div> <div>to give further help, there are some more infos needed:</div> <div>Which version of Gate are you using and which OS?</div> <div>Also, I you wish, I can run your program in my environment</div> <div>as I did for many other GATE users in the past.</div> <div>Feel free to send the macros fickly to me and I can test them</div> <div>on my system. It is difficult to help just from a simple output</div> <div>not knowing the basic setup.</div> <div><br> </div> <div>Kind regards,</div> <div><br> </div> <div>Uwe Pietrzyk<br> <div> <div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"> <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> Fakultät für Mathematik und Naturwissenschaften</div> <div style="orphans: 2; widows: 2;">Büro: 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@uni-wuppertal.de</a><br> <a href="http://www.medizinphysik.uni-wuppertal.de/">http://www.medizinphysik.uni-wuppertal.de</a><br> ----------------------------------------------------------------------/</div> </div> </div> <br> <div> <div>On 17 Nov 2015, at 11:55, Andrea González <<a href="mailto:andreita_5_92@hotmail.com">andreita_5_92@hotmail.com</a>> wrote:</div> <br class="Apple-interchange-newline"> <blockquote type="cite"><style></style> <div class="hmmessage"> <div dir="ltr">Thank you very much! <div><br> </div> <div>But If I do like the example, my source doens't decay... I have the RadioactiveDecay included in my physics list... </div> <div>Maybe something is wrong with my version of GATE.</div> <div><br> </div> <div>I have attached the spectrum with this simulations, obviously positrons are not being annihilated. Now I'm using the PENELOPE physics list...</div> <div>Now I have implemented the source as follows:</div> <div><br> </div> <div> <div><font color="#d24726">#</font></div> <div><font color="#d24726">#<span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>S O U R C E S</font></div> <div><font color="#d24726">#</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726"># source: ion</font></div> <div><font color="#d24726">/gate/source/addSource <span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span> IonSource</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/source/IonSource/setActivity <span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>1000 Bq</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/source/IonSource/gps/type<span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>Plane</font></div> <div><font color="#d24726">/gate/source/IonSource/gps/shape<span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>Circle</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/source/IonSource/gps/radius<span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>0.5 mm</font></div> <div><font color="#d24726">/gate/source/IonSource/gps/centre <span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>0.0 0.0 0.0 cm</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/source/IonSource/gps/particle<span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>ion</font></div> <div><font color="#d24726">/gate/source/IonSource/gps/ion <span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>11 22 0 0</font></div> <div><font color="#d24726">/gate/source/IonSource/setForcedUnstableFlag <span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>true</font></div> <div><font color="#d24726">/gate/source/IonSource/setForcedHalfLife <span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>81993600.0 s</font></div> <div><font color="#d24726">/gate/source/IonSource/gps/energytype <span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>Mono</font></div> <div><font color="#d24726">/gate/source/IonSource/gps/monoenergy <span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>0. MeV</font></div> <div><font color="#d24726">/gate/source/IonSource/gps/number <span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>1</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/source/IonSource/gps/angtype<span class="ecxx_Apple-tab-span" style="white-space: pre;"> </span>iso</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/source/list</font></div> </div> <div><br> <div> <hr id="stopSpelling"> From: <a href="mailto:u.pietrzyk@fz-juelich.de">u.pietrzyk@fz-juelich.de</a><br> To: <a href="mailto:andreita_5_92@hotmail.com">andreita_5_92@hotmail.com</a><br> CC: <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br> Subject: Re: [Gate-users] Best physics list for positron annihilation.<br> Date: Tue, 17 Nov 2015 10:20:39 +0000<br> <br> <div style="word-wrap:break-word;"> <div><br> </div> <div>Hi Andrea,</div> <div><br> </div> <div>in your macro you are specifying a source which emits positrons</div> <div>with a fixed energy! To simulate the range of positrons from</div> <div>Na-22 decay you better use an ion-source! </div> <div>Here is the code we use in the EduGATE example “Spectro”</div> <div>(see also: <a href="http://www.opengatecollaboration.org/EduGATE" target="_blank">http://www.opengatecollaboration.org/EduGATE</a>)</div> <div>& see macro file attached to this eMail.</div> <div><br> </div> <div>In the case of Na-22 the aliases in { } are replaced by</div> <div><br> </div> <div>Ion_Z_val -> 11</div> <div>Ion_A_val -> 22</div> <div><br> </div> <div>NOTE: this is done automatically in the Spectro example</div> <div>according to the users’ choice for the Isotope. We simply read</div> <div>the file: RadioactiveDecay3.3 used in GEANT4.</div> <div><br> </div> <div>This finally should give you more realistic data about the positron</div> <div>range, since it takes into account the energy distribution of the</div> <div>emitted positron.</div> <div><br> </div> <div>I hope this helps!</div> <div><br> </div> <div>Kind regards,</div> <div><br> </div> <div>Uwe Pietrzyk</div> <div><br> </div> <div>-----------------------------------------</div> <div> <div>#</div> <div>#<span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>S O U R C E S</div> <div>#</div> <div><br> </div> <div># source: ion</div> <div>/gate/source/addSource <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span> IonSource</div> <div><br> </div> <div>/gate/source/IonSource/setActivity <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span> {SourceActivity}</div> <div><br> </div> <div><br> </div> <div>/gate/source/IonSource/gps/type<span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>Volume</div> <div>/gate/source/IonSource/gps/shape<span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>Sphere</div> <div>#/gate/source/IonSource/gps/radius<span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>0.1 mm</div> <div>/gate/source/IonSource/gps/radius<span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>{SourceRad}</div> <div>/gate/source/IonSource/gps/centre <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>0.0 0.0 0.0 cm</div> <div><br> </div> <div>##</div> <div>## universal ion source</div> <div>## with arbitrary halflife</div> <div>##</div> <div>/gate/source/IonSource/gps/particle<span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>ion</div> <div>/gate/source/IonSource/gps/ion <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>{Ion_Z_val} {Ion_A_val} 0 0</div> <div>/gate/source/IonSource/setForcedUnstableFlag <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>true</div> <div>/gate/source/IonSource/setForcedHalfLife <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>99999999.0 s</div> <div>/gate/source/IonSource/gps/energytype <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>Mono</div> <div>/gate/source/IonSource/gps/monoenergy <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>0. MeV</div> <div>/gate/source/IonSource/gps/number <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>1</div> <div><br> </div> <div>/gate/source/IonSource/gps/angtype<span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>iso</div> <div>/gate/source/IonSource/gps/mintheta<span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>0. deg</div> <div>/gate/source/IonSource/gps/maxtheta <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>180. deg</div> <div>/gate/source/IonSource/gps/minphi <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>0. deg</div> <div>/gate/source/IonSource/gps/maxphi <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>360. deg</div> <div><br> </div> <div>/gate/source/list</div> <div><br> </div> <div>#/gate/source/IonSource/gps/confine <span class="ecxx_Apple-tab-span" style="white-space:pre;"> </span>source_vol</div> <div><br> </div> </div> <br> <div> <div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;"> <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" target="_blank">http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html</a><br> &<br> Bergische Universität Wuppertal<br> Fakultät für Mathematik und Naturwissenschaften</div> <div style="orphans:2;widows:2;">Büro: 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@uni-wuppertal.de</a><br> <a href="http://www.medizinphysik.uni-wuppertal.de/" target="_blank">http://www.medizinphysik.uni-wuppertal.de</a><br> ----------------------------------------------------------------------/</div> </div> </div> <div><br class="ecxx_webkit-block-placeholder"> </div> <div><br> </div> <div></div> </div> <div style="word-wrap:break-word;"> <div></div> <div><br> </div> <div><br> </div> <br> <div> <div>On 17 Nov 2015, at 10:47, Andrea González <<a href="mailto:andreita_5_92@hotmail.com">andreita_5_92@hotmail.com</a>> wrote:</div> <br class="ecxx_Apple-interchange-newline"> <blockquote><style></style> <div class="ecxx_hmmessage"> <div dir="ltr">Sorry, you are right! <div>I'm using 22-Na as follows:</div> <div> <div><br> </div> <div><br> </div> <div><span style="font-size:12pt;"><font color="#d24726">/gate/source/addSource na22</font></span></div> <div><font color="#d24726">/gate/source/na22/setActivity 10000 Bq</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/source/na22/gps/particle e+</font></div> <div><font color="#d24726">/gate/source/na22/setForcedUnstableFlag true</font></div> <div><font color="#d24726">/gate/source/na22/setForcedHalfLife 81993600 s</font></div> <div><font color="#d24726">#/gate/source/na22/gps/energytype Mono</font></div> <div><font color="#d24726">#/gate/source/na22/gps/monoenergy 545 keV </font></div> <div><font color="#d24726">/gate/source/na22/gps/monoenergy 195 keV </font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/source/na22/gps/type Plane</font></div> <div><font color="#d24726">/gate/source/na22/gps/shape Circle</font></div> <div><font color="#d24726">/gate/source/na22/gps/radius 0.5 mm</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/source/na22/gps/angtype iso</font></div> <div><font color="#d24726">/gate/source/na22/gps/centre 0. 0. 0. cm</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/source/list</font></div> </div> <div><br> </div> <div>Do you thing is correct?</div> <div><br> </div> <div>My physics list:</div> <div><br> </div> <div> <div><font color="#d24726">#=====================================</font></div> <div><font color="#d24726"># Electromagnetic processes</font></div> <div><font color="#d24726">#=====================================</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/physics/addProcess RadioactiveDecay</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/physics/addProcess PhotoElectric</font></div> <div><font color="#d24726">/gate/physics/processes/PhotoElectric/setModel StandardModel</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/physics/addProcess Compton</font></div> <div><font color="#d24726">/gate/physics/processes/Compton/setModel StandardModel</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/physics/addProcess GammaConversion</font></div> <div><font color="#d24726">/gate/physics/processes/GammaConversion/setModel StandardModel</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/physics/addProcess ElectronIonisation</font></div> <div><font color="#d24726">/gate/physics/processes/ElectronIonisation/setModel StandardModel e-</font></div> <div><font color="#d24726">/gate/physics/processes/ElectronIonisation/setModel StandardModel e+</font></div> <div><font color="#d24726">/gate/physics/processes/ElectronIonisation/setStepFunction e+ 0.2 0.1 mm</font></div> <div><font color="#d24726">/gate/physics/processes/ElectronIonisation/setStepFunction e- 0.2 0.1 mm</font></div> <div><font color="#d24726">/gate/physics/processes/ElectronIonisation/setLinearLossLimit electron 0.01</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/physics/addProcess Bremsstrahlung</font></div> <div><font color="#d24726">/gate/physics/processes/Bremsstrahlung/setModel StandardModel e-</font></div> <div><font color="#d24726">/gate/physics/processes/Bremsstrahlung/setModel StandardModel e+</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/physics/addProcess PositronAnnihilation</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/physics/addProcess eMultipleScattering e-</font></div> <div><font color="#d24726">/gate/physics/addProcess eMultipleScattering e+</font></div> <div><font color="#d24726">/gate/physics/addProcess/eMultipleScattering/setModel Urban95Model</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e- distanceToBoundary</font></div> <div><font color="#d24726">/gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e+ distanceToBoundary</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">#=========</font></div> <div><font color="#d24726"># Options</font></div> <div><font color="#d24726">#=========</font></div> <div><font color="#d24726"><br> </font></div> <div><font color="#d24726">/gate/physics/setEMin 0.1 keV</font></div> <div><font color="#d24726">/gate/physics/setEMax 10 GeV</font></div> <div><br> </div> </div> <div><br> </div> <div>The problem is about the annihilation range of the positrons in PMMA, because it shows a distrubution much broader than it should be...</div> <div><br> </div> <div>I really appreciate your help and comments.</div> <div><br> </div> <div>Best regards, Andrea.</div> <div><br> </div> <div><br> </div> <div><br> </div> <div><br> </div> <div><br> </div> <div><br> <div> <hr id="ecxx_stopSpelling"> From: <a href="mailto:u.pietrzyk@fz-juelich.de">u.pietrzyk@fz-juelich.de</a><br> To: <a href="mailto:andreita_5_92@hotmail.com">andreita_5_92@hotmail.com</a><br> CC: <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br> Subject: Re: [Gate-users] Best physics list for positron annihilation.<br> Date: Mon, 16 Nov 2015 15:40:00 +0000<br> <br> <div><br> </div> <div>Dear Andrea,</div> <div><br> </div> <div>you didn’t mention the type of problem, but when</div> <div>you use 22-Na as an ion source you need to specify</div> <div>the radioactive decay explicitly. In our test and examples,</div> <div>we use the following:</div> <div><br> </div> <div> <div>/gate/physics/addPhysicsList emstandard</div> <div>/gate/physics/addProcess RadioactiveDecay</div> </div> <div><br> </div> <div>and this seems to work fine.</div> <div>In case you mean something else, please let us know.</div> <div><br> </div> <div>Kind regards,</div> <div><br> </div> <div>Uwe Pietrzyk</div> <br> <div> <div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word;"> <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" target="_blank">http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html</a><br> &<br> Bergische Universität Wuppertal<br> Fakultät für Mathematik und Naturwissenschaften</div> <div style="orphans:2;widows:2;">Büro: 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@uni-wuppertal.de</a><br> <a href="http://www.medizinphysik.uni-wuppertal.de/" target="_blank">http://www.medizinphysik.uni-wuppertal.de</a><br> ----------------------------------------------------------------------/</div> </div> </div> <br> <div> <div>On 16 Nov 2015, at 15:58, Andrea González <<a href="mailto:andreita_5_92@hotmail.com">andreita_5_92@hotmail.com</a>> wrote:</div> <br class="ecxx_ecxApple-interchange-newline"> <blockquote><style></style> <div class="ecxx_ecxhmmessage"> <div dir="ltr">Hello, I'm trying to simulate positron annihilitaion for 22-Na in PMMA. <div><br> <div>I would like to know wich is the best physics list in this case, because I have problems with my list (standard EM).</div> <div><br> </div> <div>Thank you very much.</div> <div><br> </div> <div>Andrea.</div> <div><br> </div> <div><br> </div> </div> </div> </div> _______________________________________________<br> Gate-users mailing list<br> <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></blockquote> </div> <br> <br> <font face="Arial" size="1"><br> ------------------------------------------------------------------------------------------------<br> ------------------------------------------------------------------------------------------------<br> Forschungszentrum Juelich GmbH<br> 52425 Juelich<br> Sitz der Gesellschaft: Juelich<br> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. 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