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Dear Sarah,
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</div>
<div class="">some remarks:</div>
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</div>
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<ul class="MailOutline">
<li class="">If I am not mistaken, the nanoparticles you create have a radius of 500 nm, but the repeater has a step size of 5 nm, so you end up with one big chunk of overlapping volumes. I am not sure whether Gate even likes that, I had problems with that
in the past once.</li><li class="">You define the source as a cylinder. By default, a source emits particles in all directions. I don’t know what scenario you would like to simulate, but there is the option to limit the angle so that you get a parallel beam or any angle you like.
(I can give you a code example if you need it). (On that note: if one uses a parallel beam, the absorbed dose will probably be very sensitive to the orientation of the nanoparticle grid.)</li></ul>
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<div class="">Those two points might already explain why you receive less dose than you expected in the previous mail you sent.</div>
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</div>
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</div>
<div class="">Running Gate simulations in parallel shouldn’t be a problem.</div>
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</div>
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</div>
<div class="">I think there might be a way to check the absorbed dose (even though it’s a bit cumbersome). You can include phase space actors in your setup, which record every particle that leaves a certain volume, and they record e.g. the position and energy
of a particle. Hence, you can place planes (so very thin boxes, filled with, in your case, air) around your cell and then compare the ingoing and outgoing energy; the difference should be absorbed in you cell or nanoparticles. Then you can of course emit the
water sphere of the cell to see whether there’s a difference.</div>
<div class="">I attached a code example for a phase space actor, which is attached to a dedicated volume (“PhS_BeforePlane”). The options that define which parameters are saved also include direction, position and energy, which you can switch off if you want.</div>
<div class="">If I remember correctly, I always needed a crystalSD detector, otherwise the phase space actor would not record anything. Please see the example script “Geometry.mac” below, which you can use to define a detector. Just place the detector volume
somewhere away from your cell and source and disregard the output (that’s the line "/gate/CTscanner/placement/setTranslation 0. 0. 0. mm”)</div>
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</div>
<div class="">One more note about the physics list: It is highly recommended to use a pre-built physics list (e.g. emstandard opt.4) instead of building one yourself. Having said that, I don’t have any experience with the selection of physics lists.</div>
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<div class="">I hope that helps!</div>
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</div>
<div class="">Best regards,</div>
<div class="">David</div>
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</div>
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<div class="">
<div class="">#======================================================</div>
<div class=""># PHASE SPACE DETECTOR</div>
<div class="">#======================================================</div>
<div class="">#</div>
<div class=""># This snippet shows how to add a phase space actor.</div>
<div class=""><br class="">
</div>
<div class=""># First define its volume - you can also attach the</div>
<div class=""># phase space actor to an already existing volume:</div>
<div class="">/gate/world/daughters/name PhS_BeforePlane</div>
<div class="">/gate/world/daughters/insert box</div>
<div class="">/gate/PhS_BeforePlane/setMaterial Vacuum</div>
<div class="">/gate/PhS_BeforePlane/geometry/setXLength 500 mm</div>
<div class="">/gate/PhS_BeforePlane/geometry/setYLength 500 mm</div>
<div class="">/gate/PhS_BeforePlane/geometry/setZLength 2 mm</div>
<div class="">/gate/PhS_BeforePlane/placement/setTranslation 0 0 194 mm</div>
<div class="">/gate/PhS_BeforePlane/vis/setColor white</div>
<div class="">/gate/PhS_BeforePlane/vis/setVisible true</div>
<div class=""><br class="">
</div>
<div class=""># Add the phase space actor to the volume:</div>
<div class="">/gate/actor/addActor PhaseSpaceActor PhS_b</div>
<div class="">/gate/actor/PhS_b/attachTo PhS_BeforePlane</div>
<div class="">/gate/actor/PhS_b/save <span class="Apple-tab-span" style="white-space:pre">
</span> output/output-PhS-b.root</div>
<div class=""><br class="">
</div>
<div class=""># Define which parameters you would like to save:</div>
<div class="">/gate/actor/PhS_b/enableParticleName true</div>
<div class="">/gate/actor/PhS_b/enableEkine true</div>
<div class="">/gate/actor/PhS_b/enableXPosition false</div>
<div class="">/gate/actor/PhS_b/enableYPosition false</div>
<div class="">/gate/actor/PhS_b/enableZPosition false</div>
<div class="">/gate/actor/PhS_b/enableXDirection true</div>
<div class="">/gate/actor/PhS_b/enableYDirection true</div>
<div class="">/gate/actor/PhS_b/enableZDirection true</div>
<div class="">/gate/actor/PhS_b/enableWeight false</div>
<div class="">/gate/actor/PhS_b/enableMass false</div>
<div class="">/gate/actor/PhS_b/enableProductionProcess false</div>
<div class="">/gate/actor/PhS_b/enableProductionVolume true</div>
<div class="">/gate/actor/PhS_b/useVolumeFrame false</div>
<div class="">/gate/actor/PhS_b/enableTime false</div>
<div class="">/gate/actor/PhS_b/enablePrimaryEnergy false</div>
<div class="">/gate/actor/PhS_b/enableEmissionPoint false</div>
<div class="">/gate/actor/PhS_b/storeOutgoingParticles true</div>
<div class=""># PS: There are many more parameters available.</div>
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</div>
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</div>
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<div class="">
<div class="">#======================================================</div>
<div class=""># GEOMETRY.MAC</div>
<div class="">#======================================================</div>
<div class="">#</div>
<div class=""># This snippet defines a simple flat panel CT detector.</div>
<div class="">#</div>
<div class=""># The system level descriptions of the CT scanner are:</div>
<div class=""># module / cluster / pixel</div>
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</div>
<div class="">#######################################################</div>
<div class=""># CT SCANNER</div>
<div class="">#######################################################</div>
<div class="">/gate/world/daughters/name CTscanner</div>
<div class="">/gate/world/daughters/insert box</div>
<div class="">/gate/CTscanner/placement/setTranslation 0. 0. 0. mm</div>
<div class="">/gate/CTscanner/geometry/setXLength 0.1 nm</div>
<div class="">/gate/CTscanner/geometry/setYLength 0.1 nm</div>
<div class="">/gate/CTscanner/geometry/setZLength 0.1 nm</div>
<div class="">/gate/CTscanner/setMaterial Vacuum</div>
<div class="">/gate/CTscanner/vis/forceWireframe</div>
<div class="">/gate/CTscanner/vis/setColor white</div>
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</div>
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</div>
<div class="">#######################################################</div>
<div class=""># CT SCANNER -> MODULE</div>
<div class="">#######################################################</div>
<div class="">/gate/CTscanner/daughters/name module</div>
<div class="">/gate/CTscanner/daughters/insert box</div>
<div class="">/gate/module/geometry/setXLength 0.1 nm</div>
<div class="">/gate/module/geometry/setYLength 0.1 nm</div>
<div class="">/gate/module/geometry/setZLength 0.1 nm</div>
<div class="">/gate/module/setMaterial Vacuum</div>
<div class="">/gate/module/vis/forceWireframe</div>
<div class="">/gate/module/vis/setColor white</div>
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</div>
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</div>
<div class="">#######################################################</div>
<div class=""># CT SCANNER -> MODULE -> CLUSTER</div>
<div class="">#######################################################</div>
<div class="">/gate/module/daughters/name cluster</div>
<div class="">/gate/module/daughters/insert box</div>
<div class="">/gate/cluster/geometry/setXLength 0.1 nm</div>
<div class="">/gate/cluster/geometry/setYLength 0.1 nm</div>
<div class="">/gate/cluster/geometry/setZLength 0.1 nm</div>
<div class="">/gate/cluster/setMaterial Vacuum</div>
<div class="">/gate/cluster/vis/forceWireframe</div>
<div class="">/gate/cluster/vis/setColor green</div>
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</div>
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</div>
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</div>
<div class="">#######################################################</div>
<div class=""># ATTACHING THE LEVELS TO THE SYSTEM</div>
<div class="">#######################################################</div>
<div class="">/gate/systems/CTscanner/module/attach module</div>
<div class="">/gate/systems/CTscanner/cluster_0/attach cluster</div>
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</div>
<div class=""># Attach a sensitive detector:</div>
<div class="">/gate/cluster/attachCrystalSD</div>
</div>
</div>
<div class=""> </div>
</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 31 Mar2022, at 09:36, Sarah Blind <<a href="mailto:sarah.blind@univ-lorraine.fr" class="">sarah.blind@univ-lorraine.fr</a>> wrote:</div>
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<div class="">Dear Gate users,<br data-mce-bogus="1" class="">
</div>
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</div>
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<div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;" data-mce-style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000;" class="">
<div class="">I'm analysing the deposited dose in Gy of the irradiation simulation of a cell with in its inside a certain number of nanoparticles composed of 16% bismuth.<br class="">
</div>
<div class="">Looking at the deposited dose on the nanoparticles focci, for several simulations I obtain very different results and computation times:<br data-mce-bogus="1" class="">
</div>
<ul class="">
<li class="">Simulation 1 : 105,545 Gy with a computation time of ~10h,<br data-mce-bogus="1" class="">
</li><li class="">Simulation 2 : 10.07 Gy with a computation time of ~ 2h.<br data-mce-bogus="1" class="">
</li></ul>
<div class="">I run these two simulations in parallel, each in a different file and a different number for setEngineSeed.</div>
<div class=""><br data-mce-bogus="1" class="">
</div>
<div class="">I have a gamma beam and I send 300 000 Bq for a 60 secondes irradiation simulation on 35^3 nanoparticles.<br class="">
</div>
<div class="">I think the simulation 2 failed ; can the fact that I run several simulations at the same time be a problem ?<br data-mce-bogus="1" class="">
</div>
<div class=""><br data-mce-bogus="1" class="">
</div>
<div class="">If this speak to anyone, thank your for your advices!<br data-mce-bogus="1" class="">
</div>
<div class=""><br data-mce-bogus="1" class="">
</div>
<div class="">Sarah Blind<br data-mce-bogus="1" class="">
</div>
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</div>
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</div>
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</div>
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</div>
<div class="">PS: Here is my code:</div>
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</div>
<div class="">MAIN.MAC</div>
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</div>
<blockquote class="">
<div class="">/gate/geometry/setMaterialDatabase ../data/GateMaterials.db</div>
<div class=""><br class="">
/control/execute world.mac<br class="">
/control/execute physics.mac<br class="">
/control/execute detectors.mac<br class="">
<br class="">
/gate/run/initialize<br class="">
<br class="">
/control/execute 5sourceSpectrumMeV.mac<br class="">
<br class="">
/gate/application/setTimeSlice 60. s<br class="">
/gate/application/setTimeStart 0. s<br class="">
/gate/application/setTimeStop 60. s<br class="">
<br class="">
/gate/random/setEngineName MersenneTwister<br class="">
/gate/random/setEngineSeed auto<br class="">
/gate/application/start</div>
</blockquote>
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</div>
<div class="">WORLD.MAC</div>
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</div>
<blockquote class="">
<div class="">/gate/world/geometry/setXLength 30 um<br class="">
/gate/world/geometry/setYLength 30 um<br class="">
/gate/world/geometry/setZLength 30 um<br class="">
/gate/world/setMaterial Air<br class="">
<br class="">
/gate/world/daughters/name cell<br class="">
/gate/world/daughters/insert sphere<br class="">
/gate/cell/geometry/setRmin 0.0 mm<br class="">
/gate/cell/geometry/setRmax 10 um<br class="">
/gate/cell/placement/setTranslation 0 0 0 um<br class="">
/gate/cell/setMaterial G4_WATER<br class="">
/gate/cell/vis/setVisible 1<br class="">
/gate/cell/vis/setColor blue<br class="">
/gate/cell/vis/forceSolid false<br class="">
<br class="">
<br class="">
/gate/cell/daughters/name NP<br class="">
/gate/cell/daughters/insert sphere<br class="">
/gate/NP/geometry/setRmin 0 mm<br class="">
/gate/NP/geometry/setRmax 0.5 um<br class="">
/gate/NP/placement/setTranslation 0 0 0 mm<br class="">
/gate/NP/setMaterial AGuIX_bis<br class="">
<br class="">
/gate/NP/repeaters/insert cubicArray<br class="">
/gate/NP/cubicArray/setRepeatNumberX 30<br class="">
/gate/NP/cubicArray/setRepeatNumberY 30<br class="">
/gate/NP/cubicArray/setRepeatNumberZ 30<br class="">
/gate/NP/cubicArray/setRepeatVector 5 5 5 nm</div>
</blockquote>
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</div>
<div class="">PHYSICS.MAC</div>
<blockquote class="">
<div class=""><br class="">
/gate/physics/addPhysicsList QGSP_BERT_EMV</div>
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/gate/physics/Gamma/SetCutInRegion world 50 nm<br class="">
/gate/physics/Electron/SetCutInRegion world 50 nm<br class="">
<br class="">
/gate/physics/Gamma/SetCutInRegion cell 20 nm<br class="">
/gate/physics/Electron/SetCutInRegion cell 20 nm<br class="">
<br class="">
/gate/physics/Gamma/SetCutInRegion NP 0.5 nm<br class="">
/gate/physics/Electron/SetCutInRegion NP 0.5 nm<br class="">
<br class="">
/gate/random/setEngineName MersenneTwister <br class="">
<br class="">
/gate/physics/addAtomDeexcitation<br class="">
<br class="">
/gate/physics/addProcess PhotoElectric gamma<br class="">
/gate/physics/processes/PhotoElectric/setModel LivermoreModel<br class="">
/gate/physics/processes/PhotoElectric/setAugerElectron true<br class="">
/gate/physics/processes/PhotoElectric/setDeltaRayCut 10 eV<br class="">
/gate/physics/processes/PhotoElectric/setXRayCut 10 eV<br class="">
/gate/physics/processes/PhotoElectric/setStepFunction e- 0.2 0.1 nm<br class="">
<br class="">
/gate/physics/addProcess Compton gamma<br class="">
/gate/physics/processes/Compton/setModel LivermoreModel<br class="">
/gate/physics/processes/Compton/setStepFunction e- 0.2 0.1 nm<br class="">
<br class="">
/gate/physics/addProcess RayleighScattering<br class="">
/gate/physics/processes/RayleighScattering/setModel LivermoreModel<br class="">
<br class="">
/gate/physics/addProcess GammaConversion<br class="">
/gate/physics/processes/GammaConversion/setModel LivermoreModel<br class="">
<br class="">
/gate/physics/addProcess ElectronIonisation<br class="">
/gate/physics/processes/ElectronIonisation/setModel LivermoreModel e-<br class="">
/gate/physics/processes/ElectronIonisation/setModel PenelopeModel e+<br class="">
/gate/physics/processes/ElectronIonisation/setStepFunction e- 0.2 0.1 nm<br class="">
<br class="">
/gate/physics/addProcess Bremsstrahlung e-<br class="">
/gate/physics/addProcess Bremsstrahlung e+<br class="">
/gate/physics/processes/Bremsstrahlung/setModel LivermoreModel e-<br class="">
/gate/physics/processes/Bremsstrahlung/setModel PenelopeModel e+<br class="">
<br class="">
/gate/physics/addProcess eMultipleScattering e-<br class="">
/gate/physics/addProcess eMultipleScattering e+<br class="">
/gate/physics/processes/eMultipleScattering/setModel UrbanModel e-<br class="">
/gate/physics/processes/eMultipleScattering/setModel UrbanModel e+<br class="">
<br class="">
/gate/physics/SetMinKineticEnergyInRegion world 1 eV<br class="">
/gate/physics/SetMinKineticEnergyInRegion cell 1 eV<br class="">
/gate/physics/ActivateSpecialCuts gamma</div>
</blockquote>
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</div>
<div class="">DETECTOR.MAC</div>
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</div>
<blockquote class="">
<div class="">/gate/actor/addActor DoseActor dose<br class="">
/gate/actor/dose/save output/dose1.hdr<br class="">
/gate/actor/dose/attachTo cell<br class="">
/gate/actor/dose/stepHitType random<br class="">
/gate/actor/dose/setPosition 0.0 0.0 0.0 mm<br class="">
/gate/actor/dose/setSize 20 20 20 um<br class="">
/gate/actor/dose/setResolution 400 400 400<br class="">
/gate/actor/dose/saveEveryNSeconds 30</div>
</blockquote>
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</div>
<div class="">SOURCE.MAC</div>
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</div>
<blockquote class="">
<div class="">/gate/source/addSource mybeam gps<br class="">
/gate/source/mybeam/gps/particle gamma<br class="">
/gate/source/mybeam/gps/ene/type User<br class="">
/gate/source/mybeam/gps/hist/type energy<br class="">
/gate/source/mybeam/setActivity 300000. becquerel</div>
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<br class="">
[histogram]<br class="">
<br class="">
/gate/source/mybeam/gps/position 0 0 15 um<br class="">
/gate/source/mybeam/gps/pos/type Volume<br class="">
/gate/source/mybeam/gps/pos/shape Cylinder<br class="">
/gate/source/mybeam/gps/pos/inner_radius 0 mm<br class="">
/gate/source/mybeam/gps/pos/radius 10 um<br class="">
/gate/source/mybeam/gps/pos/halfz 0.01 um<br class="">
/gate/source/mybeam/gps/ang/type beam2d<br class="">
</div>
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</div>
</blockquote>
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</div>
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