[Gate-users] FW: Need help with getting started
강한규
lovehangulp at naver.com
Mon Jul 23 08:42:29 CEST 2018
-----Original Message-----
From: "강한규"<lovehangulp at naver.com>
To: "Sharif Abu Darda"<shabudarda at gmail.com>;
Cc: "강한규"<hangyookang at gmail.com>;
Sent: 2018-07-23 (월) 15:41:18
Subject: Re: [Gate-users] Need help with getting started
Dear Sharif Abu Darda, and GATE users,
It's good to hear that you figured out the problem in setting the GateMaterials.db file path by yourself.
Actually, my manual has been written for the user of vGATE which has all the example macro and GateMaterials.db files are located in the appropriate path.
Therefore, the issue of GateMaterials.db file location will not occur with vGATE.
Anyway I added the information about GateMaterials.db file in slide#24 as your comment.
If you have find any problem in my vGATE manual, please let me know.
Best regards,
Han Gyu Kang, Ph.D.
Imaging Physics Team, NIRS-QST, Japan
-----Original Message-----
From: "Sharif Abu Darda"<shabudarda at gmail.com>
To: <lovehangulp at naver.com>;
Cc:
Sent: 2018-07-19 (목) 05:22:58
Subject: Re: [Gate-users] Need help with getting started
Ok, I was able to resolve the issue, I see that I haven't configured the GateMaterials.db in the benchmarkCT.mac. There wasn't any GateMaterials.db in the CT example I downloaded from the Github repo. So, I take one from the example I downloaded from the Gate website exercises. I created a data folder in the classic folder and I configured the directory in the benchmarkCT.mac by editting the
/gate/geometry/setMaterialDatabase ../../../misc/GateMaterials.db
into
/gate/geometry/setMaterialDatabase data/GateMaterials.db
That did the trick, The simulation run fine i believe. This was not guided in the PDF guide you sent. Please add this.
[126] 21:56 vgate:~/Test/CT/classic > Gate benchmarkCT.mac
[G4]
[G4] *************************************************************
[G4] Geant4 version Name: geant4-10-03-patch-03 (20-October-2017)
[G4] Copyright : Geant4 Collaboration
[G4] Reference : NIM A 506 (2003), 250-303
[G4] WWW : http://cern.ch/geant4
[G4] *************************************************************
[G4]
[G4] ### WARNING: G4EmProcessOptions class is obsolete and will be removed in the next public release
Please, try to use G4EmParameters class and/or UI interface to EM parameters
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[G4] ### WARNING: G4EmProcessOptions class is obsolete and will be removed in the next public release
Please, try to use G4EmParameters class and/or UI interface to EM parameters
[Core-0] Initialization of actors
[Core-0]
[Core-0] **********************************************************************
[Core-0] GATE version name: gate_v8.0
[Core-0] Copyright : OpenGATE Collaboration
[Core-0] Reference : Phys. Med. Biol. 49 (2004) 4543-4561
[Core-0] Reference : Phys. Med. Biol. 56 (2011) 881-901
[Core-0] WWW : http://www.opengatecollaboration.org
[Core-0] **********************************************************************
[Core-0]
[Core-0] You are using Geant4 version 10.3.3
[Core-0] Starting macro benchmarkCT.mac
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--10-100-75-75-m-60-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--11-80-100-100-m-60-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--12-120-75-75-m-70-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--14-100-100-100-m-90-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--17-120-100-100-m-100-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--18-180-75-75-m-110-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--20-140-100-100-m-110-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--24-240-75-75-m-150-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--25-180-100-100-m-150-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--34-240-100-100-m-200-iso8859-1
/tracking/storeTrajectory 1
Attributes available for modeling and filtering with
"/vis/modeling/trajectories/create/drawByAttribute" and
"/vis/filtering/trajectories/create/attributeFilter" commands:
G4TrajectoriesModel:
Event ID (EventID): G4int
Run ID (RunID): G4int
G4Trajectory:
Charge (Ch): unit: e+ (G4double)
Track ID (ID): G4int
Initial kinetic energy (IKE): G4BestUnit (G4double)
Initial momentum magnitude (IMag): G4BestUnit (G4double)
Initial momentum (IMom): G4BestUnit (G4ThreeVector)
No. of points (NTP): G4int
PDG Encoding (PDG): G4int
Parent ID (PID): G4int
Particle Name (PN): G4String
G4TrajectoryPoint:
Position (Pos): G4BestUnit (G4ThreeVector)
WARNING: Trajectory storing has been requested. This action may be
reversed with "/tracking/storeTrajectory 0".
WARNING: The vis manager will keep up to 100 events.
This may use a lot of memory.
It may be changed with, e.g., "/vis/scene/endOfEventAction accumulate 10".
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
Rmin/gate/aluminiumBall/geometry/setRmin
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
Rmin/gate/PVCBall/geometry/setRmin
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
Rmin/gate/glassBall/geometry/setRmin
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
Rmin/gate/spineBoneBall/geometry/setRmin
===== XML PATH ====: ./Materials.xml
I/O warning : failed to load external entity "./Materials.xml"
===== XML PATH ====: 0
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
<!> *** WARNING *** <!> Unknown process: MultipleScattering
List of Enabled processes:
=== Process: PhotoElectric ===
Particle: gamma
* Model(s):
- StandardModel
=== Process: Compton ===
Particle: gamma
* Model(s):
- PenelopeModel
=== Process: RayleighScattering ===
Particle: gamma
* Model(s):
- PenelopeModel
=== Process: Bremsstrahlung ===
Particle: e+
* Model(s):
- <!> *** Warning *** <!> No model selected!
Particle: e-
* Model(s):
- StandardModel
=== Process: ElectronIonisation ===
Particle: e+
* Model(s):
- <!> *** Warning *** <!> No model selected!
Particle: e-
* Model(s):
- StandardModel
List of initialized processes:
[Core-0] Initialization of geometry
G4PhysicalVolumeModel::Validate(): A volume of the same name and
copy number ("world_phys", copy 0) still exists and is being used.
But it is not the same volume you originally specified
in /vis/scene/add/.
[Core-0] Initialization of physics
[Physic-0] WARNING: manual physic lists are being deprecated.
Please, use physic list builder mechanism instead. Related documentation can be found at:
http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics
### WARNING: G4EmProcessOptions class is obsolete and will be removed in the next public release
Please, try to use G4EmParameters class and/or UI interface to EM parameters
[Core-0] Initialization of actors
GateSourceMgr::ListSources: List of the sources in the source manager
Source --------------> xraygun
ID : 0
type : gps
activity (Bq) : 350000
startTime (s) : 0
time (s) : 0
forcedUnstable : 0
forcedHalfLife (s) : -0.693147
verboseLevel : 0
relative to vol : world
----------------------
[Acquisition-0]
[Acquisition-0] ============= Source initialization =============
[Acquisition-0]
[Acquisition-0] ============= Acquisition starts! =============
[Acquisition-0] Simulation start time = 0 sec
[Acquisition-0] Simulation end time = 180 sec
[Acquisition-0] Simulation will have = 2 run(s)
****
Number of Pixels in your detector : 10000
Number of bytes by projection : 39.0625 Kb
****
[Acquisition-0] Slice 0 from 0 to 90 s [slice=90 s]
WARNING from G4PenelopeComptonModel
Atomic de-excitation module is not instantiated, so there will not be any fluorescence/Auger emission.
Please make sure this is intended
PhotoElectric: for gamma, applyCuts: 1 SubType= 12 BuildTable= 0
LambdaPrime table from 200 keV to 100 TeV in 61 bins
===== EM models for the G4Region DefaultRegionForTheWorld ======
PhotoElectric : Emin= 0 eV Emax= 100 TeV AngularGenSauterGavrila
Compton: for gamma, applyCuts: 1 SubType= 13 BuildTable= 1
Lambda table from 100 eV to 1 MeV, 7 bins per decade, spline: 1
LambdaPrime table from 1 MeV to 100 TeV in 56 bins
===== EM models for the G4Region DefaultRegionForTheWorld ======
PenCompton : Emin= 0 eV Emax= 100 TeV
RayleighScattering: for gamma, applyCuts: 1 SubType= 11 BuildTable= 1
Lambda table from 100 eV to 100 keV, 7 bins per decade, spline: 0
LambdaPrime table from 100 keV to 100 TeV in 63 bins
===== EM models for the G4Region DefaultRegionForTheWorld ======
PenRayleigh : Emin= 0 eV Emax= 100 GeV
Bremsstrahlung: for e- SubType= 3
dE/dx and range tables from 100 eV to 100 TeV in 84 bins
Lambda tables from threshold to 100 TeV, 7 bins per decade, spline: 1
LPM flag: 1 for E > 1 GeV, VertexHighEnergyTh(GeV)= 100000
===== EM models for the G4Region DefaultRegionForTheWorld ======
eBremSB : Emin= 0 eV Emax= 1 GeV DipBustGen
eBremLPM : Emin= 1 GeV Emax= 100 TeV DipBustGen
ElectronIonisation: for e- SubType= 2
dE/dx and range tables from 100 eV to 100 TeV in 84 bins
Lambda tables from threshold to 100 TeV, 7 bins per decade, spline: 1
finalRange(mm)= 1, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
MollerBhabha : Emin= 0 eV Emax= 100 TeV
Bremsstrahlung: for e+ SubType= 3
dE/dx and range tables from 100 eV to 100 TeV in 84 bins
Lambda tables from threshold to 100 TeV, 7 bins per decade, spline: 1
LPM flag: 1 for E > 1 GeV, VertexHighEnergyTh(GeV)= 100000
===== EM models for the G4Region DefaultRegionForTheWorld ======
eBremSB : Emin= 0 eV Emax= 1 GeV DipBustGen
eBremLPM : Emin= 1 GeV Emax= 100 TeV DipBustGen
ElectronIonisation: for e+ SubType= 2
dE/dx and range tables from 100 eV to 100 TeV in 84 bins
Lambda tables from threshold to 100 TeV, 7 bins per decade, spline: 1
finalRange(mm)= 1, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
MollerBhabha : Emin= 0 eV Emax= 100 TeV
#### FrameID = 0 ####
G4VisManager: Using G4TrajectoryDrawByCharge as fallback trajectory model.
See commands in /vis/modeling/trajectories/ for other options.
WARNING: G4VisManager::EndOfEvent: Automatic event keeping suspended.
The number of events exceeds the maximum, 100, that may be kept by
the vis manager.
********************* WARNING! ********************
* Display list limit reached in OpenGL.
* Continuing drawing WITHOUT STORING. Scene only partially refreshable.
* Current limit: 50000. Change with "/vis/ogl/set/displayListLimit".
***************************************************
On Wed, Jul 18, 2018 at 9:41 PM Sharif Abu Darda <shabudarda at gmail.com> wrote:
Hello, Thanks you for your reply, I already installed vGate 8.0 version in VM in my Mac. I was able to follow the guide to install the Vi editor from the docs, Now I follow every steps to run the CT example, I edited the benchmarkCT.mac according to the guide. After saving, I tried to run the command "Gate benchmarkCT.mac", At first I got a crash pop up in Gate OS, saying the program crashed with the below log in the terminal. With repeated try, I only get the log in the terminal, but no crash pop up. I can see the visualization window opens and crashes instantly. Can you tell me why I am getting this? I am a masters student in Nuclear Engineering at King Abdulaziz university, Saudi Arabia. My thesis is depending on Gate Monte Carlo simulation software. Please help. Thanks in advance.
[122] 21:29 vgate:~/Test/CT/classic > Gate benchmarkCT.mac
[G4]
[G4] *************************************************************
[G4] Geant4 version Name: geant4-10-03-patch-03 (20-October-2017)
[G4] Copyright : Geant4 Collaboration
[G4] Reference : NIM A 506 (2003), 250-303
[G4] WWW : http://cern.ch/geant4
[G4] *************************************************************
[G4]
[G4] ### WARNING: G4EmProcessOptions class is obsolete and will be removed in the next public release
Please, try to use G4EmParameters class and/or UI interface to EM parameters
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[G4] ### WARNING: G4EmProcessOptions class is obsolete and will be removed in the next public release
Please, try to use G4EmParameters class and/or UI interface to EM parameters
[Core-0] Initialization of actors
[Core-0]
[Core-0] **********************************************************************
[Core-0] GATE version name: gate_v8.0
[Core-0] Copyright : OpenGATE Collaboration
[Core-0] Reference : Phys. Med. Biol. 49 (2004) 4543-4561
[Core-0] Reference : Phys. Med. Biol. 56 (2011) 881-901
[Core-0] WWW : http://www.opengatecollaboration.org
[Core-0] **********************************************************************
[Core-0]
[Core-0] You are using Geant4 version 10.3.3
[Core-0] Starting macro benchmarkCT.mac
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--10-100-75-75-m-60-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--11-80-100-100-m-60-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--12-120-75-75-m-70-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--14-100-100-100-m-90-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--17-120-100-100-m-100-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--18-180-75-75-m-110-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--20-140-100-100-m-110-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--24-240-75-75-m-150-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--25-180-100-100-m-150-iso8859-1
[G4-cerr] G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
-adobe-courier-bold-r-normal--34-240-100-100-m-200-iso8859-1
/tracking/storeTrajectory 1
Attributes available for modeling and filtering with
"/vis/modeling/trajectories/create/drawByAttribute" and
"/vis/filtering/trajectories/create/attributeFilter" commands:
G4TrajectoriesModel:
Event ID (EventID): G4int
Run ID (RunID): G4int
G4Trajectory:
Charge (Ch): unit: e+ (G4double)
Track ID (ID): G4int
Initial kinetic energy (IKE): G4BestUnit (G4double)
Initial momentum magnitude (IMag): G4BestUnit (G4double)
Initial momentum (IMom): G4BestUnit (G4ThreeVector)
No. of points (NTP): G4int
PDG Encoding (PDG): G4int
Parent ID (PID): G4int
Particle Name (PN): G4String
G4TrajectoryPoint:
Position (Pos): G4BestUnit (G4ThreeVector)
WARNING: Trajectory storing has been requested. This action may be
reversed with "/tracking/storeTrajectory 0".
WARNING: The vis manager will keep up to 100 events.
This may use a lot of memory.
It may be changed with, e.g., "/vis/scene/endOfEventAction accumulate 10".
[G4-cerr]
-------- EEEE ------- G4Exception-START -------- EEEE -------
*** G4Exception : GateMDBFile
issued by : GateMDBFile::GateMDBFile
Could not find material database file '../../../misc/GateMaterials.db'
*** Fatal Exception *** core dump ***
-------- EEEE -------- G4Exception-END --------- EEEE -------
[G4-cerr]
[G4-cerr] *** G4Exception: Aborting execution ***
Aborted (core dumped)
[123] 21:30 vgate:~/Test/CT/classic >
On Wed, Jul 18, 2018 at 11:52 AM 강한규 <lovehangulp at naver.com> wrote:
Dear Shabudarda,
Attached is the manual for vGATE installation and running.
I'm sure that you will be able to run GATE CT example and analyze the ROOT output file with the manual.
For Korean GATE users, I attached Korea version vGATE manual which has more information about vGATE installation.
If you have any question, just let me know.
Best regards,
Han Gyu Kang, Ph.D.
Imaging Physics Team, NIRS-QST, Japan.
-----Original Message-----
From: "Sharif Abu Darda"<shabudarda at gmail.com>
To: <Gate-users at lists.opengatecollaboration.org>;
Cc:
Sent: 2018-07-18 (수) 04:50:54
Subject: [Gate-users] Need help with getting started
I am trying to learn Gate monte carlo simulation software, I have installed the vGate in my mac OS, I need help with a video tutorial of a sample exercise that I can get started with, A sample water phantom scanning with a gamma source, to measure dose rate. A video tutorial would be much helpful. Can anyone help me with that? Please. Thanks in advance.
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