Mikhail Polkovnikov | 7 Sep 10:14 2014
Picon

Re: problem with assigning a shape to a new volume

On 07.09.2014 10:22, Ali User wrote:
Dear polkovinkov

Thank you so much for your reply to my question of:

After I enter following commands in vGate_2.1:
>
> *Idle> gate/world/daughters/name XXX*
> *Idle> gate/world/daughters/insert box*
>
> I face this error:
>
> */home/gate/Progs/Gate/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc
> (l.132): GateMaterialDatabase: could not find the definition for material
> 'Vacuum' in material files*
>
> And once I enter*Idle> /gate/geometry/setMaterialDatabase GateMaterials.db*
>   following message appears
>
> *-------- EEEE ------- G4Exception-START -------- EEEE -------*
> **** G4Exception : GateMDBFile*
> *      issued by : GateMDBFile::GateMDBFile*
> *Could not find material database file 'GateMaterials.db'*
> **** Fatal Exception *** core dump ****
> *-------- EEEE -------- G4Exception-END --------- EEEE -------*
>
> the result is the same when I type *Idle>
> /gate/geometry/setMaterialDatabase data/GateMaterials.db*
>
> what is the problem? and how can I solve this problem to define my volume?
 

but as I mentioned earlier, I am working with vGate (virtual Gate) not Gate. By that I mean vGate is a pack that is run by virtual machine, therefore i don't have access to modify it. Do you have any idea how to solve my problem in vGate?

Thank you in advance for your help 
Hi,

There are two files in VGate 2.1 in /home/gate/Progs/Gate/gate_v6.2 directory: GateMaterials.db, Materials.xml

so you can use in your macro as

/gate/geometry/setMaterialDatabase /home/gate/Progs/Gate/gate_v6.2/GateMaterials.db

or if your have a macro file in gate_v6.2 directory

/gate/geometry/setMaterialDatabase GateMaterials.db



Best regards,
Mikhail


<div>
    <div class="moz-cite-prefix">On 07.09.2014 10:22, Ali User wrote:<br>
</div>
    <blockquote cite="mid:CAAiyeaTJZQCxDJjc5oj5dyncS+LDYyt6+B9-jA5bfTWq5mmkTQ@...l.com" type="cite">
      <div dir="ltr">Dear polkovinkov
        <div><br></div>
        <div>Thank you so much for your reply to my question of:</div>
        <div><br></div>
        <span>After
            I enter following commands in vGate_2.1:</span><br><span>&gt;</span><br><span>&gt;
            *Idle&gt; gate/world/daughters/name XXX*</span><br><span>&gt;
            *Idle&gt; gate/world/daughters/insert box*</span><br><span>&gt;</span><br><span>&gt;
            I face this error:</span><br><span>&gt;</span><br><span>&gt;
            */home/gate/Progs/Gate/gate_</span><span>v6.2/source/geometry/src/≤/span><span>GateMaterialDatabase.cc</span><br><span>&gt;
            (l.132): GateMaterialDatabase: could not find the definition
            for material</span><br><span>&gt;
            'Vacuum' in material files*</span><br><span>&gt;</span><br><span>&gt;
            And once I enter*Idle&gt; /gate/geometry/≤/span><span>setMaterialDatabase
            GateMaterials.db*</span><br><span>&gt;&nbsp;
            &nbsp;following message appears</span><br><span>&gt;</span><br><span>&gt;
            *-------- EEEE ------- G4Exception-START -------- EEEE
            -------*</span><br><span>&gt;
            **** G4Exception : GateMDBFile*</span><br><span>&gt;
            *&nbsp; &nbsp; &nbsp; issued by : GateMDBFile::GateMDBFile*</span><br><span>&gt;
            *Could not find material database file 'GateMaterials.db'*</span><br><span>&gt;
            **** Fatal Exception *** core dump ****</span><br><span>&gt;
            *-------- EEEE -------- G4Exception-END --------- EEEE
            -------*</span><br><span>&gt;</span><br><span>&gt;
            the result is the same when I type *Idle&gt;</span><br><span>&gt;
            /gate/geometry/≤/span><span>setMaterialDatabase
            data/GateMaterials.db*</span><br><span>&gt;</span><br>
        <div><span>&gt;
              what is the problem? and how can I solve this problem to
              define my volume?</span></div>
        <div>&nbsp;</div>
        <div><br></div>
        <div>but as I mentioned earlier, I am working with vGate
          (virtual Gate) not Gate. By that I mean vGate is a pack that
          is run by virtual machine, therefore i don't have access to
          modify it. Do you have any idea how to solve my problem in
          vGate?</div>
        <div><br></div>
        <div>Thank you in advance for your help&nbsp;</div>
      </div>
    </blockquote>
    Hi,<br><br>
    There are two files in VGate 2.1 in /home/gate/Progs/Gate/gate_v6.2
    directory: GateMaterials.db, Materials.xml<br><br>
    so you can use in your macro as<br><br>
    /gate/geometry/setMaterialDatabase
    /home/gate/Progs/Gate/gate_v6.2/GateMaterials.db<br><br>
    or if your have a macro file in gate_v6.2 directory<br><br>
    /gate/geometry/setMaterialDatabase GateMaterials.db<br><br><br><br>
    Best regards,<br>
    Mikhail<br><br><br>
</div>
Leda Lorenzon | 6 Sep 09:47 2014
Picon

Problems with output image from example_ARF

 

Dear Gate-users,

I tried to execute the template macro files  provided in the folder /examples/example_ARF. When I execute the macro “useARFTables” I obtain the output image (“benchARFMultiProjections.hdr”  and “benchARFMultiProjections.sin” ) but when I try to open it with ImageJ I obtain an image which is not correct. The simulated source is a point one but the output image is not representing a point source. I sent you a screen shots of one projection.

Do I make anything wrong?
Please help me.
Leda

Attachment (benchARFMultiProjections.hdr): application/octet-stream, 4263 bytes
<div><div dir="ltr">

<p><span lang="EN-US">&nbsp;</span></p>

<p><span lang="EN-US">Dear
Gate-users,</span></p>

<p><span lang="EN-US">I tried to execute
the template macro files <span>&nbsp;</span>provided in the
folder /examples/example_ARF. When I execute the macro &ldquo;useARFTables&rdquo; I obtain
the output image (&ldquo;benchARFMultiProjections.hdr&rdquo; <span>&nbsp;</span>and &ldquo;benchARFMultiProjections.sin&rdquo; ) but when
I try to open it with ImageJ I obtain an image which is not correct. The simulated
source is a point one but the output image is not representing a point source. </span><span lang="EN-US">I sent you a screen shots of one projection.</span></p>

<div><span lang="EN-US">Do I make anything wrong?</span></div>
<div><span lang="EN-US">Please help me.</span></div>
<div><span lang="EN-US">Leda</span></div>
<div>
<span lang="EN-US"></span><br>
</div>

</div></div>
Paweł Kowalski | 4 Sep 12:49 2014
Picon

Re: new install help

Hello,

Unfortunatelly I do not use MacOS but linux Fedora. Maybe someone who
uses MacOS will be able to help you.

Best regards,
PK

2014-09-04 12:45 GMT+02:00 O'Doherty, Jim <jim.odoherty <at> kcl.ac.uk>:
> Hi Pawel,
>
> Thank you for the tip - that has solved the empty install folder.
>
> The QTKit I have on my mac is v7.7.3, do you know how it is possible to
> rollback to v4 so it is compatible with the Geant4 install?
>
>  QTKit:
>
>       Version: 7.7.3
>       Obtained from: Apple
>       Last Modified: 01/05/2014 03:36
>       Kind: Intel
>       64-Bit (Intel): Yes
>       Signed by: Software Signing, Apple Code Signing Certification
> Authority, Apple Root CA
>       Get Info String: QTKit 7.7.3, Copyright 2003-2012, Apple Inc.
>       Location: /System/Library/Frameworks/QTKit.framework
>       Private: No
>
>
>
> Just wondering what other users do when they encounter this issue. If I
> compile without Qt, does that mean I have no graphical interface?
>
> Regards,
> Jim
>
>
>
>
> On 04/09/2014 10:50, "Paweł Kowalski" <flukson <at> gmail.com> wrote:
>
>>> Does anybody know why the Qt4 is failing (something in the QT4.cmake
>>>file?),
>>> and also why the geant4.9.6.p03-install (and 2.1.3.1-install) folder
>>>stays
>>> empty after I "make install"? The same happens when I try install the
>>>gate
>>> code
>>
>>Qt4 is failing because you probably have qt version 5. You should
>>install qt version 4.
>>
>>Directory geant4.9.6.p03-install is empty because you set
>>CMAKE_INSTALL_PREFIX
>>/Users/jim/Documents/GEANT4/geant4.9.6.p03
>>You should set it to:
>>CMAKE_INSTALL_PREFIX
>>/Users/jim/Documents/GEANT4/geant4.9.6.p03-install
>>
>>After compilation (make) you have to type 'make install'.
>>
>>Best regards,
>>PK
>
_______________________________________________
Gate-users mailing list
Gate-users <at> lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
O'Doherty, Jim | 4 Sep 13:54 2014
Picon

new install help

Hi,

Further to my previous query about using QTKit on a mac (how do I compile
GEANT4 with my version QTKit:7.7.3 on MacOS) I also have a query about the
ROOT package:

While installing GATEv7 my configuration is:

CMAKE_BACKWARDS_COMPATIBILITY 	2.4

 CMAKE_BUILD_TYPE 		Release

 CMAKE_INSTALL_PREFIX 		/Users/jim/Documents/GEANT4/gate.7.0-install

 CMAKE_OSX_ARCHITECTURES

 CMAKE_OSX_DEPLOYMENT_TARGET

 CMAKE_OSX_SYSROOT 

 EXECUTABLE_OUTPUT_PATH

 GATE_ANALYSIS_USE_FILE 		ON

 GATE_ANALYSIS_USE_GENERAL 	ON

 GATE_DOWNLOAD_BENCHMARKS_DATA 	OFF

 GATE_DOWNLOAD_EXAMPLES_DATA     OFF

 GATE_USE_ECAT7 			OFF

 GATE_USE_GEANT4_UIVIS 		ON

 GATE_USE_GPU 			OFF

 GATE_USE_LMF 			OFF

 GATE_USE_OPTICAL 		OFF

 GATE_USE_ROOT 			ON

 GATE_USE_SYSTEM_CLHEP 		OFF

 Geant496_COMPATIBILITY 		ON

 Geant4_DIR 
			/Users/jim/Documents/GEANT4/geant4.9.6.p03-install/lib/Geant4-9.6.3

 LIBRARY_OUTPUT_PATH

 ROOTCINT_EXECUTABLE 		/Users/jim/Documents/GEANT4/root_v5.XX/bin/rootcint

Trying to configure this gives me the error:

Root Not found ! Please install Root and make it available in PATH

However I have installed root, and if I echo $PATH, I see that it is
already available in PATH:

/Users/jim/Documents/GEANT4/root_v5.XX/bin:/Applications/CMake_2.8-12.app/C
ontents/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/
local/git/bin

Has anybody else encountered this issue and any idea how I can get around
this? Should I install an older version of ROOT (I used 5.34/20)?

Thanks,
Jim

On 04/09/2014 11:49, "Paweł Kowalski" <flukson@...> wrote:

>Hello,
>
>Unfortunatelly I do not use MacOS but linux Fedora. Maybe someone who
>uses MacOS will be able to help you.
>
>Best regards,
>PK
>
>2014-09-04 12:45 GMT+02:00 O'Doherty, Jim <jim.odoherty@...>:
>> Hi Pawel,
>>
>> Thank you for the tip - that has solved the empty install folder.
>>
>> The QTKit I have on my mac is v7.7.3, do you know how it is possible to
>> rollback to v4 so it is compatible with the Geant4 install?
>>
>>  QTKit:
>>
>>       Version: 7.7.3
>>       Obtained from: Apple
>>       Last Modified: 01/05/2014 03:36
>>       Kind: Intel
>>       64-Bit (Intel): Yes
>>       Signed by: Software Signing, Apple Code Signing Certification
>> Authority, Apple Root CA
>>       Get Info String: QTKit 7.7.3, Copyright 2003-2012, Apple Inc.
>>       Location: /System/Library/Frameworks/QTKit.framework
>>       Private: No
>>
>>
>>
>> Just wondering what other users do when they encounter this issue. If I
>> compile without Qt, does that mean I have no graphical interface?
>>
>> Regards,
>> Jim
>>
>>
>>
>>
>> On 04/09/2014 10:50, "Paweł Kowalski" <flukson@...> wrote:
>>
>>>> Does anybody know why the Qt4 is failing (something in the QT4.cmake
>>>>file?),
>>>> and also why the geant4.9.6.p03-install (and 2.1.3.1-install) folder
>>>>stays
>>>> empty after I "make install"? The same happens when I try install the
>>>>gate
>>>> code
>>>
>>>Qt4 is failing because you probably have qt version 5. You should
>>>install qt version 4.
>>>
>>>Directory geant4.9.6.p03-install is empty because you set
>>>CMAKE_INSTALL_PREFIX
>>>/Users/jim/Documents/GEANT4/geant4.9.6.p03
>>>You should set it to:
>>>CMAKE_INSTALL_PREFIX
>>>/Users/jim/Documents/GEANT4/geant4.9.6.p03-install
>>>
>>>After compilation (make) you have to type 'make install'.
>>>
>>>Best regards,
>>>PK
>>

Mikhail Polkovnikov | 4 Sep 13:23 2014
Picon

Re: problem with assigning a shape to a new volume (Ali User)

Message: 4 Date: Thu, 4 Sep 2014 14:22:51 +0430 From: Ali User <gateuser2014-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> To: gate-users-ZwoEplunGu1UUpeUK0L/Pw@public.gmane.orggatecollaboration.org Subject: [Gate-users] problem with assigning a shape to a new volume Message-ID: <CAAiyeaSgWHUatD+rTPgyNZMegZjCg-rzY5-w=Qvyk+9J1q=MoA-JsoAwUIsXotQFR93xxRIaA@public.gmane.orgcom> Content-Type: text/plain; charset="utf-8" Hi every body, After I enter following commands in vGate_2.1: *Idle> gate/world/daughters/name XXX* *Idle> gate/world/daughters/insert box* I face this error: */home/gate/Progs/Gate/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc (l.132): GateMaterialDatabase: could not find the definition for material 'Vacuum' in material files* And once I enter *Idle> /gate/geometry/setMaterialDatabase GateMaterials.db* following message appears *-------- EEEE ------- G4Exception-START -------- EEEE -------* **** G4Exception : GateMDBFile* * issued by : GateMDBFile::GateMDBFile* *Could not find material database file 'GateMaterials.db'* **** Fatal Exception *** core dump **** *-------- EEEE -------- G4Exception-END --------- EEEE -------* the result is the same when I type *Idle> /gate/geometry/setMaterialDatabase data/GateMaterials.db* what is the problem? and how can I solve this problem to define my volume? Thank you
Hello,

Try copy the GateMaterials.db to the folder there are your project macro files, and try something like:

/vis/disable

/gate/geometry/setMaterialDatabase    GateMaterials.db

/gate/world/geometry/setXLength       400. cm
/gate/world/geometry/setYLength       400. cm
/gate/world/geometry/setZLength       400. cm

/gate/run/initialize

<div>
    <div class="moz-cite-prefix">On 04.09.2014 13:49,
      <a class="moz-txt-link-abbreviated" href="mailto:gate-users-request@...">gate-users-request@...llaboration.org</a> wrote:<br>
</div>
    <blockquote cite="mid:mailman.123.1409824143.1509.gate-users@...ation.org" type="cite">
      Message: 4
Date: Thu, 4 Sep 2014 14:22:51 +0430
From: Ali User <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:gateuser2014@...">&lt;gateuser2014@...&gt;</a>
To: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:gate-users@...">gate-users@...gatecollaboration.org</a>
Subject: [Gate-users] problem with assigning a shape to a new volume
Message-ID:
	<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:CAAiyeaSgWHUatD+rTPgyNZMegZjCg-rzY5-w=Qvyk+9J1q=MoA@...">&lt;CAAiyeaSgWHUatD+rTPgyNZMegZjCg-rzY5-w=Qvyk+9J1q=MoA@...com&gt;</a>
Content-Type: text/plain; charset="utf-8"

Hi every body,

After I enter following commands in vGate_2.1:

<span class="moz-txt-tag">*</span>Idle&gt; gate/world/daughters/name XXX<span class="moz-txt-tag">*</span>
<span class="moz-txt-tag">*</span>Idle&gt; gate/world/daughters/insert box<span class="moz-txt-tag">*</span>

I face this error:

*/home/gate/Progs/Gate/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc
(l.132): GateMaterialDatabase: could not find the definition for material
'Vacuum' in material files*

And once I enter <span class="moz-txt-tag">*</span>Idle&gt; /gate/geometry/setMaterialDatabase GateMaterials.db<span class="moz-txt-tag">*</span>
 following message appears

*-------- EEEE ------- G4Exception-START -------- EEEE -------*
**** G4Exception : GateMDBFile*
*      issued by : GateMDBFile::GateMDBFile*
*Could not find material database file 'GateMaterials.db'*
**** Fatal Exception *** core dump ****
*-------- EEEE -------- G4Exception-END --------- EEEE -------*

the result is the same when I type *Idle&gt;
/gate/geometry/setMaterialDatabase data/GateMaterials.db*

what is the problem? and how can I solve this problem to define my volume?

Thank you
    </blockquote>
    Hello,<br><br>
    Try copy the GateMaterials.db to the folder there are your project
    macro files, and try something like:<br><br>
    /vis/disable<br><br>
    /gate/geometry/setMaterialDatabase&nbsp;&nbsp;&nbsp; GateMaterials.db<br><br>
    /gate/world/geometry/setXLength&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 400. cm<br>
    /gate/world/geometry/setYLength&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 400. cm<br>
    /gate/world/geometry/setZLength&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 400. cm<br><br>
    /gate/run/initialize<br><br>
</div>
Jye Smith | 4 Sep 06:36 2014
Picon

Jobsplitter make error

Hi Gate,

Ive run into the below error when compiling the gjs. This is on a clean install of G4v10 and Gatev7 development version. I also tried compiling the gjs on vGate (G4v4.9.6 and Gatev7) and it compiled fine. Could this be a compatibility issue with G4v10?

Is anyone able to give some insight to whats happened? 

Cheers
Jye


ubuntu <at> ubuntu-i386:~/gate.7.0.develop/cluster_tools/jobsplitter$ make
Compiling gjs.cc...
Compiling GateMacfileParser.cc...
./src/GateMacfileParser.cc: In constructor âGateMacfileParser::GateMacfileParser(G4String, G4int, G4int, G4String*)â:
./src/GateMacfileParser.cc:41:26: error: âgetpidâ was not declared in this scope
  srand(time(NULL)*getpid());
                          ^
./src/GateMacfileParser.cc: In member function âG4int GateMacfileParser::GenerateResolvedMacro(G4String, G4int, std::ofstream&)â:
./src/GateMacfileParser.cc:137:17: warning: declaration of âbufferâ shadows a member of 'this' [-Wshadow]
  char buffer[256];
                 ^
./src/GateMacfileParser.cc: In member function âvoid GateMacfileParser::InsertSubMacros(std::ofstream&, G4int, std::ofstream&)â:
./src/GateMacfileParser.cc:225:18: warning: declaration of âbufferâ shadows a member of 'this' [-Wshadow]
   char buffer[256];
                  ^
./src/GateMacfileParser.cc: In member function âvoid GateMacfileParser::FormatMacline()â:
./src/GateMacfileParser.cc:931:9: warning: declaration of âpositionâ shadows a previous local [-Wshadow]
   G4int position=macline.find("#");
         ^
./src/GateMacfileParser.cc:927:8: warning: shadowed declaration is here [-Wshadow]
  G4int position=0;
        ^
make: *** [tmp/GateMacfileParser.o] Error 1

<div><div dir="ltr">Hi Gate,<div><br></div>
<div>Ive run into the below error when compiling the gjs. This is on a clean install of G4v10 and Gatev7 development version. I also tried compiling the gjs on vGate (G4v4.9.6 and Gatev7) and it compiled fine. Could this be a compatibility issue with G4v10?</div>
<div><br></div>
<div>Is anyone able to give some insight to whats happened?&nbsp;</div>
<div><br></div>
<div>Cheers</div>
<div>Jye</div>
<div>
<div><br></div>
<div><br></div>
<div>
<div>ubuntu <at> ubuntu-i386:~/gate.7.0.develop/cluster_tools/jobsplitter$ make</div>
<div>Compiling gjs.cc...</div>
<div>Compiling GateMacfileParser.cc...</div>
<div>./src/GateMacfileParser.cc: In constructor &acirc;GateMacfileParser::GateMacfileParser(G4String, G4int, G4int, G4String*)&acirc;:</div>
<div>./src/GateMacfileParser.cc:41:26: error: &acirc;getpid&acirc; was not declared in this scope</div>
<div>&nbsp; srand(time(NULL)*getpid());</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</div>
<div>./src/GateMacfileParser.cc: In member function &acirc;G4int GateMacfileParser::GenerateResolvedMacro(G4String, G4int, std::ofstream&amp;)&acirc;:</div>
<div>./src/GateMacfileParser.cc:137:17: warning: declaration of &acirc;buffer&acirc; shadows a member of 'this' [-Wshadow]</div>
<div>&nbsp; char buffer[256];</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;^</div>
<div>./src/GateMacfileParser.cc: In member function &acirc;void GateMacfileParser::InsertSubMacros(std::ofstream&amp;, G4int, std::ofstream&amp;)&acirc;:</div>
<div>./src/GateMacfileParser.cc:225:18: warning: declaration of &acirc;buffer&acirc; shadows a member of 'this' [-Wshadow]</div>
<div>&nbsp; &nbsp;char buffer[256];</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ^</div>
<div>./src/GateMacfileParser.cc: In member function &acirc;void GateMacfileParser::FormatMacline()&acirc;:</div>
<div>./src/GateMacfileParser.cc:931:9: warning: declaration of &acirc;position&acirc; shadows a previous local [-Wshadow]</div>
<div>&nbsp; &nbsp;G4int position=macline.find("#");</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;^</div>
<div>./src/GateMacfileParser.cc:927:8: warning: shadowed declaration is here [-Wshadow]</div>
<div>&nbsp; G4int position=0;</div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; ^</div>
<div>make: *** [tmp/GateMacfileParser.o] Error 1</div>
</div>
<div><br></div>
</div>
</div></div>
Amy Meldrum | 3 Sep 15:43 2014

Digitizer modules for PMT, and quantum efficiency of PMT?

Gate users,

I have been doing simulations using scintillators, PMTs, and optical photons. Up until now I have only taken the Hits.dat file and parsed the data using a script I have written to combine the number of photons detected per parent particle as a means of simulating a pulse that would be seen by a PMT.


I have realized that I need to account for the quantum efficiency of the PMT when doing these simulations. Initially I thought that by changing the value for EFFICIENCY in the detection surface definition in the Surfaces.xml file would be sufficient. Is this true?

Secondly, when searching for ways to simulate PMT output, the idea of using the digitizer came up frequently. Initially I shied away from using the digitizer because I did not understand how to incorporate it or what format the output would even be. Has anyone used the digitizer and its modules to recreate the output of a PMT? Such that it includes quantum efficiency, and each 'pulse' represents the number of photons detected for a given parent particle?  If so, what would the output look like? Would this be something I could use to generate a simulated spectrum?


Any help is greatly appreciated.

-Amy
<div><div dir="ltr">Gate users,<div><br></div>
<div>I have been doing simulations using scintillators, PMTs, and optical photons. Up until now I have only taken the Hits.dat file and parsed the data using a script I have written to combine the number of photons detected per parent particle as a means of simulating a pulse that would be seen by a PMT.</div>
<div><br></div>
<div><br></div>
<div>I have realized that I need to account for the quantum efficiency of the PMT when doing these simulations. Initially I thought that by changing the value for EFFICIENCY in the detection surface definition in the Surfaces.xml file would be sufficient. Is this true?</div>
<div><br></div>
<div>Secondly, when searching for ways to simulate PMT output, the idea of using the digitizer came up frequently. Initially I shied away from using the digitizer because I did not understand how to incorporate it or what format the output would even be. Has anyone used the digitizer and its modules to recreate the output of a PMT? Such that it includes quantum efficiency, and each 'pulse' represents the number of photons detected for a given parent particle? &nbsp;If so, what would the output look like? Would this be something I could use to generate a simulated spectrum?</div>
<div><br></div>
<div><br></div>
<div>Any help is greatly appreciated.</div>
<div><br></div>
<div>-Amy</div>
</div></div>
肖期德 | 3 Sep 10:15 2014
Picon

example_Radiotherapy/example3/data/linac-beam.root is what?

Dear Gate users !

How is the root file  ".../examples/example_Radiotherapy/example3/data/linac-beam.root" generated ?
It only take space 4.7MB,and look like has lots of particles and many branches.

And,as the example3 shown , It genarate a root file of 13.6M,only include 599101 photons.

<div>
    Dear Gate users !<br><br>
    How is the root file&nbsp;
    ".../examples/example_Radiotherapy/example3/data/linac-beam.root"
    generated ?<br>
    It only take space 4.7MB,and look like has lots of particles and
    many branches.<br><br>
    And,as the example3 shown , It genarate a root file of 13.6M,only
    include 599101 photons.<br><br>
</div>
David Sarrut | 3 Sep 07:44 2014
Picon
Picon

Re: Geant4 10.0 MT and GATE


yes, MT is *not* implemented in GATE : it would required some (a lot of ?) effort to make the code compliant and we agreed in the collaboration that, at the moment, it is not worth it. Really good speed up can be obtained by launching several Gate simulation (with different random seed number). 

David


On Wed, Sep 3, 2014 at 7:36 AM, Jye Smith <jye.smith-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

So MT is not yet implemented in Gate with G4 v10?

Thanks for the reply.

On 3 Sep 2014 15:31, "David Sarrut" <David.Sarrut-0ZXfWqjJkvJNgumx+FIHDcc1ZZbpBbUC@public.gmane.org> wrote:
Hello, 

yes, Gate could yet only be compiled with MT=false. 

Warning : Gate can be linked with G4 10.0 *only* with the development version of the source code available in git (develop branch), not the official release. 

If you use both Gate and G4 directly, you may need two compiled versions of G4, with MT=false for Gate and with MT=true for your own G4 simulations that use MT. 

No other modifications in the macro files.

Sincerely, 
David



On Wed, Sep 3, 2014 at 6:00 AM, Jye Smith <jye.smith-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Hi David,

Ive just been through the process of installing Gatev7.0 development with G4v10.00.p02 on a fresh install of Ubuntu server 14 (testing in virtualbox).

I complied G4 with "cmake /home/ubuntu/geant4.10.00.p02 -DCMAKE_INSTALL_PREFIX=/home/ubuntu/geant4.10.00.p02-install -DGEANT4_INSTALL_DATA=OFF "

Is your comment below about GEANT4_BUILD_MULTITHREADED=false correct or should it be GEANT4_BUILD_MULTITHREADED=ON for MT?

Compiling as above with MT=OFF I can only see 1 of 4 CPUs running when running a simulation. Besides turning MT=ON is there any other changes required to the macs?

Cheers
Jye


On Thu, Jul 10, 2014 at 3:21 PM, David Sarrut <David.Sarrut-0ZXfWqjJkvJNgumx+FIHDcc1ZZbpBbUC@public.gmane.org> wrote:
Hello, 

the develop branch of the opengate git repository has been updated : Gate is now compatible with Geant4 10.0 (must be compiled with GEANT4_BUILD_MULTITHREADED=false). 

feedback welcome, 
have fun, 
David



On Mon, Dec 2, 2013 at 2:37 PM, Marc Verderi <verderi-wBnxOHnizbs@public.gmane.org> wrote:
Dear Ian,

    Just a few words to let you know about some feature of the Geant4 10.0 MT, and to partly answer your question. Geant4 10.0, which includes this MT capability, will be released in a few days. The MT scheme adopted is to process events (in Geant4 sense) in parallel, each thread dealing with a set of events, and sharing geometry and physics tables among the threads, to minimize the memory footprint.

    GATE will certainly need an adaptation. This is of course critical, but requires only a few lines of code. The G4RunManager as to be replaced by the G4MTRunManager. Users' actions (primary generator action, stepping action, event action, and run action if needed) become thread local actions : one instance of each of these actions is instantiated per thread. Sensitive detectors and fields become also thread local, and have to be instantiated in a new method of the detector construction : ConstructSDandField() which is executed once for each thread. In this way, events can be processed independently, in parallel. The overall mechanics is controlled by a master thread, the one launched at the application startup, and which then spawn the slave threads at event loop start.

    What will be needed also is an examination of the "static" data members in the GATE classes : some of them would be static as known in the master and slave threads, some others will be static but with a thread local scope and will need some adaptation. Helper classes in the Geant4 MT version exist to help doing an easy transformation of, for example, a singleton to a thread-local singleton.
    All these transformations are compatible with a sequential processing (the up-to-now processing), and a MT-compliant code can be compiled as is for a sequential processing (provided the G4RunManager has been chosen).

    For information, tests performed on a 61 cores Intel Xeon Phi board allowed to go up to 244 threads (maximum possible number on this platform) for a single realistic application !

    Hoping I just whet your appetite ! ;)

Best regards,
Marc




On 11/26/2013 03:07 PM, Porter Ian (RBV) NHS Christie Tr wrote:
Hello All,
   My understanding is that the next version of Geant4 (v10.0) will
support multi-threading and will be released to production soon.  We are
keen to move over to this to avoid using multiple instances of GATE (1
per CPU core) on our cluster.  Can anyone tell me whether GATE will
require an upgrade in order to work with Geant4 MT?  If so, is there a
timescale for the release of the new version?  The last newsletter
mentions GATE v7.0 with GPU support, which was due out by now but has
not yet appeared.  Is this being rewritten with a view to supporting
Geant4 10.0 MT?

Many Thanks,
   -- Ian.
To download our 20:20 Vision strategy, please visit http://www.christie.nhs.uk/2020

This e-mail and any files transmitted with it are confidential and solely for the use of the intended recipient.
If you have received this e-mail in error you should not disseminate, distribute or copy it.
Please notify the sender immediately and delete this e-mail from your system.

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--
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U 1044
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
_________________________________

_______________________________________________
Gate-users mailing list
Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users




--
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U 1044
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
_________________________________



--
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U 1044
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
_________________________________
<div>
<div dir="ltr">
<div><br></div>
<div>yes, MT is *not* implemented in GATE : it would required some (a lot of ?) effort to make the code compliant and we agreed in the collaboration that, at the moment, it is not worth it. Really good speed up can be obtained by launching several Gate simulation (with different random seed number).&nbsp;</div>

<div><br></div>
<div>David</div>
</div>
<div class="gmail_extra">
<br><br><div class="gmail_quote">On Wed, Sep 3, 2014 at 7:36 AM, Jye Smith <span dir="ltr">&lt;<a href="mailto:jye.smith@..." target="_blank">jye.smith@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">
<p dir="ltr">So MT is not yet implemented in Gate with G4 v10?</p>
<p dir="ltr">Thanks for the reply.</p>
<div class="HOEnZb"><div class="h5">
<div class="gmail_quote">On 3 Sep 2014 15:31, "David Sarrut" &lt;<a href="mailto:David.Sarrut@..." target="_blank">David.Sarrut@...</a>&gt; wrote:<br type="attribution"><blockquote class="gmail_quote">

<div dir="ltr">Hello,&nbsp;<div><br></div>
<div>yes, Gate could yet only be compiled with MT=false.&nbsp;</div>
<div><br></div>
<div>Warning : Gate can be linked with G4 10.0 *only* with the development version of the source code available in git (develop branch), not the official release.&nbsp;</div>

<div><br></div>
<div>If you use both Gate and G4 directly, you may need two compiled versions of G4, with MT=false for Gate and with MT=true for your own G4 simulations that use MT.&nbsp;</div>
<div><br></div>
<div>No other modifications in the macro files.</div>

<div><br></div>
<div>Sincerely,&nbsp;</div>
<div>David</div>
<div><br></div>
</div>
<div class="gmail_extra">
<br><br><div class="gmail_quote">On Wed, Sep 3, 2014 at 6:00 AM, Jye Smith <span dir="ltr">&lt;<a href="mailto:jye.smith@..." target="_blank">jye.smith@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">
<div dir="ltr"><div class="gmail_extra">
<div class="gmail_extra">Hi David,</div>
<div class="gmail_extra"><br></div>
<div class="gmail_extra">

Ive just been through the process of installing Gatev7.0 development with G4v10.00.p02 on a fresh install of Ubuntu server 14 (testing in virtualbox).</div>
<div class="gmail_extra"><br></div>
<div class="gmail_extra">I complied G4 with "cmake /home/ubuntu/geant4.10.00.p02 -DCMAKE_INSTALL_PREFIX=/home/ubuntu/geant4.10.00.p02-install -DGEANT4_INSTALL_DATA=OFF "</div>

<div class="gmail_extra">
<br>
</div>
<div class="gmail_extra">Is your comment below about&nbsp;<span>GEANT4_BUILD_≤/span><span>MULTITHREADED=false correct or should it be&nbsp;</span><span>GEANT4_BUILD_≤/span><span>MULTITHREADED=ON for MT?</span>
</div>

<div class="gmail_extra"><br></div>
<div class="gmail_extra">Compiling as above with MT=OFF I can only see 1 of 4 CPUs running when running a simulation. Besides turning MT=ON is there any other changes required to the macs?</div>

<div class="gmail_extra"><br></div>
<div class="gmail_extra">Cheers</div>
<span><div class="gmail_extra">Jye</div></span><div><div>
<div class="gmail_extra"><br></div>
<br><div class="gmail_quote">On Thu, Jul 10, 2014 at 3:21 PM, David Sarrut <span dir="ltr">&lt;<a href="mailto:David.Sarrut@..." target="_blank">David.Sarrut@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">
<div dir="ltr">Hello,&nbsp;<div><br></div>
<div>the develop branch of the opengate git repository has been updated : Gate is now compatible with Geant4 10.0&nbsp;<span>(must be compiled with&nbsp;GEANT4_BUILD_≤/span><span>MULTITHREADED=false).&nbsp;</span><br>
</div>
<div><span><br></span></div>
<div><span>feedback welcome,&nbsp;</span></div>
<div><span>have fun,&nbsp;</span></div>

<div><span>David</span></div>
<div><span><br></span></div>
</div>
<div class="gmail_extra">
<br><br><div class="gmail_quote">

On Mon, Dec 2, 2013 at 2:37 PM, Marc Verderi <span dir="ltr">&lt;<a href="mailto:verderi@..." target="_blank">verderi@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">

Dear Ian,<br><br>
&nbsp; &nbsp; Just a few words to let you know about some feature of the Geant4 10.0 MT, and to partly answer your question. Geant4 10.0, which includes this MT capability, will be released in a few days. The MT scheme adopted is to process events (in Geant4 sense) in parallel, each thread dealing with a set of events, and sharing geometry and physics tables among the threads, to minimize the memory footprint.<br><br>
&nbsp; &nbsp; GATE will certainly need an adaptation. This is of course critical, but requires only a few lines of code. The G4RunManager as to be replaced by the G4MTRunManager. Users' actions (primary generator action, stepping action, event action, and run action if needed) become thread local actions : one instance of each of these actions is instantiated per thread. Sensitive detectors and fields become also thread local, and have to be instantiated in a new method of the detector construction : ConstructSDandField() which is executed once for each thread. In this way, events can be processed independently, in parallel. The overall mechanics is controlled by a master thread, the one launched at the application startup, and which then spawn the slave threads at event loop start.<br><br>
&nbsp; &nbsp; What will be needed also is an examination of the "static" data members in the GATE classes : some of them would be static as known in the master and slave threads, some others will be static but with a thread local scope and will need some adaptation. Helper classes in the Geant4 MT version exist to help doing an easy transformation of, for example, a singleton to a thread-local singleton.<br>

&nbsp; &nbsp; All these transformations are compatible with a sequential processing (the up-to-now processing), and a MT-compliant code can be compiled as is for a sequential processing (provided the G4RunManager has been chosen).<br><br>
&nbsp; &nbsp; For information, tests performed on a 61 cores Intel Xeon Phi board allowed to go up to 244 threads (maximum possible number on this platform) for a single realistic application !<br><br>
&nbsp; &nbsp; Hoping I just whet your appetite ! ;)<br><br>
Best regards,<br>
Marc<div><div>
<br><br><br><br>
On 11/26/2013 03:07 PM, Porter Ian (RBV) NHS Christie Tr wrote:<br><blockquote class="gmail_quote">
Hello All,<br>
&nbsp; &nbsp;My understanding is that the next version of Geant4 (v10.0) will<br>
support multi-threading and will be released to production soon. &nbsp;We are<br>
keen to move over to this to avoid using multiple instances of GATE (1<br>
per CPU core) on our cluster. &nbsp;Can anyone tell me whether GATE will<br>
require an upgrade in order to work with Geant4 MT? &nbsp;If so, is there a<br>
timescale for the release of the new version? &nbsp;The last newsletter<br>
mentions GATE v7.0 with GPU support, which was due out by now but has<br>
not yet appeared. &nbsp;Is this being rewritten with a view to supporting<br>
Geant4 10.0 MT?<br><br>
Many Thanks,<br>
&nbsp; &nbsp;-- Ian.<br>
To download our 20:20 Vision strategy, please visit <a href="http://www.christie.nhs.uk/2020" target="_blank">http://www.christie.nhs.uk/2020</a><br><br>
This e-mail and any files transmitted with it are confidential and solely for the use of the intended recipient.<br>
If you have received this e-mail in error you should not disseminate, distribute or copy it.<br>
Please notify the sender immediately and delete this e-mail from your system.<br><br>
_______________________________________________<br>
Gate-users mailing list<br><a href="mailto:Gate-users@..." target="_blank">Gate-users <at> 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>
</blockquote>
<br>
_______________________________________________<br>
Gate-users mailing list<br><a href="mailto:Gate-users@..." target="_blank">Gate-users <at> 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><span><br></span>
</div></div>
</blockquote>
</div>
<span><br><br clear="all"><div><br></div>-- <br><div dir="ltr">David Sarrut, Phd<br>Directeur de recherche CNRS<br>CREATIS, UMR CNRS 5220, Inserm U 1044<div>

Centre de lutte contre le cancer L&eacute;on B&eacute;rard<br>

28 rue La&euml;nnec, 69373 Lyon cedex 08<br>Tel : <a href="tel:04%2078%2078%2051%2051" value="+33478785151" target="_blank">04 78 78 51 51</a> / <a href="tel:06%2074%2072%2005%2042" value="+33674720542" target="_blank">06 74 72 05 42</a><br><a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>_________________________________</div>

<div>&nbsp;"2 + 2 = 5,&nbsp; for extremely large values of 2"<br>_________________________________</div>
</div>
</span>
</div>
<br>_______________________________________________<br>
Gate-users mailing list<br><a href="mailto:Gate-users@..." target="_blank">Gate-users@...</a><br><a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>
</blockquote>
</div>
<br>
</div></div>
</div></div>
</blockquote>
</div>
<br><br clear="all"><div><br></div>-- <br><div dir="ltr">David Sarrut, Phd<br>Directeur de recherche CNRS<br>CREATIS, UMR CNRS 5220, Inserm U 1044<div>Centre de lutte contre le cancer L&eacute;on B&eacute;rard<br>28 rue La&euml;nnec, 69373 Lyon cedex 08<br>

Tel : <a href="tel:04%2078%2078%2051%2051" value="+33478785151" target="_blank">04 78 78 51 51</a> / <a href="tel:06%2074%2072%2005%2042" value="+33674720542" target="_blank">06 74 72 05 42</a><br><a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>

_________________________________</div>
<div>&nbsp;"2 + 2 = 5,&nbsp; for extremely large values of 2"<br>

_________________________________</div>
</div>
</div>
</blockquote>
</div>
</div></div>
</blockquote>
</div>
<br><br clear="all"><div><br></div>-- <br><div dir="ltr">David Sarrut, Phd<br>Directeur de recherche CNRS<br>CREATIS, UMR CNRS 5220, Inserm U 1044<div>Centre de lutte contre le cancer L&eacute;on B&eacute;rard<br>

28 rue La&euml;nnec, 69373 Lyon cedex 08<br>Tel : 04 78 78 51 51 / 06 74 72 05 42<br><a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>_________________________________</div>

<div>&nbsp;"2 + 2 = 5,&nbsp; for extremely large values of 2"<br>_________________________________</div>
</div>
</div>
</div>
Michal Knap | 3 Sep 06:39 2014
Picon

Gate7.o simulation problem

Hi All,
I'm trying to run my minigammacamera simulation but i have problem with that. It looks like i'm able to run simulation but after 4 runs everything stops and i get no results (no graphs, outputs...). Can anybody help me what is wrong?
Thanks in advance

mknap <at> mknap-HP:~$ cd Gate/
mknap <at> mknap-HP:~/Gate$ source your_file.bashrc 
mknap <at> mknap-HP:~/Gate$ Gate --qt minigamma1pointsourceoncollimator1.mac
[G4] 
[G4] *************************************************************
[G4]  Geant4 version Name: geant4-09-06-patch-03    (14-March-2014)
[G4]                       Copyright : Geant4 Collaboration
[G4]                       Reference : NIM A 506 (2003), 250-303
[G4]                             WWW : http://cern.ch/geant4
[G4] *************************************************************
[G4] 
[Core-0] Initialization of geometry
[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:
[Core-0] Initialization of actors
[G4] Available UI session types: [ Qt, GAG, tcsh, csh ]
[Core-0] 
[Core-0] **********************************************************************
[Core-0]  GATE version name: gate_v7.0                                         
[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 9.6.3
[Core-0] Starting macro minigamma1pointsourceoncollimator1.mac
[Physic-0] The following Geant4's physic-list is enabled :emstandard
[Acquisition-0]                                      
[Acquisition-0] ============= Source initialization =============
[Acquisition-0]                                      
[Acquisition-0] ============= Acquisition starts! =============
[Acquisition-0] Simulation start time = 0 sec
[Acquisition-0] Simulation end time   = 150 sec
[Acquisition-0] Simulation will have  = 4 run(s)

----- HepJamesRandom engine status -----
 Initial seed = 669708517
 u[] = 0.313493 0.22101 0.720638 0.288275 0.209104 0.961876 0.0185378 0.767277 0.570899 0.11677 0.585697 0.361668 0.499346 0.969958 0.659357 0.470614 0.232287 0.851241 0.27455 0.788571 0.407255 0.205312 0.558045 0.841456 0.443543 0.0437512 0.20597 0.975022 0.180286 0.842097 0.240617 0.115375 0.0104213 0.86239 0.254429 0.284886 0.114014 0.250714 0.477909 0.527364 0.887455 0.402326 0.5341 0.418133 0.107406 0.124517 0.302133 0.489961 0.8011 0.598657 0.398494 0.285134 0.133646 0.956609 0.548981 0.0394724 0.830412 0.922722 0.527004 0.588913 0.129604 0.169863 0.043967 0.0808861 0.801898 0.583084 0.269808 0.84379 0.235689 0.208139 0.683603 0.275 0.411587 0.134052 0.253045 0.356203 0.629278 0.233236 0.444437 0.502942 0.77252 0.00816381 0.210178 0.938382 0.894515 0.511199 0.913346 0.907528 0.240269 0.448999 0.814368 0.13479 0.692496 0.707161 0.983838 0.703152 0.403158 
 c = 0.652903, cd = 0.456233, cm = 1
 i97 = 93, u[i97] = 0.707161
 j97 = 29, u[j97] = 0.842097
----------------------------------------
[Acquisition-0] Slice 0 from 0 to 37.5 s [slice=37.5 s], final stop at 150 s.
[Acquisition-0] Slice 1 from 37.5 to 75 s [slice=37.5 s], final stop at 150 s.
[Acquisition-0] Slice 2 from 75 to 112.5 s [slice=37.5 s], final stop at 150 s.
[Acquisition-0] Slice 3 from 112.5 to 150 s [slice=37.5 s], final stop at 150 s.
[Core-0] End of macro minigamma1pointsourceoncollimator1.mac

And after simulation i get this:


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".

WARNING: The vis manager will keep up to 10000 events.

This may use a lot of memory.

It may be changed with, e.g., "/vis/scene/endOfEventAction accumulate 10".

GateDetectorConstruction::insertARFSD entered

created a ARF Sensivitive Detector

created command /gate/systems/SPECThead/arf/setARFStage

Rmin/gate/Phantom/geometry/setRmin

Rmin/gate/movsource/geometry/setRmin

Confirming confinement to volume 'movsource_P_phys'...

**** Error: Volume does not exist ****

Ignoring confine condition

### === Deexcitation model UAtomDeexcitation is activated for 1 region:

DefaultRegionForTheWorld

### === G4UAtomicDeexcitation::InitialiseForNewRun()

### === PIXE model for hadrons: Empirical 1

### === PIXE model for e+-: Livermore 1

### === Deexcitation model UAtomDeexcitation is activated for 1 region:

DefaultRegionForTheWorld

### === G4UAtomicDeexcitation::InitialiseForNewRun()

### === PIXE model for hadrons: Empirical 1

### === PIXE model for e+-: Livermore 1

WARNING: G4VisManager::EndOfEvent: Automatic event keeping suspended.

The number of events exceeds the maximum, 10000, that can be kept by the vis manager.

WARNING: G4VisManager::EndOfRun: Automatic event keeping has been suspended.

The number of events in the run exceeded the maximum, 10000, that can be kept by the vis manager.

The number of events kept by the vis manager can be changed with

"/vis/scene/endOfEventAction accumulate <N>", where N is the

maximum number you wish to allow. N < 0 means "unlimited".

10000 events have been kept for refreshing and/or reviewing.

### === Deexcitation model UAtomDeexcitation is activated for 1 region:

DefaultRegionForTheWorld

### === G4UAtomicDeexcitation::InitialiseForNewRun()

### === PIXE model for hadrons: Empirical 1

### === PIXE model for e+-: Livermore 1

WARNING: G4VisManager::EndOfRun: Automatic event keeping has been suspended.

The number of events in the run exceeded the maximum, 10000, that can be kept by the vis manager.

The number of events kept by the vis manager can be changed with

"/vis/scene/endOfEventAction accumulate <N>", where N is the

maximum number you wish to allow. N < 0 means "unlimited".

10000 events have been kept for refreshing and/or reviewing.

### === Deexcitation model UAtomDeexcitation is activated for 1 region:

DefaultRegionForTheWorld

### === G4UAtomicDeexcitation::InitialiseForNewRun()

### === PIXE model for hadrons: Empirical 1

### === PIXE model for e+-: Livermore 1

WARNING: G4VisManager::EndOfRun: Automatic event keeping has been suspended.

The number of events in the run exceeded the maximum, 10000, that can be kept by the vis manager.

The number of events kept by the vis manager can be changed with

"/vis/scene/endOfEventAction accumulate <N>", where N is the

maximum number you wish to allow. N < 0 means "unlimited".

10000 events have been kept for refreshing and/or reviewing.

### === Deexcitation model UAtomDeexcitation is activated for 1 region:

DefaultRegionForTheWorld

### === G4UAtomicDeexcitation::InitialiseForNewRun()

### === PIXE model for hadrons: Empirical 1

### === PIXE model for e+-: Livermore 1

WARNING: G4VisManager::EndOfRun: Automatic event keeping has been suspended.

The number of events in the run exceeded the maximum, 10000, that can be kept by the vis manager.

The number of events kept by the vis manager can be changed with

"/vis/scene/endOfEventAction accumulate <N>", where N is the

maximum number you wish to allow. N < 0 means "unlimited".

10000 events have been kept for refreshing and/or reviewing.



Z wyrazami szacunku
Michał Knap
<div>Hi All,<div>I'm trying to run my minigammacamera simulation but i have problem with that. It looks like i'm able to run simulation but after 4 runs everything stops and i get no results (no graphs, outputs...). Can anybody help me what is wrong?</div>
<div>Thanks in advance</div>
<div><br></div>
<div>
<div>mknap <at> mknap-HP:~$ cd Gate/</div>
<div>mknap <at> mknap-HP:~/Gate$ source your_file.bashrc&nbsp;</div>
<div>mknap <at> mknap-HP:~/Gate$ Gate --qt minigamma1pointsourceoncollimator1.mac</div>
<div>[G4]&nbsp;</div>
<div>[G4] *************************************************************</div>
<div>[G4] &nbsp;Geant4 version Name: geant4-09-06-patch-03 &nbsp; &nbsp;(14-March-2014)</div>
<div>[G4] &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Copyright : Geant4 Collaboration</div>
<div>[G4] &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Reference : NIM A 506 (2003), 250-303</div>
<div>[G4] &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; WWW : <a href="http://cern.ch/geant4">http://cern.ch/geant4</a>
</div>
<div>[G4] *************************************************************</div>
<div>[G4]&nbsp;</div>
<div>[Core-0] Initialization of geometry</div>
<div>[Core-0] Initialization of physics</div>
<div>[Physic-0] WARNING: manual physic lists are being deprecated.</div>
<div>Please, use physic list builder mechanism instead. Related documentation can be found at:</div>
<div><a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics</a></div>
<div>[Core-0] Initialization of actors</div>
<div>[G4] Available UI session types: [ Qt, GAG, tcsh, csh ]</div>
<div>[Core-0]&nbsp;</div>
<div>[Core-0] **********************************************************************</div>
<div>
[Core-0] &nbsp;GATE version name: gate_v7.0 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;</div>
<div>[Core-0] &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Copyright : OpenGATE Collaboration &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;</div>
<div>[Core-0] &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Reference : Phys. Med. Biol. 49 (2004) 4543-4561 &nbsp;</div>
<div>[Core-0] &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Reference : Phys. Med. Biol. 56 (2011) 881-901 &nbsp; &nbsp;</div>
<div>[Core-0] &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; WWW : <a href="http://www.opengatecollaboration.org">http://www.opengatecollaboration.org</a> &nbsp; &nbsp; &nbsp; &nbsp;</div>
<div>[Core-0] **********************************************************************</div>
<div>[Core-0]&nbsp;</div>
<div>[Core-0] You are using Geant4 version 9.6.3</div>
<div>[Core-0] Starting macro minigamma1pointsourceoncollimator1.mac</div>
<div>[Physic-0] The following Geant4's physic-list is enabled :emstandard</div>
<div>[Acquisition-0] &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;</div>
<div>[Acquisition-0] ============= Source initialization =============</div>
<div>[Acquisition-0] &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;</div>
<div>[Acquisition-0] ============= Acquisition starts! =============</div>
<div>[Acquisition-0] Simulation start time = 0 sec</div>
<div>[Acquisition-0] Simulation end time &nbsp; = 150 sec</div>
<div>[Acquisition-0] Simulation will have &nbsp;= 4 run(s)</div>
<div><br></div>
<div>----- HepJamesRandom engine status -----</div>
<div>&nbsp;Initial seed = 669708517</div>
<div>&nbsp;u[] = 0.313493 0.22101 0.720638 0.288275 0.209104 0.961876 0.0185378 0.767277 0.570899 0.11677 0.585697 0.361668 0.499346 0.969958 0.659357 0.470614 0.232287 0.851241 0.27455 0.788571 0.407255 0.205312 0.558045 0.841456 0.443543 0.0437512 0.20597 0.975022 0.180286 0.842097 0.240617 0.115375 0.0104213 0.86239 0.254429 0.284886 0.114014 0.250714 0.477909 0.527364 0.887455 0.402326 0.5341 0.418133 0.107406 0.124517 0.302133 0.489961 0.8011 0.598657 0.398494 0.285134 0.133646 0.956609 0.548981 0.0394724 0.830412 0.922722 0.527004 0.588913 0.129604 0.169863 0.043967 0.0808861 0.801898 0.583084 0.269808 0.84379 0.235689 0.208139 0.683603 0.275 0.411587 0.134052 0.253045 0.356203 0.629278 0.233236 0.444437 0.502942 0.77252 0.00816381 0.210178 0.938382 0.894515 0.511199 0.913346 0.907528 0.240269 0.448999 0.814368 0.13479 0.692496 0.707161 0.983838 0.703152 0.403158&nbsp;</div>
<div>&nbsp;c = 0.652903, cd = 0.456233, cm = 1</div>
<div>&nbsp;i97 = 93, u[i97] = 0.707161</div>
<div>&nbsp;j97 = 29, u[j97] = 0.842097</div>
<div>----------------------------------------</div>
<div>[Acquisition-0] Slice 0 from 0 to 37.5 s [slice=37.5 s], final stop at 150 s.</div>
<div>[Acquisition-0] Slice 1 from 37.5 to 75 s [slice=37.5 s], final stop at 150 s.</div>
<div>[Acquisition-0] Slice 2 from 75 to 112.5 s [slice=37.5 s], final stop at 150 s.</div>
<div>[Acquisition-0] Slice 3 from 112.5 to 150 s [slice=37.5 s], final stop at 150 s.</div>
<div>[Core-0] End of macro minigamma1pointsourceoncollimator1.mac</div>
<div><br></div>
<div>And after simulation i get this:</div>
<div>
<p><br></p>
<p>WARNING: The vis manager will keep up to 100 events.</p>
<p>  This may use a lot of memory.</p>
<p>  It may be changed with, e.g., "/vis/scene/endOfEventAction accumulate 10".</p>
<p>WARNING: The vis manager will keep up to 10000 events.</p>
<p>  This may use a lot of memory.</p>
<p>  It may be changed with, e.g., "/vis/scene/endOfEventAction accumulate 10".</p>
<p>GateDetectorConstruction::insertARFSD  entered</p>
<p>created a ARF Sensivitive Detector</p>
<p>created command /gate/systems/SPECThead/arf/setARFStage</p>
<p>Rmin/gate/Phantom/geometry/setRmin</p>
<p>Rmin/gate/movsource/geometry/setRmin</p>
<p>Confirming confinement to volume 'movsource_P_phys'...</p>
<p>**** Error: Volume does not exist ****</p>
<p>Ignoring confine condition</p>
<p>### ===  Deexcitation model UAtomDeexcitation is activated for 1 region:</p>
<p>DefaultRegionForTheWorld</p>
<p>### === G4UAtomicDeexcitation::InitialiseForNewRun()</p>
<p>### ===  PIXE model for hadrons: Empirical  1</p>
<p>### ===  PIXE model for e+-:     Livermore  1</p>
<p>### ===  Deexcitation model UAtomDeexcitation is activated for 1 region:</p>
<p>DefaultRegionForTheWorld</p>
<p>### === G4UAtomicDeexcitation::InitialiseForNewRun()</p>
<p>### ===  PIXE model for hadrons: Empirical  1</p>
<p>### ===  PIXE model for e+-:     Livermore  1</p>
<p>WARNING: G4VisManager::EndOfEvent: Automatic event keeping suspended.</p>
<p>  The number of events exceeds the maximum, 10000, that can be kept by the vis manager.</p>
<p>WARNING: G4VisManager::EndOfRun: Automatic event keeping has been suspended.</p>
<p>  The number of events in the run exceeded the maximum, 10000, that can be kept by the vis manager.</p>
<p>  The number of events kept by the vis manager can be changed with</p>
<p>  "/vis/scene/endOfEventAction accumulate &lt;N&gt;", where N is the</p>
<p>  maximum number you wish to allow.  N &lt; 0 means "unlimited".</p>
<p>10000 events have been kept for refreshing and/or reviewing.</p>
<p>### ===  Deexcitation model UAtomDeexcitation is activated for 1 region:</p>
<p>DefaultRegionForTheWorld</p>
<p>### === G4UAtomicDeexcitation::InitialiseForNewRun()</p>
<p>### ===  PIXE model for hadrons: Empirical  1</p>
<p>### ===  PIXE model for e+-:     Livermore  1</p>
<p>WARNING: G4VisManager::EndOfRun: Automatic event keeping has been suspended.</p>
<p>  The number of events in the run exceeded the maximum, 10000, that can be kept by the vis manager.</p>
<p>  The number of events kept by the vis manager can be changed with</p>
<p>  "/vis/scene/endOfEventAction accumulate &lt;N&gt;", where N is the</p>
<p>  maximum number you wish to allow.  N &lt; 0 means "unlimited".</p>
<p>10000 events have been kept for refreshing and/or reviewing.</p>
<p>### ===  Deexcitation model UAtomDeexcitation is activated for 1 region:</p>
<p>DefaultRegionForTheWorld</p>
<p>### === G4UAtomicDeexcitation::InitialiseForNewRun()</p>
<p>### ===  PIXE model for hadrons: Empirical  1</p>
<p>### ===  PIXE model for e+-:     Livermore  1</p>
<p>WARNING: G4VisManager::EndOfRun: Automatic event keeping has been suspended.</p>
<p>  The number of events in the run exceeded the maximum, 10000, that can be kept by the vis manager.</p>
<p>  The number of events kept by the vis manager can be changed with</p>
<p>  "/vis/scene/endOfEventAction accumulate &lt;N&gt;", where N is the</p>
<p>  maximum number you wish to allow.  N &lt; 0 means "unlimited".</p>
<p>10000 events have been kept for refreshing and/or reviewing.</p>
<p>### ===  Deexcitation model UAtomDeexcitation is activated for 1 region:</p>
<p>DefaultRegionForTheWorld</p>
<p>### === G4UAtomicDeexcitation::InitialiseForNewRun()</p>
<p>### ===  PIXE model for hadrons: Empirical  1</p>
<p>### ===  PIXE model for e+-:     Livermore  1</p>
<p>WARNING: G4VisManager::EndOfRun: Automatic event keeping has been suspended.</p>
<p>  The number of events in the run exceeded the maximum, 10000, that can be kept by the vis manager.</p>
<p>  The number of events kept by the vis manager can be changed with</p>
<p>  "/vis/scene/endOfEventAction accumulate &lt;N&gt;", where N is the</p>
<p>  maximum number you wish to allow.  N &lt; 0 means "unlimited".</p>
<p>10000 events have been kept for refreshing and/or reviewing.</p>
</div>
<div>
<div dir="ltr"><br></div>
<div dir="ltr"><br></div>
<div dir="ltr">Z wyrazami szacunku<br>Micha&#322; Knap</div>
</div>
</div>
</div>
Albert Hirtl | 2 Sep 13:45 2014
Picon

Radioactive decay with general ion source and new physics list

Dear Colleagues,

I have a question regarding the new physics list mechanism in GATE v7.0. 
If I understood it correctly I do not need to specify the various 
processes explicitly if I use, e.g.,

/gate/physics/addPhysicsList emstandard_opt3

However, if I run a simulation with the general ion source

/gate/source/addSource fluor18
/gate/source/fluor18/setActivity 500 becquerel
/gate/source/fluor18/gps/particle ion
/gate/source/fluor18/gps/ion 9 18 0 0
/gate/source/fluor18/gps/energytype Mono
/gate/source/fluor18/gps/monoenergy 0. MeV
/gate/source/fluor18/setForcedUnstableFlag true
/gate/source/fluor18/setForcedHalfLife 6586 s

and if I start the simulation with

/gate/application/setTimeSlice   1 s
/gate/application/setTimeStart   0 s
/gate/application/setTimeStop    1 s
/gate/application/startDAQ

I do not get any decaying particles. In order to get a signal I have to add

/gate/physics/addProcess RadioactiveDecay

So, isn't the advantage of the new mechanism, that I do not have to 
define the processes explicitly? I guess if I ran the simulation with

/gate/application/setTotalNumberOfPrimaries

everything would be fine, right?

Additionally, if I use

/gate/physics/addPhysicsList  QGSP_BERT_EMY

I do not get any decay products no matter what I do...

Any comment would be very much appreciated.

Cheers,
Albert

-- 
Medizinische Universität Wien
Universitätsklinik für Radiologie und Nuklearmedizin
Währinger Gürtel 18-20
1090 Wien
Austria

Tel.: +43 (0) 1 / 40400 55450

Web:
http://www.meduniwien.ac.at/user/albert.hirtl
http://www.meduniwien.ac.at/moccamed/

Attachment (albert_hirtl.vcf): text/x-vcard, 409 bytes
Dear Colleagues,

I have a question regarding the new physics list mechanism in GATE v7.0. 
If I understood it correctly I do not need to specify the various 
processes explicitly if I use, e.g.,

/gate/physics/addPhysicsList emstandard_opt3

However, if I run a simulation with the general ion source

/gate/source/addSource fluor18
/gate/source/fluor18/setActivity 500 becquerel
/gate/source/fluor18/gps/particle ion
/gate/source/fluor18/gps/ion 9 18 0 0
/gate/source/fluor18/gps/energytype Mono
/gate/source/fluor18/gps/monoenergy 0. MeV
/gate/source/fluor18/setForcedUnstableFlag true
/gate/source/fluor18/setForcedHalfLife 6586 s

and if I start the simulation with

/gate/application/setTimeSlice   1 s
/gate/application/setTimeStart   0 s
/gate/application/setTimeStop    1 s
/gate/application/startDAQ

I do not get any decaying particles. In order to get a signal I have to add

/gate/physics/addProcess RadioactiveDecay

So, isn't the advantage of the new mechanism, that I do not have to 
define the processes explicitly? I guess if I ran the simulation with

/gate/application/setTotalNumberOfPrimaries

everything would be fine, right?

Additionally, if I use

/gate/physics/addPhysicsList  QGSP_BERT_EMY

I do not get any decay products no matter what I do...

Any comment would be very much appreciated.

Cheers,
Albert

--

-- 
Medizinische Universität Wien
Universitätsklinik für Radiologie und Nuklearmedizin
Währinger Gürtel 18-20
1090 Wien
Austria

Tel.: +43 (0) 1 / 40400 55450

Web:
http://www.meduniwien.ac.at/user/albert.hirtl
http://www.meduniwien.ac.at/moccamed/


Gmane