Nada Fakhoury | 18 Oct 20:39 2014
Picon

Re: Dose actor calculations

Hello again,

this is to say that I have resolved my issue. It was simply a matter  
of the dose actors' measuring direction, in other words my Depth Dose  
graph was simply ploted in reverse. Oh well...

Nada

>
> Dear all,
>
> I am experiencing a weird behavior of the dose actor. I am simulating
> a gamma source pointing towards a water volume.
>
> I first tried acquiring a depth dose curve along the central axis, and
> got a distribution that didn't quite measure up to what I expected.
> (dose increasing with depth)
>
> See here:
> https://www.dropbox.com/s/hd6da9lhapn5cju/Screenshot%20from%202014-10-11%2017%3A40%3A14.png?dl=0
>
>
> When I then changed my actor's resolution to get a dose profile in
> various depths in the volume, the distribution in depth was the
> complete opposite of what the depth dose curve at first indicated.
> (dose decreasing with depth)
>
> See here: https://www.dropbox.com/s/e3610h1fhz5r8e6/profiles.png?dl=0
>
> The setup is the same in both cases, the *only* thing that changed was
(Continue reading)

maryam khazaee | 18 Oct 14:54 2014
Picon

EnergySpectrumActor output is not the same as the energy spectrum defined by user

Dear Gate users
I defined a Y-90  source wiith user defined energy histogram, but when i use EnergySpectrumActor to check the given spectrum the output root file shows a peak in 1 MeV. I can not understand where have i gone wrong .
Regards, Khazaee
<div><div dir="ltr">
<div class="gmail_default">Dear Gate users<br>
</div>
<div class="gmail_default">I defined a Y-90&nbsp; source wiith user defined energy histogram, but when i use EnergySpectrumActor to check the given spectrum the output root file shows a peak in 1 MeV. I can not understand where have i gone wrong .<br>
</div>
<div class="gmail_default">Regards, Khazaee<br>
</div>
</div></div>
Jose Carvajal | 18 Oct 02:51 2014
Picon

Issue with creation of sources and volumes

Hello colleagues!

I'm just entering this world of Monte Carlo simulations and am in front of a source geometry i'm not sure if it's possible to build.
I understand that for each source, a geometry is intended to be created. So, given that a background radiation is a source, my question is:

Is it possible to create, say, a phantom Jaszczak with the spheres, but INCLUDING a radiation background distributed inside the water?, i.e., create a volume (for the source) consisting of the cylinder without the volumes of the spheres...
I imagine that such task is beyond Gate 6.2. Am i wrong? I hope so...

Thank you in advance,

Jose.


Sorry if my english is poor.
<div><div dir="ltr"><div class="gmail_default">Hello colleagues!<br><br>I'm just entering this world of Monte Carlo simulations and am in front of a source geometry i'm not sure if it's possible to build. <br>I understand that for each source, a geometry is intended to be created. So, given that a background radiation is a source, my question is:<br><br>Is it possible to create, say, a phantom Jaszczak with the spheres, but INCLUDING a radiation background distributed inside the water?, i.e., create a volume (for the source) consisting of the cylinder without the volumes of the spheres... <br>I imagine that such task is beyond Gate 6.2. Am i wrong? I hope so...<br><br>Thank you in advance,<br><br>Jose.<br><br><br>Sorry if my english is poor.<br>
</div></div></div>
Nada Fakhoury | 17 Oct 11:51 2014
Picon

Dose actor calculations


Dear all,

I am experiencing a weird behavior of the dose actor. I am simulating  
a gamma source pointing towards a water volume.

I first tried acquiring a depth dose curve along the central axis, and  
got a distribution that didn't quite measure up to what I expected.  
(dose increasing with depth)

See here:  
https://www.dropbox.com/s/hd6da9lhapn5cju/Screenshot%20from%202014-10-11%2017%3A40%3A14.png?dl=0

When I then changed my actor's resolution to get a dose profile in  
various depths in the volume, the distribution in depth was the  
complete opposite of what the depth dose curve at first indicated.  
(dose decreasing with depth)

See here: https://www.dropbox.com/s/e3610h1fhz5r8e6/profiles.png?dl=0

The setup is the same in both cases, the *only* thing that changed was  
the actor's resolution and for the profiles the actor's position. (For  
the central axis depth dose distribution the actor was attached at the  
top of the volume.)

Does anyone have an idea of what may be wrong?

Thank you in advance,

Nada,

**Please ignore the dose values in the graphs, they were acquired with  
different primary events and energies, but the overall behavior  
remains the same in every case. The graphs are drafts.**


Ahmed Elmekawy | 15 Oct 20:00 2014
Picon

Re: problem with voxelized phantom (Mohsen Sadat shahabi)

Hi User,

your macro should read the header which is h33, I am not sure why your macro doesn't able to read the header.


Regards,
Ahmed

On Tue, Oct 14, 2014 at 3:52 AM, Said Kaddouch <saidkaddouch-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

Dear Ahmed

I want to use Zubal voxelized phantom in my simulation. I converted the Zubal data format to interfile using

(X)Medcon as follows :


Number of images [1]? 243

General header offset to binary data [0 bytes]? 0 (or 4096)

Image header offset to binary data [0 bytes]? 0 (or 4096)

Image header repeated before each image [No]? No

Swap the pixel bytes [No]? No

Same characteristics for all images [Yes]? Yes

ALL IMAGES

----------

Absolute offset in bytes [0]? 0

Image columns [0]? 128

Image rows [0]? 128

Pixel data type:

1 -> bit

2 -> Int8 3 -> Uint8

4 -> Int16 5 -> Uint16

6 -> Int32 7 -> Uint32

10 -> float 11 -> double

12 -> ascii

20 -> RGB

Your choice [4]? 5

after running my macro with virtual GATE6.2 the following messages appear and running procedure aborts.

'!ror: Could not open header file 'zubal_phantom.i33

[Core-0] Initialization of geometry

-------- EEEE ------- G4Exception-START -------- EEEE -------

*** G4Exception : GeomSolids0002

issued by : G4Box::G4Box()

Dimensions too small for Solid: hof_zubal_solid!

hX, hY, hZ = 0, 0, 0

*** Fatal Exception *** core dump ***

-------- EEEE -------- G4Exception-END --------- EEEE -------

Gate can not open the header file. what to do to solve this problem.

can you help me please?


2014-10-13 22:59 GMT+02:00 Ahmed Elmekawy <ahmedfelmekawy-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>:
Hi Mohsen,

Yes, you can use Xmedcon program to convert whatever you need, which mean dicom or analyze format image to interfile format, that mean " xxxx.dcm  or  xxxx.hdr and xxxx.img   to  xxxx.h33 and xxxx.i33" .

Use this link ( http://xmedcon.sourceforge.net/Main/Download ) to download the package but use Windows package not Mac iso package because Mac iso doesn't have viewer screen as I tried before may be it will work with you for Mac, after install Xmedcon with windows system, you can open the image and save as the image with interfile format and  you will get image with extension h33 and i33.


Best Regards,
Ahmed 

On Sun, Oct 12, 2014 at 8:49 PM, xcao <xcao-2luAYUEiU/6n7cex9QMx8g@public.gmane.org> wrote:
hello,mohsen
    
       You may use the software xmedcon to try, it can transfer xcat data to Gate。 
 
Shelly
xcao
 
Date: 2014-10-12 16:54
Subject: Gate-users Digest, Vol 101, Issue 12
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------------------------------
 
Message: 2
Date: Sun, 12 Oct 2014 10:45:04 +0100
Subject: [Gate-users] problem with voxelized phantom
Message-ID:
Content-Type: text/plain; charset="utf-8"
 
Hello Gate Users
I want to use Zubal phantom in gate and downloaded zubal .dat file from internet.
I converted this file to .hdr+ .img files using imagej software. I used this files for voxelized phantom
and it do not work.
Now i think maybe converting the .dat file to .h33 + .i33 files works. I searched whole internet an there is nothing about .i33 file.
Can anyone help me for converting .dat file to .i33 file?(i already added intrerfile_Tp pluging to imagej, but there is nothing about .i33 or .h33)
thanks in advance
mohsen
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<div>
<div dir="ltr">
<div>
<div>
<div>Hi User,<br><br>
</div>your macro should read the header which is h33, I am not sure why your macro doesn't able to read the header.<br>
</div>
<div><br></div>
<div><br></div>Regards,<br>
</div>Ahmed<br>
</div>
<div class="gmail_extra">
<br><div class="gmail_quote">On Tue, Oct 14, 2014 at 3:52 AM, Said Kaddouch <span dir="ltr">&lt;<a href="mailto:saidkaddouch@..." target="_blank">saidkaddouch@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">
<div dir="ltr">
<p lang="en-US">Dear Ahmed<br></p>
<p lang="en-US">I want to
use Zubal voxelized phantom in my simulation. I converted the Zubal data format to interfile using
</p>
<p lang="en-US">(X)Medcon
as follows :</p>
<p lang="en-US"><br></p>
<p lang="en-US">	Number
of images [1]? 243
</p>
<p lang="en-US">	General
header offset to binary data [0 bytes]? 0
 (or 4096)</p>
<p lang="en-US">	Image
  header offset to binary data [0 bytes]? 0
 (or 4096)</p>
<p lang="en-US">	Image
  header repeated before each image [No]? No
</p>
<p lang="en-US">	Swap
the pixel bytes [No]? No
</p>
<p lang="en-US">	Same
characteristics for all images [Yes]? Yes
</p>
<p lang="en-US">
</p>
<p lang="en-US">	ALL
IMAGES
</p>
<p lang="en-US">	----------
</p>
<p lang="en-US">	Absolute
offset in bytes [0]? 0
</p>
<p lang="en-US">	Image
columns [0]? 128
</p>
<p lang="en-US">	Image
rows    [0]? 128
</p>
<p lang="en-US">	Pixel
data type:
</p>
<p lang="en-US">
</p>
<p lang="en-US">		
 1  -&gt;  bit
</p>
<p lang="en-US">		
 2  -&gt;  Int8 		  3 -&gt; Uint8
</p>
<p lang="en-US">		
 4  -&gt;  Int16		  5 -&gt; Uint16
</p>
<p lang="en-US">		
 6  -&gt;  Int32		  7 -&gt; Uint32
</p>
<p lang="en-US">		
10  -&gt;  float		 11 -&gt; double
</p>
<p lang="en-US">		
12  -&gt;  ascii
</p>
<p lang="en-US">		
20  -&gt;  RGB
</p>
<p lang="en-US">
</p>
<p lang="en-US">	Your
choice [4]? 5
</p>
<p lang="en-US"> after
running my macro with virtual  GATE6.2  the following messages appear
and running procedure aborts.</p>

<p lang="en-US">
</p>
<p lang="en-US">
</p>
<p lang="en-US">'!ror:
Could not open header file 'zubal_phantom.i33
</p>
<p lang="en-US">[Core-0]
Initialization of geometry
</p>
<p lang="en-US">
</p>
<p lang="en-US">--------
EEEE ------- G4Exception-START -------- EEEE -------
</p>
<p lang="en-US">***
G4Exception : GeomSolids0002
</p>
<p lang="en-US">     
issued by : G4Box::G4Box()
</p>
<p lang="en-US">Dimensions
too small for Solid: hof_zubal_solid!
</p>
<p lang="en-US">     hX,
hY, hZ = 0, 0, 0
</p>
<p lang="en-US">***
Fatal Exception *** core dump ***
</p>
<p lang="en-US">--------
EEEE -------- G4Exception-END --------- EEEE -------
</p>
<p lang="en-US">
</p>
<p lang="en-US">
</p>

<p lang="en-US">Gate can
not open the header file. what to do to solve this problem.</p>
<p lang="en-US">can you help me please?<br></p>
</div>
<div class="HOEnZb"><div class="h5">
<div class="gmail_extra">
<br><div class="gmail_quote">2014-10-13 22:59 GMT+02:00 Ahmed Elmekawy <span dir="ltr">&lt;<a href="mailto:ahmedfelmekawy <at> gmail.com" target="_blank">ahmedfelmekawy@...</a>&gt;</span>:<br><blockquote class="gmail_quote">
<div dir="ltr">
<div>
<div>
<div>Hi Mohsen,<br><br>
</div>Yes, you can use Xmedcon program to convert whatever you need, which mean dicom or analyze format image to interfile format, that mean " xxxx.dcm&nbsp; <span>or</span>&nbsp; xxxx.hdr and xxxx.img &nbsp;<span> to&nbsp;</span> xxxx.h33 and xxxx.i33" .<br><br>
</div>Use this link ( <span><a href="http://xmedcon.sourceforge.net/Main/Download" target="_blank">http://xmedcon.sourceforge.net/Main/Download</a></span> ) to download the package but use Windows package not Mac iso package because Mac iso doesn't have viewer screen as I tried before may be it will work with you for Mac, after install Xmedcon with windows system, you can open the image and save as the image with interfile format and&nbsp; you will get image with extension h33 and i33.<br><br><br>
</div>Best Regards,<br>Ahmed&nbsp; <br>
</div>
<div><div>
<div class="gmail_extra">
<br><div class="gmail_quote">On Sun, Oct 12, 2014 at 8:49 PM, xcao <span dir="ltr">&lt;<a href="mailto:xcao@..." target="_blank">xcao@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">

<div>
<div>hello&#65292;mohsen</div>
<div>&nbsp;&nbsp;&nbsp;&nbsp;</div>
<div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;You&nbsp;may&nbsp;use the software 
xmedcon to try&#65292; it can&nbsp;transfer xcat data to 
Gate&#12290;<span>&nbsp;</span>
</div>
<div>
<span></span>&nbsp;</div>
<div><span>Shelly</span></div>
<div><span>xcao</span></div>
<div>&nbsp;</div>
<div>
<div>
<div>From:&nbsp;<a href="mailto:gate-users-request@...ollaboration.org" target="_blank">gate-users-request</a>
</div>
<div>Date:&nbsp;2014-10-12&nbsp;16:54</div>
<div>To:&nbsp;<a href="mailto:gate-users@...on.org" target="_blank">gate-users</a>
</div>
<div>Subject:&nbsp;Gate-users Digest, Vol 101, Issue 12</div>
</div>
</div>
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<div>than&nbsp;"Re:&nbsp;Contents&nbsp;of&nbsp;Gate-users&nbsp;digest..."</div>
<div>------------------------------</div>
<div>&nbsp;</div>
<div>Message:&nbsp;2</div>
<div>Date:&nbsp;Sun,&nbsp;12&nbsp;Oct&nbsp;2014&nbsp;10:45:04&nbsp;+0100</div>
<div>From:&nbsp;Mohsen&nbsp;Sadat&nbsp;shahabi&nbsp;&lt;<a href="mailto:s.mohsen_shahabi@..." target="_blank">s.mohsen_shahabi@...</a>&gt;</div>
<div>To:&nbsp;"<a href="mailto:gate-users@...n.org" target="_blank">gate-users@...</a>"</div>
<div>&lt;<a href="mailto:gate-users@..." target="_blank">gate-users@...</a>&gt;</div>
<div>Subject:&nbsp;[Gate-users]&nbsp;problem&nbsp;with&nbsp;voxelized&nbsp;phantom</div>
<div>Message-ID:</div>
<div>&lt;<a href="mailto:1413107104.80514.YahooMailNeo@....yahoo.com" target="_blank">1413107104.80514.YahooMailNeo@...ir2.yahoo.com</a>&gt;</div>
<div>Content-Type:&nbsp;text/plain;&nbsp;charset="utf-8"</div>
<div>&nbsp;</div>
<div>Hello&nbsp;Gate&nbsp;Users</div>
<div>I&nbsp;want&nbsp;to&nbsp;use&nbsp;Zubal&nbsp;phantom&nbsp;in&nbsp;gate&nbsp;and&nbsp;downloaded&nbsp;zubal&nbsp;.dat&nbsp;file&nbsp;from&nbsp;internet.</div>
<div>I&nbsp;converted&nbsp;this&nbsp;file&nbsp;to&nbsp;.hdr+&nbsp;.img&nbsp;files&nbsp;using&nbsp;imagej&nbsp;software.&nbsp;I&nbsp;used&nbsp;this&nbsp;files&nbsp;for&nbsp;voxelized&nbsp;phantom</div>
<div>and&nbsp;it&nbsp;do&nbsp;not&nbsp;work.</div>
<div>Now&nbsp;i&nbsp;think&nbsp;maybe&nbsp;converting&nbsp;the&nbsp;.dat&nbsp;file&nbsp;to&nbsp;.h33&nbsp;+&nbsp;.i33&nbsp;files&nbsp;works.&nbsp;I&nbsp;searched&nbsp;whole&nbsp;internet&nbsp;an&nbsp;there&nbsp;is&nbsp;nothing&nbsp;about&nbsp;.i33&nbsp;file.</div>
<div>Can&nbsp;anyone&nbsp;help&nbsp;me&nbsp;for&nbsp;converting&nbsp;.dat&nbsp;file&nbsp;to&nbsp;.i33&nbsp;file?(i&nbsp;already&nbsp;added&nbsp;intrerfile_Tp&nbsp;pluging&nbsp;to&nbsp;imagej,&nbsp;but&nbsp;there&nbsp;is&nbsp;nothing&nbsp;about&nbsp;.i33&nbsp;or&nbsp;.h33)</div>
<div>thanks&nbsp;in&nbsp;advance</div>
<div>mohsen</div>
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</blockquote>
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</div>
S. Saghamanesh | 15 Oct 18:45 2014
Picon

Re: GPS Bremsstrahlung spectra

The bremsstrahlung should be specified in the physics section by "/gate/physics/processes/bremsstrahlung/...". But I guess you mean you want to define a continuous spectrum (bremsstrahlung spectrum) for your source. So you can use of a "User" or "Arb" type of gps energy as below:

/gate/source/mysource/gps/particle gamma
/gate/source/
mysource/gps/energytype User
/gate/source/
mysource/gps/histname energy
/gate/source/
mysource/gps/emin 1.00 keV
/gate/source/
mysource/gps/emax 35.00 keV
/gate/source/
mysource/gps/histpoint 0.001  0.
/gate/source/
mysource/gps/histpoint 0.0015  0.
/gate/source/
mysource/gps/histpoint 0.0020  0.2776
.
.
.
/gate/source/Xtube/gps/histpoint 0.0350  12960

you should go on with completing all your user-defined spectrum histogram. you can refer to Gate benchmarks or examples (CT benchmark) as well as the Gate user guide (section: defining a source/defining energy type).

Good luck
Soman


On Wednesday, October 15, 2014 4:26 PM, Nada Fakhoury <nfachour-JAjqph6Yjy+tU/mMRLST0w@public.gmane.org> wrote:



Dear all,

I am quite new at using Gate, so I have many questions, but I will 
trouble you today with just the one.

I am trying to simulate a Linac beam, so as a first step I am trying 
to approach it with the gps commands.
So I am wondering, does Gate support the bremsstrahlung command?

I tried defining it as

/gate/source/mybeam/gps/particle gamma
/gate/source/mybeam/gps/ene/type Brem
/gate/source/mybeam/gps/ene/min 1 eV
/gate/source/mybeam/gps/ene/max 6 MeV

for starters, but I am getting a repeated error saying

*****EXPMIN=0. Choose different E's or Temp
*****EXPMAX=0. Choose different E's or Temp


I tried defining my source as done in the examples and the RT 
benchmark, but I get a dose distribution that seems way off... ( 
https://www.dropbox.com/s/hd6da9lhapn5cju/Screenshot%20from%202014-10-11%2017%3A40%3A14.png?dl=0
)


Thank you in advance,

Nada.




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<div><div>
<div dir="ltr"></div>
<div class="">The 
bremsstrahlung should be specified in the physics section by 
"/gate/physics/processes/bremsstrahlung/...". But I guess you mean you 
want to define a continuous spectrum (bremsstrahlung spectrum) for your 
source. So you can use of a "User" or "Arb" type of gps energy as below:</div>
<div class=""><br class="" clear="none"></div>
<div class="" dir="ltr">

</div>
<div class="">
<span class="">/gate/source/mysource/gps/particle
gamma<br class="" clear="none">
/gate/source/≤/span><span class=""><span class="">mysource</span>/gps/energytype User<br class="" clear="none">
/gate/source/≤/span><span class=""><span class="">mysource</span>/gps/histname energy<br class="" clear="none">
/gate/source/≤/span><span class=""><span class="">mysource</span>/gps/emin 1.00 keV<br class="" clear="none">
/gate/source/≤/span><span class=""><span class="">mysource</span>/gps/emax 35.00 keV<br class="" clear="none">
/gate/source/≤/span><span class=""><span class="">mysource</span>/gps/histpoint 0.001<span class="">&nbsp;
</span>0.<br class="" clear="none">
/gate/source/≤/span><span class=""><span class="">mysource</span>/gps/histpoint 0.0015<span class="">&nbsp;
</span>0.<br class="" clear="none">
/gate/source/≤/span><span class=""><span class="">mysource</span>/gps/histpoint 0.0020<span class="">&nbsp;
</span>0.2776<br class="" clear="none"></span><span class=""></span>
</div>
<div class=""><span class="">.</span></div>
<div class=""><span class="">.</span></div>
<div class=""><span class="">.<br class="" clear="none"></span></div>
<div class="" dir="ltr">

</div>
<div class=""><span class="">/gate/source/Xtube/gps/histpoint
0.0350<span class="">&nbsp; </span>12960<br class="" clear="none"></span></div>

<span class=""></span><div class="">
<br class="" clear="none"><span class=""></span>
</div>
<div class="" dir="ltr"><span class="">you
 should go on with completing all your user-defined spectrum histogram. 
you can refer to Gate benchmarks or examples (CT benchmark) as well as 
the Gate user guide (section: defining a source/defining energy type).</span></div>
<div class="" dir="ltr">
<br class="" clear="none"><span class=""></span>
</div>
<div class="" dir="ltr"><span class="">Good luck</span></div>
<span class="">Soman</span> <div class="qtdSeparateBR">
<br><br>
</div>
<div class="yahoo_quoted"> <div> <div> <div dir="ltr">  On Wednesday, October 15, 2014 4:26 PM, Nada Fakhoury &lt;nfachour@...&gt; wrote:<br> </div>  <br><br><div class="y_msg_container">
<br>Dear all,<br><br>I am quite new at using Gate, so I have many questions, but I will&nbsp; <br>trouble you today with just the one.<br><br>I am trying to simulate a Linac beam, so as a first step I am trying&nbsp; <br>to approach it with the gps commands.<br>So I am wondering, does Gate support the bremsstrahlung command?<br><br>I tried defining it as<br><br>/gate/source/mybeam/gps/particle gamma<br>/gate/source/mybeam/gps/ene/type Brem<br>/gate/source/mybeam/gps/ene/min 1 eV<br>/gate/source/mybeam/gps/ene/max 6 MeV<br><br>for starters, but I am getting a repeated error saying<br><br>*****EXPMIN=0. Choose different E's or Temp<br>*****EXPMAX=0. Choose different E's or Temp<br><br><br>I tried defining my source as done in the examples and the RT&nbsp; <br>benchmark, but I get a dose distribution that seems way off... (&nbsp; <br><a href="https://www.dropbox.com/s/hd6da9lhapn5cju/Screenshot%20from%202014-10-11%2017%3A40%3A14.png?dl=0" target="_blank">https://www.dropbox.com/s/hd6da9lhapn5cju/Screenshot%20from%202014-10-11%2017%3A40%3A14.png?dl=0 </a> <br>)<br><br><br>Thank you in advance,<br><br>Nada.<br><br><br><br><br>_______________________________________________<br>Gate-users mailing list<br><a ymailto="mailto:Gate-users@..." href="mailto:Gate-users@...tecollaboration.org">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><br><br>
</div>  </div> </div>  </div> </div></div>
zhangran | 15 Oct 17:28 2014
Picon

MHD File cannot be read

Dear Gate users,

    I met this problem when I tried to run the electron_radiotherapy example.

MetaImage: Read: Cannot open data file
GateMHDImage.cc (l.185): MHD File cannot be read: data/Rando.mhd

Does it ever happen to anyone else?

Thanks.

Ran
Nada Fakhoury | 15 Oct 14:55 2014
Picon

GPS Bremsstrahlung spectra


Dear all,

I am quite new at using Gate, so I have many questions, but I will  
trouble you today with just the one.

I am trying to simulate a Linac beam, so as a first step I am trying  
to approach it with the gps commands.
So I am wondering, does Gate support the bremsstrahlung command?

I tried defining it as

/gate/source/mybeam/gps/particle gamma
/gate/source/mybeam/gps/ene/type Brem
/gate/source/mybeam/gps/ene/min 1 eV
/gate/source/mybeam/gps/ene/max 6 MeV

for starters, but I am getting a repeated error saying

*****EXPMIN=0. Choose different E's or Temp
*****EXPMAX=0. Choose different E's or Temp

I tried defining my source as done in the examples and the RT  
benchmark, but I get a dose distribution that seems way off... ( 

https://www.dropbox.com/s/hd6da9lhapn5cju/Screenshot%20from%202014-10-11%2017%3A40%3A14.png?dl=0

)

Thank you in advance,

Nada.

jehangir khan | 15 Oct 13:18 2014
Picon

Gate simulation on multiprocessor using MPI

Hi,

we have built cluster machine (6nodes) and MPI is installed. It goes fine to run simulation on main machine using MPI. But it does not communicate to nodes.

As I did not install job splitter and job merge, Do I need to install job splitter and job merger even I have MPI.

is it possible to run GATE simulation on multiprocessor for using MPI?

Can anyone provide some more information or links inorder to run simulation on multi processor using MPI.

Best regards

Jehangir 

<div><div dir="ltr">
<div>Hi, <br>
</div>
<div dir="ltr">
<p>we
 have built cluster machine (6nodes) and MPI is installed. It goes fine to run simulation on main machine using MPI. But it does not communicate to nodes.</p>
<p>As I did not install job splitter and job merge, Do I need to install job splitter and job merger even I have MPI. <br></p>
<p>is it possible to run GATE simulation on multiprocessor for using MPI?</p>
<p> Can anyone provide some more information or links inorder to run simulation on multi processor using MPI. <br></p>
<p>Best regards <br></p>
<p>Jehangir&nbsp; </p>
</div>
</div></div>
Ana Margarida Mota | 15 Oct 13:02 2014
Picon

Gate material data base-soft tissue

Hello,

Does anyone could tell me what is the definition for material 'SoftTissue'  to add to the material txt file?

Thank you very much!

Regards
<div><div dir="ltr">Hello,<div><br></div>
<div>
<span>Does anyone could tell me what is the definition for material 'SoftTissue' &nbsp;to add to the material txt file?</span><br>
</div>
<div><span><br></span></div>
<div><span>Thank you very much!</span></div>
<div><span><br></span></div>
<div><span>Regards</span></div>
</div></div>
Grevillot Loic | 15 Oct 12:40 2014
Picon

Re: Can't run with 100 million particles

Of course not!

If you buy 2 times 10 apples or 1 time 20 apples you get in both cases 20 apples.

Reference to papers used for uncertainty calculations are available – please look at Gate reference papers!

Please use the list, other people may benefit of discussion and my contributions are on free time which is very limited at the moment…

 

Kind regards,

 

Loïc Grevillot

 

 

 

From: S. Saghamanesh [mailto:s.saghamanesh <at> yahoo.com]
Sent: Mittwoch, 15. Oktober 2014 12:34
To: Grevillot Loic
Subject: Re: [Gate-users] Can't run with 100 million particles

 

 

Thanks for your note. However, due to the linear operation of this addition, I'll have a greater uncertainty!

For example, I have two simulations with uncertainties of sigma1 = 0.7 (70%) and sigma2 = 0.6 (60%). After the addition, I'll have the total uncertainty of sqrt(sigma1^2 + sigma2^2) = 0.92 (92%). 

So I wanted to reduce my uncertainty by increasing my statistics (through several simulations), but ultimately I'd obtain a greater uncertainty. Am I right on this?

 

Best

Soman

 

On Monday, October 13, 2014 8:41 AM, Grevillot Loic <loic.grevillot <at> medaustron.at> wrote:

 

You can manually run 10 different simulations. Make sure to change output names for each simu and then make a simple addition.

 

Sincerely,

 

Loïc

 

 

 

From: S. Saghamanesh [mailto:s.saghamanesh <at> yahoo.com]
Sent: Samstag, 11. Oktober 2014 13:53
To: Grevillot Loic; gate-users <at> lists.opengatecollaboration.org
Subject: Re: [Gate-users] Can't run with 100 million particles

 

Dear Loïc,

 

I've tried to run my main macro file through the following command:

 "/control/loop myMain.mac mycounter 1 10 10"

which is supposed to run 10 simulations with 10 million particles with different seeds (by /gate/random/setEngineSeed auto). But It runs only the first 10 million particles and doesn't keep run the remains.

Do you have any idea what's wrong with this command? I guess it's the only way I can proceed with 100 million primaries without getting error.

 

Best regards

Soman

 

On Friday, October 3, 2014 9:10 AM, Grevillot Loic <loic.grevillot <at> medaustron.at> wrote:

 

Dear Soman,

 

You said you need to run 100 million primaries and artifacts appear after 10 million.

My suggestion is therefore to run 10 simulations of 10 million particles (fully equivalent to a single simu of 100 million). You just have to make sure the seeds are different for every simulation, which can be easily achieved using the following command:

/gate/random/setEngineSeed auto

 

Best,

Loïc

 

From: S. Saghamanesh [mailto:s.saghamanesh <at> yahoo.com]
Sent: Freitag, 3. Oktober 2014 07:30
To: Grevillot Loic
Subject: Re: [Gate-users] Can't run with 100 million particles

 

Hi,

 

Thanks a lot for your note. I use of splitting 1000 for my emitted photons but I still have unacceptable uncertainties, so I have to run with 100 million particles. Do you tell me if I run 10 simulations with 10 million particles, it would lessen the uncertainty? I guess it wouldn't, because I have uncertain results with a single simulation of 10 million particles.

 

Thanks in advance for your help

- Soman

 

 

On Wednesday, October 1, 2014 3:41 PM, Grevillot Loic <loic.grevillot <at> medaustron.at> wrote:

 

Dear Soman,

 

We noticed a similar simulation “artifact” when a too high number of particles was used. We also noticed that the effect is dependent on the particle type and simulation parameters (cut, step size).

We will try correcting the bug for the next release. In the meantime I advise you to run 10 simulations of 10 million particles.

 

Sincerely,

 

Loïc

 

 

 

From: gate-users-bounces <at> lists.opengatecollaboration.org [mailto:gate-users-bounces <at> lists.opengatecollaboration.org] On Behalf Of S. Saghamanesh
Sent: Mittwoch, 1. Oktober 2014 09:29
To: gate-users <at> lists.opengatecollaboration.org
Subject: [Gate-users] Can't run with 100 million particles

 

Hi,

 

Is there any limitation on the number of primary particles generated in Gate7.0 ? It seems running code with more than 10 million particles leads to false results. I need to run my code with 100 millions particles, but after checking (with a very simple example), I noticed that no more than 20 million particles would be generated.

 

Thanks for your comments.

- Soman

Disclaimer:
Please notice our E-Mail Disclaimer http://www.medaustron.at/email-disclaimer/  

 

 

Disclaimer:
Please notice our E-Mail Disclaimer http://www.medaustron.at/email-disclaimer/  

 

 

Disclaimer:
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Disclaimer:
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<div>
<div class="WordSection1">
<p class="MsoNormal"><span>Of course not!<p></p></span></p>
<p class="MsoNormal"><span>If you buy 2 times 10 apples or 1 time 20 apples you get in both cases 20 apples.<p></p></span></p>
<p class="MsoNormal"><span>Reference to papers used for uncertainty calculations are available &ndash; please look at Gate reference papers!<p></p></span></p>
<p class="MsoNormal"><span>Please use the list, other people may benefit of discussion and my contributions are on free time which is very limited at the moment&hellip;<p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span lang="DE">Kind regards,<p></p></span></p>
<p class="MsoNormal"><span lang="DE-AT"><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span lang="DE-AT">Lo&iuml;c Grevillot</span><span lang="DE-AT"><p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<div>
<div>
<p class="MsoNormal"><span>From:</span><span> S. Saghamanesh [mailto:s.saghamanesh <at> yahoo.com]
<br>Sent: Mittwoch, 15. Oktober 2014 12:34<br>To: Grevillot Loic<br>Subject: Re: [Gate-users] Can't run with 100 million particles<p></p></span></p>
</div>
</div>
<p class="MsoNormal"><p>&nbsp;</p></p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<div>
<p class="MsoNormal"><span>Thanks for your note. However, due to the linear operation of this addition, I'll have a greater uncertainty!<p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>For example, I have two simulations with uncertainties of sigma1 = 0.7 (70%) and sigma2 = 0.6 (60%). After the addition, I'll have
 the total uncertainty of sqrt(sigma1^2 + sigma2^2) = 0.92 (92%).&nbsp;<p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>So I wanted to reduce my uncertainty by increasing my statistics (through several simulations), but ultimately I'd obtain a greater
 uncertainty. Am I right on this?<p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
</div>
<div>
<p class="MsoNormal"><span>Best<p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>Soman<p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>On Monday, October 13, 2014 8:41 AM, Grevillot Loic &lt;<a href="mailto:loic.grevillot <at> medaustron.at">loic.grevillot <at> medaustron.at</a>&gt; wrote:</span><span><p></p></span></p>
</div>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>You can manually run 10 different simulations. Make sure to change output names for each simu and then make a simple addition.</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="DE">Sincerely,</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="DE-AT">&nbsp;</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="DE-AT">Lo&iuml;c</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>From:</span><span> S. Saghamanesh [<a href="mailto:s.saghamanesh <at> yahoo.com">mailto:s.saghamanesh <at> yahoo.com</a>]
<br>Sent: Samstag, 11. Oktober 2014 13:53<br>To: Grevillot Loic; <a href="mailto:gate-users <at> lists.opengatecollaboration.org">
gate-users <at> lists.opengatecollaboration.org</a><br>Subject: Re: [Gate-users] Can't run with 100 million particles</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;<p></p></span></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>Dear&nbsp;</span><span>Lo&iuml;c,</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>I've tried to run my main macro file through the following command:</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;"/control/loop myMain.mac mycounter 1 10 10"</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>which is supposed to run 10 simulations with 10 million particles with different seeds (by&nbsp;</span><span>/gate/random/setEngineSeed
 auto</span><span>). But It runs only the first 10 million particles and doesn't keep run the remains.</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>Do you have any idea what's wrong with this command? I guess it's the only way I can proceed with 100 million primaries without getting
 error.</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>Best regards</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>Soman</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>On Friday, October 3, 2014 9:10 AM, Grevillot Loic &lt;<a href="mailto:loic.grevillot <at> medaustron.at" target="_blank">loic.grevillot <at> medaustron.at</a>&gt;
 wrote:</span><span><p></p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;<p></p></span></p>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>Dear Soman,</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>You said you need to run 100 million primaries and artifacts appear after 10 million.</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>My suggestion is therefore to run 10 simulations of 10 million particles (fully equivalent to a single simu of 100 million). You just
 have to make sure the seeds are different for every simulation, which can be easily achieved using the following command:</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>/gate/random/setEngineSeed auto</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>Best,</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>Lo&iuml;c</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>From:</span><span> S. Saghamanesh [<a href="mailto:s.saghamanesh <at> yahoo.com" target="_blank">mailto:s.saghamanesh <at> yahoo.com</a>]
<br>Sent: Freitag, 3. Oktober 2014 07:30<br>To: Grevillot Loic<br>Subject: Re: [Gate-users] Can't run with 100 million particles</span><span><p></p></span></p>
</div>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;<p></p></span></p>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>Hi,</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>Thanks a lot for your note. I use of splitting 1000 for my emitted photons but I still have unacceptable uncertainties, so I have to
 run with 100 million particles. Do you tell me if I run 10 simulations with 10 million particles, it would lessen the uncertainty? I guess it wouldn't, because I have uncertain results with a single simulation of 10 million particles.</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>Thanks in advance for your help</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>- Soman</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>On Wednesday, October 1, 2014 3:41 PM, Grevillot Loic &lt;<a href="mailto:loic.grevillot <at> medaustron.at" target="_blank">loic.grevillot <at> medaustron.at</a>&gt;
 wrote:</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;<p></p></span></p>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>Dear Soman,</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>We noticed a similar simulation &ldquo;artifact&rdquo; when a too high number of particles was used. We also noticed that the effect is dependent
 on the particle type and simulation parameters (cut, step size).</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>We will try correcting the bug for the next release. In the meantime I advise you to run 10 simulations of 10 million particles.</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span lang="DE">Sincerely,</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span lang="DE-AT">&nbsp;</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span lang="DE-AT">Lo&iuml;c</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
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<p class="MsoNormal"><span>From:</span><span>
<a href="mailto:gate-users-bounces <at> lists.opengatecollaboration.org" target="_blank">
gate-users-bounces <at> lists.opengatecollaboration.org</a> [<a href="mailto:gate-users-bounces <at> lists.opengatecollaboration.org" target="_blank">mailto:gate-users-bounces <at> lists.opengatecollaboration.org</a>]
On Behalf Of S. Saghamanesh<br>Sent: Mittwoch, 1. Oktober 2014 09:29<br>To: <a href="mailto:gate-users <at> lists.opengatecollaboration.org" target="_blank">
gate-users <at> lists.opengatecollaboration.org</a><br>Subject: [Gate-users] Can't run with 100 million particles</span><span><p></p></span></p>
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<p class="MsoNormal"><span>Hi,</span><span><p></p></span></p>
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<p class="MsoNormal"><span>Is there any limitation on the number of primary particles generated in Gate7.0 ? It seems running code with more than 10 million particles
 leads to false results. I need to run my code with 100 millions particles, but after checking (with a very simple example), I noticed that no more than 20 million particles would be generated.</span><span><p></p></span></p>
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<p class="MsoNormal"><span>Thanks for your comments.</span><span><p></p></span></p>
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<p class="MsoNormal"><span>- Soman</span><span><p></p></span></p>
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Gmane