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None Information about the structure of the data for low energy silicon model.  by Ismail <Ismail>,   Nov 11, 00:11
Hello,

I'm interested in extending the model of low energy silicon model to silica and I'm wondering of someone understand the structure of the date for the model in the 4GLELOW data files.

None Re: Information about the structure of the data for low energy silicon model.  by Sebastien INCERTI <Sebastien INCERTI>,   Nov 11, 00:51
Re: None Information about the structure of the data for low energy silicon model. (Ismail)
Hello,

Please contact us if you want to discuss the possibility to extend Geant4 very low energy models to other materials.

Thank you,

Sebastien Incerti (incerti@cenbg.in2p3.fr)

Question How to model carbon ions using DNA physics?  by Ivan Konobeev <Ivan Konobeev>,   Jul 24, 05:43
Hello

Could you please help me. This question is probably very basic however I can't find the answer.

I'm using Geant4 v.10.04.p01 with Visual Studio 2017. I'm trying to model carbon ions (A = 12, Z = 6) in dnaphysics example (which attaches default DNA constructor to World region). To do that I made minor changes to dnaphysics.in macro file: I just replaced default particle which was 100 keV proton with 2.4 MeV carbon ion. These are the changes that I made to dnaphysics.in:

From:

  /tracking/verbose 0
  /gun/particle proton
  /gun/energy 100 keV
  /run/beamOn 2

Was changed to:

  /tracking/verbose 1
  /gun/particle ion
  /gun/ion 6 12
  /gun/energy 2400 keV
  /run/beamOn 10000000

Then I executed the program with:

RelWithDebInfo\dnaphysics dnaphysics.in

Output of the program:

*********************************************************************************************************
* G4Track Information:   Particle = C12,   Track ID = 1,   Parent ID = 0
*********************************************************************************************************

Step#    X(mm)    Y(mm)    Z(mm) KinE(MeV)  dE(MeV) StepLeng TrackLeng  NextVolume ProcName
    0        0        0        0       2.4        0        0         0       World initStep
    1 1.91e-08        0        0         0      2.4 1.91e-08  1.91e-08       World GenericIon_G4DNAIonisation

*********************************************************************************************************
* G4Track Information:   Particle = C12,   Track ID = 1,   Parent ID = 0
*********************************************************************************************************

Step#    X(mm)    Y(mm)    Z(mm) KinE(MeV)  dE(MeV) StepLeng TrackLeng  NextVolume ProcName
    0        0        0        0       2.4        0        0         0       World initStep
    1  9.1e-08        0        0         0      2.4  9.1e-08   9.1e-08       World GenericIon_G4DNAIonisation

So carbon ions with energy 2.4 MeV are immediately consumed by water medium having track length below 1 nanometer. I believe these results are incorrect. In G4EmDNAPhysics.cc file I saw commented instructions:

  genericIonsManager->GetIon("carbon");

  if ( particleName == "carbon" ) {
        ph->RegisterProcess(new G4DNAIonisation("carbon_G4DNAIonisation"), particle);
  }

Uncommenting those did't change anything. Also it is unclear from where the particle "carbon" can be "included" since there is no "carbon" particle in "geant4_10_04_p01\source\particles" directory.

So is it possible to use Geant4-DNA constructors to model carbon ions? How can I do that?

Thank you.

Question Negative energy deposit by e-_G4DNAIonisation process  by Ivan Konobeev <Ivan Konobeev>,   Jun 20, 07:15
Hello

Could you please help me.

I used "dnaphysics" example and replaced default primary particles (100 keV protons) with 1.3 MeV gammas in "dnaphysics.in" control file. No other changes to the project were made.

The problem is that "e-_G4DNAIonisation" process sometimes (rare but regulary) gives negative value of energy deposition which is returned by "step->GetTotalEnergyDeposit()" command in SteppingAction.cc file or can also be seen using "/tracking/verbose 1" in control file.

This is how it looks with "/tracking/verbose 1":

*********************************************************************************************************
* G4Track Information:   Particle = e-,   Track ID = 2,   Parent ID = 1
*********************************************************************************************************

Step#    X(mm)    Y(mm)    Z(mm) KinE(MeV)  dE(MeV) StepLeng TrackLeng  NextVolume ProcName
    0   0.0372        0        0      0.77        0        0         0       World initStep
    1   0.0374 4.01e-05 -3.47e-05      0.77 -0.000498  0.00013   0.00013       World e-_G4DNAIonisation
    2   0.0374 4.25e-05 -3.68e-05     0.769 1.34e-05 7.88e-06  0.000138       World e-_G4DNAIonisation
    3   0.0374 4.66e-05 -4.03e-05     0.769        0 1.33e-05  0.000151       World e-_G4DNAElastic
    4   0.0375 7.35e-05 -6.72e-05     0.769 1.08e-05 9.53e-05  0.000246       World e-_G4DNAIonisation
...

You can see here that -0.000498 MeV were deposited in "World" volume. This also happens to low-energy electrons (< 1 keV) that deposit (by module) energy that exceeds their kinetic energy.

For my study those negative energy depositions are very sufficient because they correspond to very large local dose depositions at nanoscale and cannot be neglected. For example, this 0.000498 MeV corresponds to about 80000 Gy in 10x10x10 nm voxel.

Could you please tell me:

Do those negative energy depositions correspond to some physical process? If so then how is it referred to in physics?

If they do not correspond to physical process then how should I interpret such results? Would it be correct to equate those negative energy depositions to zero energy depositions?

Thank you.

None Re: Negative energy deposit by e-_G4DNAIonisation process  by Sebastien INCERTI <Sebastien INCERTI>,   Jul 02, 03:41
Re: Question Negative energy deposit by e-_G4DNAIonisation process (Ivan Konobeev)
Thank you for reporting this issue caused by atomic deexcitation activation, a fix will be available in our next release.

Warning Bug in dnaphysics example  by Ivan Konobeev <Ivan Konobeev>,   Jun 15, 08:07
Hello

I would like to report a bug in

examples -> extended -> medical -> dna -> dnaphysics

example of Geant4 10.04.p01. I would appreciate if one of devs would confirm that it is a bug and reply to this message.

To reproduce this bug one should make these changes in "dnaphysics.in" control file:

/tracking/verbose 0 -> /tracking/verbose 1

/gun/particle proton -> /gun/particle e-

/gun/energy 100 keV -> /gun/energy 10 keV

Then run example with "dnaphysics.in" file as argument. For example:

Debug\dnaphysics dnaphysics.in

You will see that electrons with kinetic energy of EXACTLY 10 keV can only suffer elastic scattering and cannot ionise other electrons or deposit any energy in water medium at all. The only process that occurs is "e-_G4DNAElastic". If one changes energy of electrons to 9.9 keV or 10.1 keV this problem dissapears.

Activating physics with

RegisterPhysics(new G4EmDNAPhysics());

in PhysicsList instead of using mixed standard and DNA physics with G4EmDNAPhysicsActivator also solves the problem.

The source of the problem is likely in G4EmDNAPhysicsActivator who attaches two models for e-_G4DNAIonisation process: DNAEmfietzoglouIonisationModel (from 0 eV to 10 keV) and DNABornIonisationModel (from 10 keV to 1 MeV). So these models probably do not cover energy of exactly 10 keV so that e-_G4DNAIonisation process does not occur in simulation process at all.

This bug probably will not affect results of any simulations unless user sets energy of source to exactly 10 keV. But if he does he will obtain wrong results.

None Re: Bug in dnaphysics example  by Sebastien INCERTI <Sebastien INCERTI>,   Jun 18, 02:07
Re: Warning Bug in dnaphysics example (Ivan Konobeev)
Thank you Ivan for your report.

We will fix this in the coming weeks.

Best regards,

Sebastien

None Pdb file for pdb4dna  by João Júlio <João Júlio>,   02 Apr, 2018
Hi,

I've been trying to import a pdb file from a genomic sequence from a bacteria that i have generated myself using a software named Avogrado but when I try to load it on pdb4dna I get this message:

/PDB4DNA/det/loadPDB RecA.pdb Load PDB file : RecA.pdb.

G4Material WARNING: duplicate name of material Galactic PDBlib::load >> No header found !!!! **************** atomisticView(...) **************** Number of loaded chains = 0 Number of Atoms = 0 Number of Hydrogens = 0 Number of Carbons = 0 Number of Oxygens = 0 Number of Nitrogens = 0 Number of Sulfurs = 0 Number of Phosphorus = 0 Number of undifined atoms =0

-------- EEEE ------- G4Exception-START -------- EEEE -------
*** G4Exception : GeomSolids0002
      issued by : G4Box::G4Box()
Dimensions too small for Solid: Bounding!
     hX, hY, hZ = -inf, -inf, -inf
*** Fatal Exception *** core dump ***
-------- EEEE -------- G4Exception-END --------- EEEE -------

*** G4Exception: Aborting execution *** Abortado (imagem do núcleo gravada)

How can I fix this problem? Thanks

None Re: Pdb file for pdb4dna  by M. Hahn <M. Hahn>,   02 Apr, 2018
Re: None Pdb file for pdb4dna (João Júlio)
Hi,
its just a guess, but from the error message it seems that there are
problems with the volumes

"
> *** G4Exception : GeomSolids0002
>       issued by : G4Box::G4Box()
> Dimensions too small for Solid: Bounding!
"

Try to increase the dimensions of the "Box" this error message refers to.

Best regards
Marc


>
> *** Discussion title: DNA/Very Low Energy
>
> Hi,
>
> I've been trying to import a pdb file from a genomic sequence from a
> bacteria that i have generated myself using a software named Avogrado
> but when I try to load it on pdb4dna I get this message:
>
> /PDB4DNA/det/loadPDB RecA.pdb Load PDB file : RecA.pdb.
>
> G4Material WARNING: duplicate name of material Galactic PDBlib::load >>
> No header found !!!! **************** atomisticView(...)
> **************** Number of loaded chains = 0 Number of Atoms = 0 Number
> of Hydrogens = 0 Number of Carbons = 0 Number of Oxygens = 0 Number of
> Nitrogens = 0 Number of Sulfurs = 0 Number of Phosphorus = 0 Number of
> undifined atoms =0
>
> -------- EEEE ------- G4Exception-START -------- EEEE -------
> *** G4Exception : GeomSolids0002
>       issued by : G4Box::G4Box()
> Dimensions too small for Solid: Bounding!
>      hX, hY, hZ = -inf, -inf, -inf
> *** Fatal Exception *** core dump ***
> -------- EEEE -------- G4Exception-END --------- EEEE -------
>
> *** G4Exception: Aborting execution *** Abortado (imagem do núcleo
> gravada)
>
> How can I fix this problem? Thanks
>
> -------------------------------------------------------------
> Visit this GEANT4 at hypernews.slac.stanford.edu message (to reply or
> unsubscribe) at:
> http://hypernews.slac.stanford.edu/HyperNews/geant4/get/dnaverylowe/28.html
>
None Pdb file for pdb4dna  by João Júlio <João Júlio>,   02 Apr, 2018
Hi,

I've been trying to import a pdb file from a genomic sequence from a bacteria that i have generated myself using a software named Avogrado but when I try to load it on pdb4dna I get this message:

/PDB4DNA/det/loadPDB RecA.pdb Load PDB file : RecA.pdb.

G4Material WARNING: duplicate name of material Galactic PDBlib::load >> No header found !!!! **************** atomisticView(...) **************** Number of loaded chains = 0 Number of Atoms = 0 Number of Hydrogens = 0 Number of Carbons = 0 Number of Oxygens = 0 Number of Nitrogens = 0 Number of Sulfurs = 0 Number of Phosphorus = 0 Number of undifined atoms =0

-------- EEEE ------- G4Exception-START -------- EEEE -------
*** G4Exception : GeomSolids0002
      issued by : G4Box::G4Box()
Dimensions too small for Solid: Bounding!
     hX, hY, hZ = -inf, -inf, -inf
*** Fatal Exception *** core dump ***
-------- EEEE -------- G4Exception-END --------- EEEE -------

*** G4Exception: Aborting execution *** Abortado (imagem do núcleo gravada)

How can I fix this problem? Thanks

None Simulations with a CCD -   by Joao Miguel Da Rocha <Joao Miguel Da Rocha>,   14 Mar, 2018
Dear Geant4 collaboration,

I am producing a simulation ( with other people) of our detector, a CCD. Our CCD in Geant4 is simply 3 volumes, Two dead layers (on the top and bottom of the CCD) and a sensitive part. The two dead layers are 1um thick each, and the sensitive part is 673um thick.

Our goal is to get for a Dark Matter experiment, to simulate our background coming from contamination. Our energy range is 50 eV to few MeV electron-equivalent .

We use the 10.2.2 version of G4.

To test our physics list we simulate low energies electrons ( 10 keV) going through a 2 µm silicon cube ( like the ones of the MicroElectronics paper : https://www.sciencedirect.com/science/article/pii/S0168583X12004314).

So we have 4 different configurations:

-Livermore with the Urban Model

-Livermore with the Goudsmit Saunderson Model

-Livermore with the Low Energy Wentzel Model

-MicroElectronics

This 4 configuration for the projected range ( the sum of the length of the projection of the steps of an electron trajectory on its initial direction axis ( Z in our case) gives us different results, apart from Goudsmit and Urban models that gives almost same.

I attach one of my plots showing the difference between the MicroElectronics and Livermore with UrbanModel.

I am thus looking for some point of view of expert from the Geant4 collaboration. Which configuration should be the most accurate in our case, taking into account all the latest development ?

looking forward to hearing from you, Thanks!

João

   Attachment:
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2018/03/14/07.03-14729-ZLowMicrovsUrban10keV.pdf

Question Tracking hadrons below 1kev  by Helga Holmestad <Helga Holmestad>,   29 Nov, 2017
Hi I want to track hadrons at very low energy. I have tried to use the electromagnetic single scattering list, but it always seems like there is a cutoff at 1keV. When the particle reaches this energy it looses all its energy in one step. Is it possible to track hadrons to such low energy at all?

Question Re: Tracking hadrons below 1kev  by Helga Holmestad <Helga Holmestad>,   29 Nov, 2017
Re: Question Tracking hadrons below 1kev (Helga Holmestad)
I looked deeper into this problem. I that a minimum kinetic energy is set for all particles, and for hadrons and muons this is set to 1keV. This energy can be changes with the command /process/em/lowestMuHadEnergy 10 eV. However, I am suprised that none of the physics list for low energy does this? Is there a reason for that?

None Electrons below 1keV  by Christopher Walker <Christopher Walker>,   29 Nov, 2017
Hello,
   I am using  geant4-10-02-patch-02 on Ubuntu.

I hope to track electrons down to ~10eV (or even lower). I am using parts of the microelectronics example in association with example B2a (for a sensitive detector). I find that the hits are never below 1 keV. I came across this website which suggests a possible causes and solutions:

https://twiki.cern.ch/twiki/bin/view/Geant4/LoweAtomicDeexcitation

However, the suggested options such as putting this line:
 G4ProductionCutsTable::GetProductionCutsTable()->SetEnergyRange(250*eV, 1*GeV);

in the SetCuts() method of the PhysicsList did not solve the problem.

Also this UI command did not solve it: /process/em/lowestElectronEnergy 10 eV

Using this UI command /cuts/setLowEdge 250 eV

I get the following output: illegal application state -- command refused

Does anyone have any further suggestions ?

Thanks Chris

None Re: Electrons below 1keV  by Christopher Walker <Christopher Walker>,   30 Nov, 2017
Re: None Electrons below 1keV (Christopher Walker)
Following on from the similar thread by Helga Holmestad (also posted recently) in this forum category, I tried: /process/em/lowestElectronEnergy 10 eV

The UI command was accepted, but I still do not detect electrons with energy less than about 1 keV. I have also looked through the Geant4-DNA examples and so far found nothing in the code which would cause a sensitive detector to detect electrons at a lower energy.

Thanks Chris

None Re: Electrons below 1keV  by Christopher Walker <Christopher Walker>,   01 Dec, 2017
Re: None Re: Electrons below 1keV (Christopher Walker)
In case anyone is following this thread, I find that the command:
 /process/em/lowestElectronEnergy 10 eV

works in the example TestEm5, but doesn't work in my code which consists of a mixture of the B2a example code and the microelectronics example PhysicsList.

I am now trying to determine what might be the cause, but if anyone has an idea, please let me know !

Thanks Chris

Note Re: Electrons below 1keV  by Helga Holmestad <Helga Holmestad>,   01 Dec, 2017
Re: None Re: Electrons below 1keV (Christopher Walker)
If you show me your inputcode I can take a look

None Re: Electrons below 1keV  by Christopher Walker <Christopher Walker>,   01 Dec, 2017
Re: Note Re: Electrons below 1keV (Helga Holmestad)
Dear Helga,
    Thanks very much for taking a look. I'm afraid I am about to leave work and won't be back at work again until Wednesday next week. However, I will keep a check on my emails and on the forum. However, if I have forgotten a file, then I'm afraid I will have to upload it next week.
Thank you again.
Best Wishes
Chris

   Attachment:
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.23-93958-B2ActionInitialization.cc
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.23-32479-2aDetectorConstruction.cc
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.23-51797-B2aDetectorMessenger.cc
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.23-31341-B2EventAction.cc
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.23-73932-PrimaryGeneratorAction.cc
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.23-38968-B2RunAction.cc
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.24-86365-B2TrackerHit.cc
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.24-14146-B2TrackerSD.cc
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.24-87809-G4ElectronCapture.cc
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.24-94283-PhysicsList.cc
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.24-3159-exampleB2a.cc
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.25-2247-B2ActionInitialization.hh
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.25-62963-2aDetectorConstruction.hh
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.25-98265-B2aDetectorMessenger.hh
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.26-68970-B2EventAction.hh
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.26-62986-PrimaryGeneratorAction.hh
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.26-5628-B2RunAction.hh
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.26-29484-B2TrackerHit.hh
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.26-79381-B2TrackerSD.hh
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.26-75877-G4ElectronCapture.hh
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/12/01/07.27-47008-PhysicsList.hh

Note Re: Electrons below 1keV  by Helga Holmestad <Helga Holmestad>,   01 Dec, 2017
Re: None Re: Electrons below 1keV (Christopher Walker)
Can you also send the inputfile, that is the .mac file where you write the command to set the lower energy limit

None Re: Electrons below 1keV  by Christopher Walker <Christopher Walker>,   02 Dec, 2017
Re: Note Re: Electrons below 1keV (Helga Holmestad)
Dear Helga,
   My .mac file is below. Please remember that I compiled against geant4.10.02.p02 
The /cuts/setLowEdge command only works before the /run/initialize, but neither this command or the later /process/em command seem to have an effect on the lowest energy that I detect.
Best Wishes
Chris

# Macro file for example B2
# 
# Can be run in batch, without graphic
# or interactively: Idle> /control/execute run1.mac
#
# Change the default number of workers (in multi-threading mode) 
#/run/numberOfWorkers 4
#
# Initialize kernel
/cuts/setLowEdge 250 eV

/run/initialize

#
# Default kinematics: 
# proton 3 GeV in direction (0.,0.,1.)
# 1 event with tracking/verbose
#
#/tracking/verbose 1
#/run/beamOn 1
#
# 1 event with printing hits
#
/tracking/verbose 0

/hits/verbose 2

#/run/beamOn 1

#
# set target and chamber material
#
#/B2/det/setTargetMaterial G4_WATER
#/B2/det/setChamberMaterial G4_Ar
#/run/beamOn 3
# 
# set a magnetic field and max allowed step length
# 3 event with printing hits
#
#/globalField/verbose 1
#/globalField/setValue 0.2 0 0 tesla
#/B2/det/stepMax 1.0 mm
#/gun/energy 0.3 GeV
#/run/beamOn 3
#
# electron 300 MeV in the direction (0.,0.,1.)
# 3 event with detailed printing
#
/process/em/lowestElectronEnergy 10 eV

/gun/position 0. 0. -100. um

/particle/select e-

/gun/energy 2 keV

/run/beamOn 100

None Re: Electrons below 1keV  by Christopher Walker <Christopher Walker>,   02 Dec, 2017
Re: None Re: Electrons below 1keV (Christopher Walker)
Further to my last message, I have been investigating a bit more.

The /process/em command to set the lowest electron energy is controlled by the class G4EmParameters. I see that this class is used by a number of other Physics Model/List classes, but not the ones for the Microelectronics Physics example. I guess this is the reason why I cannot change the lowest electron energy using the /process/em command.

I will look into the Physics classes that the Microelectonics model uses to see if the model can be "simply" modified to allow use of sensitive detectors at low energies. Evidently the model generates electrons at low energies...

Best Wishes Chris

Idea Re: Electrons below 1keV  by Helga Holmestad <Helga Holmestad>,   05 Dec, 2017
Re: None Re: Electrons below 1keV (Christopher Walker)
Hi I tried using the physics list from your code. And I am able to track particles down to whatever low value I set in the inputfile. In order to actully see them I had to set the defaultCutValue really small. You can try 0.01nm and see if you see the low energy electronds then.

None Re: Electrons below 1keV  by Christopher Walker <Christopher Walker>,   06 Dec, 2017
Re: Idea Re: Electrons below 1keV (Helga Holmestad)
Dear Helga,
    Thankyou for your efforts. I can also see electrons down to very low energy, but only by switching on verbose settings. 
I have also managed to create a root file by outputting tracking events using the AnalysisManager class. 
However, what I would really like to do is to use a sensitive detector and detect the low energy electrons in such a detector. Did you manage to do this? 
My detector still only sees electrons above 1 keV (I did as you suggested and changed the SetCuts value to 0.01nm).

Best Wishes Chris

Question Re: Electrons below 1keV  by Michael H. Kelsey <Michael H. Kelsey>,   06 Dec, 2017
Re: None Re: Electrons below 1keV (Christopher Walker)
On Wed, 06 Dec 2017 12:15:36 GMT, Christopher Walker wrote:
> Thank you for your efforts. I can also see electrons down to very low energy, but only by switching on verbose settings. 
> I have also managed to create a root file by outputting tracking events using the AnalysisManager class. 
> However, what I would really like to do is to use a sensitive detector and detect the low energy electrons in such a detector. Did you manage to do this? 
> My detector still only sees electrons above 1 keV (I did as you suggested and changed the SetCuts value to 0.01nm).

Sorry to jump in late on this. If you can see the low energy electrons in the tracking verbose output, then your sensitive detector must be able to see them as well. The SD is passed every step of every track, just as the verbose output sees it. Is there a chance that your SD includes a cut on either energy or particle type? Have you put in at the very first line of ProcessHits a simple cout statement to print the particle name and energy?

  -- Michael Kelsey

None Re: Electrons below 1keV  by Christopher Walker <Christopher Walker>,   10 Dec, 2017
Re: Question Re: Electrons below 1keV (Michael H. Kelsey)
Hi Michael and Helga,
    thanks for your help on this. I had been thinking that it was a problem with the PhysicsList, so I replaced the Microelectronics example PhysicsList with another and then I started to detect electrons below 1 keV. Then I saw your messages and I realised that it shouldn't be anything to do with the PhysicsList, so I put the original PhysicsList back and I still see the low energy electrons. Hence I am somewhat mystified as to what the problem was before.
   At any rate, I seem to have made some progress over the weekend, but now I must return to do some experimental work, so I my Geant4 efforts will have to be cut back for a little while.

Thank you again. Chris

Note Re: Electrons below 1keV  by Helga Holmestad <Helga Holmestad>,   06 Dec, 2017
Re: None Re: Electrons below 1keV (Christopher Walker)
Hi When I tried to run your program it ended with segfault after a few steps, therefore I tested by replacing the physics list in a small test program I have. In my sensitive detector I see the low energy particles.

Question PhysicsList for Svalue  by ebrahim <ebrahim>,   12 Nov, 2017
Dear all Users

I want to adapt Svalue example for the situation that there is Nanoparticles is inside the Absorber volume, so I need to change physicsList , I need corresponding DNA physics in the Absorber and Livermore physics for the nanoparticle as my region which is inside Absorber ,the default physics is based on Modular I want to know How can do it with Modular method ,
Question G4EmDNAPhysicsActivator not working for ions  by Batom <Batom>,   15 Sep, 2017
Dear users,

In dnaphysics example, G4EmDNAPhysicsActivator not working for ions (i.e., carbon ion). Has anyone tried it?

Best, Batom.

Question Ion particles in svalue example  by Kirstie Caravani <Kirstie Caravani>,   29 Aug, 2017
Hi,

I am very new to using Geant4, and I was trying to simulate Ac 225 and its decay chain in the svalue example. I know the svalue example is working as I was able to run the default e- particle 300.00eV and the svalue was calculated as expected. However with the following macro:

/gun/particle ion
/gun/ion 89 225
/run/beamOn 1000

The run summary shows 0eV energy deposited and 0Gy/Bq.s as the S value. I even tried a larger sphere but had the same results. What would I need to change in the original files (possibly the physics list I guess) to be able to simulate ions (not only Ac 225, but of course others used in nuclear medicine)?

Thanks,
Kirstie.
None Re: Ion particles in svalue example  by Sebastien INCERTI <Sebastien INCERTI>,   30 Aug, 2017
Re: Question Ion particles in svalue example (Kirstie Caravani)
Hello Kirstie,

Yes exactly, you would need to adapt the physics list (other than Geant4-DNA) to your needs (EM physics, rad. decay...).

Best regards,

Sebastien

Question Re: Ion particles in svalue example  by Kirstie Caravani <Kirstie Caravani>,   30 Aug, 2017
Re: None Re: Ion particles in svalue example (Sebastien INCERTI)
Hello Sebastien,

Thank you very much for your response. I have tried adapting the physics lists from microbeam and rdecay01 into that of svalue, and it will now calculate the energy deposited (it didn't previously) but still shows 0 for the S value.

>The run is 1000 Ac225 of 300.00 eV through a sphere of radius 2.88 cm of G4_WATER (density: 1.00 g/cm3 )
>Total Energy deposited = 28.639 MeV +- 896.267 keV
>S value = 0.000 Gy/Bq.s +- 0.000 Gy/Bq.s
>Track length of primary track = 18.771 nm +- 0.000 fm
> Projected range = -68.380 um +- 1.299 cm
>Nb of steps of primary track = 2.00 +- 0.00
>Step size = 9.386 nm +- 0.000 fm

I realise I probably have more than necessary as I was hoping for a result and to tidy the code afterwards.
Could you or someone else please have a look at my physics list and perhaps point me in the right direction? Thank you.

Attachment:
http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/08/30/06.34-50255-PhysicsList.cc

Kind regards,
Kirstie.
Question G4DNA Carbon Ions  by Nicholas Henthorn <Nicholas Henthorn>,   28 Jul, 2017
Hi All,

I’m using Geant4-DNA (v10.2 patch-01) to simulate the transport of Carbon-12(6+) ions across a water volume (1 g/cm3). With default cut value set to 1 nm. Energy range of the production cuts table is set between 1 eV and 10 GeV.

When calculating the primary ion LET I’ve noticed what looks to be some possibly odd behaviour. Between 1191 MeV and 1192 MeV there seems to be a discontinuity in the LET (each point is the average from 5E+5 primaries).

(Graph is attached)

I’ve set up a water box of side length 10um. As the Carbon enters the volume (first step in volume) its position and kinetic energy are recorded. When the Carbon leaves the volume (last step in volume) its position and kinetic energy are recorded. I’m calculating the LET as this change in energy divided by the straight-line length connecting the first and last step.

All secondary e- are killed through the stacking action (fKill).

I’m defining the Carbon primary through the GPS, e.g.: /gps/position 0 0 -5.1 um /gps/direction 0 0 1 /gps/particle GenericIon /gps/ion 6 12 6 /gps/energy 1100 MeV

Has anyone else seen this? Or does anyone know what’s causing this?

Any advice would be greatly appreciated. Thanks,

Nick

   Attachment:
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/07/28/02.01-41674-LET.png

None Re: G4DNA Carbon Ions  by Ziad Francis <Ziad Francis>,   28 Jul, 2017
Re: Question G4DNA Carbon Ions (Nicholas Henthorn)
Dear Nicolas,

please describe further about your physicslist, are you using any other processes for ions or only G4DNAIonisation process (a copy of the code would help).

Ziad

None Re: G4DNA Carbon Ions  by Nicholas Henthorn <Nicholas Henthorn>,   28 Jul, 2017
Re: None Re: G4DNA Carbon Ions (Ziad Francis)
Dear Ziad,

I'm building the default G4 DNA physics list, without defining other processes:

#include "PhysicsList.hh"
#include "G4SystemOfUnits.hh"
#include "G4EmDNAPhysics.hh"
#include "G4EmStandardPhysics.hh"

PhysicsList::PhysicsList()
: G4VModularPhysicsList()
{
    SetDefaultCutValue(1.0*nm);
    SetVerboseLevel(0);
    RegisterPhysics(new G4EmDNAPhysics());
    //RegisterPhysics(new G4EmStandardPhysics());
    G4ProductionCutsTable::GetProductionCutsTable()->SetEnergyRange(1*eV, 10*GeV);
}

PhysicsList::~PhysicsList() { }

Best,

Nick

None Re: G4DNA Carbon Ions  by Ziad Francis <Ziad Francis>,   28 Jul, 2017
Re: None Re: G4DNA Carbon Ions (Nicholas Henthorn)
Dear Nicholas,

after verifying the cross sections nothing comes out meaning all seems smooth. However, the issue is most probably caused by the switch between normal and relativistic formulas in the G4DNARuddIonisationExtendedModel Class, and specifically in functions RejectionFunction and ProposedSampledEnergy, the value at which we use relativistic formulas is around ~100 MeV/amu and for carbon ions it corresponds to ~ 1200 MeV.

So if you definitely need to eliminate this you'll have to decrease all the energy limits down to let's say zero (in the file G4DNARuddIonisationExtendedModel.cc) and therefore you'll have only relativistic formulas in action, however since we never tried this you will have to validate what you obtain before using it, to make sure the proper energy loss is still there.

Anyway we will be addressing this issue for our next release, but until then you may look for the magic numbers ((tau/MeV)<5.447761194e-2) and ((k/MeV)/(particle->GetPDGMass()/MeV) <= 0.1 ) and change this into ((tau/MeV)<0) and ((k/MeV)/(particle->GetPDGMass()/MeV) <= 0 ), recompile Geant4 and your application and check the rest out.

Hope this helps a bit Ziad

None Re: G4DNA Carbon Ions  by Nicholas Henthorn <Nicholas Henthorn>,   28 Jul, 2017
Re: None Re: G4DNA Carbon Ions (Ziad Francis)
Thanks for your help Ziad.

Following your advice i get the attached, which certainly removes the discontinuity

Nick

   Attachment:
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2017/07/28/11.06-10268-LET.png

Question What is coupledTransportation?  by Huagang Yan <Huagang Yan>,   24 Jan, 2017
When I checked which processes deposit high energy in a hit, I got coupledtransportation, msc, and eioni, which deposits more than 1.4 keV in water in single hits.

What is coupledtransportation? By the way, I wonder how such an amount of energy can be deposited in a water molecule? what will the molecule do with this energy next? break apart with fast parts?

Is there any reference I can read in order to understand the Geant4-DNA processes?

Any help is highly appreciated.

Huagang.

Question Is this a problem in microdosimetry?  by Huagang Yan <Huagang Yan>,   07 Nov, 2016
For region Target, the cut is 1 nm, but corresponding energy limit should be far less than 990 eV. How come the energy threshold is 990 eV? Is this a problem?

   Attachment:
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2016/11/07/08.19-74480-snapshot.jpg

Question maximum energy transfer - 60.18 eV ?  by Batom <Batom>,   23 Sep, 2016
Hi All,

Please explain that why maximum energy transfer is only 60.18 eV when use G4EmDNAPhysics process? That maximum value did not change for different incident particles and secondary electrons.

thank you.

Feedback Re: maximum energy transfer - 60.18 eV ?  by Ziad Francis <Ziad Francis>,   28 Sep, 2016
Re: Question maximum energy transfer - 60.18 eV ? (Batom)
Dear Batom,

I reverified the G4DNARuddIonisationExtendedModel class no issues were found there. I ran simulations with 600 MeV Iron Ions and both the stopping power and the secondary electrons spectra are good (maximum electron energy around ~22 keV). The maximum secondary energies are obtained according to the formulas presented in Plante and Cuccinotta paper (New Journal of Physics 10, 125020, 2008).

Hope this helps.

Ziad

None Re: maximum energy transfer - 60.18 eV ?  by Batom <Batom>,   28 Sep, 2016
Re: Feedback Re: maximum energy transfer - 60.18 eV ? (Ziad Francis)
Dear Ziad,

Thank you for your reply! I also obtained ~ 22-23 keV of electrons maximum kinetic energy for 600 MeV/u Iron ions. But, 60.18 eV - is maximum value of energy deposition (energy transfer). This value did not change (or increase) when different kinetic energies of incident ions (1000 MeV/u Iron ion, or 500 MeV/u Carbon and/or 50 MeV protons). Have a cut-value for energy deposition in the G4EmDNAPhysics constructor?

Thank you for your helping to understand it! Batom.

Feedback Re: maximum energy transfer - 60.18 eV ?  by Ziad Francis <Ziad Francis>,   30 Sep, 2016
Re: None Re: maximum energy transfer - 60.18 eV ? (Batom)
Dear Batom, The G4DNA processes are all discrete processes ... so far, so energy depositions are limited by the target (water) binding energies and by the end of track particle killing procedure. So for water molecule you would see energies around 10.7eV, 13, 17eV, 37.7eV and 537 eV (very rarely).

In other words yes it is normal to obtain a maximum energy transfer of 60 eV it does not depend on the particle itself, but rather on the target material in our case.

Ziad

Ok Re: maximum energy transfer - 60.18 eV ?  by Batom <Batom>,   30 Sep, 2016
Re: Feedback Re: maximum energy transfer - 60.18 eV ? (Ziad Francis)
Dear Ziad,

Thank you so much! I see it, then obtained a maximum energy transfer of ~ 539 eV by G4DNA process with multiple events.

Once again, thank you for your time and consideration!

Question general question for physics model combination  by Batom <Batom>,   13 Sep, 2016
Dear Expert, We know that Geant4-DNA physics and Geant4-Standard physics were integrated in the extended example "microdosimetry". If I add following physics models into PhysicsList.cc of the example "microdosimetry" from advanced example "hadrontherapy", regarding this integration what do you suggest me ?

G4HadronElasticPhysics, G4HadronPhysicsQGSP_BIC, G4StoppingPhysics, G4IonBinaryCascadePhysics, G4EmExtraPhysics, G4NeutronTrackingCut, G4DecayPhysics, G4RadioactiveDecayPhysics

Thank you for your comments.

Question delta-rays track of DNA-Physics and Livermore-Physics   by Batom <Batom>,   06 Sep, 2016
Dear Experts,

I compared the track structure of 600 MeV/u Iron ion in 200 um box for three physics processes of DNA-Physics, Livermore-Physics and Standard-Physics. In the case of DNA-Physics, secondary electrons should be travel long distance from track core of energetic Iron ions. But, I does not see delta-rays like Livermore and Standard physics. I have some questions:

1. Please explain that why does not travel away delta-rays from track core of Iron particle at DNA-Physics? 2. Have a cut-value of high energy electrons for DNA-Physics? How (or possible) to obtain track structure of Iron ions in few hundred micrometer by DNA-Physics like Livermore-Physics (with energetic delta-rays)?

3. My some results of DNA and Livermore physics are so different: In the case of Livermore and Standart physics, probability of particle hits is increasing with increase LET. Contrariwise, probability of particle hits is decreasing with increase LET for DNA-Physics. Here, values of LET are higher than 100 keV/um. I just wordering that probability why decrease for DNA-Physics? If its true, I need to some explination.

Results attached in follow.

Thank you for your advise! Best Regards, Batom.

   Attachment:
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2016/09/06/08.55-28435-Fe600_200um.jpg

None Re: delta-rays track of DNA-Physics and Livermore-Physics   by Ziad Francis <Ziad Francis>,   07 Sep, 2016
Re: Question delta-rays track of DNA-Physics and Livermore-Physics (Batom)
Dear Batom,

can you produce the initial energy spectra for the first generation electrons produced by ions for the 3 different physics lists?

Ziad

None Re: delta-rays track of DNA-Physics and Livermore-Physics   by Batom <Batom>,   07 Sep, 2016
Re: None Re: delta-rays track of DNA-Physics and Livermore-Physics (Ziad Francis)
Dear Ziad,

Thank your for your reply. Yes, I produced initial kinetic energy spectrum of electrons from 600 MeV/u Iron ion in 200 um box. In the case of DNAPhysics, max value of electrons kinetic energy is 23.4 keV, and For LivermorePhysics- 288.2 keV, for StandardPhysics - 641.8 keV. So, initial kinetic energy of secondary electrons produced by DNAPhysics is 10 and 30 times less than Livermore and Standard PhysicsLists. Please see as attached files of initial energy spectra of electrons for 3 different physics list. Here, unit is keV, and to attach, energy printed only above 20 keV, because large file produced by DNAPhysics.

P.S. I also compared track of ions with other Monte-Carlo codes at DNA scale, which codes produced energetic delta-rays with long travel from track core.

Best Regards, Batom.

   Attachment:
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2016/09/07/06.41-37703-Ekin-DNAPhyics.txt
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2016/09/07/06.41-54463-Ekin-Livermore.txt
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2016/09/07/06.41-24450-Ekin-Standard.txt

More Re: delta-rays track of DNA-Physics and Livermore-Physics   by Batom <Batom>,   06 Sep, 2016
Re: Question delta-rays track of DNA-Physics and Livermore-Physics (Batom)
I obtained track structure of mentioned particle in above volume using by example "microdosimetry". In this example, the DNA-physics model is generated in "Target" volume. Here, we can see that different track structure by the example "microdosimetry" and "dnaphysics". In the constructor "G4EmDNAPhysics.cc", have a HighEnergyLimit?

Question Reversing microdosimetry example  by <anne-catherine.heuskin@unamur.be>,   08 Jul, 2016
Dear Geant4 Users,

I would like to adapt the microdosimetry example: instead of having standard physics in the world, and DNA in a region, I need to have DNA in the world and Livermore physics in a region.

However, when I try to set Livermore models for my region and deactivate DNA in this region, Livermore gets used everywhere.

Here is what I wrote for proton ionisation:

//For world

ph->RegisterProcess(new G4DNAIonisation("proton_G4DNAIonisation"), particle);

G4hIonisation* hIoni = new G4hIonisation(); hIoni->SetEmModel(new G4DummyModel(),1); hIoni->SetEmModel(new G4DummyModel(), 2); hIoni->SetStepFunction(0.2, 50 * um); ph->RegisterProcess(hIoni, particle);

//For region
mod = new G4DNARuddIonisationModel();
mod->SetActivationLowEnergyLimit(100 * MeV);
em_config->SetExtraEmModel("proton", "proton_G4DNAIonisation",
		mod, reg, 0.0, 0.5*MeV);

mod = new G4DNABornIonisationModel();
mod->SetActivationLowEnergyLimit(100 * MeV);
em_config->SetExtraEmModel("proton", "proton_G4DNAIonisation",
		mod, reg, 0.5*MeV, 100 * MeV);

mod = new G4BraggModel(); em_config->SetExtraEmModel("proton", "hIoni", mod, reg, 0.0, 2 * MeV, new G4IonFluctuations());

mod = new G4BetheBlochModel(); em_config->SetExtraEmModel("proton", "hIoni", mod, reg, 2 * MeV, 10 * TeV, new G4UniversalFluctuation());

I can't figure out why it's not working. Does someone have any idea? Thanks !

None Re: Reversing microdosimetry example  by M. Hahn <M. Hahn>,   13 Jul, 2016
Re: Question Reversing microdosimetry example
Hi! In your Physicslist just activate global DNA physics by

 emPhysicsList = new G4EmDNAPhysics();
 emPhysicsList->ConstructParticle();
 emPhysicsList->ConstructProcess(); 

If I remember correctly it will anyway just work/being applied for G4_WATER material. But check that with the documentation.

Than set your other processes by

		mod = new G4PenelopeIonisationModel();
		em_config->SetExtraEmModel("e-","e-_G4PenelopeIonisationModel",mod,"REGION",1*MeV,1000*MeV);

		mod = new G4PenelopeBremsstrahlungModel();
		em_config->SetExtraEmModel("e-","e-_G4PenelopeBremsstrahlungModel",mod,"REGION",1*MeV,1000*MeV);

whereby REGION has to be replaced with the name (G4String) of the region as defined in your DetectorConstruction while using the g4region constructor.

e.g. ... = G4Region("REGION")

More Re: Reversing microdosimetry example  by <anne-catherine.heuskin@unamur.be>,   13 Jul, 2016
Re: None Re: Reversing microdosimetry example (M. Hahn)
Hi ! Thank you, I did what you suggested. Still it doesn't work.

I used the constructor of G4EmDNAPhysics first. Then I created processes I need for my region with dummy models in the world, and set models for these processes in my region with G4EmConfigurator.

This is similar to what I did before, except that I don't handle DNA processes myself and that I don't deactivate them (anyway they wouldn't work in the metal).

As a result, I get both DNA and Livermore activated in the world (water). As if G4EmConfigurator does not care about regions...

None Re: Reversing microdosimetry example  by M. Hahn <M. Hahn>,   13 Jul, 2016
Re: More Re: Reversing microdosimetry example
That sounds weird. As a workaround you could just restrict the parallel active regions to certain energy ranges. So that the one you don't need, is only active in energy ranges which don't apply for your experiment.

But to properly find the error, it would be helpful to see the whole code of the class. An the applications output.

More Re: Reversing microdosimetry example  by <anne-catherine.heuskin@unamur.be>,   13 Jul, 2016
Re: None Re: Reversing microdosimetry example (M. Hahn)
   Attachment:
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2016/07/13/06.53-27868-CombinedPhysicsList.cc
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2016/07/13/06.53-34820-log.out

Here is what I got originally (see attached files). I am setting up DNA everywhere, and set dummy models for livermore processes in the world. Then deactivate DNA in region, and assign livermore models in region.

The log looks OK to me. However, I get "Livermore" tracks in the world in the visual.

I did another test where I don't deactivate DNA in metal region (shouldn't be important anyway). And I get twice the expected dose in my world volume (one part from DNA (ok), and one part from livermore I guess (not ok)).

This makes me think that G4EmConfigurator is part of the problem

I would be grateful for any ideas :) Thanks !

None Re: Reversing microdosimetry example  by M. Hahn <M. Hahn>,   13 Jul, 2016
Re: More Re: Reversing microdosimetry example
Maybe the problem lies in the DetectorConstruction? Are your regions overlapping? Like Au-nanoparticles in water defined as spheres within a water box? Then you have to exclude the volume of the Au from the water by using something like "G4SubtractionSolid" if I remember correctly. But I am not 100% sure about that. It's quite a while...

More Re: Reversing microdosimetry example  by <anne-catherine.heuskin@unamur.be>,   14 Jul, 2016
Re: None Re: Reversing microdosimetry example (M. Hahn)
Thank you for all ideas ! I appreciate your help.

Well, my water box is the world and gold in scattered in there. So yes, regions overlaps in the sense that DefaultRegionForTheWorld is overlapping with region for gold. But there is no way around, is there ?

I have been checking processes occuring by setting verbose to 2 : there is Livermore/standard in gold region (ok) AND world (not ok); DNA processes are not occuring at all.

None Re: Reversing microdosimetry example  by M. Hahn <M. Hahn>,   14 Jul, 2016
Re: More Re: Reversing microdosimetry example
When you define a solid by a certain basic geometry like a box, you can substract another arbitary form. This is done by "G4SubtractionSolid". This way you can avoid the overlap. You could create a box with holes in it, like a cheese for example.

More Re: Reversing microdosimetry example  by <anne-catherine.heuskin@unamur.be>,   15 Jul, 2016
Re: None Re: Reversing microdosimetry example (M. Hahn)
Of course, but I don't think it would help here. I have only two volumes: - one is the world, and is associated to DefaultRegionForTheWorld - one is gold (and is daughter of the world volume), and is associated to a gold region

What I mean is because the world contains everything, DefaultRegionForTheWorld overlaps with any other region, by definition.

It could be an error in the DetectorConstruction, but everything is building properly. I assign my region in the regular way:

G4Region* regionNP = new G4Region("NP");

regionNP->AddRootLogicalVolume(m_VolumeNP);

If the second line is commented, I get DNAphysics everywhere (ok). If it's not, I get Livermore everywhere, which is definitely nor what I expect.

I starting to doubt that I can get out of this :/

None Re: Reversing microdosimetry example  by M. Hahn <M. Hahn>,   13 Jul, 2016
Re: More Re: Reversing microdosimetry example
As a quick hel for debugging you can set

/tracking/verbose 2 /run/verbose 2

and you'll get much more detailed output for every scattering event what might help you check which process actually leads to an event. And if both models contribute to in the same region.

Question Export images in Geant4  by Alaoui Faical <Alaoui Faical>,   13 Jun, 2016
Hello, Please, is it possible to export images (MRI mouse, uniformed objects,..) in Geant4 ?

Thx

None Very low energy tracks in Vacuum get stopped  by Tom Roberts <Tom Roberts>,   19 Apr, 2016
I am trying to track very low energy particles in vacuum (G4_Galactic). For instance, an e- with KE=1 eV (p=0.001 MeV/c, beta=0.002).

This used to work, for at least a decade up to and including geant4-09-06-patch-02.

In geant4-10-02 the track is stopped immediately (process=Stopped:Transportation). Indeed there seems to now be a threshold of 1 keV below which tracks are stopped as soon as they are created, even in vacuum.

Where is this documented? How can I change that threshold?

Tracking very low-energy e- is not very useful; my real interest is muonium for which I have written code, including processes MuoniumDecay and MuoniumSurface which adsorbs them onto any surface they hit. MuoniumDecay gives two neutrinos, a 5-53 MeV e+, and a 13.6 eV e- (boost to the lab doesn't change these very much). We have an E field that immediately accelerates the very slow e- into a detector. I want to track very slow Mu atoms in vacuum, let them adsorb onto surfaces, and see where they decay, including their e- when they decay in vacuum.

Sad wholenuclearDNA example  by shaksbeer <shaksbeer>,   02 Dec, 2015
Dear G4 Users

I have tried to execute wholenuclearDNA example , but I experienced 2 problems .

1- it said that G4UIQt.hh: No such file or directory but when I comment it , it run

2- once I run /run/beamOn 10 , I have empty root file ?

Looking forward to give a hand on this .

Thanks.

Question About world's material in dosimetry example  by Balder <Balder>,   21 Oct, 2015
Dear Geant4 experts/users, I have a question about microdosimetry example. As you know, the world is fill with water even though Geant4-DNA is not used in it -just dummy models. Therefore, it will be any difference if the world's material is changed to Al for example, instead water? Many thanks,

Balder.

Question Experimental test/validation of scattering cross sections etc.  by M. Hahn <M. Hahn>,   12 Jul, 2015
Dear all,

are their any measurements of elastic/inelastic scattering crossections on liquid water available?

While digging through the literature it seems to me that all validation of geant4-dna was done against data from the gas phase. In general most of the measurements focus on gas phase and extrapolate the results to the liquid phase. With the exception of a publication by Michaud et al measuring low energy electron scattering on ice.

Am I mistaken to say that this approach seems to be reasonable for higher energies, but that it might be problematic in the low energy limit? Don't we have to take into account the special properties (water-water interaction, vibrational excitations, cluster/water-networks, reorientation ...) of liquid water to obtain reasonable crossections?

I would be grateful for any clarification, literature recommendation or information if there was or wasn't done some work in this direction. Thank you very much and best regards. M.Hahn

Question wholeNuclearDNA example runing  by Adel Pirnia <Adel Pirnia>,   06 May, 2015
please please help me Hello all I had to run wholeNuclearDNA example (Geant4-10.01.p01) without Qt viewer, so I change the viewer to OpenGl by changing the code in the main program. The example runs and the visualization gives me a picture. now I want to change the primary information of it, like primary projectile particle or energy, in the readMe file notes about a file named wholenucleardna.mac that I cant see it, in the primaryGeneratorAction there are no any information about that, and when I tell the program about my purposes (gun/particle and gun/energy) and run that (run/beamOn)the process does correctly but any information about the output data will not be appeared in the terminal or any root file will not be created, instead this message will be appeared: You have entered a viewer secondary X event loop. Quit it with an 'Escape' viewer button

how can I access to the output data? please please help me

best wishes

None Re: wholeNuclearDNA example runing  by Mathieu Karamitros <Mathieu Karamitros>,   06 May, 2015
Re: Question wholeNuclearDNA example runing (Adel Pirnia)
Hello Adel,

Sorry for the late feedback. Indeed, the README is not pointing to the right file. The macro file is wholeNuclearDNA.in

The dna examples use command line options. To see the available options, just call your dna application with '-h' at the end : ./wholeNuclearDNA -h

You will see an option to create the root files.

Best, Mathieu

Question Re: wholeNuclearDNA example runing  by Adel Pirnia <Adel Pirnia>,   06 May, 2015
Re: None Re: wholeNuclearDNA example runing (Mathieu Karamitros)
Thank you Mathieu Karamitros There were several helpful options, but when I ran "root plot.C" command to see the output data these messages was appeared at the end of process and it show me nothing:

adel@adel-X450LCP:~/geant4/workdir/NewFolder/wbuild$ root plot.C 
   ------------------------------------------------------------
  | Welcome to ROOT 6.02/08                http://root.cern.ch |
  |                               (c) 1995-2014, The ROOT Team |
  | Built for linuxx8664gcc                                    |
  | From tag v6-02-08, 13 April 2015                           |
  | Try '.help', '.demo', '.license', '.credits', '.quit'/'.q' |
   ------------------------------------------------------------

root [0] 
Processing plot.C...
/home/adel/geant4/workdir/NewFolder/wbuild/./plot.C:22:21: error: member reference type
      'TFile' is not a pointer; maybe you meant to use '.'?
ntuple = (TNtuple*)f->Get("ntuple"); 
                   ~^~
                    .
/home/adel/geant4/workdir/NewFolder/wbuild/./plot.C:24:3: error: member reference type
      'TCanvas *' is a pointer; maybe you meant to use '->'?
c1.cd(1);
~~^
  ->
root [1] 

Question Re: wholeNuclearDNA example runing  by Adel Pirnia <Adel Pirnia>,   06 May, 2015
Re: Question Re: wholeNuclearDNA example runing (Adel Pirnia)
I changed the marks that message pointed to them, to the suggested marks, but below messages did appeared:

adel@adel-X450LCP:~/geant4/workdir/NewFolder/wbuild$ root plot.C 
   ------------------------------------------------------------
  | Welcome to ROOT 6.02/08                http://root.cern.ch |
  |                               (c) 1995-2014, The ROOT Team |
  | Built for linuxx8664gcc                                    |
  | From tag v6-02-08, 13 April 2015                           |
  | Try '.help', '.demo', '.license', '.credits', '.quit'/'.q' |
   ------------------------------------------------------------

root [0]

Processing plot.C...

hadd Target file: wholeNuclearDNA.root

hadd Source file 1: wholeNuclearDNA_t0.root

Error in <TFile::ReadBuffer>: error reading all requested bytes from file

wholeNuclearDNA_t0.root, got 188 of 300

Error in <TFile::Init>: wholeNuclearDNA_t0.root failed to read the file type data.

Error in <TFileMerger::AddFile>: cannot open file wholeNuclearDNA_t0.root

hadd exiting due to error in wholeNuclearDNA_t0.root

 *** Break *** segmentation violation

None Re: wholeNuclearDNA example runing  by Mathieu Karamitros <Mathieu Karamitros>,   07 May, 2015
Re: Question Re: wholeNuclearDNA example runing (Adel Pirnia)
Hi Adel,

It seems that you are using MT. In MT, each thread creates a root file. If a thread has no track to proceed, the created root file is empty. So to fix this issue, you would have to beam at least two particles.

However, it is strange that hadd is complaining about concatenating an empty root, some information might be missing. We'll have a look at it.

Cheers, Mathieu

Question Re: wholeNuclearDNA example runing  by Adel Pirnia <Adel Pirnia>,   07 May, 2015
Re: None Re: wholeNuclearDNA example runing (Mathieu Karamitros)
Dear Mathieu Karamitros

Hello

Thank you for following the problem, however I did your suggestion for running 2 or 3 particles, but messages in the terminal was the same, I thought that may bee the root program has a problem but it runs it's examples correctly. It is really important to me to see output data of this example, so thank you again for trying to fix the problem.

Best wishes

Question High Energy Proton Transport  by William Donahue <William Donahue>,   05 Feb, 2015
Hi,

I have a question regarding the transport of protons. For a project i am working on i need some validation data for a proton with 15 MeV energy stopping in in water. I need the full track structure generated so i figured G4DNA was the way to go. I loaded the dnaphysics example up and made modification to the code to make a large water phantom (14x15x10 mm^3), new source position, and output to CSVs.

The problems i am having are the following

1) The proton is not transported until all the energy is lost. In some cases the last process is a charge conversion but there is no hydrogen transport. So it seems like energy is not conserved. a 9 MeV proton should travel about 7 mm but i am getting a distance of 100 um travel

2) Is there any way to incorporate proton elastic collisions in the model? This would be helpful for my project.

Any help would be greatly appreciated.

Question For particle 56Fe, simulation not working  by Batom <Batom>,   15 Jan, 2015
Dear Experts!

For particle Fe, simulation not working on example "dnaphysics" and "chem". How to solve this problem?

Regards, Batom.

Question demonstrate initial radiation interation in the tissue + 1question  by Batom <Batom>,   13 Jan, 2015
Dear, Experts!

1. How to demonstrate initial radiation interation in the tissue at time stage from 10^-24 sec to 10^-14 sec (Taylor & Francis Ltd, 1983.) ? Here, Will be nuclear interaction at time 10^-24 - 10^-18 sec ? Also, Which I need to use GlabalTime or LocalTime?

2. Why did not include nuclear (or hadronic) process in PhysicsList of "DNA examples" on Geant4? Is it calculation possible or not ?

Regards,

Batom.

Question how to get track information from 1fs to 1ps (physico-chemical stage)?  by Batom <Batom>,   07 Jan, 2015
Hello, experts!

How to simulate physico-chemical stage on example "chem(1,2,3)"? I would like to print the coordinates of tracks from 1fs to 1ps.

Please advise me, how i can do it?

Regards.

Question problem to compil extended example DNA_wholeNuclearDNA  by maxime tomezak <maxime tomezak>,   15 Dec, 2014
Hello,

I am Novice to use Geant4, and my question is about example compilation. I have a problem to compile extended example DNA_wholeNuclearDNA. I work on virtual station delivered by IN2P3/CNRS last version. I have message below after make : thanks for help me

Maxime T

[root@localhost wholeNuclearDNA-build]# cmake -DGeant4_DIR=$G4DIR ../wholeNuclearDNA -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Configuring done -- Generating done -- Build files have been written to: /home/local1/Desktop/examples-build/wholeNuclearDNA-build [root@localhost wholeNuclearDNA-build]# make -j4 Scanning dependencies of target wholeNuclearDNA [ 10%] [ 20%] [ 30%] Building CXX object CMakeFiles/wholeNuclearDNA.dir/wholeNuclearDNA.cc.o Building CXX object CMakeFiles/wholeNuclearDNA.dir/src/ActionInitialization.cc.o Building CXX object CMakeFiles/wholeNuclearDNA.dir/src/CommandLineParser.cc.o [ 40%] Building CXX object CMakeFiles/wholeNuclearDNA.dir/src/PrimaryGeneratorAction.cc.o [ 50%] Building CXX object CMakeFiles/wholeNuclearDNA.dir/src/SteppingAction.cc.o [ 60%] Building CXX object CMakeFiles/wholeNuclearDNA.dir/src/PhysicsList.cc.o [ 70%] Building CXX object CMakeFiles/wholeNuclearDNA.dir/src/RunAction.cc.o [ 80%] Building CXX object CMakeFiles/wholeNuclearDNA.dir/src/DetectorConstruction.cc.o /home/local1/Desktop/examples-build/wholeNuclearDNA/wholeNuclearDNA.cc: In function ‘int main(int, char**)’: /home/local1/Desktop/examples-build/wholeNuclearDNA/wholeNuclearDNA.cc:174: error: ‘class G4UIQt’ has no member named ‘AddViewerTabFromFile’ /usr/local/clhep/2.1.4.1/include/CLHEP/Units/PhysicalConstants.h: At global scope: /usr/local/clhep/2.1.4.1/include/CLHEP/Units/PhysicalConstants.h:80: warning: ‘CLHEP::electron_charge’ defined but not used /usr/local/clhep/2.1.4.1/include/CLHEP/Random/Randomize.h:70: warning: ‘CLHEP::HepRandomGenActive’ defined but not used [ 90%] Building CXX object CMakeFiles/wholeNuclearDNA.dir/src/ChromosomeParameterisation.cc.o make[2]: *** [CMakeFiles/wholeNuclearDNA.dir/wholeNuclearDNA.cc.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[1]: *** [CMakeFiles/wholeNuclearDNA.dir/all] Error 2 make: *** [all] Error 2

   Attachment:
      http://hypernews.slac.stanford.edu/HyperNews/geant4/get/AUX/2014/12/15/22.12-83169-ample_wholeNuclearDNA.odt

None Re: problem to compil extended example DNA_wholeNuclearDNA  by maxime tomezak <maxime tomezak>,   21 Dec, 2014
Re: Question problem to compil extended example DNA_wholeNuclearDNA (maxime tomezak)
Hello,

My first problem is solved with last last version of Virtual Geant4. But now I have problem for read root file.

I have this message for pdb4dna example :

Processing analysis.C... Info in <TFile::Recover>: pdb4dna_output.root, recovered key TDirectoryFile:pdb4dna_output at address 180 Warning in <TFile::Init>: no StreamerInfo found in pdb4dna_output.root therefore preventing schema evolution when reading this file. Error: illegal pointer to class object hist1 0x0 1312 analysis.C:35: *** Interpreter error recovered ***

Thanks for your help

MT

None Re: problem to compil extended example DNA_wholeNuclearDNA  by Yann Perrot <Yann Perrot>,   26 Jan, 2015
Re: None Re: problem to compil extended example DNA_wholeNuclearDNA (maxime tomezak)
Maxime's problem concerning pdb4dna has been resolved. The ROOT output file was empty. Be sure to run particles before the output analysis. The command to run the application is:

pdb4dna -mac <your_macro_name> -mt <number_Of_Threads>

Yann

Idea Geant4-DNA  by Sebastien INCERTI <Sebastien INCERTI>,   11 Nov, 2014
This is the forum category dedicated to Geant4-DNA and related very low energy extensions.

See http://geant4-dna.org.

None Welcome  by Dennis H. Wright <Dennis H. Wright>,   11 Nov, 2014
Welcome to the forum on DNA and Very Low Energy Extensions.

 Add Message Add Message
to: "DNA/Very Low Energy"

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