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Discussion of DNA and very low energy extensions

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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.

1 None: Re: Information about the structure of the data for low energy silicon model.   (Sebastien INCERTI - Nov 11, 00:51) new
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.

1 None: Re: Negative energy deposit by e-_G4DNAIonisation process   (Sebastien INCERTI - Jul 02, 03:41)
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.

1 None: Re: Bug in dnaphysics example   (Sebastien INCERTI - Jun 18, 02:07)
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

1 None: Re: Pdb file for pdb4dna   (Marc B. Hahn - 02 Apr, 2018)
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?

1 Question: Re: Tracking hadrons below 1kev   (Helga Holmestad - 29 Nov, 2017)
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

1 None: Re: Electrons below 1keV   (Christopher Walker - 30 Nov, 2017)
(_ None: Re: Electrons below 1keV   (Christopher Walker - 01 Dec, 2017)
(_ Note: Re: Electrons below 1keV   (Helga Holmestad - 01 Dec, 2017)
(_ None: Re: Electrons below 1keV   (Christopher Walker - 01 Dec, 2017)
(_ Note: Re: Electrons below 1keV   (Helga Holmestad - 01 Dec, 2017)
(_ None: Re: Electrons below 1keV   (Christopher Walker - 02 Dec, 2017)
(_ None: Re: Electrons below 1keV   (Christopher Walker - 02 Dec, 2017)
(_ Idea: Re: Electrons below 1keV   (Helga Holmestad - 05 Dec, 2017)
(_ None: Re: Electrons below 1keV   (Christopher Walker - 06 Dec, 2017)
1 Note: Re: Electrons below 1keV   (Helga Holmestad - 06 Dec, 2017)
2 Question: Re: Electrons below 1keV   (Michael H. Kelsey - 06 Dec, 2017)
1 None: Re: Electrons below 1keV   (Christopher Walker - 10 Dec, 2017)
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.
1 None: Re: Ion particles in svalue example   (Sebastien INCERTI - 30 Aug, 2017)
(_ Question: Re: Ion particles in svalue example   (Kirstie Caravani - 30 Aug, 2017)
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

1 None: Re: G4DNA Carbon Ions   (Ziad Francis - 28 Jul, 2017)
(_ None: Re: G4DNA Carbon Ions   (Nicholas Henthorn - 28 Jul, 2017)
(_ None: Re: G4DNA Carbon Ions   (Ziad Francis - 28 Jul, 2017)
(_ None: Re: G4DNA Carbon Ions   (Nicholas Henthorn - 28 Jul, 2017)
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.

1 Feedback: Re: maximum energy transfer - 60.18 eV ?   (Ziad Francis - 28 Sep, 2016)
(_ None: Re: maximum energy transfer - 60.18 eV ?   (Batom - 28 Sep, 2016)
(_ Feedback: Re: maximum energy transfer - 60.18 eV ?   (Ziad Francis - 30 Sep, 2016)
(_ Ok: Re: maximum energy transfer - 60.18 eV ?   (Batom - 30 Sep, 2016)
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

1 More: Re: delta-rays track of DNA-Physics and Livermore-Physics   (Batom - 06 Sep, 2016)
2 None: Re: delta-rays track of DNA-Physics and Livermore-Physics   (Ziad Francis - 07 Sep, 2016)
1 None: Re: delta-rays track of DNA-Physics and Livermore-Physics   (Batom - 07 Sep, 2016)
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 !

1 None: Re: Reversing microdosimetry example   (M. Hahn - 13 Jul, 2016)
(_ More: Re: Reversing microdosimetry example   (anne-catherine.heuskin@unamur.be - 13 Jul, 2016)
(_ None: Re: Reversing microdosimetry example   (M. Hahn - 13 Jul, 2016)
(_ More: Re: Reversing microdosimetry example   (anne-catherine.heuskin@unamur.be - 13 Jul, 2016)
1 None: Re: Reversing microdosimetry example   (M. Hahn - 13 Jul, 2016)
2 None: Re: Reversing microdosimetry example   (M. Hahn - 13 Jul, 2016)
1 More: Re: Reversing microdosimetry example   (anne-catherine.heuskin@unamur.be - 14 Jul, 2016)
... 2 Message(s)
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

1 None: Re: wholeNuclearDNA example runing   (Mathieu Karamitros - 06 May, 2015)
(_ Question: Re: wholeNuclearDNA example runing   (Adel Pirnia - 06 May, 2015)
(_ Question: Re: wholeNuclearDNA example runing   (Adel Pirnia - 06 May, 2015)
(_ None: Re: wholeNuclearDNA example runing   (Mathieu Karamitros - 07 May, 2015)
(_ Question: Re: wholeNuclearDNA example runing   (Adel Pirnia - 07 May, 2015)
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

1 None: Re: problem to compil extended example DNA_wholeNuclearDNA   (maxime tomezak - 21 Dec, 2014)
(_ None: Re: problem to compil extended example DNA_wholeNuclearDNA   (Yann Perrot - 26 Jan, 2015)
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.

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