Although, during work with RegisterConstructor(“emlivermore”); which in PhysicsList.cc of g4test/neuron/src. I do not have this problem!
sarahabdelaziz@Sarahs-MacBook-Pro neuron-build % make
[ 5%] Building CXX object CMakeFiles/neuron.dir/src/PhysicsList.cc.o
[ 10%] Linking CXX executable neuron
[100%] Built target neuron
sarahabdelaziz@Sarahs-MacBook-Pro neuron-build % nano neuron.in
sarahabdelaziz@Sarahs-MacBook-Pro neuron-build % ./neuron -mac neuron.in -mt 2 -dnachemON -network NeuralNETWORK.dat
**************************************************************
Geant4 version Name: geant4-11-02-patch-02 [MT] (21-June-2024)
<< in Multi-threaded mode >>
Copyright : Geant4 Collaboration
References : NIM A 506 (2003), 250-303
: IEEE-TNS 53 (2006), 270-278
: NIM A 835 (2016), 186-225
WWW : http://geant4.org/
**************************************************************
===== neuron is started with 2 threads of MT MODE =====
NeuronLoadDataFile::NeuralNetworkDATAfile: opened NeuralNETWORK.dat
Total number of compartments into Neuron : 18376
Livermore + DNAphysics is activated!
DNAChemistry is activated!
---- Begin of Neuron Construction! ----
==========================================================
Side length of word volume is calculated : 699.017 um
Radius of homogeneous medium is calculated : 349.509 um
Overall dimensions (um) of neuron morphology :
width = 640 height = 280 depth = 25
Volume (um3), surface (um2) and mass (ug) of Bounding Slice are calculated :
4.48e+06; 404400; 4.48
Volume (um3), surface (um2) and mass(ug) of Neuron are calculated :
100726; 140835; 0.100726
Total number of compartments into Neuron : 18376
Shift values (um) for Neuron translation are calculated :
shiftX = 0 shiftY = 0 shiftZ = 0
---- Soma for construction: ----
Total number of compartments into Soma : 96
---- Dendrites for construction: ----
Total number of compartments into Dendrites: 18279
---- Axon not found! ----
---- Spines not found! ----
---- End of Neuron Construction! ----
==========================================================
=======================================================================
====== Electromagnetic Physics Parameters ========
=======================================================================
LPM effect enabled 1
Enable creation and use of sampling tables 0
Apply cuts on all EM processes 0
Use combined TransportationWithMsc Disabled
Use general process 0
Enable linear polarisation for gamma 0
Enable photoeffect sampling below K-shell 1
Enable sampling of quantum entanglement 0
X-section factor for integral approach 0.8
Min kinetic energy for tables 100 eV
Max kinetic energy for tables 100 TeV
Number of bins per decade of a table 20
Verbose level 1
Verbose level for worker thread 0
Bremsstrahlung energy threshold above which
primary e+- is added to the list of secondary 100 TeV
Bremsstrahlung energy threshold above which primary
muon/hadron is added to the list of secondary 100 TeV
Lowest triplet kinetic energy 1 MeV
---
=======================================================================
====== Atomic Deexcitation Parameters ========
=======================================================================
Fluorescence enabled 1
Directory in G4LEDATA for fluorescence data files fluor
Auger electron cascade enabled 0
PIXE atomic de-excitation enabled 0
De-excitation module ignores cuts 0
Type of PIXE cross section for hadrons Empirical
Type of PIXE cross section for e+- Livermore
=======================================================================
====== DNA Physics Parameters ========
=======================================================================
Use fast sampling in DNA models 0
Use Stationary option in DNA models 0
Use DNA with multiple scattering of e- 0
Use DNA e- solvation model type 11003
=======================================================================
### === Deexcitation model UAtomDeexcitation is activated for 3 regions:
DefaultRegionForTheWorld 1 0 0
Soma 1 0 0
Dendrites 1 0 0
### === Ignore cuts flag: 0
phot: for gamma SubType=12 BuildTable=0
LambdaPrime table from 200 keV to 100 TeV in 174 bins
===== EM models for the G4Region DefaultRegionForTheWorld ======
LivermorePhElectric : Emin= 0 eV Emax= 100 TeV SauterGavrila Fluo
compt: for gamma SubType=13 BuildTable=1
Lambda table from 100 eV to 1 MeV, 20 bins/decade, spline: 1
LambdaPrime table from 1 MeV to 100 TeV in 160 bins
===== EM models for the G4Region DefaultRegionForTheWorld ======
LivermoreCompton : Emin= 0 eV Emax= 1 GeV Fluo
KleinNishina : Emin= 1 GeV Emax= 100 TeV Fluo
conv: for gamma SubType=14 BuildTable=1
Lambda table from 1.022 MeV to 100 TeV, 20 bins/decade, spline: 1
===== EM models for the G4Region DefaultRegionForTheWorld ======
Livermore5DConversion : Emin= 0 eV Emax= 100 TeV ModifiedTsai
Rayl: for gamma SubType=11 BuildTable=1
Lambda table from 100 eV to 150 keV, 20 bins/decade, spline: 0
LambdaPrime table from 150 keV to 100 TeV in 176 bins
===== EM models for the G4Region DefaultRegionForTheWorld ======
LivermoreRayleigh : Emin= 0 eV Emax= 100 TeV CullenGenerator
-----
msc: for proton SubType= 10
===== EM models for the G4Region DefaultRegionForTheWorld ======
WentzelVIUni : Emin= 0 eV Emax= 100 TeV Nbins=240 100 eV - 100 TeV
StepLim=Minimal Rfact=0.2 Gfact=2.5 Sfact=0.6 DispFlag:1 Skin=3 Llim=1 mm
hIoni: for proton XStype:3 SubType=2
dE/dx and range tables from 100 eV to 100 TeV in 240 bins
Lambda tables from threshold to 100 TeV, 20 bins/decade, spline: 1
StepFunction=(0.1, 0.05 mm), integ: 3, fluct: 1, linLossLim= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
Bragg : Emin= 0 eV Emax= 2 MeV deltaVI
BetheBloch : Emin= 2 MeV Emax= 100 TeV deltaVI
hBrems: for proton XStype:1 SubType=3
dE/dx and range tables from 100 eV to 100 TeV in 240 bins
Lambda tables from threshold to 100 TeV, 20 bins/decade, spline: 1
===== EM models for the G4Region DefaultRegionForTheWorld ======
hBrem : Emin= 0 eV Emax= 100 TeV ModifiedMephi
===== Limit on energy threshold has been applied
hPairProd: for proton XStype:1 SubType=4
dE/dx and range tables from 100 eV to 100 TeV in 240 bins
Lambda tables from threshold to 100 TeV, 20 bins/decade, spline: 1
Sampling table 17x1001; from 7.50618 GeV to 100 TeV
===== EM models for the G4Region DefaultRegionForTheWorld ======
hPairProd : Emin= 0 eV Emax= 100 TeV ModifiedMephi
CoulombScat: for proton XStype:1 SubType=1 BuildTable=1
Lambda table from threshold to 100 TeV, 20 bins/decade, spline: 0
ThetaMin(p) < Theta(degree) < 180, pLimit(GeV^1)= 0.139531
===== EM models for the G4Region DefaultRegionForTheWorld ======
eCoulombScattering : Emin= 0 eV Emax= 100 TeV
nuclearStopping: for proton SubType=8 BuildTable=0
===== EM models for the G4Region DefaultRegionForTheWorld ======
ICRU49NucStopping : Emin= 0 eV Emax= 1 MeV
msc: for GenericIon SubType= 10
===== EM models for the G4Region DefaultRegionForTheWorld ======
UrbanMsc : Emin= 0 eV Emax= 100 TeV
StepLim=Minimal Rfact=0.2 Gfact=2.5 Sfact=0.6 DispFlag:1 Skin=3 Llim=1 mm
ionIoni: for GenericIon XStype:3 SubType=2
dE/dx and range tables from 100 eV to 100 TeV in 240 bins
Lambda tables from threshold to 100 TeV, 20 bins/decade, spline: 1
StepFunction=(0.1, 0.001 mm), integ: 3, fluct: 1, linLossLim= 0.02
===== EM models for the G4Region DefaultRegionForTheWorld ======
LindhardSorensen : Emin= 0 eV Emax= 100 TeV deltaVI
----
===== EM models for the G4Region DefaultRegionForTheWorld ======
eCoulombScattering : Emin= 0 eV Emax= 100 TeV
=========================================================================
--> G4TaskRunManager::CreateAndStartWorkers() --> Initializing workers...
=========================================================================
Visualization Manager instantiating with verbosity "warnings (3)"...
Visualization Manager initialising...
Registering graphics systems...
You have successfully registered the following graphics systems.
Registered graphics systems are:
ASCIITree (ATree)
DAWNFILE (DAWNFILE)
G4HepRepFile (HepRepFile)
RayTracer (RayTracer)
VRML2FILE (VRML2FILE)
gMocrenFile (gMocrenFile)
TOOLSSG_OFFSCREEN (TSG_OFFSCREEN)
TOOLSSG_OFFSCREEN (TSG_OFFSCREEN, TSG_FILE)
OpenGLImmediateQt (OGLIQt, OGLI)
OpenGLStoredQt (OGLSQt, OGL, OGLS)
OpenGLImmediateX (OGLIX, OGLIQt_FALLBACK)
OpenGLStoredX (OGLSX, OGLSQt_FALLBACK)
Qt3D (Qt3D)
TOOLSSG_X11_GLES (TSG_X11_GLES, TSGX11, TSG_QT_GLES_FALLBACK)
TOOLSSG_QT_GLES (TSG_QT_GLES, TSGQt, TSG)
TOOLSSG_QT_ZB (TSG_QT_ZB, TSGQtZB)
Default graphics system is: TSG_OFFSCREEN (based on batch session).
Default window size hint is: 600x600-0+0 (based on G4VisManager initialisation).
Note: Parameters specified on the command line will override these defaults.
Use "vis/open" without parameters to get these defaults.
Registering model factories...
You have successfully registered the following model factories.
Registered model factories:
generic
drawByAttribute
drawByCharge
drawByOriginVolume
drawByParticleID
drawByEncounteredVolume
Registered models:
None
Registered filter factories:
attributeFilter
chargeFilter
originVolumeFilter
particleFilter
encounteredVolumeFilter
Registered filters:
None
You have successfully registered the following user vis actions.
Run Duration User Vis Actions: none
End of Event User Vis Actions: none
End of Run User Vis Actions: none
Some /vis commands (optionally) take a string to specify colour.
"/vis/list" to see available colours.
### === Deexcitation model UAtomDeexcitation is activated for 3 regions:
DefaultRegionForTheWorld 1 0 0
Soma 1 0 0
Dendrites 1 0 0
### === Auger flag: 1
### === Ignore cuts flag: 1
G4VisManager: Using G4TrajectoryDrawByCharge as fallback trajectory model.
See commands in /vis/modeling/trajectories/ for other options.
========================================================================================
--> G4TaskRunManager::CreateAndStartWorkers() --> Creating 2 tasks with 1 events/task...
========================================================================================
G4WT0 > End of tracking primary particle, its final energy is :28.7285 MeV
G4WT1 > End of tracking primary particle, its final energy is :28.7947 MeV
G4WT0 > Physics stage ends
G4WT0 > *** G4Scheduler starts processing
G4WT0 > *** G4Scheduler did not start because no track was found to be processed
G4WT0 > ___________________________________
G4WT1 > Physics stage ends
G4WT1 > *** G4Scheduler starts processing
G4WT1 > *** G4Scheduler did not start because no track was found to be processed
G4WT1 > ___________________________________
======= The summary of simulation results 'neuron' ========
Primary particle = proton
Kinetic energy of beam = 30 A*MeV
Particle traversals the neuron = 1 of 2
Full LET of beam as formulas = 1.864 keV/um
Mean LET of beam as simulation = 1.6897 +- 0.017192 keV/um
Mean track length of beam = 717.46 +- 0.00057621 um
Particle fluence = 130.29 particles/cm^2
Fluence dose (full) = 3.891e-07 Gy
Fluence dose ber beam = 1.9455e-07 Gy
List of generated physical process:
eIoni= 1182
hIoni= 942
msc= 1376
List of generated particles outside neuron structure:
e- : 961 Emean = 1.1696 keV ( 242.19 eV --> 58.006 keV) Eflow/event = 562.02 keV
Number of secondary particles inside neuron structure:
e- : 1
Number of molecular products inside neuron structure:
time: 1 ps - 10 ps
Total energy (MeV) deposition :
All volume: 2.4246
Bounding slice: 0.48238
Neuron: 0.00012086
Soma: 0
Dendrites: 0.00012086
Axon: 0
Number of compartments traversed by particle tracks :
Soma: 0 of total: 96
Dendrites: 1 of total: 18279
Axon: 0 of total: 0
Dendritic (or Axon) compartmental energy deposits
at the distance from Soma have been written into *.out files:
Dend3DEdep.out, Axon3DEdep.out, Soma3DEdep.out
Outputs of energy deposition per event written in data file:
OutputPerEvent.out
Calculation time = 1.33618 s
Graphics systems deleted.
Visualization Manager deleting...
sarahabdelaziz@Sarahs-MacBook-Pro neuron-build %
Also, I noticed that DNA Physics Parameters as shown above is the same for two cases. Dose it mean there is a problem related to EMDNAphysics model process?