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12. Output Files#
12.1. Stdout and Stderr#
Important to check during macro testing and before long runs! The standard output (stdout) contains useful G4 warning messages, which warns the user about bad macro settings, like volume overlaps, ignored parameters, which do not raise error, so code can run with unintentional, wrong settings.
By default, this is printed to command-line, but when submitting to a typical computer cluster node,
this is usually redirected automatically to a file (g4see_<#>.sh.o<JobID> or similar).
It can be also intentionally redirected by user with the > bash operator to a file.
The standard error (stderr) messages (resulted e.g. by non valid macro commands) are printed when G4SEE terminates with an error.
These are also printed to command-line, or usually redirected automatically to file (g4see_<#>.sh.e<JobID> or similar) on typical computer clusters.
12.2. The event counter file#
The file n_event_t<N>.out (where <N> is the thread ID) is being updated regularly during simulation by printing the number of already simulated events per thread.
This is useful when G4SEE is running on a cluster node, and the user has no access to the standard output (stdout) file containing information on the simulation progress.
12.3. The g4see.out output file#
Some info about run (date, G4SEE version, CPU time, I/O) and input macro. This file is only printed at the end of the simulation run.
#####################################################################################
# G4SEE OUTPUT FILE #
#####################################################################################
Simulation started: 2022/09/19 16:30:46
Geant4 release: geant4-11-00-patch-02 [MT] (25-May-2022)
G4SEE version: v0.5
G4SEE tag: v0.5
G4SEE commit ID: 06822d21
G4SEE branch: master
Multi-Threaded mode
Number of threads used: 2
Number of primary particles: 100
Total CPU time (s): 18.6748
CPU time / primary (s): 0.186748
Output directory: /home/work/g4see/build/output
Input macro file: /home/work/g4see/build/examples/detailed_scoring_example.mac
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Input Macro Commands +
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
/run/numberOfThreads 2
##############
### Geometry
# BULK MATERIAL WIDTH unit THICK unit BIAS
/SEE/geometry/Bulk G4_Si 20 mm 300 um true
...
12.4. Standard Scoring Histograms#
At the end of runs, output histogram files are created by each job (or thread if applicable) in output folder of that specific job (e.g. out_0, out_1, …).
Histograms can be dumped to file regularly during a simulation run, which can be controlled via the /SEE/scoring/dumpHistogramsAfter command.
Naming of histogram files: <quantity>_<id>_hist_t<N>.out
<quantity>:EdeporEkin<id>: scoring (histogram) ID defined by user via/SEE/scoring/addScoringmacro command<N>: thread ID run simulation and created the file
In both single- and multi-threaded mode (by default), these histograms have to be merged manually after run, see How to Run.
Histogram types:
Edep: Energy Deposited histogram
Enable via
/SEE/scoring/addScoring Edep <id>macro commandBins: Total energy deposited event-by-event in sensitive volume, unit: MeV
Counts: Number of occurrence multiplied by inverse event biasing weights
Ekin: Particle Kinetic Energy histograms
Enable via
/SEE/scoring/addScoring Ekin <id> <particle>macro commandBins: Particle Kinetic Energy (Ekin) particle-by-particle when entering or produced in sensitive volume, unit: MeV
Counts: Number of occurrence multiplied by inverse particle biasing weights
Standard scoring histograms in their header also contains 1 underflow bin (below scoring range) and 1 overflow bin (above scoring range), therefore histograms contain all the events, even outside scoring range.
Example of a job/thread Edep_<id>_hist_t<N>.out file:
Edep Counts
underflow 9.000e+00
overflow 0
1.000e-01 6.000e+00
1.023e-01 1.400e+01
1.047e-01 4.700e+01
1.072e-01 1.010e+02
1.096e-01 1.780e+02
1.122e-01 2.780e+02
1.148e-01 3.730e+02
1.175e-01 5.330e+02
...
9.550e-01 0
9.772e-01 0
1.000e+00
During merging of the N pieces of raw job/thread histogram file, the following columns are calculated and printed to the final <quantity>_<id>_histogram.out file:
Bins: same binning as in job/thread histograms
Counts: sum of the counts (to get the average, just divide this by N)
StdDev(corr): absolute, corrected sample standard deviation of the final population, estimated from samples
\(StdDev_{corr} = s = \sqrt{ \frac{1}{N-1} \sum_i^N(Y_i - \overline{Y})^2 } \), where \(Y_i\) are the bin counts of job/thread histograms and \(\overline{Y}\) is their average
(to get uncorrected sample standard deviation: \(s^2 = \frac{N}{N-1} \sigma_Y^2\))
Example of a merged Edep_<id>_histogram.out file:
Edep Counts StdDev(corr)
underflow 1.420e+02 2.809e+00
overflow 0 0
1.000e-01 1.740e+02 3.437e+00
1.023e-01 4.340e+02 5.580e+00
1.047e-01 9.030e+02 1.192e+01
1.072e-01 1.767e+03 2.072e+01
1.096e-01 3.275e+03 3.942e+01
1.122e-01 5.440e+03 6.223e+01
1.148e-01 8.038e+03 9.112e+01
1.175e-01 1.099e+04 1.241e+02
...
9.550e-01 0 0
9.772e-01 0 0
1.000e+00
Standard Scoring histogram of 14.8 MeV neutrons in Si diode#
12.5. Detailed Scoring Hits data#
When Detailed Scoring feature of G4SEE is enabled, then each thread saves hits of SV particle-by-particle to Hits_t<N>.out output file.
In Detailed Scoring, all particles are scored and printed to Hits file, which have entered or was produced in the Sensitive Volume (SV).
These files can grow very fast in file size, can easily take up huge amount of file storage space!
It is strongly recommended to check what is the expected total Hits file size before starting a longer simulation run!
Particle hits data are dumped to file regularly during a DS simulation run after exceeding a memory or event limit,
which can be controlled via the /SEE/scoring/detailed/dumpMemoryLimit and dumpEventLimit commands.
Columns (in the same order as in Hits file):
event: event number {mandatory}particle: name of particle {mandatory}weight: inverse biasing weight of particle/event if XS biasing was used {mandatory}Z: particle atomic number {optional, default: false}A: particle mass (nucleon) number {optional, default: false}track: track (particle) ID {optional, default: true}parent: parent particle ID {optional, default: true}E_kin: kinetic energy of particle when entering or produced in SV (unit: MeV) {optional, default: true}pos_x,pos_y,pos_z: x, y, z coordinates of particle position when entering or produced in SV (unit: mm) {optional, default: false}mom_x,mom_y,mom_z: x, y, z coordinates of particle momentum when entering or produced in SV (unit: MeV/c) {optional, default: false}process: creator process of particle, ‘biasWrapper()’ indicates that XS biasing was used for that process {optional, default: false}volume: name of the volume where particle produced {optional, default: false}E_dep: total energy deposited by particle in SV (unit: MeV) {optional, default: true}N_dep: total non-ionizing energy deposited by particle in SV (unit: MeV) {optional, default: false}counts: number of grouped e-, e+ or gamma particles in event {optional, default: true}E_exc: excitation energy of nuclei, if it is produced in excited state (unit: MeV) {optional, default: false}
Example of a Hits_t<N>.out Detailed Scoring output file (showing only 3 proton events):
event particle weight Z A track parent E_kin pos_x pos_y pos_z mom_x mom_y mom_z process volume E_dep N_dep counts E_exc
0 proton 1.008e+00 1 1 1 0 9.7886e+00 -1.95e-08 -3.75e-07 -5.00e-04 6.93e-02 -4.05e-02 -1.36e+02 primary World 1.8389e+00 0 1 0
0 e- 1.051e+00 0 0 20 1 1.7251e-02 -1.59e-04 1.04e-04 -2.15e-02 5.25e-02 -1.34e-02 -1.22e-01 hIoni Sensitive 1.7251e-02 0 1 0
0 e- 1.273e+00 0 0 91 1 1.7018e-02 -7.51e-04 -1.05e-04 -1.11e-01 -5.53e-03 -3.93e-02 -1.27e-01 hIoni Sensitive 1.5718e-02 0 1 0
0 e- 1.319e+00 0 0 118 1 1.8867e-02 -5.28e-04 -1.16e-04 -1.29e-01 -4.95e-03 -8.60e-03 -1.40e-01 hIoni Sensitive 1.6024e-02 0 1 0
0 e- 1.329e+00 0 0 124 1 1.5299e-02 -4.61e-04 -1.39e-04 -1.33e-01 -5.03e-02 -2.97e-02 -1.12e-01 hIoni Sensitive 1.5299e-02 0 1 0
0 ga(e-) nan 0 0 -1 1 nan nan nan nan nan nan nan nan Sensitive 8.0312e-01 0 289 0
0 ga(e-) nan 0 0 -2 91 nan nan nan nan nan nan nan eIoni Sensitive 1.3006e-03 0 1 0
0 ga(e-) nan 0 0 -3 118 nan nan nan nan nan nan nan eIoni Sensitive 2.8434e-03 0 2 0
1 proton 1.006e+00 1 1 1 0 9.9739e+00 0 0 -5.00e-04 -9.57e-02 -8.19e-02 -1.37e+02 primary World 5.7929e-02 0 1 0
1 neutron 1.028e-03 0 1 9 1 1.5393e+00 7.28e-06 2.66e-05 -1.15e-02 4.12e+01 2.26e+01 -2.63e+01 b(protonInelastic) Sensitive 0 0 1 0
1 gamma 1.028e-03 0 0 10 1 2.3996e+00 7.28e-06 2.66e-05 -1.15e-02 9.60e-01 1.99e+00 9.30e-01 b(protonInelastic) Sensitive 0 0 1 0
1 P30 1.028e-03 15 30 12 1 2.6201e-01 7.28e-06 2.66e-05 -1.15e-02 -4.17e+01 -2.37e+01 -1.11e+02 b(protonInelastic) Sensitive 2.6201e-01 0 1 0
1 ga(e-) nan 0 0 -1 1 nan nan nan nan nan nan nan hIoni Sensitive 2.0196e-02 0 7 0
1 ga(gamma) nan 0 0 -2 1 nan nan nan nan nan nan nan b(protonInelastic) Sensitive 0 0 1 0
2 proton 1.002e+00 1 1 1 0 1.0049e+01 6.97e-08 -2.39e-07 -5.00e-04 3.67e-02 -8.86e-02 -1.38e+02 primary World 1.4359e+00 0 1 0
2 e- 1.127e+00 0 0 44 1 1.7355e-02 -5.79e-04 -7.58e-04 -5.08e-02 -3.43e-02 -4.60e-02 -1.21e-01 hIoni Sensitive 1.4933e-02 0 1 0
2 e- 1.177e+00 0 0 65 1 1.9941e-02 -5.67e-04 -9.63e-04 -6.99e-02 2.43e-02 7.73e-03 -1.42e-01 hIoni Sensitive 1.8540e-02 0 1 0
2 e- 1.349e+00 0 0 131 1 1.6440e-02 -1.24e-03 -1.32e-03 -1.34e-01 1.52e-04 4.82e-02 -1.21e-01 hIoni Sensitive 1.5360e-02 0 1 0
2 Si28 1.632e-03 14 28 230 1 5.4918e-01 -3.87e-03 -3.70e-04 -2.40e-01 -3.31e+01 -5.24e+01 -1.57e+02 b(protonInelastic) Sensitive 5.4918e-01 0 1 0
2 proton 1.632e-03 1 1 231 1 2.4233e+00 -3.87e-03 -3.70e-04 -2.40e-01 2.58e+01 5.01e+01 3.71e+01 b(protonInelastic) Sensitive 2.0739e+00 1.0748e-03 1 0
2 gamma 1.632e-03 0 0 232 1 3.1873e+00 -3.87e-03 -3.70e-04 -2.40e-01 1.80e+00 2.54e+00 -6.81e-01 b(protonInelastic) Sensitive 0 0 1 0
2 gamma 1.632e-03 0 0 233 1 1.7836e+00 -3.87e-03 -3.70e-04 -2.40e-01 1.41e-02 1.32e+00 -1.19e+00 b(protonInelastic) Sensitive 0 0 1 0
2 ga(e-) nan 0 0 -1 1 nan nan nan nan nan nan nan nan Sensitive 6.1624e-01 0 237 0
2 ga(e-) nan 0 0 -2 44 nan nan nan nan nan nan nan eIoni Sensitive 2.4222e-03 0 2 0
2 ga(e-) nan 0 0 -3 65 nan nan nan nan nan nan nan eIoni Sensitive 1.4008e-03 0 1 0
2 ga(e-) nan 0 0 -4 131 nan nan nan nan nan nan nan eIoni Sensitive 1.0804e-03 0 1 0
2 ga(e-) nan 0 0 -5 231 nan nan nan nan nan nan nan nan Sensitive 3.4940e-01 0 212 0
DS is enabled with
/SEE/scoring/detailed true10 MeV proton primaries (Gaussian energy with 200 keV std. dev.) with
protonInelasticinteractions XS biased (indicated withb())Kinetic energy thresholds used for individual particle scoring: 15 keV for e\(^-\) and 1 MeV for \(\gamma\)
e\(^-\) and \(\gamma\) are grouped by their ancestors (indicated with
ga()), groups have negative track IDAll the optional quantities are enabled (thus scored and printed) using all the commands like
/SEE/scoring/detailed/addMomentumCSV file format is disabled (just for better visual display)
Another example of Detailed Scoring output with different settings (showing only 4 neutron events):
event particle weight track parent E_kin process E_dep counts E_exc
15 neutron 2.021e-03 1 0 1.4800e+01 primary 0 1 0
15 proton 2.021e-03 2 1 3.2360e+00 b(neutronInelastic) 2.6470e+00 1 0
15 gamma 2.021e-03 3 1 5.4022e+00 b(neutronInelastic) 0 1 0
15 gamma 2.021e-03 4 1 2.1153e+00 b(neutronInelastic) 0 1 0
15 Al28m 2.021e-03 5 1 1.5723e-01 b(neutronInelastic) 1.5723e-01 1 3.064e+01
15 g(e-) nan -1 nan nan nan 5.8904e-01 331 0
16 neutron 1.008e-03 1 0 1.4800e+01 primary 0 1 0
16 Si28 1.008e-03 2 1 1.0745e+00 b(neutronInelastic) 1.0745e+00 1 0
16 neutron 1.008e-03 3 1 4.0265e+00 b(neutronInelastic) 0 1 0
16 gamma 1.008e-03 4 1 7.9169e+00 b(neutronInelastic) 0 1 0
16 gamma 1.008e-03 5 1 1.7821e+00 b(neutronInelastic) 0 1 0
17 neutron 2.151e-03 1 0 1.4800e+01 primary 0 1 0
17 proton 2.151e-03 2 1 3.6445e+00 b(neutronInelastic) 2.9932e+00 1 0
17 gamma 2.151e-03 3 1 3.7906e+00 b(neutronInelastic) 0 1 0
17 gamma 2.151e-03 4 1 2.9867e+00 b(neutronInelastic) 0 1 0
17 Al28 2.151e-03 5 1 5.1960e-01 b(neutronInelastic) 5.1960e-01 1 0
17 g(e-) nan -1 nan nan nan 6.5123e-01 351 0
18 neutron 1.400e-03 1 0 1.4800e+01 primary 0 1 0
18 e- 1.400e-03 17 2 1.0328e-02 hIoni 8.9250e-03 1 0
18 proton 1.400e-03 2 1 4.8414e+00 b(neutronInelastic) 3.7430e+00 1 0
18 gamma 1.400e-03 3 1 5.6328e+00 b(neutronInelastic) 0 1 0
18 Al28m 1.400e-03 4 1 4.3648e-01 b(neutronInelastic) 4.3648e-01 1 3.064e+01
18 g(e-) nan -1 nan nan nan 1.0894e+00 535 0
/SEE/scoring/detailed trueis used to enable DS14.8 MeV mono-energetic neutron primaries with
neutronInelasticinteractions XS biased (indicated withb())Default kinetic energy thresholds for individual particle scoring are used (10 keV for e\(^-\) and 100 keV for \(\gamma\))
No ancestor grouping enabled, so just regular grouping (max. 1 e\(^-\) group and 1 \(\gamma\) group per event, indicated with
g()), groups have negative track IDAdditional to the default scored quantities, excitation energy and creator process scoring are also enabled
Detailed Scoring data of 14.8 MeV neutrons in Si diode#