Add support for region labels to egs_kerma #1235
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Authors of the EGSnrc files are unequivocally identified in the git commit log. However, we also want to preserve the names of authors and contributors inside text files headers, as much as possible, in case the files are extracted from the repository (or the repository eventually moves to another version control system). This script compares, for each modified file in a commit range (passed as the first argument, master..HEAD by default), the commit authors of the file against the authors and contributors listed in the file header. It reports the missing names, and returns 1 (error) if some authors are missing, or 0 (success) otherwise. Binary files are excluded from the comparison, as well as files that do not contain authorship information. The latter are reported at the end of the output, skipping over files that do not contain author information (e.g., image files). This script is intended to run automatically as a github action. It implies that all commit authors should be listed under "Contributors", regardless of the significance of the contribution, so that the script runs cleanly. The output of the github action should always be inspected before merging to check the files that don't contain authorship information.
Clarify that multiple-scattering transport is triggered only if the intended electron step is longer than a skin depth, even in bulk media away from any region boundaries. This improves efficiency, because a multiple-scattering step costs about the same as 3 single-scattering steps (the default skin depth is 3 mean free paths). Below a skin depth, it is more efficient (and more accurate) to use single-scattering.
Fix the output message in the egslst file for BEAMnrc simulations about the number of brems events the took place. When DBS was turned on, it would always read zero.
Fix a bug in egs_phsp_scoring where the electron energy for IAEA phase-spaces was written as the total energy instead of the kinetic energy. This was a critical bug.
Fix a bug where the source collection fluence was not calculated properly when multiple transformations were performed on a single base source.
The documentation in the source code for core EGSnrc parameters options is updated match HEN_HOUSE/src/get_inputs.mortran
This fix divides phase space sources used in parallel runs into npar*nchunk equal segments, where npar is the number of parallel runs and nchunk is the number of chunks (defaults to 10). Each chunk of the parallel run is then assigned its own segment of the phase space source outside of which it will not sample. This scheme, identical to that used in the EGSnrc mortran codes, should ensure relatively even sampling of the phase space source over the entire parallel run.
Any remaining histories after completion of npar*nchunk simulations chunks reuse particles from the last segment of the phase space file.
Fix typo in hownear when particle in bounding box determining which of the repeated geometries to check: Using nz rather than nxy when computing index of repeated geometry array results in addressing array index out of bounds with subsequent segfault error. Showed when electron transport turned ON up during dose calculations around a CivaDot source using egs_dose_scoring and egs_app and 2 microns regions. It did not affect photon-only nor egs_kerma calculations since there is no call to hownear. ;-)
Fix a bug in egs_circle_perpendicular that made the geometry invalid for any cases where the circle was expected to face away from the z-axis.
Changes to be committed: modified: egs++/ausgab_objects/egs_fluence_scoring/egs_fluence_scoring.h
- Added virtual methods setRussianRoulette and splitTopParticleIsotropically needed by the radiative splitting object. Changes to be committed: modified: egs++/egs_application.h
- Added two new methods needed by the radiative splitting object and provided more information in comments. - Turn ON/OFF EGSnrc internal radiative splitting (UBS) void setRadiativeSplitting( const EGS_Float &nsplit ); - Turn ON/OFF EGSnrc internal Russian Roultette + UBS void setRussianRoulette( const EGS_Float &iSwitchRR ); - Split particle uniformly in 4Pi void splitTopParticleIsotropically( const EGS_Float &fsplit ); Changes to be committed: modified: egs++/egs_advanced_application.h
- Added two new methods needed by the radiative splitting object and provided more information in comments. - Turn ON/OFF EGSnrc internal radiative splitting (UBS) void setRadiativeSplitting( const EGS_Float &nsplit ); - Turn ON/OFF EGSnrc internal Russian Roultette + UBS void setRussianRoulette( const EGS_Float &iSwitchRR ); - Split particle uniformly in 4Pi void splitTopParticleIsotropically( const EGS_Float &fsplit ); Changes to be committed: modified: egs++/egs_advanced_application.cpp
Change the output spectra from egs_gammaspec to report the energy at the middle of each energy bin, instead of the lower edge of the bin.
Fix a bug where some ensdf files from the nndc caused a segmentation fault for egs_radionuclide source. This was due to comment lines following gamma records in the file. The code did not check to see if a normalization record existed before trying to use it, and this has been fixed.
Fix a bug in egs_ensdf that resulted in the x-rays and auger electrons in the ensdf file for Zn-65 not being used. This has no impact if the relaxations are set to the default of using EADL data.
- Total fluence normalization bug during output: expression norm /= volume[k]; reduces normalization for F[k] by V[k-1]*V[k-2]*...*V[1] changed to norm = norma/volume[k]; - Eliminate misleading message in fluence scoring When scoring photon fluence, no message related to electron fluence calculation method should be issued. Thanks to Alexandra Bourgouin for drawing my attention to this issue! Fixes issue #1002 - Read user-requested normalization not only when differential fluence requested as it is also needed for integral fluence
Same bug affecting total fluence whereby in the case of differential fluence scoring in multiple regions the normalization for region i was divided by the volume of the precedent regions.
If estimating differential fluence for several regions, one might want to turn off diff fluence output to terminal. This can be achieved by setting verbose = no In the AO input block. Added a clarifying message stating that diff fluence is output as a Grace plot file.
It was being read outside that block which didn't make sense and was error prone as one would have expected to find it inside that block.
Forgot to use proper spacing in IF block for diff fluence scaling inputs.
BUG: Commit 8023cd0 labels fluorescent photons from EII as secondaries. The pertinent block for UBS and BCSE requires knowledge of the local region number IRL, which is only set later in AUSGAB. FIX: Set IRL above the UBS/BCSE block in the AUSGAB routine. Funnily enough this bug only showed when using BEAMnrc as library, not during BEAM simulations. Perhaps IRL was taking values below smaller than the dimension of the IREGION_TO_BIT array, set to 3000.
Follow-up on previous commit: Why did the bug not appear during standalone BEAMnrc runs? During direct BEAMnrc simulations, when IRL isn't set in the block to split EII-generated secondary photons, it takes value 2, the first region of the geometry, set during previous calls to AUSGAB. When using BEAMnrc as a library with other applications, the memory location IRL is pointing to can change, taking an arbitrary number. In my case it was a very large integer.
Add libclean target to standard beam_makefile which removes BEAMnrc library related files. Until now one had to do this manually!
Fixes
=====
- Average source energy calculation was assuming a statistical weight of
1 and lumping all particles together. Now weight is accounted for, and
average energy for photons and charge particles scored separately.
Moreover, average energy of scoring photons is also estimated.
- Typos in differential fluence xmgrace file output
Additions
=========
- Flexible scoring region input spares user from having to enter huge
number of regions one at the time. Here are the different input
schemes:
a) Individual entries using 'scoring regions' input key Simply enter
scoring regions individually
b) Initial and final region pairs using `scoring region ranges`
Expects pairs of initial and final scoring regions
c) Groups of regions using 'scoring start region' and 'scoring stop
region' input keys. Requires using two input keys on two lines,
similar to what is done for the dose scoring ausgab object.
d) Equally spaced scoring regions using key 'Incremental scoring
regions' The most general scheme, expects triplets of initial,
final and increment regions allowing the definition of ranges where
scoring is performed at specified intervals (increments) between
regions. Note that using an increment of 1 is equivalent to schemes
b) and c).
If an error in these inputs is detected, code aborts with a warning
message, rather than simply ignoring the error.
- Scoring regions mass input schemes:
Using `scoring region masses` input key
a) One value per region, regardless of scoring region input scheme
b) One value per group (pair or triplet) when using scoring input
options b, c, or d above.
c) One value for all regions (positive)
d) One value for whole scoring volume (negative)
Using `scoring volume mass` input key assumes mass for whole scoring
volume as in d).
- Fluence calculation expanded to estimating integral fluence on all
scoring regions ir for each calculation geometry ig, Ftot(ig,ir), and
differential fluence (spectrum) Fdiff(ig,E), for each calculation
geometry ig in the total scoring volume.
TODO: Add option to specify spectral scoring regions rather than using
all scoring regions.
- Estimate average mass-energy absorption coefficient in each scoring
region when integral fluence is calculated.
- Fix small typo in output
The new, more natural way of projection input, had a typo in the projection variable iproj
Apply astyle 3.1 to a recent rebase on the develop branch.
Add the feature to select regions for source emission for the isotropic source depending on the medium. The medium selection can include media, or exclude them. Region selections are combined with the media selections using an AND operation, so that a valid region must meet both criteria.
Fix track sorting used for dynamic .ptracks files containing time indices. Usually the original .ptracks file is overwritten by the sorted one, but on Windows file deletion may be blocked. As a workaround for this situation, the sorted .ptracks file is left as a separate file.
Also improve the label replacement algorithm to allow for inputs that have a mix of parameters that are not regions. For example, "start stop delta", where the delta is the increment value.
mainegra
approved these changes
Jan 10, 2025
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Also improve the label replacement algorithm to allow for inputs that have a mix of parameters that are not regions. For example, "start stop delta", where the delta is the increment value.
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git diff --ignore-space-spaceto best view the differences. You can do this on github using the gear symbol underFiles changed.