Merge branch develop into master for 2023 release #965
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Remove superfluous command in entry point source_check_emin copied from entry point source_get_emax during implementation, which was setting the value for emax. Not really clear to me why this was happening but it turns out that having emax as an argument in one entry point would force to also have in the other entry point to avoid SEGFAULT errors. However, line has been removed as it shouldn't have been there in the first place!
Before this change, there was a small risk of buffer overflow in the tutor7pp fluence scoring arrays. The value r2 was checked to be less than 400, and then the scoring bin number (from 0 to 199) is calculated using the expression (int)(sqrt(r2)*10.). The problem with this check is that certain double precision values less than 400 can nevertheless have a square root equal to exactly 20.0 due to floating-point rounding. For example, taking the square root of the double 399.99999999999994 results in 20.0 under certain conditions, not a value slightly less than 20.0 as would be expected. The default g++ rounding mode is round-to-nearest, so even with the square root's true value being under 20.0, the resulting double can be rounded upwards to 20.0 if the true value is closer to 20.0 than the previous representable float. Then, scoring in bin 200 results in buffer overflow in the scoring array. This change ensures the resulting scoring array bin integer is in bounds (< 200), eliminating the potential for buffer overflow.
Check that the current region index (ir) is not -1 for region dose scoring. Before this change, there was an out-of-bounds read in d_reg_index when the region was -1 (outside the geometry).
Vacuum has a special medium number -1, while all other media get offsets from 0 to nmedia. Before this change, there was a buffer overflow if media dose scoring was used with a geometry that had vacuum as one of the media. The vector massM is indexed by medium number, but for any vacuum regions, it would read and write memory at the memory location one before the buffer bounds: massM[-1]. Skipping the vacuum region masses shouldn't matter, as vacuum dose is always zero. massM is only used later on with non-vacuum media, so skipping vacuum regions is the right choice instead of an alternative like appending the vacuum mass to massM.
Bug: results depend on the order in which the material composition is defined. Reported by Iymad Mansour who observed that egs_brachy simulations of an irradiation with an isotropic 35 keV photon point source, embedded in a steel applicator, produced 5% differences in the surface dose of a water phantom when the order of the steel components was changed. Reproduced with egs_kerma for a 35 keV photon point source surrounded by a 1 mm steel encapsulation embedded in a spherical water phantom. Kerma at the spherical water shell next to the encapsulation differs by 4%. Cause: sampling element and atomic shell for photo-electric interaction with MCDF-XCOM shell-wise using unsorted array zelem rather than pe_zsorted. Solution: using sorted array pe_zsorted fixes the issue.
Fix a mistake in the previous fix for non-alpha numeric characters in the job name in egs-parallel jobs resulting in a crash. The previous fix removed non-alphanum characters from the start of the original job name, but actually we needed to remove from the start of the trimmed 14 character job name.
Change a few occurrences of endl to \n in egs++ scoring routines, to increase performance by about 50%. The reason for this is that endl performs a buffer flush each time, which is not necessary. The performance hit was very noticeable for large arrays, like a 300x300x300 3ddose file.
Add a record of the git hash, branch and compile time to the c++ makefiles. This allows the c++ codes to access those parameters as defines. Advanced applications now output those values during initEGSnrcBackEnd().
Add the compilation time of an application to the printout of git hash and branch, and add these messages to the mortran codes. Also add a check for applications in the makefile to compare with the HEN_HOUSE versions and print a warning if there are differences. With the git information now printed to machine.mortran, it is not necessary to pass it as c++ compile flags. However, I will leave these flags for future use.
Also replace an old reference to nmake with mingw32-make.
Change the git branch and commit reporting to be passed as defines at compile time, instead of being generated during the configuration of EGSnrc. This fixes the issue where users could switch branches but not run the configuration script, resulting in the wrong git branch and commit being output.
As discussed in issue #745 ensure that one EGS_TrackScoring object is define to prevent bugs at write time when multiple objects try to write to the same file.
Fix memory leaks in EGS_AdvancedApplication: interpolation arrays are never freed, and transportp is allocated by EGS_Input::getInputItem but never freed. Also Fix memory leak in EGS_ObjectFactory::createObjects: EGS_Input* input is allocated by EGS_Input::takeInputItem but never freed. Memory leaks reported by AddressSanitizer.
After compiling egs_view with asan support, there was a buffer overflow
error traced back to the memcpy call in ImageWindow::paintEvent.
ERROR: AddressSanitizer: dynamic-stack-buffer-overflow ...
READ of size 400 at 0x7ffe71889e40 thread T0
#0 0x7f543595ecdf (/usr/lib/x86_64-linux-gnu/libasan.so.5+0x99cdf)
#1 0x55dc3acdbb15 in memcpy
#2 0x55dc3acdbb15 in ImageWindow::paintEvent(QPaintEvent*)
#3 0x7f5434f86047 in QWidget::event(QEvent*)
The issue is that memcpy will always copy sizeof(lastRegions) bytes into
the array regions. But before this change, regions could be shorter than
lastRegions, leading to a buffer overflow. After this change, maxreg is
always set to N_REG_MAX, the length of lastRegions.
In the solution to one of the questions in the getting-started manual, the total dose was calculated as the sum of dose to regions, instead of appropriately weighted by the relative volume of each region. This was corrected, as well as another typo in the instructions. Reported by @mjukdisk in discussion #780.
Fix a GUI error that occurred in DYNJAWS jaw definitions when clicking the button to calculate the jaw settings from the field size and SSD. The button triggered a function that was duplicated with the same name in SYNCJAWS, leading to the error. As the fix, the syncjaws version of the function has been renamed. This bug has existed since SYNCJAWS was added to the GUI.
Set the minimum distance between component modules in BEAMnrc to 1e-5 cm (macro $MIN_GAP). Previously this minimum gap was set to 0.01 cm. Given that the code is normally used in double-precision nowadays, there is no point in leaving such a large value as the default. This change follows for looking into issue #773.
Add the source-axis distance to the z position of the particle before it is written to the phase space file. This change only affects IAEA phsp sources, and only when scoring particles in BEAMnrc coordinates.
Fix a minor bug in FLURZnrc where it expected the wrong number of inputs when reading in the SLOTE parameter from the egsinp file. This did not result in any actual issues, but an error message was printed to the screen about the user providing the wrong number of inputs.
Implement a graceful exit from the addphsp application if the total number of particles is greater than 2^32-1, the maximum count that can be stored in the header. Only enforce this for a phase space in EGSnrc format.
- EGS_Interpolator: increase array size when creating an interpolator based on an array of value pairs to have an extra bin to prevent round-off errors. This is also done by PEGS4 when determining fit parameters for each interval. The extra bin uses the same parameters as the previous one, i.e., it extrapolates. - Add auxiliary methods to application classes to get electron step size, energy deposited and app source type. - Fluence scoring: at a plane, in regions for all particles.
Get proper stopping power interpolator depending on charge.
- Add "clean" target for dose and fluence scoring objects (instead of manually deleting files when building the ausgab object). Need to add to the rest of the ausgab objects! - One can now define DEBUG=-DDEBUG to turn on some debugging messages that I found useful. - Add MYDEF for user defines: use MYDEF=-DDEBUG to activate debugging messages and variables.
Reworked the classes for planar and volumetric fluence scoring to descend from a common base class which contains many commonalities, to avoid code duplication. Should have started that way!
Add auxiliary functions to application classes, required by the fluence scoring ausgab object.
- Add a method to get the charge of a base source, which returns -99 by default, matching the unknown type of the fluence scoring ausgab object. A base source does not know the charge of its particles unless it is later derived from a simple source. For instance a collection of sources, a beam source, or a phase space source will contain multiple type of particles. - Sources derived from the class EGS_SimpleSource return the source particle's charge. - Add a method to get source charge from the application.
Add an application-level method to obtain the maximum energy of the source. This proves useful for ausgab objects that need this information.
- Add option to define regions from where to score planar fluence to improve efficiency of charged particle calculations. - Move many common tasks to the base class EGS_FluenceScoring. - Fix group scoring region definitions. - Improve logic for defining scoring regions in planar scoring class. - Document classes with Doxygen comments.
- Add the ability to divide fluence in total and primary fluence. - Add the ability to calculate integral and differential fluence. - Improve output format. - Investigate the effect of scoring integral charged particle fluence using either EDEP (within differential scoring block) or directly TVSTEP: a) Identical for FLURZ-like calculation b) Small, negligible differences using stprO3 and stpwrO5 This allows extraction of the integral fluence scoring from the blocks for differential fluence. When one is only interested in the integral fluence, the calculation is up to 10% faster using a TVSTEP-based approach. Current implementation allows switching between EDEP-based and TVSTEP-based integral fluence calculation via the pre-processor define USETVSTEP. To use TVSTEP-based integral dose calculation use: make MYDEFS=-DUSETVSTEP Next iteration will only use the TVSTEP-based approach for integral fluence as both approaches result in negligible differences. - Add mechanism to track the distribution of number of energy bins covered when spreading EDEP. This is activated via the define variable DEBUG: to use it, build the fluence scoring ausgab object using: make MYDEFS=-DDEBUG One can also trace the difference between the step derived from spreading EDEP over the energy grid and TVSTEP via DEBUG.
- Add input blocks to define the energy grid and the scoring options based on the scoring type. - Improve output format.
Remove example for base class and add specific blocks for planar an volumetric scoring inputs.
- Remove initial approach to score charged particle integral fluence from each contribution to the differential fluence. Now is uses TVSTEP and computes integral fluence in one go. - Remove checks for pre-processor directive USETVSTEP as it not needed anymore. - Polish documentation.
This new ausgab object scores fluence in user-defined regions (volumetric) or at a circular or rectangular field (planar) located in an arbitrary position in space. Scoring can be done for either photons, electrons or positrons. Scoring for multiple particle types is accomplished by defining multiple fluence scoring ausgab objects.
Add a missing include of the array c++ class library. This avoids compiler errors that occurred on macOS.
Add ausgab calls before and after a photonuclear interaction, in order to handle cross section enhancement (xcse) correctly. Without these calls, there is no compensation for the enhanced cross section, hence the photonuclear cross section is effectively increased by the xcse factor. Also add the photonuclear event trapping in Fano calculations, for consistency. However, the Fano calculation fails when photonuclear attenuation is turned on anyway, because the photon is discarded without depositing its energy. Also update a couple loops that print out the ausgab flags (IAUSFL) values, to include the photonuclear attenuation option value.
ftessier
requested review from
mainegra,
rtownson and
blakewalters
and removed request for
a team
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