Notes for V3.4 (June 2018)¶
Note
V3.4 was the first public version of USINE released in June 2018. Minor corrections were implemented in July 2018.
Tag V3.4 (2018/06)¶
Bug fixes (in this release)
- 2018/07/19 - corr#1
- Minor bug fixed in TUXSections (to skip XS reaction not present in list when loading file)
- Minor bug fixed in E6 (bug related to XS file renaming done just before the release)
- Better conversion for quantities on different E-type (updated .ref files)
- ‘IsELossCoulombIon’ split in ‘IsELossCoulomnb’ and ‘IsELossIon’ in init.TEST.par and int.Model1D.par (to fix minor bug in E2)
- Better instructions for user for option E2
- Added section “Models and equations” in documentation
- Updated .gitlab-ci.yml to generate properly usine.pdf and access it from online documentation
Prior to release
- 2018/06
- Added IsWind() in list of switches (for comparison plots)
- Small bug fixes in comparison plot axes name
- Consistent renaming of XS files (and header description)
- Bug fixed for rhole calculation
- CMakeList.txt modified to also compile on mac OS
- 2018/05
- Prepared version for AMS collaboration (internal use)
- Added init.Model1D.par initialisation file for model 1D
- Merged master into v4-dev branch
- Removed TU*Spline*, SolMod1D, TUCRFluxes… (in v4-dev)
- 2018/04
- Removed display of model*bias when no nuisance parameter
- Information on errors for displayed data and fit data added on graphs
- Read Tc 50% (instead of Tc) in TUAtomProperties
- removed files usine.tutorial.odp and usine.tutorial.pdf (now in this doc)
- removed file usine.v3.3.log (now in this doc -this file!)
- Minor bug fixed in minimisation status print
- Sphinx documentation (git added) available at $USINE/doc/_build/html/index.html
- Important change for init.TEST.par (and accordingly in TUInitParList.cc), see the documentation: new format
group @ subgroup @ parameter @ M=? @ value
, a few subgroups reassigned to different group, a few subgroup names modified, a few parameters renamed, and hopefully better syntax to select template for source spectrum / spatial distribution. - Sort correctly by growing Z in option D0 (and bug fixed) + added fluxes
- Default values for initialisation file modified to ‘better match’ B/C data and fluxes
- More message for MINUIT/MINOS status
- Graph for model with data nuisance parameters added
- Clean-up unused/dummy methods in all classes also to avoid redundancy (TU***List vs TU***Entry methods)
- Significant modifications in TUDataSet to handle possibility of data with same exp/qty but different etype (e.g., AMS-02 data for B/C are in kEKN and kR)
- Added parameter in parfile to select ‘a’ ‘(fluxes shown times E^a) for displays for fits
- Added residuals (data-model)/model in fit results
- Bugs fixed (valgrind analysis): radioactive decay equilibrium comparison (option -ED3+), CoeffReac1stOrder (was using index out of range), a few comparisons to indices (no impact on runs and test functions), TUMisc:RemoveDuplicates(), number of free pars displayed (with -m2)
- 2018/03
- combos to display: B/C,O → B/C,O:kEKN;B/C:kR to enable fit of a mix of KEKN ad KR data (syntax of -l option changed accordingly)
- Paths with env variable (e.g., $USINE) replaced in prints
- Path correctly stripped in some tests (to be user location independent)
- Reference files added for -i and -e options in integration tests
- Minor bug fixed to avoid duplicated in TUInitParList.cc
- Minor bug fixed for multiple XS as free parameters
- Added USINE advertisement on plots
- More inelastic XS added (thanks Yoann!) + removed dummy name in format
- Moved obsolete
BEGIN_MACROS...END_MACROS
statements in src/TU*.cc files (THtml root documentation no longer used) into usine.MACROS/ as .C ROOT macros - Removed
#if !defined(R__ALPHA) && !defined(R__SOLARIS) && !defined(R__ACC) && !defined(R__FBSD)
and#endif
enclosingNamespaceImp(TU...)
in src/*.cc for namespaces - Added usine -i and -e options in integration tests
- Option A1 split in A1 & A2 (for GCR/SS plots)
- Renamed TUPhysicsProcesses → TUInteractions, SigTot*.dat → SigInel*.dat
- Enabled more free parameters for XS (EAxisScale, EnhancePowHE, EThresh, SlopeLE in addition to Norm): either for explicit reactions or all reactions
- Renamed usine.version.txt → usine.v3.3.log, crprop_charts* → crcharts*, crprop_abundances2003.dat → solarsystem_abundances2003.dat, usine_run.cc → usine.cc
- Single executable usine for all options (removed all src/usine_*.cc!)
- ./bin/usine -tUSINE to test USINE installation/stability (usine.test file removed, new usine.tests/*.ref – one file per class)
- FILE *f as argument added in TEST() methods in all classes
- Removed directory inputs/OBSOLETE/
- 2018/01
- Bug fixed with source parameters in minimisation
- Test of minimisation added (in usine.test)
- Fitable/nuisance parameter for ‘half-life’ (BETA or EC) added
- 2017/12
- Added user output directory in ‘usine_run -t’ command line
- Several mini-bug fixed in D1, D2A, and D2B run options
- Precision issue fixed in normalisation to data (during propagation)
- More parameters to control precision (in initialisation file and code): EPS_INTEGR (integrations), EPS_ITER (iterations), EPS_NORMDATA (normalise data)
- USINE 80’s logo added and simplification of usine_run.cc
- 2017/10
- Minor fix in parameter file
- replace all char[]/sprintf by string/Form() because of random crashes with long names…
- 2017/08
- Contribution to \(\chi^2\) of covariance matrix re-implemented (to enable item below)
- Any error systematics on data enabled as a nuisance parameter (model bias)
- 2017/07
- More options for XS ranking D0, D1, D2A, and D2B (multi-file enabled, outputs plots
- Annoying memory leak fixed (especially for D options)
- git name USINE-DEV changed to USINE
- Initialisation file format: new syntax ‘#’→’@’ and ‘//’→’#’ (to be consistent with other input files, i.e. ‘#’ indicates a comment)
- Renamed inputs/XSEC_* into inputs/XS_*, and added inputs/XS_NUCLEI/GHOST_SEPARATELY (XS files added by Y. Génolini from GALPROP)
- Memory leak in TUXSections fixed
- Re-factoring/modifications of option D0 and D1
- 2017/05
- XS parameters added as NUISANCE for list of reactions (norm)
- New parameters in initialisation file: ‘IsMINOS’ (to evaluate correctly errors after minimisation), UsineRun@Display@QtiesExpsEType and ErrType (kERRSYST, kERRSTAT, kERRTOT, kERRCOV:DIR) for display. For option kERRCOV:DIR, seek for covariance matrix in DIR and add in chi2
- 2017/03
- Extra plots (for dominant production reactions) with “./bin/usine_run -t” (options E1 to E9)
- TUQueries renamed to TUMisc, TUGlobalEnum to TUEnum
- New code parameters IsDecayFedBETA and IsDecayFedEC (useful to run comparisons plots)
- In Bessel re-summation (2D model), Bringmann’s trick to accelerate convergence implemented
- TUPhysics: physics and astrophysics values/conversion updated to PDG 2016
- Documentation: typos in formulas corrected (missing 2H factors, etc.)
- Now use user-range information for NUISANCE parameters (if parameter out of this range, chi2 returns a large number)
- Model calculation on data E bin instead of Emean (parameter ‘IsUseBinRange’ and ‘NExtraInBinRange’ with power-law on each sub-bin assumed)
- New parameter for boundary conditions on energy numerical inversion, separately for NUC, ANTINUC, and LEPTON
- Bug fixed in in chi2 for multiple exp/qty fits (printing error)
- Unused inline functions removed, code cleaned with ‘cppcheck –enable=all include/TU*.h src/TU*.cc’, updated FindROOT.cmake and CMakeLists.txt updated
- 2017/02
- Source parameters enabled as free parameters
- Fit parameter ‘X’ enabled as ‘X’ or ‘log10(X)’ with the keywords LIN and LOG
- Enabled fit parameters either as FIT or NUISANCE
- Take correctly into account asymmetric error bars
- Fit-able parameters listed with option -m1
- Normalisation of source abundances to data on/off enabled
- Bug fixed related to source abundances