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 enclosing NamespaceImp(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