Changes between Version 17 and Version 18 of HowToNeut

Timestamp:

Jan 8, 2017, 4:10:52 PM (8 years ago)

Author:

Clarence Wret

Comment:

--

HowToNeut

@@ -7 +7 @@
 Contact: Clarence Wret (`c.wret14@imperial.ac.uk`)
 
-You can also try: Patrick Stowell (`p.stowell@sheffield.ac.uk`), Callum Wilkinson (`callum.wilkinson@lhep.unibe.ch`), Luke Pickering (`luke.pickering08@imperial.ac.uk`) or Hayato-san (`hayato@icrr.u-tokyo.ac.jp`)
+You can also try: [mailto:p.stowell@sheffield.ac.uk Patrick Stowell]
+[mailto:callum.wilkinson@lhep.unibe.ch Callum Wilkinson], [mailto:luke.pickering08@imperial.ac.uk Luke Pickering],
+or [mailto:hayato@icrr.u-tokyo.ac.jp Hayato-san].
 }}}
+
+[=#point_compile]
 == Compiling NEUT and running neutroot2 ==
 
@@ -17 +21 @@
 NEUT has two dependencies: ROOT and CERNLIB. You need to have `$ROOTSYS`, `$CERN` and `$CERN_LEVEL` environment variables set-up to compile NEUT. These should all be specified by the user in `$NEUT_ROOT/src/neutsmpl/EnvMakeneutsmpl.csh`. 
 
-Compilation is done (somewhat inconveniently) by running `./Makeneutsmpl` in `$NEUT_ROOT/src/neutsmpl/`: this sources the above `EnvMakeneutsmpl.csh`, runs through a host of makefiles, sets up symlinks and builds the project. If you have some time on your hands and want to fix the build process by e.g. CMake, please contact us or Hayato-san.
+Compilation is done by running `./Makeneutsmpl` in `$NEUT_ROOT/src/neutsmpl/`: this sources the above `EnvMakeneutsmpl.csh`, runs through a host of makefiles, sets up symlinks and builds the project.
 
 Running the main executable is done by `./neutroot2 NEUT_CARD_FILE.card OUTPUT_ROOT_FILE.root`, where `NEUT_CARD_FILE.card` is a card file compliant with your chosen NEUT version, and `OUTPUT_ROOT_FILE.root` is the ROOT output file where the events are to be saved. This output file contains all the event information and is the input for NUISANCE analyses.
 
 Examples of NEUT card files can be found in the `$NEUT_ROOT/src/neutsmpl/Cards` directory, or have a look at what team NUISANCE used for 2016 analyses at 
-[wiki:Winter2016] and https://imperialcollegelondon.app.box.com/files/0/f/13226969736/neut_cards
-
+[wiki:Winter2016] and at our [https://imperialcollegelondon.app.box.com/files/0/f/13226969736/neut_cards box].
 
 Hot tip: NEUT can be quite verbose and you might want to pipe the output to file (or /dev/null...) rather than dump it to screen. This can actually speed up NEUT considerably.
@@ -32 +35 @@
 NEUT has a load of defaults set on run-time if the user does not supply them, which means you're running with "reference" NEUT.
 
-Some things are good to specify though, and here's a list for generating all modes on T2K H2O. We can specify how many events we want, the input flux in TH1D format, the incoming neutrino type, the flux file, number of bound protons and neutrons and free protons, what interaction modes, and so on.
+Selecting different models is done in the cardfile, and all the inputs that a user can specify is found in `src/neutcore/necard.F`.
 
-The "C" at the start of each line is just a comment and will not be parsed by NEUT.
+We can specify how many events we want, the input flux in TH1D format, the incoming neutrino type, the flux file, number of bound protons and neutrons and free protons, what interaction modes, and so on.
 
-The `EVCT-MPV 3` says the flux is coming from a file, `EVCT-FILENM` specifies the file location of the flux, `EVCT-HISTNM` is the name of the TH1D inside `EVCT-FILENM`, and `EVCT-INMEV` specifies if the input histogram is in MeV or not.
+Here's a list for generating all modes on T2K H2O. The "C" at the start of each line is just a comment and will not be parsed by NEUT.
+
 
 {{{
@@ -70 +74 @@
 }}}
 
+The `EVCT-MPV 3` says the flux is coming from a file, `EVCT-FILENM` specifies the file location of the flux, `EVCT-HISTNM` is the name of the TH1D inside `EVCT-FILENM`, and `EVCT-INMEV` specifies if the input histogram is in MeV or not.
+
+
 = NEUT inputs for NUISANCE =
 
-The output of `neutroot2`, contains a `neutvect` object which has all the information about the event in it. This is read in by NUISANCE to generate predictions. `neutroot2` also saves the predicted flux and event rate predictions automatically into the output file so NUISANCE already has everything it needs.
+The output of `neutroot2`, contains a ROOT file containing `nevents` `neutvect` objects which has all the information about each event in it. This is read in by NUISANCE to generate predictions. `neutroot2` also saves the predicted flux (`flux_numu`) and event rate (`evtrt_numu`) predictions automatically into the output file so NUISANCE already has everything it needs.
 
 To read NEUT inputs the NEUT type just needs to be specified in the NUISANCE input card file, e.g. for MiniBooNE CCQE:
@@ -79 +86 @@
 
 = Using NEUT !ReWeight =
+NUISANCE has full support of running NEUT with its reweighting engine. We can generate error-bands, perform generator tunings to specific data-sets, and so on all through NUISANCE.
+
+== Compiling the reweight classes in NEUT ==
+To compile NEUT's reweighting engine, make sure you've got the main executables compiled (see [#point_compile above]), and
+
+{{{
+$ cd $NEUT_ROOT/src/reweight
+$ make clean
+$ make all
+}}}
+
+to compile the reweighting engine.
+
+== Running NUISANCE with NEUT !ReWeight ==
+{{{
+#!div class="important"
+We recommend talking to Hayato-san or us (or other NEUT experts) before fitting parameters to make sure that they are not deprecated.
+}}}
+
+The syntax for running NEUT with reweighting in NUISANCE is very similar to how it's done in [wiki:HowToGenie GENIE] and [wiki:HowToNuWro NuWro] too.
+
+The user specifies the parameter(s) and the range which should be varied as:
+
+`neut_parameter  MaCCQE  0.0  -4.0  4.0  1.0  FREE`
+
+where `MaCCQE` is the parameter to be varied, `0.0` is the starting values, `-4.0` is the minimum value, `4.0` is the maximum value, `1.0` is the step-size to take, and `FREE` means the parameter is free to vary in the minimisation. 
+
+We can also specify `FIX` for the parameters if we want to reweight a systematic parameter to some value other than nominal and keep it there. This is useful for using best-fit parameter constraints from one experiment to predict another experiment (e.g. fit to MiniBooNE and predict MINERvA data, or fit to bubble-chamber data to predict T2K data).
+
+The whole list of parameters can be found in `$NEUT_ROOT/src/reweight/NSyst.h` and the `return`ed `std::string`s (e.g. `MaCCQE` and `CA5RES`). 
+
+The starting, minimum, maximum and step values are all in units of 1-sigma uncertainties. So `-4.0` for the minimum means -4*1-sigma ranges, and `0.0` for the starting value means the nominal value nominal.
+
+The hard-coded 1-sigma uncertainty defaults for NEUT can be found in `$NEUT_ROOT/src/reweight/NSystUncertainity.cc` and the `NSystUncertainty::SetDefaults(void)` function. These are in the physical units (e.g. MaCCQE has +/- 0.165 GeV uncertainty in NEUT for 1 sigma)
+
+The hard-coded nominal defaults for NEUT can be found in `$NEUT_ROOT/src/reweight/NFortFns.cc`. These are also the physical units of the parameter (e.g. MaCCQE default is 1.21 GeV in NEUT).
+
+The actual physical parameter value is found by `par_value = nominal * (1 + par_var * 1-sigma)`.
+
+The output of the fit is in the units of `par_var`, not `par_value`. So an output for `MaCCQE` of `0.7` would equate to `1.21*(1+1*0.165) = 1.35` GeV.
 
 
 = Joint Flux Inputs =
-`neutroot2` does not yet natively support combined beams or targets so if you want to use the measurement classes that require this (e.g. MINERvA CC0pi nue+nuebar) you will have to setup a JOINT input. See HowToJointInput for more information on how to achieve this.
+
+`neutroot2` does not yet natively support combined beams or targets so if you want to use the measurement classes that require this (e.g. MINERvA CC0pi nue+nuebar) you will have to setup a JOINT input. See [wiki:HowToJointInput this] for more information on how to achieve this.