2007-10-17 21:47  Robert Hatcher <rhatcher@fnal.gov>

	* Production/asciidb/dogwood/bhend/: BFLDDBIPLANEMAP.csv,
	  BFLDDBIPLANEMAPVLD.csv, catalogue.db:

	A table in the new format (w/ [MAP|SCALE]FULLGAP[1|2] and BDOTSCALE)
	that has linear combinations for the first and last 9 planes of each
	supermodule.  VLD is set for all time but only kData (not kMC/kReroot).
	The CoilTools::IsReverse() should now take care of the sign for
	new code (current development and future dogwood).

	If we adopt this it would be spun into a production database ...
	this ASCII DB is for testing purposes only.

	Previous commit was against "cedar_phy/bhcurv" (this is "dogwood/bhend")
	because of starting with a copy that include the CVS subdir...
	those commits have been backed out using "cvs admin -o rev file".

2007-10-17 21:20  scavan

	* setup/packages-R1.24.4:

	point release for the farm

	with workaround for MRCC/satrack issue

	with /cvs/minoscvs/rep1/minossoft/CandSubShowerSR/AlgSubShowerSRList.cxx bug fixed

2007-10-17 20:58  hartnell

	* NuMuBar/tools/farm.pl:

	Modify so it works for Justin

2007-10-17 20:44  scavan

	* MuonRemoval/SelectEvent.cxx:

	This bypasses a bug that occurs when both sa and sr tracks are created in the reconstruction before MRCC is called

	the bug is that
	  if(cth_test->IsEquivalent(rc))
	When cth_test points to a CandFitTrackSAHandle and rc points to a CandFitTrackCamHandle
	segfaults

	the work around is to just not compare a CandFitTrackSAHandle to a CandFitTrackCamHandle
	     if(strncmp("CandFitTrackSAHandle",cth_test->ClassName(),20)==0)continue;        if(cth_test->IsEquivalent(rc)){
	.....

2007-10-17 20:35  evans

	* NuMuBar/tools/sam.pl:

	The perl script now pulls out the user's user name and sticks it on
	the front of the sam project name.

2007-10-17 20:12  hartnell

	* NuMuBar/NuDSTAna.cxx:

	Adapt to removed variables not being present (don't try and print them)

2007-10-17 20:12  hartnell

	* NtupleUtils/: NuEvent.cxx, NuEvent.h, NuExtraction.cxx,
	  NuReco.cxx:

	Removed some majority curvature variabls that weren't important as well
	as the 6th and 7th shower info. This is probably a 10% size reduction.

2007-10-17 20:10  evans

	* NuMuBar/tools/sam.pl:

	Adding today's date and time to the sam project name. Making pwd the
	place for the output files.

2007-10-17 19:26  hartnell

	* NuMuBar/NuAnalysis.cxx:

	Bring Majority Curvature back from the wilderness... Justin's perftool
	findings have brought the Ntuple making back to being close to IO-bound
	when MajC is included. Horray!

2007-10-17 19:17  evans

	* NtupleUtils/MajorityCurvature.cxx:

	Removing an unused variable.

2007-10-17 19:12  evans

	* NtupleUtils/: MajorityCurvature.cxx, MajorityCurvature.h:

	Discovered Google Perftools and made my majority curvature code at
	least a factor of 5 faster. No change in the user interface or
	results.

2007-10-17 18:07  Brian Rebel <brebel@fnal.gov>

	* NCUtils/NCAnalysisUtils.cxx:

	fix bug in extended model I

2007-10-17 17:57  bckhouse

	* Production/Cedar_phy/restructure-chris/:
	  reco_MC_daikon_far_cedar_phy.C,
	  headers/set_calibrator_daikon_far.h:

	reco_MC_daikon_far_cedar_phy.C

2007-10-17 17:54  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCAnalysisUtils.h,
	  Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolationModule.cxx:

	make the calls for different oscillation models a little more intelligent,
	ie name them something other than FindSurvivalProbability.

	also use the NCType::NuMuToXXX modes when determining which probability
	to apply for a given event.

2007-10-17 17:49  bckhouse

	* Production/Cedar_phy/restructure-chris/reco_MC_far_cedar_phy.C:

	Accidentally left superfluous forward declarations in.

2007-10-17 17:43  bckhouse

	* Production/Cedar_phy/restructure-chris/:
	  reco_MC_daikon_near_cedar_phy.C, headers/set_calibrator_daikon.h,
	  headers/io/attach_output_mc.h:

	New files needed for reco_MC_near_cedar_phy.C

2007-10-17 17:43  bckhouse

	* Production/Cedar_phy/restructure-chris/headers/util/:
	  get_record_title.h, run.h:

	reco_MC_daikon_near_cedar_phy.C

2007-10-17 17:41  bckhouse

	* Production/Cedar_phy/restructure-chris/reco_MC_near_cedar_phy.C:

	Fix output filename.

2007-10-17 17:19  hartnell

	* NuMuBar/macros/mVsTime.C:

	Make coil current, coilIsOk and coilIsReverse plots vs time

2007-10-17 17:19  hartnell

	* NuMuBar/NuDSTAna.cxx:

	Add PID cut to 1st set of vs time plots

2007-10-17 17:17  hartnell

	* NuMuBar/NuTime.cxx:

	Insert 1e12 pot scale factor

2007-10-17 16:10  Robert Hatcher <rhatcher@fnal.gov>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/build_pythia6.sh:

	Better control over removal or not of pythia6 dummy routines PDFSET,
	STRUCTM, STRUCTP using:
	   --dummies=besttry (default) means try to link to CERNLIB libraries
	          pdflib[804] mathlib kernlib; if any of the libraries can't
	          be found then don't remove the dummies
	   --dummies=remove means always remove dummy routines, try to link to
	          whatever libraries can be found
	   --dummies=keep means always keep dummies, don't try to link to CERNLIB

	General cleanup to make sections more clearly separated.

2007-10-17 14:49  arms

	* Contrib/rhatcher/gminos_jobs/umn_bulk_copy.sh:

	Update bulk copy script to account for changes to the setup_umn_bundle.sh script

2007-10-17 13:51  hartnell

	* NtupleUtils/NuExtraction.cxx:

	Cleaned out around 10 unused headers

2007-10-17 12:51  bckhouse

	* Production/Cedar_phy/restructure-chris/:
	  reco_near_cosmic_cedar_phy.C, headers/set_msg_levels_cosmic.h,
	  headers/cosmic/cosmic_configure.h,
	  headers/cosmic/cosmic_create_path.h,
	  headers/cosmic/cosmic_do_report.h,
	  headers/cosmic/cosmic_set_filter.h,
	  headers/cosmic/cosmic_set_prescaling.h:

	First draft of reco_near_cedar_phy.C

2007-10-17 12:47  bckhouse

	*
	  Production/Cedar_phy/restructure-chris/headers/io/attach_output.h:

	Take more parameters.

2007-10-17 11:40  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/DataCacheManager/config/sno.site_ral_sno.local_disks:

	Add Directory used to hold resource locks

2007-10-17 11:28  scavan

	* CandSubShowerSR/AlgSubShowerSRList.cxx:

	modified lies 949 and 957 to fix an occasional core dump

	was

	while(PlanePH[maxPlane+counter]>0||(maxPlane+counter)==249)

	now is

	while((maxPlane+counter)>=0&&(PlanePH[maxPlane+counter]>0||(maxPlane+counter)==249))

2007-10-17 11:24  scavan

	* CandSubShowerSR/AlgSubShowerSRList.cxx:

	modified lies 949 and 957 to fix an occasional core dump

	was

	  while(PlanePH[maxPlane+counter]>0||(maxPlane+counter)==249)

	now is

	  while((maxPlane+counter)>=0&&(PlanePH[maxPlane+counter]>0||(maxPlane+counter)==249))

2007-10-17 05:32  Robert Hatcher <rhatcher@fnal.gov>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/build_pythia6.sh:

	Look around for the necessary CERNLIB libraries pdflib[804], mathlib and
	kernlib; if they can't be found then don't remove the dummy routines
	PDFSET, STRUCTM, STRUCTP.  The non-removal can also be forced by the
	flag --keep-dummies.  If the dummies are left in place then a call to
	one of them will result in a PYSTOP (fortran STOP) at some arbitrary
	place ... generally not nice.  Supplying our own source to build for
	these libraries is a daunting task, so if you want them you'll need
	to have CERNLIB installed somewhere it can find: $CERNLIB $CERNLIBS
	$CERN_DIR/lib or $CERN_ROOT/lib.  This will avoid leaving the libPythia6.so
	with unresolved externals that can't be trivally satisfied during
	a ROOT session:  gSystem->Load("libPythia6.so")

	The source code can be forced to be refetched from the web source via
	the command line flag:--refetch.

2007-10-16 23:42  arms

	* Contrib/rhatcher/gminos_jobs/: gminos_cfg_L010000_near_bhcurv.py,
	  gminos_cfg_L010000_rock_bhcurv.py,
	  gminos_cfg_L010170_near_bhcurv.py,
	  gminos_cfg_L010170_rock_bhcurv.py,
	  gminos_cfg_L010185_far_beam_bhcurv.py,
	  gminos_cfg_L010185_far_invert_bhcurv.py,
	  gminos_cfg_L010185_far_nutau_bhcurv.py,
	  gminos_cfg_L010200_near_bhcurv.py,
	  gminos_cfg_L010200_rock_bhcurv.py,
	  gminos_cfg_L100200_far_beam_bhcurv.py,
	  gminos_cfg_L100200_far_invert_bhcurv.py,
	  gminos_cfg_L100200_far_nutau_bhcurv.py,
	  gminos_cfg_L100200_near_bhcurv.py,
	  gminos_cfg_L100200_rock_bhcurv.py,
	  gminos_cfg_L150200_near_bhcurv.py,
	  gminos_cfg_L150200_rock_bhcurv.py,
	  gminos_cfg_L250200_far_beam_bhcurv.py,
	  gminos_cfg_L250200_far_invert_bhcurv.py,
	  gminos_cfg_L250200_far_nutau_bhcurv.py,
	  gminos_cfg_L250200_near_bhcurv.py,
	  gminos_cfg_L250200_rock_bhcurv.py:

	Prepare daikon_04/bhcurv beam MC cfg scripts

2007-10-16 22:19  hartnell

	* NuMuBar/: macros/makeDstSam.C, tools/sam.pl:

	Now pass the MaxNumberOfFiles to the script as an argument.

	Adapt perl script to use new form.

2007-10-16 22:04  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCAnalysisUtils.h, NCOscProb.cxx,
	  NCOscProb.h, NCType.h, Extraction/NCAnalysisModule.cxx,
	  Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolation.h,
	  Extrapolation/NCExtrapolationJK_fit.cxx,
	  Extrapolation/NCExtrapolationJK_fit.h,
	  Extrapolation/NCExtrapolationMQ.cxx,
	  Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationModule.h,
	  macros/nearFarExtrapolation.C:

	more changes to calculate new oscillation probabilities.

	some structural changes, such as passing vectors of parameters rather than
	individual parameters.  had to change JK and MQ methods to accomodate.

	new oscillation probability functions added to NCOscProb

2007-10-16 21:36  Robert Hatcher <rhatcher@fnal.gov>

	* WebDocs/external_products.html:

	A quick-ish update including:
	  * preferred compiler gcc 3.2 --> 3.4
	  * add description of building pythia6 library
	  * update ROOT section
	     - on how to check out code with Subversion
	     - enable pythia6, xml, asimage subpackage
	     - make cintdlls is essentially a no-op now (part of basic build)
	     - give warning about SRT's setting of MAKEFILE and MAKEFLAGS
	  * how to get and/or install Subversion
	Things could probably still do with some cleaning up but most of the
	basics are now there.y

2007-10-16 21:28  hartnell

	* NuMuBar/macros/Config.C:

	Was loading different libraries in different scripts... this should be
	the more complete set.

2007-10-16 21:08  Robert Hatcher <rhatcher@fnal.gov>

	* SRT_MINOS/SoftRelTools/arch_spec_googleperftools.mk:

	be a bit more circumspect in how one tests for non-blank HAS_PERFTOOLS
	(not just defined but non-blank).

2007-10-16 20:44  hartnell

	* NuMuBar/macros/: FileListSpecial.C, chargeSeparation.C, dstAna.C,
	  makeDst.C, makeDstSam.C, microDst.C, microDstCC.C:

	Using the new Config object throughout

2007-10-16 20:43  hartnell

	* NuMuBar/macros/concatenateDSTs.C:

	A macro to concatenate the DSTs. Not fast, but it deals with the
	histograms properly.

2007-10-16 20:39  hartnell

	* NuMuBar/macros/Config.C:

	An object to do the loading of libraries and setting of msg levels
	(borrowed from MeuCal)

2007-10-16 20:27  boehm

	* NueAna/: ANtpEventInfoAna.cxx, AnalysisInfoAna.cxx,
	  NueStandard.cxx, NueStandard.h, Extrapolation/Comparator.h,
	  Extrapolation/NueBackground.h, Extrapolation/NueExtrapHelper.cxx,
	  Extrapolation/NueExtrapHelper.h,
	  Extrapolation/NueFNExtrapolation.cxx,
	  Extrapolation/NueFNHelper.h, Extrapolation/NueGui.cxx,
	  Extrapolation/NueGui.h, Extrapolation/NueSystematic.cxx,
	  Extrapolation/NueSystematic.h, Extrapolation/Selection.cxx,
	  Extrapolation/Selection.h, Extrapolation/Systematic.cxx,
	  Extrapolation/Systematic.h, Module/NueBeamMonModule.cxx,
	  NueAnaTools/LinkDef.h, NueAnaTools/Selection.cxx,
	  NueAnaTools/Selection.h:

	A whole slew of changes in two broad categories:

	Updates for Ent:
	 - anainfo.inFiducialVolume now filled by the Standard Fiducial Volume
	 - srevent.coilCurrent filled by Alec's new CoilTools
	 - POT counting set to only count pots when CoilIsOK and In forward running
	   (again using coil tools)

	 - Moved the Selection namespace from Extrapolation into NueAnaTools and extended it
	to include MCNN and FidCut
	 - This allows for a new NueStandard functions of the form
	PassesSelection(NueRecord*, Selection) which will work for everything making a nice simple interface

	Updates for Systematics code:
	 - takes modern PIDS
	 - new systematic TrkLike for track like planes
	 - make use of the NueStandard namespace for the cuts
	 - change skzp to use the SKZPweight calculator and to use the current error envelopes
	 - change the definition of emfraction used for the EM v HadCalib split
	 - change the gui to handle cleanly not having all systematics available

2007-10-16 20:19  hartnell

	* NuMuBar/: NuAnalysis.cxx, NuAnalysis.h, NuBeam.cxx, NuBeam.h:

	Fixed a bug with pot counting that I introduced at the weekend. When the
	coil was bad the pots were still being summed.

	More rationalisation and factorisation of the code.

2007-10-16 19:47  scavan

	* Production/Cedar_phy/MRCC/: reco_MC_daikon_far_MRCC_cedar_phy.C,
	  reco_MC_daikon_far_MRCC_cedar_phy_cal.C,
	  reco_MC_daikon_far_cosmic_MRCC_cedar_phy.C,
	  reco_MC_daikon_near_MRCC_cedar_phy.C,
	  reco_MC_daikon_near_cosmic_MRCC_cedar_phy.C,
	  reco_MC_far_MRCC_cedar_phy.C,
	  reco_MC_far_cosmic_MRCC_cedar_phy.C,
	  reco_MC_near_MRCC_cedar_phy.C, reco_far_all_MRCC_cedar_phy.C,
	  reco_far_spill_MRCC_cedar_phy.C,
	  reco_near_cosmic_MRCC_cedar_phy.C,
	  reco_near_spill_MRCC_cedar_phy.C,
	  reco_near_spill_MRCC_special_runs_cedar_phy.C,
	  srsafitter/reco_MC_daikon_far_MRCC_cedar_phy_srsafitter.C,
	  srsafitter/reco_MC_daikon_far_cosmic_MRCC_cedar_phy_srsafitter.C,
	  srsafitter/reco_MC_daikon_near_MRCC_cedar_phy_srsafitter.C,
	  srsafitter/reco_far_all_MRCC_cedar_phy_srsafitter.C,
	  srsafitter/reco_near_spill_MRCC_cedar_phy_srsafitter.C:

	fixed problems with MRCC scripts

2007-10-16 17:57  nwest

	* GridTools/Scripts/jobs/: run_test_job.perl,
	  test_edg-job-get-output.text, test_edg-job-status.text,
	  test_edg-job-submit.text:

	Add utility to to submit and monitor short, simple jobs on the GRID

2007-10-16 17:29  bckhouse

	* Production/Cedar_phy/restructure-chris/: reco_MC_far_cedar_phy.C,
	  reco_MC_near_cedar_phy.C, headers/set_calibrator_far_mc.h,
	  headers/set_msg_levels_far_mc.h,
	  headers/mc_reco_far/mc_reco_far_configure.h,
	  headers/mc_reco_far/mc_reco_far_create_path.h,
	  headers/mc_reco_far/mc_reco_far_do_report.h,
	  headers/reroot/reroot_configure.h:

	First draft of reco_MC_far_cedar_phy.C

2007-10-16 16:56  bckhouse

	* Production/Cedar_phy/restructure-chris/:
	  reco_MC_near_cedar_phy.C, headers/reroot/reroot_configure.h:

	reroot_configure() now takes GevPerMip as a parameter.

2007-10-16 15:52  hartnell

	* NtupleUtils/NuExtraction.cxx:

	When extracting the coilIsOk might as well get the coil current as well

2007-10-16 15:21  hartnell

	* NuMuBar/: NuDSTAna.cxx, NuDSTAna.h, NuPlots.cxx:

	Added:
	NuDSTAna::ConcatenateDSTs
	This just concatenates files with absolutely no cuts. The histograms
	containing the pot, times, etc info are also dealt with.

	Also, now use the histograms to determine the earliest and latest times
	across multiple files.

2007-10-16 15:17  hartnell

	* NtupleUtils/: NuCuts.cxx, NuExtraction.cxx:

	Use CoilTools to get the coil current (Thanks to Robert for the
	suggestion). This should be a lot faster.

2007-10-16 13:14  bckhouse

	*
	  Production/Cedar_phy/restructure-chris/headers/io/attach_output_mc.h:

	Forgot a file.

2007-10-16 12:41  ishi

	* setup/packages-development:

	New modules G3PTSim and GeoSwimmer are added.

2007-10-16 12:21  bckhouse

	* Production/Cedar_phy/restructure-chris/:
	  reco_far_spill_cedar_phy.C, headers/set_calibrator_far.h,
	  headers/set_msg_levels_far.h, headers/io/attach_blinded_output.h:

	First draft of reco_far_spill_cedar_phy.C

2007-10-16 12:18  bckhouse

	* Production/Cedar_phy/restructure-chris/:
	  reco_near_spill_MRCC_cedar_phy.C, reco_near_spill_cedar_phy.C,
	  headers/use_new_hv_table.h,
	  headers/far_spill/far_spill_configure.h,
	  headers/far_spill/far_spill_configure_filters.h,
	  headers/far_spill/far_spill_create_path.h,
	  headers/far_spill/far_spill_do_report.h,
	  headers/io/attach_output.h, macros/load_libs.C:

	Files for reconstructing far detector.

2007-10-16 10:00  bckhouse

	*
	  Production/Cedar_phy/restructure-chris/headers/util/set_cand_output_bntp.h:

	Add missing line.

2007-10-16 05:46  dap56

	* Mad/MadPIDAnalysis.cxx:

	Added code from Niki to access ND coil current from DB

2007-10-16 03:53  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/fnal_ups/neugen3/: v3_5_2.table, v3_5_2.version,
	  v3_5_3.table, v3_5_3.version:

	ups setup file for neugen3.

2007-10-15 22:29  hartnell

	* NuMuBar/macros/: chargeSeparation.C, dstAna.C, makeDst.C,
	  makeDstSam.C, microDst.C, microDstCC.C:

	Add gSystem->Load("libDcsUser"); before NtupleUtils

2007-10-15 22:02  hartnell

	* NtupleUtils/: NuCuts.h, NuExtraction.cxx, NuExtraction.h:

	Missed these...

	Implementing CoilToils (from Alec Habig with database caching from Robert)

2007-10-15 21:58  hartnell

	* NtupleUtils/NuCuts.cxx:

	Minor change to MSG

2007-10-15 21:40  hartnell

	* NtupleUtils/NuCuts.cxx:

	Adapt to new CoilTools::IsOk.

2007-10-15 21:39  hartnell

	* NuMuBar/: NuAnalysis.cxx, NuPlots.cxx, NuTime.cxx:

	Extract the new coilIsOk variables. Switch from coilOn to coilIsOk.

2007-10-15 21:28  hartnell

	* NtupleUtils/: NuEvent.cxx, NuEvent.h:

	Removed:
	  Bool_t coilOn;

	Added:
	  Bool_t coilIsOk;
	  Bool_t coilIsReverse;

	To use Robert's new CoilTools.

2007-10-15 20:19  hartnell

	* NuMuBar/macros/mVsTime.C:

	Macro to make plots of quantities vs time.

	Very useful for data quality monitoring!

2007-10-15 20:14  hartnell

	* NuMuBar/NuDSTAna.cxx:

	Added code to sum the potSinceLastEvent: have to do this whenever events
	are cut out.

2007-10-15 20:11  hartnell

	* NuMuBar/NuTime.cxx:

	Add a load more variables to plots vs time

2007-10-15 19:56  hartnell

	* NuMuBar/NuAnalysis.cxx:

	Committed wrong configuration last night... DO want to cut on coil
	current, etc. Also, use kFullDST anaVersion.

	(will try and implement Robert's new coil code now...)

2007-10-15 19:39  Robert Hatcher <rhatcher@fnal.gov>

	* DatabaseUpdater/dbu_sampy.C:

	copy of script being used to fill new DB tables in offline_dev and create
	the SAM python files.

2007-10-15 17:13  koskinen

	* NCUtils/Extrapolation/NCExtrapolation.cxx:

	Fixed issue with fLocFElectron variable being uninitialized in
	NCExtrapolation constructors.

2007-10-15 16:35  Sue Kasahara <schubert@hep.umn.edu>

	* G3PTSim/TGeant3/TGeant3.cxx:

	Undo commit of yesterday to reduce verbosity of StopRun.  It's not that
	this method was overly verbose, but rather that the method was being
	called frequently by an older version of GeoSwimmer (already fixed
	by Masaki in the development version).

2007-10-15 16:33  bckhouse

	* Production/Cedar_phy/restructure-chris/macros/tsql_override.C:

	This file was based on an old version of the tsql override code.
	Should just use the version in asciidb/ instead.

2007-10-15 15:58  bckhouse

	* Production/Cedar_phy/restructure-chris/:
	  reco_MC_near_cedar_phy.C, headers/mc_reco/mc_reco_configure.h,
	  headers/mc_reco/mc_reco_create_path.h,
	  headers/mc_reco/mc_reco_do_report.h,
	  headers/reroot/reroot_configure.h,
	  headers/reroot/reroot_create_path.h,
	  headers/reroot/reroot_do_report.h:

	Commit draft of reco_MC_near_cedar_phy.C

	Some of these files may well need renaming/moving.

2007-10-15 14:29  koskinen

	* NCUtils/Extrapolation/NCExtrapolationJK_fit.cxx:

	Edited the FillResults histogram to return the oscillated background plots

2007-10-15 13:48  scavan

	* Production/Cedar_phy/MRCC/:
	  reco_MC_daikon_far_cosmic_MRCC_cedar_phy.C,
	  reco_MC_daikon_near_cosmic_MRCC_cedar_phy.C,
	  reco_MC_far_MRCC_cedar_phy.C,
	  reco_MC_far_cosmic_MRCC_cedar_phy.C,
	  reco_MC_near_MRCC_cedar_phy.C, reco_far_all_MRCC_cedar_phy.C,
	  reco_far_spill_MRCC_cedar_phy.C,
	  reco_near_cosmic_MRCC_cedar_phy.C,
	  reco_near_spill_MRCC_cedar_phy.C,
	  reco_near_spill_MRCC_special_runs_cedar_phy.C:

	modified MRCC scripts to accept arguments nSkip and nRun with defaults nSkip=0 and nRun=100000

2007-10-15 13:39  bckhouse

	* Production/Cedar_phy/restructure-chris/macros/add_to_path.C:

	Add a macro add_to_path(TString release). Adds Production/release to ROOT's macro and include paths.

2007-10-15 13:15  bckhouse

	*
	  Production/Cedar_phy/restructure-chris/headers/io/attach_output.h:

	Add arguement to control whether candidate files are written out. Set to true by default.

2007-10-15 13:10  bckhouse

	* Production/Cedar_phy/restructure-chris/:
	  reco_near_spill_MRCC_cedar_phy.C, reco_near_spill_cedar_phy.C,
	  headers/io/set_input_data.h:

	Minor changes.

2007-10-15 13:07  bckhouse

	* Production/Cedar_phy/restructure-chris/: headers/tsql_override.h,
	  headers/io/attach_output.h, headers/util/load_libs.h,
	  macros/load_libs.C, macros/tsql_override.C:

	Similarly move tsql_override() to macros/

2007-10-15 13:03  bckhouse

	* Production/Cedar_phy/restructure-chris/:
	  reco_near_spill_MRCC_cedar_phy.C, reco_near_spill_cedar_phy.C,
	  headers/attach_mrcc_path.h:

	Change load_libs to a .C file so it can be used interactively.

2007-10-15 12:12  musser

	* CandFitTrackCam/: AlgFitTrackCam.cxx, AlgFitTrackCam.h,
	  AlgFitTrackCamList.cxx, CandFitTrackCam.cxx, CandFitTrackCam.h,
	  CandFitTrackCamHandle.cxx, CandFitTrackCamHandle.h,
	  FitTrackCamListModule.cxx, FitTrackCamListModule.h:

	removal of range bias.
	pass both bias and unbiased q/p - add member to handle to support this
	improvements to vertex location
	provide avg Bfield along track

2007-10-15 11:36  Nick West <n.west1@physics.oxford.ac.uk>

	* setup/setup_minossoft_csf.sh:

	Use the new GRID setup script

2007-10-15 11:08  Nick West <n.west1@physics.oxford.ac.uk>

	* setup/setup_minossoft_csf.csh:

	Use the new GRID setup script

2007-10-15 11:00  nwest

	* setup/setup_minossoft_oxford.csh:

	Use the new GRID setup script

2007-10-15 10:47  nwest

	* GridTools/docs/ChangeLog:

	Minor updates: RSD GridTools assemble and install; Scripts setup

2007-10-15 10:46  nwest

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/install_GridTools.sh:

	Remove component libraries - GridTools installed a single library.

2007-10-15 10:46  nwest

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/assemble_GridTools.sh:

	Abort assemble if MOG_TOOLS appears to point to an RSD installed version (installed_libraries exists)

2007-10-15 10:45  nwest

	* GridTools/: DataCacheManager/init.pm,
	  DataCacheManager/docs/dcm.html,
	  RemoteSoftwareDeployment/doc/rsd.html,
	  RemoteSoftwareDeployment/driver/initialise_globals.pm,
	  Scripts/maintenance/version_number:

	Update to version V00-07-41

2007-10-15 08:17  nwest

	* GridTools/Scripts/setup/setup_minos_lcg_grid.sh:

	Use "pro" link, if it exists, to define the best version, rather than
	take the one with the highest version number.

2007-10-15 08:17  nwest

	* GridTools/Scripts/: docs/Scripts.html,
	  setup/setup_minos_lcg_grid.csh:

	Support the use of MOG_TOOLS and MOG_SCRIPTS as a way of locating
	supporting scripts without having to cd to directory holding them.

2007-10-15 08:12  nwest

	* GridTools/Ganga/docs/ganga.html:

	Current version of Ganga now 4.4.1

2007-10-15 05:43  nwest

	* DatabaseMaintenance/tools/checksum_partial_rebuild.pl:

	Remove the setting of the DBM_SELECT_SEQNO environmental variable and
	allow the differential checksumming optimise the rebuild.  Do this as
	it's selection can lead to the sanity check failing i.e. if further
	data has been added to the table since the checksum log was created.

2007-10-15 03:06  Sue Kasahara <schubert@hep.umn.edu>

	* CandNtupleSR/Module/NtpSRModule.cxx:

	Back out Jim's commit today to fill mc truth particle min/maxE.  This is now
	filled as part of NtpMCStdHep.

2007-10-15 02:49  Sue Kasahara <schubert@hep.umn.edu>

	* MCNtuple/Module/: NtpMCModule.cxx, NtpMCModule.h:

	Fill NtpMCStdHepHit data member of NtpMCStdHep.
	New private data method:
	  bool BuildStdHepToDigiHit(const TClonesArray* stdheparray,
	                            const TClonesArray* simdigihitarray);
	to build map of stdhep particles to associated digihits, where
	those digihits are directly deposited by the particle and are
	not veto shield hits.

2007-10-15 02:28  Sue Kasahara <schubert@hep.umn.edu>

	* MCNtuple/: NtpMCStdHep.cxx, NtpMCStdHep.h:

	New stdhep data member:
	 NtpMCStdHepHit dethit[2];   // record info about first/last detector digihit
	to store information derived from the first/last *detector* (veto shield
	excluded) digiscinthit associated with the stdhep particle.
	Use NtpMCStdHepHit::IsValid() to determine the validity of the hit, i.e. to
	test if no hits were recorded.

2007-10-15 02:20  Sue Kasahara <schubert@hep.umn.edu>

	* MCNtuple/: LinkDef.h, NtpMCStdHepHit.cxx, NtpMCStdHepHit.h:

	New class to record information about a stdhep particle energy deposition
	hit as derived from an associated digiscinthit.  To be used to record
	information about the first & last hit deposited by a stdhep particle.

2007-10-14 23:43  hartnell

	* NuMuBar/tools/sam.pl:

	More jobs to run.

	Alex: some of your dates were missing the ":ss" so I just added ":00".

2007-10-14 23:09  arms

	* Contrib/rhatcher/gminos_jobs/:
	  gminos_cfg_CosmicLE_near_bhcurv.py, run_umn.sh,
	  setup_umn_bundle.sh:

	Commit changes necessary to produce ND CosmicLE samples. Rename location for UMN flux files.

2007-10-14 22:57  hartnell

	* NuMuBar/NuAnalysis.cxx:

	Minor mods... should be the last commit for tonight.

2007-10-14 22:48  musser

	* G3PTSim/TGeant3/TGeant3.cxx:

	suppress verbose 'run stopped' cout

2007-10-14 22:43  musser

	* CandNtupleSR/Module/NtpSRModule.cxx:

	subsitute improved versions of min/max track energy calls to TruthHelper
	C

2007-10-14 22:39  hartnell

	* NuMuBar/NuDSTAna.cxx:

	The FullDSTs now have the bad spills written out, so added a cut to the
	standard set to remove them:
	lib.cuts.IsGoodBeamDetPOTCountingStage()

	When making micro DSTs update the nu.potSinceLastEvt variables since
	many events get cut out.

	Add more vs time plot for events with minimal cuts.

2007-10-14 22:36  musser

	* CandShowerSR/DBtxt_AlgShowerSR_Beam.C:

	subsitute John Marshall's wt cc calibration constants

2007-10-14 22:34  hartnell

	* NuMuBar/: NuTime.cxx, NuTime.h:

	Added some new variables to plot vs time.

	Now make AllQ plots as well as PQ and NQ.

2007-10-14 22:32  musser

	* DataUtil/: TruthHelper.cxx, TruthHelper.h:

	add min/max E support

2007-10-14 22:16  musser

	* RecoBase/CandShowerHandle.cxx:

	misc shower energy tweaks

2007-10-14 21:13  Robert Hatcher <rhatcher@fnal.gov>

	* DcsUser/CoilTools.h:

	Make GetCoilState() and GetMagNear() publically accessible -- like the
	comment stated their intent to be.

2007-10-14 21:12  hartnell

	* NtupleUtils/: NuCounter.cxx, NuCounter.h, NuCuts.cxx, NuCuts.h:

	Added:
	  IsGoodBeamDetPOTCountingStage()
	to remove bad spills and !coilOn.

	Count these too.

2007-10-14 20:38  Sue Kasahara <schubert@hep.umn.edu>

	* CVSROOT/check_access:

	Add Jim to CandFitTrackCam.

2007-10-14 20:37  Sue Kasahara <schubert@hep.umn.edu>

	* CandNtupleSR/Module/: NtpSRModule.cxx, NtpSRModule.h:

	Remove fill of NtpSRTrack::mcminE/mcmaxE data members and reference
	to TruthHelper.  NtpSRModule version number should always be zero
	since this module is not i/o'able.

2007-10-14 20:32  Sue Kasahara <schubert@hep.umn.edu>

	* CandNtupleSR/NtpSRTrack.h:

	Remove:
	  Float_t mcmaxE; // maximum digiScintHit Energy
	  Float_t mcminE; // minimum digiScintHit Energy
	since these don't belong here.
	Update version number 7 to 8.

2007-10-14 20:10  hartnell

	* NuMuBar/NuDSTAna.cxx:

	Adapt to the new anaVersion: kFullDST

2007-10-14 20:06  hartnell

	* NuMuBar/macros/makeDst.C:

	Added:
	  //j.Path("NuDST").Mod("NuModule").Set("UseOldMethod=1");

2007-10-14 20:03  hartnell

	* NuMuBar/NuModule.h:

	Add fUseOldMethod data member

2007-10-14 19:59  hartnell

	* NuMuBar/: NuAnalysis.cxx, NuModule.cxx:

	Have reverted ChargeSeparationOneSnarl so as to reproduce previous
	results. However the default is now the new MakeFullDST(). To use the
	old method use this in the macro:
	j.Path("NuDST").Mod("NuModule").Set("UseOldMethod=1");

	Fixed a small (0.2%) bug in the number of events that got written out
	depending on the analysis version. Was only checking if the primary
	track was in the loose fid vol, now check all tracks so that a different
	track can be chosen at the second stage.

2007-10-14 19:42  Sue Kasahara <schubert@hep.umn.edu>

	* CVSROOT/check_access:

	Add Jim to DataUtil and G3PTSim commit list.

2007-10-14 14:16  hartnell

	* NuMuBar/NuPlots.h:

	coilOn is now part of NuEvent

2007-10-14 14:15  hartnell

	* NuMuBar/: NuAnalysis.cxx, NuAnalysis.h:

	Work in progress...

	Added a new function to be used in making the FullDSTs.

	void NuAnalysis::MakeFullDST(const NtpStRecord* pntp,
	                             const NtpBDLiteRecord* pntpBD,
	                             const NtpFitSARecord* pntpSA)

	This function should be faster as it does not produce the 100s of
	analysis plots that ChargeSeparationOneSnarl used to. The coil current
	and goodBeamSntp is no longer cut on here, has to be done at the
	microDST stage. The goodBeamSntp and coilOn variables are now written to
	the NuDST.

	The potSinceLastEvt variables are now filled: this should allow pots per
	day/week/month to be derived.

	I will revert ChargeSeparationOneSnarl to it's previous behaviour so as
	not to change things for other users.

2007-10-14 14:04  hartnell

	* NuMuBar/: NuPlots.cxx, NuTime.cxx:

	Minor mods

2007-10-14 14:02  hartnell

	* NtupleUtils/: NuExtraction.cxx, NuReco.cxx:

	Filling the new NC discriminator variables

2007-10-14 13:58  hartnell

	* NtupleUtils/: NuEvent.cxx, NuEvent.h:

	Added NC discriminator variables:

	   Float_t evtphsigcor;//evt.ph.sigcor
	   Float_t evtphsigmap;//evt.ph.sigmap

	   Int_t ntrklike;//the number of trk-like planes
	   Float_t trkphsigcor;//trk.ph.sigcor
	   Float_t trkphsigmap;//trk.ph.sigmap

	and variables to say whether the coil was on and if the beam was good
	according to the data in the sntp file:

	   Bool_t goodBeamSntp;//uses the beam data in the sntp file
	   Bool_t coilOn;//if coil current passes the cut

	Previously these variables were cut on when the DST was made... but for
	VsTime plots you need to have this info in the DST.

	Also added variables to allow POT counting including snarls with zero
	events:

	   Float_t potSinceLastEvt;//includes pot count for spills w/ no evts
	   Float_t potSinceLastEvtGood;//as above but also good beam+det spills
	   Float_t potSinceLastEvtBad;//as above but for bad beam+det spills

2007-10-14 13:51  hartnell

	* NtupleUtils/: NuCuts.cxx, NuCuts.h:

	Added IsCoilOn() to be used when making the FullDSTs and counting POTs

2007-10-13 23:33  musser

	* CandEventSR/: AlgEventSR.cxx, AlgEventSSList.cxx:

	fill event dcos variables

2007-10-13 23:19  musser

	* CandNtupleSR/: NtpSRFitTrack.h, NtpSRMomentum.h, NtpSRTrack.h,
	  Module/NtpSRModule.cxx, Module/NtpSRModule.h:

	add bave and min/maxE variable to fit track branch

2007-10-13 22:52  musser

	* RecoBase/: AlgTrack.cxx, CandFitTrack.cxx, CandFitTrack.h,
	  CandFitTrackHandle.cxx, CandFitTrackHandle.h,
	  CandShowerHandle.cxx:

	Update CandShowerHandle::SetEnergy, add ability to hold ave mag field along track

2007-10-13 22:07  hartnell

	* NuMuBar/macros/: dstAna.C, mEnergy.C:

	Minor improvements...

2007-10-13 22:01  hartnell

	* NuMuBar/NuTime.cxx:

	Extended the VsTime plot making code so that it is now trivial to add
	new variables.

2007-10-13 21:59  hartnell

	* NuMuBar/NuAnalysis.cxx:

	The coil current was not being written out to the ntuple... it got lost
	in an earlier code rearrangement.

	Now writing to the new "pot" variable.

	No longer cutting on IsGoodBeam here since it will abort in certain
	configurations. This cut is now done at a later stage.

2007-10-13 21:55  hartnell

	* NtupleUtils/: NuCuts.cxx, NuEvent.cxx:

	IsGoodBeam will now abort if it encounters bad beam in the ND... since
	it would silently mess up the pot counting at present.

2007-10-13 21:53  hartnell

	* NtupleUtils/NuEvent.h:

	Added:
	  Float_t pot;//pot in current spill

	Actually hard to use properly since in an event based ntuple you don't
	see the spills with zero events. Furthermore, you could have two events
	in one spill... I plan to add a variable that integrates the pot between
	events and takes account of spills with 2+ events.

2007-10-13 19:43  hartnell

	* NuMuBar/: NuDSTAna.cxx, NuDSTAna.h:

	Have done a lot of factorization of the code. I had done too much cut
	and paste. The std cuts are now in 2 simple functions: Pre-selction cuts
	and final cuts. The multiple calls to NuPlots are also now in their own
	functions.

	These methods are intended to be the ones to run to make standard sets
	of plots:

	  void StdCCAna();//std CC analysis
	  void StdNMBAna();//std NuMuBar analysis

2007-10-13 03:20  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCAnalysisUtils.h, NCOscProb.cxx,
	  NCOscProb.h, Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolation.h,
	  Extrapolation/NCExtrapolationJK_fit.cxx,
	  Extrapolation/NCExtrapolationJK_fit.h,
	  Extrapolation/NCExtrapolationMQ.cxx,
	  Extrapolation/NCExtrapolationModule.cxx:

	changes for using alfons' parameterization for the oscillation probabilities.

	add NCExtrapolation::FindSurvivalProbability method to make it easier to
	switch between different models

2007-10-12 22:24  hartnell

	* NuMuBar/: NuDSTAna.cxx, NuDSTAna.h:

	Added VsTime to loop over NuDST and make lots of variables vs time plots

	Added DoIOSimple.

2007-10-12 22:24  hartnell

	* NuMuBar/: NuTime.cxx, NuTime.h:

	Added code to make vs. time plots in different binnings. Just a start
	for now... more to come.

2007-10-12 22:22  hartnell

	* NuMuBar/: NuPlots.cxx, NuPlots.h:

	FillNtupleEarliestLatestTime at NuDST generation time so that
	appropriate date ranges can be set on plots at a later stage.

2007-10-12 21:49  ahimmel

	* NuMuBar/tools/sam.pl:

	Added RunJob3 to process RunII data prior to the "April Showers" problem.

2007-10-12 20:05  arms

	* Contrib/rhatcher/gminos_jobs/gminos_cfg_CosmicLE_near_bhcurv.py:

	new config for ND low energy cosmic muon MC

2007-10-12 19:59  Robert Hatcher <rhatcher@fnal.gov>

	* Loon/GNUmakefile:

	add reference to arch_spec_googleperftools.mk which will link the -lprofiler
	in to the loon executable by default (if possible, should be no failure
	if it can't be found).  By default this costs nothing.  Profiling is only
	done if it is externally enabled by defining $CPUPROFILE.

2007-10-12 19:54  Robert Hatcher <rhatcher@fnal.gov>

	* SRT_MINOS/SoftRelTools/arch_spec_googleperftools.mk:

	an SRT arch_spec config makefile fragment for use with Google's
	PerfTools package.  Looks for $PERFTOOLS_DIR, but if not found defaults
	to $INSTALLATION.  If it can't find the -lprofiler library then
	nothing gets linked.

	By default it only needs to be linked in, but then profiling is not
	specific to any routine but the executable as a whole.  To compile in calls
	to it  use:
	     #include <google/profiler.h>
	in the source code and add:
	     include SoftRelTools/arch_spec_googleperftools.mk
	to the relevant GNUmakefile.

2007-10-12 19:12  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/vld/CosmicLE/bfield/: PTSim_g3Config.C,
	  exe_gminos_ptsim.sh, gminos_base.ffr, gminos_kine.ffr,
	  kine_6_0_0_10_300_0_1500.gif, pedisplay.C, ptsim_G3_eggplant.C,
	  reco_MC_gminos.C, reco_MC_ptsim.C, reco_minos.gaf_list:

	Scripts to generate muon trajectories using gminos and ptsim
	with continuous energy loss only activated.  The purpose is to
	detect differences in bfield implementation.
	kine_6_0_0_10_300_0_1500.gif shows a ptsim trajectory overlayed over
	that of gminos for the favorite test case muon which passes through
	the coil region, twice. The trajectories agree with each other to
	a couple mm.

2007-10-12 18:46  boehm

	* NueAna/: NueStandard.cxx, NueStandard.h:

	Adding new functions to NueStandard:

	PassesSysPreSelection - an extended preselection "space" which allows for variations in preselected quantities to be varied in systematic studies.

	Passes(ANN/SSPID/Cut)Selection - cuts on three of the standard PID variables

	As usual function is overloaded to take a NueRecord or the variables in question

2007-10-12 17:45  koskinen

	* NCUtils/Extrapolation/: NCExtrapolationModule.cxx,
	  NCExtrapolationModule.h:

	Added a new flag to the Module which sets whether to add nue to the
	analysis effects.

2007-10-12 17:41  bckhouse

	* Production/Cedar_phy/restructure-chris/:
	  reco_near_spill_MRCC_cedar_phy.C, headers/attach_mrcc_path.h,
	  headers/util/get_record_title.h:

	Fix up refactored muon script.
	Extract common code into get_record_title()

2007-10-12 16:52  bckhouse

	* Production/Cedar_phy/restructure-chris/:
	  reco_near_spill_MRCC_cedar_phy.C, reco_near_spill_cedar_phy.C,
	  headers/attach_mrcc_path.h:

	Muon removal script.

2007-10-12 16:44  nwest

	* GridTools/Scripts/setup/setup_minos_lcg_grid.sh:

	Switch to Ganga 4.4.1 14 September 2007

2007-10-12 16:14  nwest

	* GridTools/docs/data_lfc_lcg.html:

	LFC Vo rename /grid/minos -> /grid/minos.vo.gridpp.ac.uk

2007-10-12 16:14  nwest

	* GridTools/: Scripts/docs/Scripts.html,
	  Scripts/setup/locate_and_run_setup_wn.sh,
	  Scripts/setup/set_routines.sh, Scripts/setup/set_sh_env.sh,
	  Scripts/setup/set_shell_env.pm,
	  Scripts/setup/setup_minos_lcg_grid.csh,
	  Scripts/setup/setup_minos_lcg_grid.sh,
	  Scripts/setup/setup_ui.csh, Scripts/setup/setup_ui.sh,
	  Scripts/setup/setup_wn.sh, docs/ChangeLog:

	Major clean up and simplification of setup scripts and associated
	documentation.

2007-10-12 16:14  nwest

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/install_GridTools.sh:

	Place copies of the GridTools/Scripts setup scripts in s/w top level
	directory to simply access when running on the GRID.

2007-10-12 16:14  nwest

	* GridTools/RemoteSoftwareDeployment/: doc/rsd.html,
	  driver/cmd_install.pm:

	Add RSD_SW_DIR to install API

2007-10-12 16:13  nwest

	* GridTools/: DataCacheManager/init.pm,
	  DataCacheManager/docs/dcm.html,
	  RemoteSoftwareDeployment/driver/initialise_globals.pm,
	  Scripts/maintenance/version_number:

	Update to version V00-07-40.

2007-10-12 16:07  bckhouse

	* Production/Cedar_phy/restructure-chris/headers/: io/set_input.h,
	  spill/spill_configure.h:

	Remove old named file.

2007-10-12 16:06  bckhouse

	* Production/Cedar_phy/restructure-chris/:
	  reco_near_spill_cedar_phy.C, headers/io/set_input_data.h:

	Rename file.

2007-10-12 16:04  bckhouse

	*
	  Production/Cedar_phy/restructure-chris/headers/io/attach_output.h:

	Fix stupid typo. Now the script doesn't crash early on.

2007-10-11 22:01  Robert Hatcher <rhatcher@fnal.gov>

	* BField/: BField.cxx, BField.h, BfldDbiPlaneMap.cxx,
	  BfldDbiPlaneMap.h, BfldLoanPool.cxx, BfldLoanPool.h:

	Extend BfldDbiPlaneMap so that it can hold maps/scales for full plane
	coverage in the inter-steel gap; fall back to using line current if
	no map is specified or if explicitly set to do so via UseLineCurrentInGap
	setting of BfldLoanPool config.  Also extend DB table with column to hold
	Bdot scale factor, rather than mixing it into the map scale #, so that
	we can choose at run time whether to apply those factors.

2007-10-11 19:37  scavan

	* Production/Cedar_phy/MRCC/: reco_MC_daikon_far_MRCC_cedar_phy.C,
	  reco_MC_daikon_far_MRCC_cedar_phy_cal.C,
	  reco_MC_daikon_far_cosmic_MRCC_cedar_phy.C,
	  reco_MC_daikon_near_MRCC_cedar_phy.C,
	  reco_MC_daikon_near_cosmic_MRCC_cedar_phy.C,
	  reco_MC_far_MRCC_cedar_phy.C,
	  reco_MC_far_cosmic_MRCC_cedar_phy.C,
	  reco_MC_near_MRCC_cedar_phy.C, reco_far_all_MRCC_cedar_phy.C,
	  reco_far_spill_MRCC_cedar_phy.C,
	  reco_near_cosmic_MRCC_cedar_phy.C,
	  reco_near_spill_MRCC_cedar_phy.C,
	  reco_near_spill_MRCC_special_runs_cedar_phy.C,
	  srsafitter/reco_MC_daikon_far_MRCC_cedar_phy_srsafitter.C,
	  srsafitter/reco_MC_daikon_far_cosmic_MRCC_cedar_phy_srsafitter.C,
	  srsafitter/reco_MC_daikon_near_MRCC_cedar_phy_srsafitter.C,
	  srsafitter/reco_far_all_MRCC_cedar_phy_srsafitter.C:

	modified all currently used scripts to also write out the MRCC tree in the ntupleMRNT.root file

	MRCC scripts are in the Production/Cedar_phy/MRCC directory

2007-10-11 16:52  hartnell

	* NtupleUtils/doc/: NuDST.html, cssSystematicsDSTs.html:

	Doh, forgot to upload these from 3 weeks ago... collaboration meeting
	panic mode obviously...

2007-10-11 14:16  Robert Hatcher <rhatcher@fnal.gov>

	* Production/asciidb/set_tsql_override.C:

	Actually _commit_ the change to allow ASCII_DB_SET to allow "_" as a valid
	separator between different 'sets' (read subdirs).

2007-10-11 13:58  bckhouse

	* Production/Cedar_phy/restructure-chris/headers/:
	  io/attach_output.h, io/set_input.h, spill/spill_configure.h,
	  spill/spill_configure_filter.h, spill/spill_configure_shower.h,
	  spill/spill_create_path.h, spill/spill_do_report.h,
	  util/get_run_number.h, util/load_libs.h, util/run.h,
	  util/set_cand_output_bntp.h, util/set_ntpst_output_bntp.h:

	The rest of the files.

2007-10-11 13:58  bckhouse

	* Production/Cedar_phy/restructure-chris/headers/:
	  apply_spectrometer_fudge.h, configure_ugli.h, set_calibrator.h,
	  set_msg_levels.h, tsql_override.h, use_new_hv_table.h:

	More restructuring files.

2007-10-11 13:57  bckhouse

	*
	  Production/Cedar_phy/restructure-chris/reco_near_spill_cedar_phy.C:

	My first draft of script restructuring.

2007-10-11 13:48  asousa

	* CVSROOT/check_access:

	Giving the new batchers Chris and Matt write permissions to Production package.

2007-10-11 10:23  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/: DataCacheManager/get_site_info.pm,
	  RemoteSoftwareDeployment/driver/get_site_info.pm:

	Make extraction of SL version from /etc/redhat-release case insensitive - Oxford and RAL were different

2007-10-11 07:05  Nick West <n.west1@physics.oxford.ac.uk>

	* setup/msrt:

	When pruning a release and checking that a package isn't used by
	another release, skip check if package directory doesn't exist in that
	release to avoid cosmetic warning about missing directory.

2007-10-10 23:57  ahimmel

	* NuMuBar/macros/alex/: FileListSpecial.C, Initialize.C,
	  LoadPlots.C, VarList_6.C, VarList_7_border.C, VarList_7_brev.C,
	  VarList_8.C, VarList_8_border.C, VarList_weeks.C, bRevAna.C,
	  cssAna.C, mBRevAccept.C, mBRevBkgPer.C, mBRevBorder.C,
	  mBRevContamination.C, mBRevNumbers.C, mBRevRatio.C,
	  mBRevSpectra.C, mBRevWeeks.C, mBorder.C, mCSS.C, map.C:

	Adding my scripts to CVS in their own folder so I can move them from release
	to release.

2007-10-10 23:01  Robert Hatcher <rhatcher@fnal.gov>

	* Validity/: LinkDef.h, VldTimeStamp.h:

	Make the annoying message:
	  Warning in <TClassTable::Add>: class timespec already in TClassTable
	go away.  This is because both ROOT and this class were making adding timespec
	to the dictionary.  Since ROOT is doing it we don't have to any more.
	To get the headers to VldTimeStamp right we can just include TTimeStamp.h
	(which is their version of the same class).  At some point the differences
	between this class and the ROOT version should be sorted out and VldTimeStamp
	be made a derived (if necessary due to additional methods) class of the
	ROOT class.

2007-10-10 19:07  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	remove debugging cout

2007-10-10 19:00  koskinen

	* NCUtils/Extrapolation/NCExtrapolationJK_fit.cxx:

	Fixed a typo that had numu to nue behaving as nue to nue in the
	FillDataMCHistograms for the FD function.

2007-10-10 18:46  hartnell

	* NuMuBar/macros/makeDstSam.C:

	Adapt to Liz's upgrades to IoModule

2007-10-10 18:45  hartnell

	* NuMuBar/tools/: farm.pl, sam.csh:

	Latest

2007-10-10 18:44  hartnell

	* NuMuBar/tools/sam.pl:

	My all in one script for queurying SAM, starting a SAM project and
	then submitting jobs to the batch farm to consume all the files in the
	project

2007-10-10 18:25  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCAnalysisUtils.h, NCOscProb.cxx,
	  NCType.h, Extrapolation/NCBeam.cxx,
	  Extrapolation/NCEnergyBin.cxx, Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolationMQ.cxx,
	  Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationModule.h, macros/ncccSeparationNC.C:

	changes to handle nu_e events are now in place.

2007-10-10 17:48  boehm

	* NueAna/NueAnaTools/: NueConvention.cxx, NueConvention.h,
	  OscProb.cxx:

	OscProb wasn't actually calculating values for the anti-nus, also renamed the functions to be a little bit more informative

2007-10-10 17:48  arms

	* Contrib/rhatcher/gminos_jobs/gminos_jobs.py:

	Slight modification to deal with a new naming convention for CosmicLE stdhep files

2007-10-10 15:48  ishi

	* GeoSwimmer/GeoSwimApplication.cxx:

	StopTrack() instead of StopRun().

2007-10-10 15:10  boehm

	* NueAna/MCNNVars.h:

	Advancing the ClassDef number

2007-10-10 15:03  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/vld/CosmicLE/: ValidationLog, cosmicVtx.gif,
	  drawCosmicVtx.C, genCosmicVtxHist.C:

	Scripts to generate and draw cosmic ray vertices in a box defined by
	the far detector hall dimensions.  cosmicVtx.gif shows that the vertices
	are clearly within the hall dimensions.
	ValidationLog therefore updated to note that any rock composition/density
	differences between the gminos & ptsim run won't make any
	difference to the simulation results.

2007-10-10 14:29  boehm

	* NueAna/NueAnaTools/: NueConvention.cxx, NueConvention.h,
	  OscProb.cxx:

	Oscprob codes have been moved into the NueConventions namespace to prevent possible library issues

2007-10-10 13:24  rustem

	* UnfoldingData/: AlgUnfold.h, CellVec.h, Matrix.cxx,
	  Near/AlgAssignNear.cxx, Near/AlgAssignNear.h,
	  Near/AlgAssignNear2d.cxx, Near/AlgAssignNear2d.h,
	  Review/AlgFile.cxx, Review/AlgFile.h, Review/ComplexKey.h,
	  Review/PlotTest.h, Review/PlotUnfold.h, Review/PlotVector.h,
	  Smooth/AlgMinuitFit.cxx, Smooth/AlgMinuitFit.h, Smooth/FitFcn.h,
	  Smooth/PolNFcn.cxx, Smooth/PolNFcn.h, Test/AlgAssignTest.cxx,
	  Test/AlgAssignTest.h, Unfold/AlgUnfoldEM.cxx,
	  Unfold/AlgUnfoldEM.h:

	A development snapshot of the unfolding package.

2007-10-10 13:14  hartnell

	* NuMuBar/NuAnalysis.cxx:

	Was still running ExtractConfig is the original place, now removed.

2007-10-10 13:00  hartnell

	* NuMuBar/NuAnalysis.cxx:

	Remove a debugging statement.

2007-10-10 12:49  hartnell

	* NuMuBar/: NuAnalysis.cxx, NuAnalysis.h:

	Deal with the case that the first snarl has no beam information. The
	beam information is used to set pdfs, etc so just keep looping until a
	GoodSpill is obtained. This should only happen rarely...

2007-10-10 12:18  asousa

	* NCUtils/Extrapolation/: NCBeam.cxx, NCBeam.h,
	  NCExtrapolation.cxx:

	Adding true energy histograms to output file.

2007-10-10 11:12  hartnell

	* NuMuBar/macros/microDstCC.C:

	Macro to make micro dsts with CC analysis reconstruction and cuts

2007-10-10 11:11  hartnell

	* NuMuBar/: NuDSTAna.cxx, NuDSTAna.h:

	Added a function to make micro DSTs with the CC analysis reconstruction
	and cuts

2007-10-10 10:38  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/docs/ChangeLog:

	Minor RSD updates

2007-10-10 10:38  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/driver/initialise_globals.pm:

	Use get_site_info to set up $SYS::HOST_PLATFORM

2007-10-10 10:38  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/: doc/rsd.html,
	  driver/help.txt, driver/manage_soft_links.pm:

	Force platform specific soft links e.g new-SL4

2007-10-10 10:38  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/: DataCacheManager/init.pm,
	  DataCacheManager/docs/dcm.html,
	  Scripts/maintenance/version_number:

	Update version number to V00-07-31

2007-10-10 10:38  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/: DataCacheManager/get_site_info.pm,
	  RemoteSoftwareDeployment/driver/get_site_info.pm:

	Add os_type: Operating System type e.g. SL4

2007-10-10 09:09  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/docs/jobs_tutorial.html:

	Deprecate RSD job submission system, Add link entry for Ganga

2007-10-10 09:07  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/docs/admin_procedures.html:

	Add link for obtaining account on UI at RAL

2007-10-10 09:06  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/docs/admin_install_software.html:

	Add some example RSD commands to assemble and install

2007-10-10 09:04  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/docs/gbs.html:

	Add configuration FGITopDir

2007-10-10 03:11  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/vld/CosmicLE/mcmon/: GNUmakefile, LinkDef.h,
	  MCMonitorCosmic.cxx, MCMonitorCosmic.h,
	  MCMonitorCosmicHistograms.cxx, MCMonitorCosmicHistograms.h,
	  compare_gminos_ptsim_far_cosmicLE.mcmoncosmic.ps, loadlib.C,
	  makeMCMonitorPlots.C, outputMCMonitorPlots.C:

	A modified version of MCMonitor suitable for cosmics.  The output
	file compare_gminos_ptsim_far_cosmicLE.mcmoncosmic.ps shows the
	comparisons for 10 CosmicLE files. The plots show that there is very
	good agreement overall, although there is on average 1 additional hit
	strip per snarl using ptsim in place of gminos.  The reconstructed
	showers have slightly more planes per shower and energy
	per shower(~2%).

2007-10-09 21:05  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: Extrapolation/NCEnergyBin.cxx,
	  Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolation.h,
	  Extrapolation/NCExtrapolationMQ.cxx,
	  Extrapolation/NCExtrapolationModule.cxx,
	  macros/ncccSeparationNC.C:

	finish adapting extrapolation base class and MQ extrapolation to be able
	to handle inverted beam files.  make the module handle them too.
	add fTheta13 to the extrapolation base class and set it in the registry
	for when we want to make f_s vs theta_13 plots.

	remove TinyXML from macro

2007-10-09 21:02  koskinen

	* NCUtils/Extrapolation/NCExtrapolationJK_fit.cxx:

	JK_fit now handles inclusion of numu->nue oscillation.

2007-10-09 20:31  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/vld/CosmicLE/ValidationLog:

	Validation log summarizing the status of the findings using Jeff's MeuCal
	test and the questions to be resolved.

2007-10-09 20:12  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: LinkDef.h, NCAnalysisUtils.cxx, NCAnalysisUtils.h,
	  NCOscProb.cxx, NCOscProb.h, NCType.h,
	  Extraction/NCReaderHelper.cxx, Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolationMQ.cxx:

	make NCOscProb a namespace and change the name of the MuDisappearance method
	to TauAppearance.

	add entries to NCType for different oscillation modes, NuMuToNuMu etc.

	add new find survival probability function to NCAnalysisUtils to make use
	of the NCOscProb namespace.

	adapt MQ extrapolation and base class to use the new survival prob method.

	fix up the LinkDef.h

2007-10-09 19:53  koskinen

	* NCUtils/Extrapolation/NCExtrapolationJK_fit.cxx:

	The JK_fit method is outfitted to handle oscillated nue events

2007-10-09 19:52  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/vld/CosmicLE/: exe_gminos.sh, exe_ptsim.sh,
	  ptsim_G3_eggplant.C, reco_MC_daikon_far_cosmic_cedar_phy.C,
	  reco_MC_eggplant_far_cosmic_cedar_phy.C:

	Add scripts used in simulation & reconstruction of CosmicLE data.

2007-10-09 19:33  scavan

	* Production/Cedar_phy/restructure1/: commonfunctions.C,
	  reco_MC_daikon_far_cedar_phy.C, x.C:

	second form of restructuring

2007-10-09 19:24  koskinen

	* NCUtils/Extrapolation/NCExtrapolationJK_fit.cxx:

	Corrected the inclusion of the CC tau background in the NC sample.
	Changed some variables to represent the addition of Beam Nue events, to
	avoid confusion with future addition of oscillated Nue events.

2007-10-09 18:48  scavan

	* Production/Cedar_phy/restructure/: reco_near_spill_cedar_phy.C,
	  common_scripts/dbi_setup.h, common_scripts/getrunnumber.h,
	  common_scripts/header.h, common_scripts/job_setup.h,
	  common_scripts/loadlib.h, common_scripts/set_tsql.h,
	  common_scripts/setcalibrator.h, common_scripts/setmessagelevel.h,
	  common_scripts/setoutput.h:

	starting to prototype restructuring of scripts

2007-10-09 17:38  Sue Kasahara <schubert@hep.umn.edu>

	* Util/UtilIstHEP.cxx:

	Turn off obnoxious "unknown isthep code" messages.

2007-10-09 16:54  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/build_config_table.dat:

	Add minossoft:S07-09-20-R1-26-build_1

2007-10-09 16:44  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/: doc/rsd.html,
	  driver/cmd_launch.pm, driver/help.txt:

	Allow launch to PBS to specify queue

2007-10-09 15:38  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCBeam.cxx, NCBeam.h, NCEnergyBin.cxx,
	  NCEnergyBin.h, NCExtrapolation.cxx, NCExtrapolationJK.cxx,
	  NCExtrapolationJK_fit.cxx, NCExtrapolationMQ.cxx,
	  NCExtrapolationNS.cxx:

	fix up naming conventions.  make the changes

	Tau -> NuMuToNuTau
	Electron -> NuMuToNuE
	ElectronBeam -> NuEToNuE

	these changes are in the NCBeam and NCEnergyBin objects, and referenced in
	the extrapolation objects.

	fix bug in MQ extrapolation that used the NuMuToNuE instead of NuEToNuE.

2007-10-09 15:24  scavan

	* Production/Cedar_phy/: reco_MC_daikon_far_cedar_phy_cal.C,
	  reco_MC_near_cedar_phy_cal.C, reco_near_mb_cedar_phy.C,
	  reco_near_spill_cedar_phy_test.C,
	  srsafitter/reco_MC_daikon_far_cedar_phy_srsafitter.C,
	  srsafitter/reco_MC_daikon_far_cosmic_cedar_phy_srsafitter.C,
	  srsafitter/reco_MC_daikon_near_cedar_phy_srsafitter.C,
	  srsafitter/reco_far_all_cedar_phy_srsafitter.C,
	  srsafitter/reco_near_spill_cedar_phy_srsafitter.C:

	cvs commit of recently added processing scripts for calibration runs, miniboone run, test run, and srsafitter runs

2007-10-09 15:23  scavan

	* Production/Cedar_phy/reco_MC_daikon_near_cosmic_cedar_phy.C:

	updated gev/mips to 0.001792

2007-10-09 14:25  hartnell

	* DataUtil/EnergyCorrections.cxx:

	One of the useful new messages was missing a "new line" at the end of it.

2007-10-09 13:46  rustem

	* PhysicsNtuple/: DataBlock.cxx, Select/SelectNeutrino.cxx,
	  kNNAlg/Node.cxx, kNNAlg/Node.h:

	Cap number of warning messages in DataBlock to 10, these messages show up
	when FillBeam algorithm is not executed. Change defaults for
	SelectNeutrino:

	kNN > 0.3 for charged current events
	q/p < -0.005 for charged current muon neutrino events

	New function in Node.h that searches k-nearest neighbours, where k is
	computed using event weight and not event count.

2007-10-09 04:39  nwest

	* GridTools/docs/admin_group.html:

	Add reference to Virtual Organisation Operations Policy

2007-10-09 00:38  jpochoa

	* NueAna/: LinkDef.h, MCNNBestMatch.cxx, MCNNBestMatch.h,
	  MCNNVars.cxx, MCNNVars.h:

	Added N best matches information (stored in MCNNBestMatch objects) to MCNNVars

2007-10-08 22:22  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	put NCType:: in front of file type designators

2007-10-08 22:07  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolationNS.cxx,
	  NCExtrapolationNS.h:

	fix up the add event methods to be able to use nue appearance files

2007-10-08 21:56  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCType.h, Extrapolation/NCBeam.cxx,
	  Extrapolation/NCBeam.h, Extrapolation/NCEnergyBin.cxx,
	  Extrapolation/NCEnergyBin.h, Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolation.h,
	  Extrapolation/NCExtrapolationDP.cxx,
	  Extrapolation/NCExtrapolationDP.h,
	  Extrapolation/NCExtrapolationJK.cxx,
	  Extrapolation/NCExtrapolationJK_fit.cxx,
	  Extrapolation/NCExtrapolationMQ.cxx,
	  Extrapolation/NCExtrapolationMQ.h,
	  Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationModule.h,
	  Extrapolation/NCExtrapolationNS.cxx,
	  Extrapolation/NCExtrapolationRS.cxx,
	  Extrapolation/NCExtrapolationRS.h, NumRec/MinosMinimization.cxx,
	  NumRec/MinosMinimization.h:

	make changes to handle reading in of nu_e appearance related files

2007-10-08 20:53  koskinen

	* NCUtils/Extrapolation/: NCExtrapolationJK_fit.cxx,
	  NCExtrapolationJK_fit.h:

	The NCExtrapolationJK_fit now uses the extra fitting variables defined by
	the base class. I removed the extraneous varaibles from the header file
	that duplicated those in the base class. All chi-squared calculations are
	done using the base class' designation that the fitting variables go from
	-sigma to +sigma and now 1 +/- sigma. The survival probability is now
	calculated by the NCAnalysisUtils function instead of a similar version
	encoded in the JK_fit code.

2007-10-08 19:49  Sue Kasahara <schubert@hep.umn.edu>

	* G3PTSim/gphys/gphysi.F:

	Comment out the TGeant3 introduced code that hardwires the unit output
	number to external file 'gphysi.dat', instead of using LOUT.  The gphysi
	print messages will now appear in the ptsim log file.

2007-10-08 19:03  bckhouse

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h,
	  NCExtrapolationJK_fit.cxx, NCExtrapolationJK_fit.h,
	  NCExtrapolationMQ.cxx:

	Back out last set of changes.

2007-10-08 18:27  kreymer

	* CVSROOT/check_access:

	Added nwest, to allow kerberized access

2007-10-08 17:57  bckhouse

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h,
	  NCExtrapolationJK_fit.cxx, NCExtrapolationJK_fit.h,
	  NCExtrapolationMQ.cxx:

	Remove the extraVars* parameters from MakeDeltaChiSqrMaps.
	It now uses the fNuisanceParameters* member variables, which should get set automatically.
	Update MQ and JK_fit to work with these changes.

	Unfortunately I seem to have broken JK_fit so it converges to the wrong values.

2007-10-07 15:49  boehm

	* CVSROOT/check_access:

	Adding Pedro to those awesome enough to modify NueAna

2007-10-05 23:41  llhsu

	* NCUtils/Extrapolation/: NCExtrapolationNS.cxx,
	  NCExtrapolationNS.h:

	Updating changes to date in the BeamMatrix method so that it can be merged with changes for theta13 fitting

2007-10-05 16:29  bckhouse

	* NCUtils/Extrapolation/NCExtrapolation.cxx:

	Minor tidying.

2007-10-05 15:51  bckhouse

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h:

	Don't recreate the Minuit object for every point on the contour. This saves a trivial amount of overhead, and ought to let Minuit use its previous knowledge of the function. Sadly this doesn't seem to give any further increase in speed.

2007-10-05 08:45  hartnell

	* MeuCal/MeuPlots.cxx:

	Bit more printout to get at the strip lengths.

2007-10-05 04:38  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/macro/: PTSim_decayConfig.C,
	  PTSim_g3Config.C:

	Remove a few blank lines.

2007-10-05 04:37  Sue Kasahara <schubert@hep.umn.edu>

	* MCApplication/: MCApplication.cxx, MCApplication.h:

	Add additional "Info" level print statements to log configuration and
	decay scripts.

2007-10-05 01:18  dap56

	* Mad/: MadPIDAnalysis.cxx, macros/CCPID_example.C:

	Changed default release for MC to "CedarPhyV02 DaikonV00"

2007-10-05 00:08  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolation.cxx,
	  NCExtrapolationMQ.cxx:

	in MQ object handle hadronic calibrations correctly

	in base class initial weights to 0 for systematic uncertainty parameters

2007-10-04 21:04  koskinen

	* NCUtils/Extrapolation/NCExtrapolationJK_fit.cxx:

	Added some code to include the current knowledge of nue's in the FD.
	Updated the findsurvivalprobability code to appropriately reflect the tiny,
	tiny contribution of the NC taus

2007-10-04 19:13  rustem

	* PhysicsNtuple/Plot/: PlotResol.cxx, PlotResol.h:

	Couple minor changes to PlotResol algorithm.

2007-10-04 19:04  rustem

	* PhysicsNtuple/macros/make_ntuple.C:

	Finally, I have a single macro that makes ntuple files for both data and
	Monte-Carlo! Life will never be the same from this moment on...

2007-10-04 19:02  rustem

	* PhysicsNtuple/AlgAdapt.cxx:

	AlgAdapt is no longer a pure ABC class, it has two base class
	functions that are used by inherited classes. I personally
	prefer pure ABC classes, but in this case it is just simpler
	to add them to the base class becaus I did not want to add
	them to the Anp namespace as global functions.

2007-10-04 19:00  rustem

	* PhysicsNtuple/Config/PlotResol.xml:

	Definitions of histograms used by PlotResol algorithm.

2007-10-04 18:59  rustem

	* PhysicsNtuple/Plot/: PlotResol.cxx, PlotResol.h:

	Plotting algorithm that plots resolution of neutrino energy for various bins of true
	energy.

2007-10-04 18:58  rustem

	* PhysicsNtuple/: AlgAdapt.h, AlgCaddy.h, DataBlock.cxx,
	  Particle.cxx, Particle.h, RecoNu.h, RunAlgEvent.cxx,
	  RunAlgSnarl.cxx, RunAlgSnarl.h, RunAlgStore.cxx, RunFinder.cxx,
	  Truth.cxx, Truth.h, Vertex.cxx, Vertex.h, Config/PlotReson.xml,
	  Config/PlotVtx.xml, Plot/CountHist.cxx, Plot/CountHist.h,
	  Plot/PlotEff.cxx, Plot/PlotEff.h, Plot/PlotPur.cxx,
	  Plot/PlotPur.h, Plot/PlotReson.cxx, Plot/PlotReson.h,
	  Plot/PlotTruth.cxx, Plot/PlotTruth.h, Plot/PlotVtx.cxx,
	  Select/SelectBeam.cxx, Select/SelectBeam.h,
	  Select/SelectCount.cxx, Select/SelectCount.h,
	  Select/SelectFiducial.cxx, Select/SelectFlux.cxx,
	  Select/SelectKinem.cxx, Select/SelectKinem.h,
	  Select/SelectNeutrino.cxx, Store/FillBeam.cxx,
	  kNNAlg/FillkNN.cxx, kNNAlg/FillkNN.h, kNNAlg/LikeModule.cxx,
	  kNNAlg/LikeModule.h, macros/make_data.C, macros/make_mc.C:

	A development snapshot of PhysicsNtuple package. Add many refinements in the plotting
	algorithms, plus lots of other minor improvement/changes.

2007-10-04 16:56  bckhouse

	* NCUtils/macros/nearFarExtrapolation.C:

	Fix typo.

2007-10-04 16:30  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/macro/PTSim_g3Config.C:

	Disable G3 debug output.

2007-10-04 16:29  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/PTSimApplication.cxx:

	Reduce verbosity at kInfo level to one line per snarl.

2007-10-04 16:09  bckhouse

	* NCUtils/: Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolation.h,
	  Extrapolation/NCExtrapolationModule.cxx,
	  macros/nearFarExtrapolation.C:

	Add two new parameters to control the contour finding:
	AllowBestFitOutsideRange and AllowContoursOutsideRange
	These toggle the penalty terms that keep the fitter inside physical limits.
	Warnings:
	1. If the best fit point is unphysical but the contours are constrained in the physical region they most likely will not be found.
	2. Certain pathalogical contours (normally protected against by the requirement to be in the physical region) may get the contour finder stuck.

2007-10-04 15:53  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationJK_fit.cxx:

	remove random typo

2007-10-04 15:28  koskinen

	* NCUtils/Extrapolation/NCExtrapolationJK_fit.cxx:

	Modified the call to the chi-squared addition of the nuisance parameters
	to reflect that extraVarsMin in the derived class is 1-sigma.

2007-10-04 15:15  koskinen

	* NCUtils/Extrapolation/NCExtrapolationJK_fit.cxx:

	Changes to the JK_fit method include the following

	- Inclusion of penalty terms on non-oscillation fitting terms
	- Initialization of key variables to zero
	- Explicit calls to set whether NC and/or CC data are loaded for fitting
	  depending on registry flags

	of note is that in it's current form the nuisance parameters will only
	be properly calculated for values whose default value is zero.

2007-10-04 14:08  boehm

	* NueAna/: NueStandard.cxx, NueStandard.h:

	Adding New Functions

	PassesNonHEPreSelection to handle new request to trim files to all cuts but the high energy cut

2007-10-04 12:55  bckhouse

	* NCUtils/macros/nearFarExtrapolation.C:

	Fix references to $SCRATCH.
	Add lines setting all the different file limits explicitly.

2007-10-04 07:25  ishi

	* CVSROOT/: check_access, modules:

	Add new module GeoSwimmer.

2007-10-04 07:20  ishi

	* GeoSwimmer/: GNUmakefile, GeoSwimApplication.cxx,
	  GeoSwimApplication.h, GeoSwimParticle.cxx, GeoSwimParticle.h,
	  GeoSwimStack.cxx, GeoSwimStack.h, GeoSwimZCondition.cxx,
	  GeoSwimZCondition.h, GeoSwimmer.cxx, GeoSwimmer.h, LinkDef.h:

	GeoSwimmer codes.

2007-10-04 07:03  ishi

	* GeoGeometry/GeoGeometry.cxx:

	Rough boundary condition for Swim Medium.

2007-10-04 01:08  arms

	* Contrib/rhatcher/gminos_jobs/: gminos_cfg_AtmosNu_far_max.py,
	  gminos_ffr.py, run_umn.sh, umn_check_logs.sh:

	Preliminary commits to make running far atmospheric neutrinos possible

2007-10-03 20:54  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCEnergyBinGradients.cxx:

	give histograms unique names including detector and beam type specifications

2007-10-03 17:54  boehm

	* NueAna/: NueStandard.cxx, NueStandard.h,
	  NueAnaTools/NueConvention.cxx, NueAnaTools/NueConvention.h:

	Adding PassesMREFiducial and PassesMREPReselection functions

	Also making the energy cuts 1 < energy < 8 instead of <= in both cases

2007-10-03 17:22  koskinen

	* NCUtils/Extrapolation/NCExtrapolation.cxx:

	Added the NCBackground and CCBackground to the list of possible systematics
	to be included in the NCUtils fits.

2007-10-03 17:03  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolationJK.cxx,
	  NCExtrapolationMQ.cxx:

	back out accidental commit to limit fs to 0. in JK method

	use proper values for systematics fits in MQ method after commits from
	jason to the base class

2007-10-03 15:19  Brett Viren <bv@bnl.gov>

	* CVSROOT/framework.list:

	Strangely, now that Mark has moved on to greener pastures, he no
	longer wishes to receive the poetic nuances of MINOSSOFT commit
	messages.  I can only hope that he will still receive solace from
	reading Double-CHOOZ commit messages.

2007-10-03 14:58  koskinen

	* NCUtils/NCType.h:

	Corrected a typo for the Hadronic Calibration

2007-10-03 14:17  koskinen

	* NCUtils/NCType.h:

	Changing the name of the HadronicCalibrations to their new nomenclature of
	Absolute and Relative in the NCType.h

2007-10-03 14:01  boehm

	* NueAna/: NueStandard.cxx, NueStandard.h:

	Forgot to actually commit in the NueStandard Files

2007-10-03 04:39  Robert Hatcher <rhatcher@fnal.gov>

	* Production/asciidb/cedar_daikon/noalignnd/: UGLIDBISCINTMDL.csv,
	  UGLIDBISCINTMDLVLD.csv, catalogue.db, mkvld.C:

	An UGLIDBISCINTMDL table that matches the daikon perfect geometry.  One
	can use this to force data to be reconstructed with the same geometry.

2007-10-03 04:29  Robert Hatcher <rhatcher@fnal.gov>

	* Production/asciidb/set_tsql_override.C:

	An improved and generalized version of set_tsql_override(); used to be
	found embedded in Cedar_phy/bfield.C.  This version can handle
	ASCII_DB_PATH and ASCII_DB_SET env variables that have more than one
	value (comma or [semi]colon separated).  The test for MC file naming
	is more stringent but still handles the "brev", "bhcurv" and
	"bhcurvrev" cases.  Put this in the "asciidb" subdir since it really
	isn't specific (anymore) to any particular release.

2007-10-02 22:56  arms

	* Contrib/rhatcher/gminos_jobs/gminos_cfg_CosmicMu_far_bhcurv.py:

	Add FD full spectrum CosmicMu script to use new Bfield maps, new rock material, air gap Bfield, etc for daikon_03 or higher

2007-10-02 22:47  koskinen

	* NCUtils/Extrapolation/NCExtrapolation.cxx:

	The values for extraVarsMin and Max have been changed for the extra parameters
	(systematics) to not include the addition of one, i.e. the value for
	Normalization is no longer 1 + Sigma. The addition of one for the extra
	parameters must be added in the derived class. This change makes it easier
	to add nuisance parameters because the fitting functions now return the
	actual deviation instead of 1 + deviation.

2007-10-02 20:44  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	dont fill mc for DQM plots when running over MDC or MC only files

2007-10-02 19:56  boehm

	* NueAna/: LinkDef.h, NueAnaTools/NueConvention.cxx,
	  NueAnaTools/NueConvention.h:

	Adding the NueStandard namespace into the framework in order to have standardized
	DataQuality, Fiducial Volume, and Preselection cuts

	Some of the new fiducial information is stored in functions in NueConventions::IsInXXFiducial_Nue_Standard functions

2007-10-02 19:08  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCType.h,
	  Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolation.h,
	  Extrapolation/NCExtrapolationJK.cxx,
	  Extrapolation/NCExtrapolationJK_fit.cxx,
	  Extrapolation/NCExtrapolationJK_fit.h,
	  Extrapolation/NCExtrapolationMQ.cxx,
	  macros/nearFarExtrapolation.C:

	change NearHadronicCalibration --> RelativeHadronicCalibration
	       NearFarHadronicCalibration --> AbsoluteHadronicCalibration

	in NCAnalysisUtils::FindRecoWeight()

	-use adjusted values for ShowerEnergy (ie the old absolute calibration) only
	if the AbosluteHadronicCalibration is not turned on.
	-apply the relative hadronic calibration only to the far detector, not the
	near

2007-10-02 18:28  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolationModule.cxx,
	  NCExtrapolationModule.h:

	make separate file limit counts for data and mc to speed up the debugging

2007-10-02 13:24  hartnell

	* MeuCal/macros/: Config.C, FileListSpecial.C, meuPlots.C:

	Add
	gSystem->Load("libNtpFitSA.so");

	before
	gSystem->Load("libNtupleUtils.so");

2007-10-01 21:04  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCType.h:

	make locations of oscillation parameters in the minuit fits defined in NCType

	fix release type for MC

2007-10-01 21:03  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h,
	  NCExtrapolationMQ.cxx, NCExtrapolationMQ.h:

	add variables to base class for using the minuit based fitter.

	add minuit based fitter calls to MQ extrapolation...verified to work with
	MC.

2007-10-01 16:53  Robert Hatcher <rhatcher@fnal.gov>

	* CVSROOT/check_access:

	complete Jeff Hartnell's request for additions to NtupleUtils & NuMuBar
	by adding idanko/izdanko.

2007-10-01 15:08  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCBeam.cxx, NCBeam.h,
	  NCExtrapolationModule.cxx, NCExtrapolationModule.h:

	fix up filling of NC and CC events for all ND beams.

	more DQM histograms in the extrapolation module

2007-10-01 02:15  Robert Hatcher <rhatcher@fnal.gov>

	* RerootExodus/RerootToTruthModule.cxx:

	supplement TempTags registry entries for newly created SimSnarl; had "stream",
	add "tree", "file", "index".

2007-10-01 02:12  Robert Hatcher <rhatcher@fnal.gov>

	* RerootExodus/: RerootExodus.cxx, RerootExodus.h:

	Add GetRerootFileName() function for convenience.

2007-10-01 02:10  Robert Hatcher <rhatcher@fnal.gov>

	* DataUtil/: GetTempTags.cxx, GetTempTags.h:

	Utility functions for getting TempTags info from records (without having
	to deal with the dual inheritance hierarchy).

2007-10-01 02:09  Robert Hatcher <rhatcher@fnal.gov>

	* DataUtil/LinkDef.h:

	make sure DataUtil namespace is declared to CINT.

2007-09-30 21:36  Minos CVS group account.  Do not commit from here!

	* Contrib/rhatcher/gminos_jobs/temp:

	removing temp test

2007-09-30 21:34  Minos CVS group account.  Do not commit from here!

	* Contrib/rhatcher/gminos_jobs/temp:

	My CVS test

2007-09-30 21:25  Minos CVS group account.  Do not commit from here!

	* Contrib/rhatcher/gminos_jobs/run_wm.sh:

	minor changes

2007-09-30 16:49  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCBeam.cxx:

	always add both NC and CC events for the near detector, no matter what
	fUseNC or fUseCC is set to.  those events are not blinded.

	fUseNC or fUseCC still used to determine if one, the other, or both
	types of events should be put into the fit

2007-09-30 14:29  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationJK_fit.cxx:

	test flag for using NC and CC before filling results histograms

2007-09-29 19:12  boehm

	* StandardNtuple/: NtpStRecord.cxx, NtpStRecord.h:

	Added a function GetRelease() to the standard ntuple.  This takes the place of the block of code that users would normally run in order to get ReleaseType value.

2007-09-29 14:48  boehm

	* Conventions/ReleaseType.cxx:

	Changing the Output string of R1.24.3 to say CedarPhy not Cedar

2007-09-28 20:41  mualem

	* Contrib/rhatcher/gminos_jobs/cit_bulk_copy.sh:

	minor changes

2007-09-28 20:15  mualem

	* Contrib/rhatcher/gminos_jobs/run_cit.sh:

	minor cleanup

2007-09-28 20:13  mualem

	* Contrib/rhatcher/gminos_jobs/submit_cit.sh:

	only minor changes

2007-09-28 17:37  rjn

	* DataUtil/: EnergyCorrections.cxx, EnergyCorrections.h:

	Adding the latest version of EnergyCorrections to the repository. I'm sure this is going to upset somebody, but then again it always does.

2007-09-28 17:14  koskinen

	* NCUtils/Extrapolation/: NCExtrapolationJK_fit.cxx,
	  NCExtrapolationJK_fit.h:

	The JK_fit extrapolation method now functions using the fitter in NCUtils.
	Changes revolved around speeding up calculating the chi-squared function
	as well as removing histograms that are no longer filled or used.

2007-09-28 15:54  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	add condition to remove q > 0 CC events from data set in FinalEventCheck

2007-09-28 15:44  boehm

	* Conventions/: ReleaseType.cxx, ReleaseType.h:

	Adding CedarPhyDaikon as defined to be R1.24.2 + Daikon00

	CalB may now be lost in the shuffle though due to R1.24.2 as a full set produced in the same environment.

2007-09-28 14:04  boehm

	* Conventions/ReleaseType.cxx:

	Fixing a bug in ReleaseType::AsString handling CedarPhy versions

2007-09-27 22:54  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCAnalysisUtils.h,
	  Extraction/NCAnalysisModule.cxx,
	  Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolationModule.cxx:

	fix ReleaseType in NCAnalysisUtils to send the energy correction methods
	the correct release.  it is hard coded right now, but should be fixed later.

	in NCExtrapolation fix a typo in the output to the screen

	NCExtrapolationModule add a plot to show the radial distribution of the
	selected events

2007-09-27 19:50  koskinen

	* NCUtils/Extraction/NCExtractionTO.cxx:

	Corrected a typo for the near detector

2007-09-27 19:42  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extraction/NCExtractionTO.cxx:

	remove 1.8% pulse height adjustment for pre-cedar reco

2007-09-27 17:20  bckhouse

	* NCUtils/: Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolation.h,
	  Extrapolation/NCExtrapolationJK_fit.cxx,
	  Extrapolation/NCExtrapolationModule.cxx,
	  macros/nearFarExtrapolation.C:

	Make the contour finder controlling paramers an option in the macro instead of having to be set in code.

2007-09-27 16:41  bckhouse

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h:

	Add a function GetLazyBestFitPoint(). Once the minimization part of the contour finding is done it will return the best fit point. As before - only for hybrid method currently.

2007-09-27 16:29  bckhouse

	* NCUtils/Extrapolation/NCExtrapolation.cxx:

	Write out the individual contours as TGraphs as well as the TCanvas plot.
	Increase the contour finder cache to a few meg.

	Note : these and the previous changes are only implemented for the hybrid method.

2007-09-27 15:55  bckhouse

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h:

	Add extra parameters to NCExtrapolation::MakeDeltaChiSqrMaps to control which oscillation paramters to draw contours for. This should make it possible to parallelise the contour finding onto 9 machines.

2007-09-27 06:25  Robert Hatcher <rhatcher@fnal.gov>

	* DcsUser/: CoilTools.cxx, CoilTools.h:

	I've modified CoilTools to use a singleton model with an internal
	cache (i.e. it uses the DBI extended context to get a day's worth
	of data and rummages throught that as necessary) for the
	BFLDDBICOILSTATUS (FarDet) and DCS_MAG_NEAR (NearDet) tables.
	By being a singleton it can hold on to a cached set and make
	use of the proximity of subsequent snarls.

	I've tested this by doing a scan across a 2 week period (at 1 sec
	intervals = DB resolution).  This compiled script was run on my 2GHz
	laptop against either minos-db1 (which had a load=1 at the time) or
	a local MySQL server.  The large "Real" (=clock) time reflects the
	effort of the MySQL server as well as the C++ script.

	            minos-db1        localhost
	code  det   Real    CPU      Real    CPU
	old   near  0:12:58 195.580  0:07:10 189.190
	old   far   0:12:26 245.790  0:08:06 241.370
	new   near  0:00:10   7.760  0:00:08   7.630
	new   far   0:00:05   2.310  0:00:02   2.210

2007-09-26 22:03  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: Extrapolation/NCExtrapolationModule.cxx,
	  macros/nearFarExtrapolation.C:

	fix bug in plotting of dqm quantities, update macro to use cedar_phy directory

2007-09-26 20:01  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/gminos_cfg_CosmicLE_far_bhcurv.py:

	tweak comment (no overlays, no recalc #'s) about changing rock/linr TMED.

2007-09-26 16:40  arms

	* Contrib/rhatcher/gminos_jobs/run_cit.sh:

	Add more flexible GOODLINES gminos log verification to cit script from umn script.

2007-09-26 16:33  arms

	* Contrib/rhatcher/gminos_jobs/gminos_cfg_CosmicLE_far_bhcurv.py:

	Add a cfg file for producing low energy FD cosmic muons with the new Bfield maps (218-220). Includes field in the air gaps and new rock material.

2007-09-25 20:58  bckhouse

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	Add a default value for the LazyContoursUseMinuit so that it actually works.

2007-09-25 20:19  koskinen

	* Contrib/koskinen/MuonDist/: DoThings1_C.d, DoThings2_C.d,
	  DoThings4.C~, FitConf.h~, fit_combined_feb07.inp~, test.inp~,
	  test1.inp~:

	Removed missed temp files.

2007-09-25 20:17  koskinen

	* Contrib/koskinen/MuonDist/: DoThings.C~, DoThings1.C~,
	  DoThings2.C~, DoThings3.C~, DoThings3_C.d, DoThings4_C.d,
	  DoThings_C.d, FitConf.cxx~, LinkDef.h~, MuDistSpline.cxx~,
	  MuDistSpline.h~, MuDistSplineFunctions.cxx~,
	  MuDistSplineFunctions.h~, grid_effic_hits.C~,
	  grid_effic_hits.cxx~, run_MuDistSpline.C~, run_MuDistSpline1.C~,
	  run_MuDistSpline2.C~, run_MuDistSpline3.C~, run_MuDistSpline4.C~:

	Removed a litany of temp files.

2007-09-25 20:06  Sue Kasahara <schubert@hep.umn.edu>

	* MCApplication/MCApplication.cxx:

	Add Tin isotope (Sn115) to list of defined ion types.  Tin makes up
	a very small fraction of the steel plane composition.

2007-09-25 19:23  Sue Kasahara <schubert@hep.umn.edu>

	* GeoGeometry/GeoGeometry.cxx:

	Adjust near & far MARS volume half-width in z from 200 m to 250 m, since
	a handful of near det rock vertices extend out to the -250->-200 m range.
	It would be nice to have the MARS volume dimensions included in the
	database.

2007-09-25 19:22  koskinen

	* NCUtils/NCType.h:

	Added JK_fit method to the list of available NC extrapolation methods

2007-09-25 19:21  koskinen

	* NCUtils/Extrapolation/: LinkDef.h, NCExtrapolation.cxx,
	  NCExtrapolationJK_fit.cxx, NCExtrapolationJK_fit.h,
	  NCExtrapolationModule.cxx, NCExtrapolationModule.h:

	Adding a separate F/N method that uses a fitting routine selected from
	the base class to find oscillation parameters instead of a grid search.
	Because of the massive architecture change vs. the normal JK method, a
	handleful of previous features are not fully implemented in this new
	method, i.e. DoSystStudy.

2007-09-25 18:41  Sue Kasahara <schubert@hep.umn.edu>

	* MCApplication/MCApplication.cxx:

	Bug fix to initialization of swim media.  The last medium in the
	"non swim" media list was incorrectly being configured for continuous
	energy loss as a swim medium.

2007-09-25 18:35  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	make sure to fill the DQM plots only for the events selected, ie either NC
	, CC, or both

2007-09-25 16:18  Brian Rebel <brebel@fnal.gov>

	* AnalysisNtuples/: ANtpRecoInfo.cxx, ANtpRecoInfo.h:

	add data member to hold difference in time between spill and event

2007-09-25 16:18  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: Extraction/NCAnalysisModule.cxx,
	  Extraction/NCAnalysisModule.h,
	  Extrapolation/NCExtrapolationModule.h,
	  Extrapolation/NCExtrapolationModule.cxx:

	add code for data quality plot making in modules

2007-09-24 17:44  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationMQ.cxx:

	call the FillDeltaChiSqrMaps function

2007-09-24 11:04  hartnell

	* NtupleUtils/doc/cssSystematicsDSTs.html:

	Add location of cedar_phy_6months

2007-09-24 08:45  ahimmel

	* NuMuBar/NuPlots.cxx:

	Added energy and shower energy to BRevPlots.

2007-09-24 08:35  ahimmel

	* NuMuBar/NuPlots.cxx:

	Update to FillBRev() and FillDetectorEdge()

2007-09-23 19:43  Robert Hatcher <rhatcher@fnal.gov>

	* CVSROOT/check_access:

	At Jeff Hartnell's request add some names to NtupleUtils and NuMuBar.

2007-09-23 17:58  hartnell

	* NtupleUtils/NuReco.cxx:

	Finally got uvz2xyz to work (I hope) on the third attempt... cut and
	paste is a killer!

2007-09-22 22:28  zarko

	* Contrib/zarko/BeamFit/MakePlot.C:

	[no log message]

2007-09-22 22:09  zarko

	* Contrib/zarko/BeamFit/: DoTheFit.C, FitBeam.cxx, FitBeam.h,
	  FitConf.cxx, FitConf.h, FitData.h, FitMuon.cxx, FitMuon.h,
	  FitPTRW.cxx, FitPTRW.h, GNUmakefile, LinkDef.h, MakePlot.C,
	  MuonAlcEff.cxx, MuonAlcEff.h, runaparamfit.C,
	  data/MRCCratio.root,
	  data/data_hist_cedardaikon_highstat_ro_scaled.root,
	  data/data_hist_cedardaikon_ro_scaled.root, data/fluka05ptxf.root,
	  data/nue_data_hist.root, data/numu_data_hist.root,
	  data/numubar_data_hist.root,
	  data/truehists-chargesigncut-upto120-rebin.root,
	  data/truehists-reclaim.root, input/fit_mm.inp:

	First commit of the code used for fitting data from muon monitors.

2007-09-22 20:56  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/: PTSimApplication.cxx, PTSimApplication.h:

	Changes to PTSimApplication::Stepping to improve performance.

2007-09-22 20:45  Sue Kasahara <schubert@hep.umn.edu>

	* G3PTSim/TGeant3/TGeant3.cxx:

	Revised TGeant3::ProdProcess, used to determine the mechanism
	resulting in the production of secondaries in the current step, to improve
	performance.

2007-09-22 19:34  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/count_overlay_files.py:

	A script for making a directory listing of /pnfs/minos/mcin_data looking
	for particular daikon xx files and classifying then looking for gaps
	in runs and such.  Probably only useful at FNAL.

2007-09-22 19:31  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/:
	  gminos_cfg_L010185_bhcurv_overlay.py,
	  gminos_cfg_L010185_near_bhcurv.py,
	  gminos_cfg_L010185_rock_bhcurv.py:

	Change NearDet bhcurv configs to use Daikon 04 (in anticipation of actually
	getting one tagged/built).  One should still be able to use these, if
	needed, for Daikon 03 by using the  -k VegRelease,3 command line flag.

2007-09-22 17:39  tjyang

	* NueAna/: ANtpTruthInfoBeamAna.cxx, ANtpTruthInfoBeamNue.cxx,
	  ANtpTruthInfoBeamNue.h, StdHepInfo.cxx, StdHepInfo.h,
	  StdHepInfoAna.cxx:

	add neutrino interaction target: itg
	add baryon xf

2007-09-22 17:09  evans

	* NtupleUtils/NuFluxHelper.cxx:

	[no log message]

2007-09-22 16:55  evans

	* NtupleUtils/NuFluxHelper.cxx:

	Adding the ability to do SKZP reweighting for run I & run II combined.

2007-09-22 14:52  hartnell

	* NuMuBar/tools/sam.csh:

	A whole bunch of SAM commands I've been playing with

2007-09-22 14:50  hartnell

	* NuMuBar/tools/farm.pl:

	Can now run at FNAL as well as RAL

2007-09-22 14:49  hartnell

	* NuMuBar/macros/: PlotFunctions.C, mCuts.C, makeStdPlots.C:

	makeStdPlots.C is used to dump out lots of plots by calling lots of the
	other macros in the same directory.

2007-09-22 14:26  hartnell

	* NuMuBar/macros/makeDstSam.C:

	Script to make DSTs using SAM to provide the files. This uses Liz's
	test version of IoModules... will update soon.

2007-09-22 13:51  hartnell

	* NtupleUtils/doc/cssSystematicsDSTs.html:

	Still didn't get u/v and x/y the right way round... should be right now

2007-09-22 13:48  hartnell

	* NtupleUtils/doc/cssSystematicsDSTs.html:

	Forgot to hit save before

2007-09-22 13:47  hartnell

	* NtupleUtils/doc/cssSystematicsDSTs.html:

	Couple of updates

2007-09-22 13:29  hartnell

	* NtupleUtils/NuReco.cxx:

	Bug fix: had my uvz2xyz the wrong way round.

2007-09-22 11:17  hartnell

	* NtupleUtils/doc/: NuDST.html, cssSystematicsDSTs.html:

	Update the documentation. NuDSTs for bhcurv data sets are listed.

2007-09-21 19:49  Liz Buckley-Geer <buckley@fnal.gov>

	* IoModules/: IoInputModule.cxx, IoInputModule.h:

	Make it possible to run a loon job on a pre-existing project that has been started using sam start project. Added new config variable StartNewProject. The default is 1 which will always start a new project. If set to 0 it will connect to an already running project. This allows users to run multiple loon jobs over datasets containg large numbers of files. The web tutorial has been updated to document this new feature

2007-09-21 19:22  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCType.h, Extrapolation/NCBeam.cxx,
	  Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolationMQ.cxx,
	  Extrapolation/NCExtrapolationModule.cxx,
	  NumRec/MinosMinimization.cxx:

	NCType:

	Add array of strings to hold run type names for use in making canvases, etc

	NCBeam:

	a couple of instances of loops over energy bins being defined by size of the
	NC NCEnergyBin vector...doesnt work when you arent fitting NC events.  fix
	that to loop over NC and CC energy bins separately

	NCExtrapolation:

	make use of change in NCType

	NCExtrapolationMQ:

	add lines to turn on the shower and track energy systematics for the FD.
	make sure to grab the kRunAll runtype for all beams

	NCExtrapolationModule:

	remove some debug MAXMSG calls

	MinosMinimization

	comment out some print out statements, change int to uint when testing
	size of vectors

2007-09-20 23:42  tjyang

	* Contrib/tjy/hadvalidation/HadAna/: HadAna.cxx, HadAna.h,
	  run_comp.C:

	rewritting the code

2007-09-20 20:54  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCBeam.cxx:

	fix bug in scale factor calculation for case when adding beams

2007-09-20 20:21  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCBeam.cxx, NCExtrapolation.cxx,
	  NCExtrapolationJK.cxx:

	fix bugs for when only using CC or only NC in JK method.

	fix display of POT inside NCExtrapolation constructor

	fix more bugs in NCBeam for case of only using NC or CC

2007-09-20 18:21  George Irwin <gmieg@slac.stanford.edu>

	* setup/packages-S07-09-20-R1-26:

	First commit

2007-09-20 15:35  llhsu

	* NCUtils/Cuts/NCAnalysisCutsNC.cxx:

	Added typecast to int in PassesFinalSelection

2007-09-20 13:28  bckhouse

	* NCUtils/macros/nearFarExtrapolationSyst.C:

	Remember to add the option to the systematic study macro too.

2007-09-20 13:26  bckhouse

	* NCUtils/: Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolation.h, macros/nearFarExtrapolation.C:

	Add an option to choose which fitting algorithm to use.

2007-09-20 12:58  bckhouse

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h:

	Add a hybrid fitting method: minimization with Minuit, contour finding with my code.
	Really sorry about all the duplicate code - as soon as a decision is made which ones to keep I will remove/merge the implementations.

2007-09-20 12:53  evans

	* NtupleUtils/NuHistos.cxx:

	Furthermore, removing the generatorWeight from the reweighting: this
	can be put into nu.rw if required.

2007-09-20 12:49  evans

	* NtupleUtils/NuHistos.cxx:

	Changing the reweighting in the code to fill Matrix Method histograms
	to use nu.rw instead of nu.beamWeight, to enable easier run 1 v. run 2
	configuration.

2007-09-20 11:34  hartnell

	* NuMuBar/: NuDSTAna.cxx, NuDSTAna.h, NuPlots.cxx, NuPlots.h:

	Added MMRereco() method for Justin so that he can use the NuDSTs to
	create the histograms needed for the matrix method. This should speed
	things up considerably.

	Not yet tested fully.

	NuPlots no longer uses mc.releaseType but mc.simFlag, which already
	exists in the NuDST ntuples.

2007-09-20 11:28  hartnell

	* NtupleUtils/: NuMCEvent.h, NuExtraction.cxx, NuMCEvent.cxx:

	Might as well add this too...

	      Int_t anaVersion;//different cuts etc

2007-09-20 11:02  hartnell

	* NtupleUtils/: NuExtraction.cxx, NuMCEvent.cxx, NuMCEvent.h:

	Added variables and code to extract them. Not needed right now but might
	be.

	   Int_t timeSec;//fHeader.fVldContext.fTimeStamp.fSec
	   Int_t timeNanoSec;//fHeader.fVldContext.fTimeStamp.fNanoSec
	   Double_t timeSeconds;//VldTimeStamp.GetSeconds() sec+nanoSec/1e9
	   Double_t trigtime;//evthdr.trigtime
	   Int_t releaseType;//Conventions/ReleaseType.h definition

2007-09-20 10:59  bckhouse

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h:

	Add the ability to name the extra (systematic) parameters to the fitting.

2007-09-20 03:43  llhsu

	* NCUtils/Cuts/NCAnalysisCutsNC.cxx:

	Loosened cuts for strip file generation.  Allowing mc events that were generated in the true fiducial volume as well as the reconstructed fiducial volume.  Removed cleaning cuts for ND

2007-09-20 03:32  llhsu

	* NCUtils/Extrapolation/NCExtrapolation.cxx:

	Added isCleanHighMultSnarl cut (for ND) to AddEvent.  This is redundant at the moment and does nothing

2007-09-20 03:22  llhsu

	* NCUtils/NCAnalysisUtils.cxx:

	Bugfix in SetInfoObjects call to NCAnalysisCuts::SetInfoObjects missing fTruthInfoBeam

2007-09-19 22:49  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCBeam.cxx, NCBeam.h,
	  NCExtrapolationJK.cxx, NCExtrapolationModule.cxx:

	NCBeam:

	add data members fUseNC and fUseCC to make sure only the correct set of events
	is used when you want to fit one or the other

	NCExtrapolationModule:

	add condition to test for "blind" in file name when running over far data uDST

	NCExtrapolationJK:

	make sure to test fUseNC and fUseCC when doing fit - only include the events
	that are turned on

2007-09-19 22:43  Brian Rebel <brebel@fnal.gov>

	* NCUtils/NCType.cxx:

	forgot to commit the coversion functions

2007-09-19 18:29  arms

	* Contrib/rhatcher/gminos_jobs/: run_umn.sh, setup_umn_bundle.sh:

	New code in setup_XXX_bundle.sh for picking daikon vegetable number from the command-line is broken if no command-line args are given. Not sure how to fix it, so note it and pass args in run_umn.sh

2007-09-19 18:03  ahimmel

	* NuMuBar/NuPlots.cxx:

	In advertently submitted file in development.  This is the correct file.

2007-09-19 18:01  ahimmel

	* NuMuBar/: NuDSTAna.cxx, NuPlots.cxx, NuPlots.h:

	Broke up FillBRev() to have a separate FillDetectorEdge() method to fill
	detector edge plots.  Added to DetectorEdge plots.

2007-09-19 17:39  koskinen

	* Contrib/koskinen/MuonDist/: DoThings.C, FitBeam.cxx, FitConf.cxx,
	  MuDistSpline.cxx, MuDistSpline.h, MuDistSplineFunctions.cxx,
	  MuDistSplineFunctions.h, test.inp:

	Added Id tags as well as specific notes in the more important .cxx files.

2007-09-19 17:30  koskinen

	* Contrib/koskinen/MuonDist/: BeamConfigs.txt, DoThings.C,
	  DoThings.C~, DoThings1.C, DoThings1.C~, DoThings1_C.d,
	  DoThings2.C, DoThings2.C~, DoThings2_C.d, DoThings3.C,
	  DoThings3.C~, DoThings3_C.d, DoThings4.C, DoThings4.C~,
	  DoThings4_C.d, DoThings_C.d, FitBeam.cxx, FitBeam.h, FitConf.cxx,
	  FitConf.cxx~, FitConf.h, FitConf.h~, GNUmakefile, LinkDef.h,
	  LinkDef.h~, MuDistSpline.cxx, MuDistSpline.cxx~, MuDistSpline.h,
	  MuDistSpline.h~, MuDistSplineFunctions.cxx,
	  MuDistSplineFunctions.cxx~, MuDistSplineFunctions.h,
	  MuDistSplineFunctions.h~, MuDistSpline_cxx.d,
	  fit_combined_feb07.inp, fit_combined_feb07.inp~,
	  grid_effic_hits.C~, grid_effic_hits.cxx~, run_MuDistSpline.C,
	  run_MuDistSpline.C~, run_MuDistSpline1.C, run_MuDistSpline1.C~,
	  run_MuDistSpline2.C, run_MuDistSpline2.C~, run_MuDistSpline3.C,
	  run_MuDistSpline3.C~, run_MuDistSpline4.C, run_MuDistSpline4.C~,
	  test.inp, test.inp~, test1.inp, test1.inp~:

	Created a contrib folder for the Muon Monitor flux code. The MuDistSplineFunctions
	file takes care of turning the g4numi data into efficiency curves. The
	MuDistSpline has numerous functions, but mainly is used to produce
	muon distributions at the 3 Muon Alcoves using the muon efficiency curves
	as well as the muons from the gnumi weighted muon ntuples.

2007-09-19 15:43  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCType.h, Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationModule.h:

	fix pot counting to handle run types as well.

	add methods to NCType to convert from beam type + run type to an index and
	back again.

	in NCExtrapolationModule make the map<int, double> for POT counting use
	the new index rather than just the beam type number.

	in NCExtrapolation get the pot from the map using the correct index.

	for MC always use the POT from run type I

2007-09-19 14:22  asousa

	* NCUtils/NCAnalysisUtils.cxx:

	Fixing implementation of FD cleaning sytematics. No adjustments were being made.

2007-09-19 13:58  Brian Rebel <brebel@fnal.gov>

	* NCUtils/NCType.h:

	forgot to commit some new run type designators

2007-09-18 21:49  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCBeam.cxx, NCBeam.h, NCEnergyBin.cxx,
	  NCEnergyBin.h, NCExtrapolation.cxx, NCExtrapolation.h,
	  NCExtrapolationJK.cxx, NCExtrapolationModule.cxx:

	changes to handle run I and run II data gracefully. add methods to
	NCEnergyBin and NCBeam to add together bins and beams.  the NCBeam::Add()
	method simply calls the NCEnergyBin::Add() method.  the NCEnergyBin::Add()
	method gets the information about MC and data events using the
	GetMCXXXInformation and GetDataInformation functions of NCEnergyBin to
	combine the two bins.  it sets everything just as in the AddEvent method.

	add CombineRuns() method to NCExtrapolation to handle combining the
	different run data sets.  if only one run (ie preshutdown or postshutdown)
	is present for a given beam the beam run type is changed to new NCType::kRunAll
	value.

	extrapolation methods should look for the NCType::kRunAll value when selecting
	beams from the fBeams vector.

	the changes have been tested using only MC and MCAsData and are shown to not
	alter the way the code works.

2007-09-18 18:17  ahimmel

	* NuMuBar/NuPlots.cxx:

	Added TrkEndX broken down by plane type (U, V, Full, Partial).

2007-09-18 10:42  ahimmel

	* NuMuBar/NuPlots.cxx:

	Added TrkEndX,U,V variables with selections to test the position in data
	vs. monte carlo of the edge of the detector.

2007-09-18 08:30  ahimmel

	* NuMuBar/: NuPIDInterface.cxx, NuPIDInterface.h:

	Submitted for JPOchoa

	Everything is ready to fill the variable poIDKin (which is "Pedro's
	new kinematics-only pid").

	All we have to do is to call another PIDCalculator object, but this time
	set it to "PYC". In other words,

	PIDCalculator *pidcalc = new PIDCalculator("PYC");

	(and you should have another one with "QYC" used for calculating poID).

	And then call pidcalc->GetNuBarPID(....) giving it exactly the same
	arguments you give the other pidcalc, including the same LoadPDF object;
	the difference is that for this second PIDCalculator the q/p/Sigma q/p
	information will be ignored.

2007-09-17 20:04  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/: setup_cit_bundle.sh,
	  setup_ral_bundle.sh, setup_tufts_bundle.sh, setup_umn_bundle.sh,
	  setup_wm_bundle.sh:

	setup_subbundle.sh now sets NEUGEN3_VERSION depending on DAIKON_VERSION
	so one no longer needs to do it in the site specific setup script.

	For site scripts that didn't have the capability add the potential for
	handling an optional argument which is the daikon version number (use
	whatever value used to be hard-coded into the script as the default).

2007-09-17 20:00  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/: setup_fnal_bundle.csh,
	  setup_fnal_bundle.sh:

	setup_subbundle.[c]sh sets NEUGEN3_VERSION based on DAIKON_VERSION
	so we no longer explicitly set it in this site specific script.

2007-09-17 19:59  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/: run_ral.sh, run_tufts.sh,
	  run_umn.sh, run_wm.sh:

	DAIKON_VERISON ==> DAIKON_VERSION

2007-09-17 19:57  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/: setup_subbundle.csh,
	  setup_subbundle.sh:

	DAIKON_VERSION daikon_04 (and beyond) will use NEUGEN_VERSION v3_5_3;
	make this happen automagically.  These will also use MODBYRS5_xsec.dat
	by default.

	Begin migration away from typo DAIKON_VERISON -> DAIKON_VERSION by having
	both get set (primary is DAIKON_VERSION).

2007-09-17 19:01  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	file count limits should only apply to mc, not to data. fixed SetPOTValue
	and AddEventsToExtrapolation to reflect this fact

2007-09-17 17:58  hartnell

	* NtupleUtils/: NuReco.cxx, NuReco.h:

	Deal with the new variables and also added:

	   TVector3 xyz2uvz(Float_t x,Float_t y,Float_t z,VldContext vc) const;
	   TVector3 uvz2xyz(Float_t u,Float_t v,Float_t z,VldContext vc) const;

	for convenience (uses Ugli).

2007-09-17 17:56  hartnell

	* NtupleUtils/NuExtraction.cxx:

	Extract all the new variables

2007-09-17 17:55  hartnell

	* NtupleUtils/: NuMCEvent.cxx, NuMCEvent.h:

	Add these to MC info too:

	   Float_t ppvx;//mc.flux.ppvx = parent production vtx x, e.g. decay pipe
	   Float_t ppvy;//mc.flux.ppvy
	   Float_t ppvz;//mc.flux.ppvz
	   Int_t ptype;//mc.flux.ptype

2007-09-17 17:54  hartnell

	* NtupleUtils/: NuEvent.cxx, NuEvent.h:

	Added more SA fitter variables, plus a variable for Pedro's new
	kinematics-only-pid, and also the neutrino parent vtx location in the
	beam line:

	   Float_t trkvtxdcoszSA;//fitsa.fit.dcosz
	   Float_t xTrkVtxSA;//calculated from u&v
	   Float_t yTrkVtxSA;//calculated from u&v
	   Float_t zTrkVtxSA;//fitsa.fit.z
	   Float_t uTrkVtxSA;//fitsa.fit.u
	   Float_t vTrkVtxSA;//fitsa.fit.v

	   Float_t poIDKin;//PO's PID variable (kinematics only)

	   Float_t ppvx;//mc.flux.ppvx = parent production vtx x, e.g. decay pipe
	   Float_t ppvy;//mc.flux.ppvy
	   Float_t ppvz;//mc.flux.ppvz
	   Int_t ptype;//mc.flux.ptype

2007-09-17 17:01  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/: PTSimApplication.cxx, PTSimApplication.h,
	  PTSimModule.cxx:

	Improve performance a little by storing sensitive medium ids separate
	from full list of medium ids, so sensitive mediums can be identified
	quicker during stepping.

2007-09-17 12:54  asousa

	* NCUtils/Extrapolation/NCExtrapolationMQ.cxx:

	Fixing a typo that prevented syst. study output file from being written out.

2007-09-17 10:20  ahimmel

	* NuMuBar/: NuPlots.cxx, NuPlots.h:

	FillEffPur:

	Fixed fillint of AllTrue for efficiency (removed AllTrueNC) - this is now
	done before any selection cuts.  Added SelectedFalse and SelectedFalseNC
	to create contamination = 1 - efficiency plots:

	contamination = SelectedFalse(NC) / Selected(NC)
	purity        = SelectedTrue(NC) / Selected(NC)
	efficiency    = SelectedTrue(NC) / AllTrue

	Also, added a ytitle argument to FormatPlot with default = "".

2007-09-16 22:17  asousa

	* NCUtils/: NCAnalysisUtils.cxx, NCType.h,
	  macros/nearFarExtrapolation.C,
	  macros/nearFarExtrapolationSystExt.C:

	Adding FD cleaning systematics described in Phill's thesis. Included on/off switching statements in the running macros.

2007-09-16 21:26  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/PTSimModule.cxx:

	Only use NeuKinList on input to determine number of events in snarl if
	present and not empty.

2007-09-15 02:00  arms

	* Contrib/rhatcher/gminos_jobs/gminos_cfg_reverse_bhcurv.py:

	Actually commit this file!

2007-09-15 01:59  arms

	* Contrib/rhatcher/gminos_jobs/run_umn.sh:

	New mods file for bhcurv with reversed Bfield. Rearrange order of cfg files in call to gminos_jobs in run_umn.sh. Was not picking up mods from  reverse_bhcurv b/c BField is defined in gminos_cfg_CosmicMu_near_bhcurv. Works properly now.

2007-09-14 23:20  arms

	* Contrib/rhatcher/gminos_jobs/umn_bulk_copy.sh:

	Make the bulk copy script smarter using getopts

2007-09-14 19:07  George Irwin <gmieg@slac.stanford.edu>

	* NueAna/MuonRemovalInfoAna.cxx:

	Add ' #include <cassert> ' for GCC 3.3.4

2007-09-14 19:01  Minos CVS group account.  Do not commit from here!

	* Contrib/rhatcher/gminos_jobs/: run_wm.sh, setup_wm_bundle.sh:

	[no log message]

2007-09-14 14:12  Nathaniel Tagg <n.tagg1@physics.ox.ac.uk>

	* TriD/: TridGLFrame.cxx, TridPageDetector.cxx, TridSketches.cxx,
	  TridSketches.h:

	Add anti-aliasing hint.
	Add stipple and line width to line sketches.
	Use fractional line widths to draw FD supermodule wireframe

2007-09-14 13:41  annah1

	* NueAna/: MuonRemovalInfo.cxx, MuonRemovalInfo.h,
	  MuonRemovalInfoAna.cxx, NueRecord.h:

	Added some original shower variables into MRI tree (like vertex, planes, strips)

2007-09-14 13:30  hartnell

	* NtupleUtils/macros/: MakeMMFluxHelpers.C, RunMMPrediction.C,
	  nuDemo.C:

	Need to gSystem->Load("libNtpFitSA.so");
	due to new dependence on the SA fit ntuple.

2007-09-14 12:58  hartnell

	* NuMuBar/macros/: chargeSeparation.C, dstAna.C, microDst.C:

	Need to gSystem->Load("libNtpFitSA.so");
	due to new dependence on the SA fit ntuple.

2007-09-14 00:26  arms

	* Contrib/rhatcher/gminos_jobs/umn_bulk_copy.sh:

	Revise bash substring matching so that any matching substring is looked for, not just one at the beginning of the subdirectory name

2007-09-13 23:35  arms

	* Contrib/rhatcher/gminos_jobs/: run_umn.sh, umn_check_logs.sh:

	Make GOODLINES check smarter so that it doesn't get foiled by extra or missing spaces in the log file lines looked for

2007-09-13 22:09  rustem

	* PhysicsNtuple/Hist1d.h:

	It is cassert, silly...

2007-09-13 22:00  rustem

	* PhysicsNtuple/Hist1d.h:

	Hist1d template needs include for assert.

2007-09-13 21:38  rustem

	* PhysicsNtuple/Select/: SelectFlux.cxx, SelectFlux.h,
	  SelectKinem.cxx, SelectKinem.h:

	Add two new algorithms. These two AlgSnarl algorithms are used as nodes in
	a graph tree, ie they configure and call other AlgSnarl algorithms.

	SelectFlux creates a tree of algorithms, where each branch is weighted
	with different flux values: beam weights, beam error envelope, best fits
	parameters, etc.

	SelectKinem creates a tree of algorithms, where each branch processes
	events that are selected by QES, RES or DIS cuts.

2007-09-13 21:34  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/gminos_jobs.py:

	Somehow the --reroot commmand flag handling was missing (how did the
	FarDet jobs get reroot'ed?).
	Also give more explicit example of what the -f (cosmic mu stdhep) file
	naming convention should be.

2007-09-13 21:32  rustem

	* PhysicsNtuple/Draw/: DrawSpan.cxx, DrawSpan.h, DrawUtil.cxx,
	  DrawUtil.h, EventAdcTab.cxx, EventAdcTab.h, EventHitTab.cxx,
	  EventHitTab.h, SnarlAdcTab.cxx, SnarlAdcTab.h, SnarlTime.txt,
	  SnarlTimeTab.cxx, SnarlTimeTab.h, StdHepTab.cxx, StdHepTab.h,
	  TabConfig.txt:

	Commit the code for the event display. I was really hoping to add more
	functionality and iron out couple minor bugs with reading the
	configuration files but it is not going to happen anytime soon, if at all.
	Enjoy it as it is...

2007-09-13 21:29  rustem

	* PhysicsNtuple/Config/PlotVtx.xml:

	An xml file that contains the definitions for the vertex histograms.

2007-09-13 21:28  rustem

	* PhysicsNtuple/: AlgAdapt.h, Plot/PlotVtx.cxx, Plot/PlotVtx.h:

	Add renamed PlotVtx class. Add a ABC for a new algorithm: AlgAdapt is an
	abstract interface for an algorithm that reweights data and Monte-Carlo.

2007-09-13 21:26  rustem

	* PhysicsNtuple/: TruthReco.cxx, TruthReco.h,
	  Config/PlotVertex.xml, Plot/PlotVertex.cxx, Plot/PlotVertex.h:

	Remove obsolete classes: TruthReco code is now in Truth.h and Truth.cxx
	files, PlotVertex is renamed to PlotVtx (and significantly improved as
	well).

2007-09-13 21:23  rustem

	* PhysicsNtuple/: DataBlock.cxx, DataBlock.h, Event.h, Factory.h,
	  Handle.h, Header.cxx, Header.h, Hist1d.h, LinkDef.h, RecoNu.h,
	  RunAlgSnarl.cxx, RunAlgSnarl.h, Truth.cxx, Truth.h,
	  Config/PlotBasic.xml, Config/PlotEvent.xml, Config/PlotKinem.xml,
	  Config/PlotReson.xml, Config/PlotTruth.xml, Draw/RecordStore.cxx,
	  Hist/HistMan.cxx, Hist/HistMan.h, Plot/CountHist.cxx,
	  Plot/CountHist.h, Plot/LinkDef.h, Plot/Plot.cxx, Plot/Plot.h,
	  Plot/PlotBasic.cxx, Plot/PlotBasic.h, Plot/PlotData.cxx,
	  Plot/PlotData.h, Plot/PlotEff.cxx, Plot/PlotEff.h,
	  Plot/PlotEvent.cxx, Plot/PlotEvent.h, Plot/PlotPur.cxx,
	  Plot/PlotPur.h, Plot/PlotReson.cxx, Plot/PlotReson.h,
	  Plot/PlotSelect.cxx, Plot/PlotSelect.h, Plot/PlotShower.cxx,
	  Plot/PlotShower.h, Plot/PlotTrack.cxx, Plot/PlotTrack.h,
	  Plot/PlotTruth.cxx, Plot/PlotTruth.h, Select/SelectNeutrino.cxx,
	  Select/SelectNeutrino.h, Store/FillDataModule.cxx,
	  Store/FillTruth.cxx, Store/FillTruth.h, Store/Interface.cxx,
	  Store/Interface.h, kNNAlg/FillkNN.cxx, kNNAlg/FillkNN.h,
	  macros/make_data.C, macros/make_mc.C:

	Commit all the changes from the last month or so. There are many of them,
	too many to list them all. I guess I just write a lot of code:-) Overall,
	the design of the package has not changed but there are many improvements
	and refinements. In particular:

	1) Hist1d<T> is now fully fledged histogram template that implements
	smoothing, merging and conversion to/from TH1 class.

	2) All plotting routines have been significantly improved and are now
	capable of making production quality histograms.

	3) Plot.h and Plot.cxx contain useful classes that simplify plotting of
	data and Monte-Carlo histograms.

2007-09-13 19:55  boehm

	* NueAna/: MuonRemovalInfo.cxx, MuonRemovalInfo.h,
	  MuonRemovalInfoAna.cxx, MuonRemovalInfoAna.h, macros/LoadLibs.C:

	Adding q/p, sigmaq/p and the other 3 CC pid to the MRI branch of the NueAna record.

	Also Andy Changed CandMorgue so the Libraries needed to be updated

2007-09-13 19:44  boehm

	* Conventions/: ReleaseType.cxx, ReleaseType.h:

	Adding R1.24.3 as another relasetype to handle the daikon 03 files that are being generated with fancy bfield

2007-09-13 19:32  hartnell

	* NtupleUtils/: NuExtraction.cxx, NuExtraction.h, NuReco.cxx,
	  NuReco.h:

	Extract and copy the new SA variables

2007-09-13 19:30  hartnell

	* NtupleUtils/: NuEvent.cxx, NuEvent.h:

	Added these variables:

	   Int_t trkIndex;//trk.index, position in TClonesArray in sntp file

	   Int_t trkfitpassSA;//variables from the SA track fitter
	   Int_t chargeSA;//definitions same as variables without SA postfix
	   Float_t qpSA;
	   Float_t sigqpSA;
	   Float_t chi2SA;
	   Float_t ndofSA;
	   Float_t probSA;

2007-09-13 19:22  hartnell

	* NuMuBar/: NuAnalysis.cxx, NuAnalysis.h, NuModule.cxx, NuTime.cxx:

	Now ask for NtpFitSARecord from mom and pass to NuAnalysis

2007-09-13 19:21  hartnell

	* NuMuBar/macros/makeDst.C:

	Add stream NtpFitSA and do gSystem->Load("libNtpFitSA.so");

2007-09-13 16:47  Brian Rebel <brebel@fnal.gov>

	* NCUtils/NCType.h:

	change 1 sigma value for NearFarHadronic calibration to 11%.

2007-09-13 16:07  boehm

	* MuonRemoval/: AlgRmMu.cxx, CandRmMu.cxx, CandRmMu.h,
	  CandRmMuHandle.cxx, CandRmMuHandle.h, NtpMREvent.cxx,
	  NtpMREvent.h:

	Attempting to add to the q/p variable into the MuonRemoval data block

2007-09-13 16:06  boehm

	* NueAna/macros/RunTrimmer.C:

	wont work

2007-09-13 15:37  Sue Kasahara <schubert@hep.umn.edu>

	* GeoGeometry/GeoGeometry.cxx:

	Change the default mediums for near and far detector rock & liners.
	         Old     --------->   New
	Far:     MARS: "ROCK"         MARS: "GREENSTONE"
	         LINR: "CONCRETE"     LINR: "GREENSTONE"
	Near:    MARS: "DOLOMITE"     MARS: "NEARBEDROCK"
	         LINR: "CONCRETE"     LINR: "NEARBEDROCK"

2007-09-13 15:09  Minos CVS group account.  Do not commit from here!

	* Contrib/boehm/Docs/IntensityNote/Intensity.tex:

	can i commit?

2007-09-13 13:06  ahimmel

	* NuMuBar/NuPlots.cxx:

	Added track end variables and stopping/exiting to BRevAna.

2007-09-13 11:28  hartnell

	* NuMuBar/NuDSTAna.cxx:

	Remove a couple more lines to simplify further.

2007-09-13 11:26  hartnell

	* NuMuBar/NuDSTAna.cxx:

	Remove the GetEvtEnergy line from CSSAna. It was harmless but may invoke
	questions.

2007-09-13 09:49  tinti

	* Contrib/barr/na49an/na49an.cxx:

	save the latest version before drastic changes

2007-09-12 21:08  Robert Hatcher <rhatcher@fnal.gov>

	* setup/setup_minossoft_FNALU_parser.sh:

	using "-r controlroom" now picks R1.26/GCC_3_4 rather than R1.22/GCC_3_2.

2007-09-12 20:55  Minos CVS group account.  Do not commit from here!

	* Contrib/rhatcher/gminos_jobs/setup_cit_bundle.sh:

	forgot one of the the files.

2007-09-12 20:54  Minos CVS group account.  Do not commit from here!

	* Contrib/rhatcher/gminos_jobs/: cit_bulk_copy.sh, run_cit.sh,
	  submit_cit.sh:

	caltech farm scripts, initial versions

2007-09-12 20:36  George Irwin <gmieg@slac.stanford.edu>

	* NtupleUtils/NuHistos.cxx:

	Add ' #include "TROOT.h" '

2007-09-12 20:16  asousa

	* NCUtils/Extrapolation/: NCExtrapolationJK.cxx,
	  NCExtrapolationMQ.cxx:

	Small fix so that "ChangeMCAsData" string in the macro setting is taken into account when figuring out the short output files.

2007-09-12 20:07  arms

	* Contrib/rhatcher/gminos_jobs/: run_umn.sh, umn_bulk_copy.sh:

	Fix a small typo in run_umn.sh for checking options to use a stdhep file as input. Improve documentation in umn_bulk_copy.sh

2007-09-12 19:40  Sue Kasahara <schubert@hep.umn.edu>

	* G3PTSim/TGeant3/TGeant3.cxx:

	Move abort on failure to find matching secondary production process
	further up in method TGeant3::ProdProcess.

2007-09-12 19:39  Sue Kasahara <schubert@hep.umn.edu>

	* MCApplication/MCApplication.cxx:

	Add additional ion types with Z > 28 to cover those defined by GMINOS,
	for completeness.

2007-09-12 17:29  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/: Ganga/GangaMinos.ini, Scripts/docs/Scripts.html,
	  docs/admin_group.html, docs/admin_install_software.html,
	  docs/admin_procedures.html, docs/data_lfc_lcg.html,
	  docs/data_tutorial.html, docs/glossary.html, docs/links.html,
	  docs/sites.html, docs/status_lcg-info.html,
	  docs/status_lcg-infosites.html, docs/status_tutorial.html:

	Begin the VO name migration:-

	  minos -> minos.vo.gridpp.ac.uk

	now that RAL T1 supports the new name, at least to the point where
	"Hello World" runs.  Currently this is a mess.  The name "minos"
	permeates many components of the GRID (software tag, service classes,
	directory names, environmental variables) and I simply don"t know how
	many of them strictly track the VO name.  Even when they do they
	sometimes require the "." to be replaced by "_".  The LFC does not yet
	support the new name nor, I think, does Castor.  So things are likely
	to be broken for a while.

2007-09-12 17:13  hartnell

	* NuMuBar/: NuAnalysis.cxx, NuDSTAna.cxx:

	Use the new CalcPOT... method.

	Micro DSTs created from now on will have the hTotalPot histogram.

	When multiple files are concatenated the hTotalPot histograms are summed
	if they exist. Otherwise the CalcPOT... method is used.

2007-09-12 17:11  hartnell

	* NtupleUtils/: NuHistos.cxx, NuHistos.h:

	Added method to create a single histogram "hTotalPot" that tells you the
	pots for ND/FD data/MC. This simplifies things significantly.

	Just do (on files made with latest code):
	hTotalPot->Integral()
	to get the pots for the file.

	I need to add a manual override for FD data (will add it when needed).

	Float_t NuHistos::CalcPOTsFromHistos(std::string sNamePostfix) const

2007-09-12 17:06  hartnell

	* NuMuBar/NuBeam.cxx:

	Make spillsPerFile=1 for FD MC.

2007-09-12 16:48  asousa

	* NCUtils/: Extrapolation/NCExtrapolationModule.cxx,
	  macros/nearFarExtrapolationSystExt.C:

	After weekend changes, systematics shifts stopped being applied when running systematic study. Updating code to recover previous behavior and chnaging the macro accrodingly.

2007-09-12 15:06  Brian Rebel <brebel@fnal.gov>

	* NCUtils/NCType.h:

	back out change to normalization default because NCANalysisUtils adds 1
	to whatever the input value is.

2007-09-12 14:39  evans

	* NtupleUtils/: NuMatrixFitter.cxx, NuMatrixFitter.h,
	  NuMatrixMethod.cxx, NuMatrixMethod.h:

	The extrapolation and fitting is now working (likelihood fit only: I
	need to rebin the histograms before a chi2 fit will work). The code
	can either do the standard CC analysis's extrapolation, or a CPT fit.

2007-09-12 13:26  ahimmel

	* NuMuBar/: NuDSTAna.cxx, NuDSTAna.h, NuPlots.cxx, NuPlots.h:

	Add NuPlots::FillEffPur(NuEvent, bool) and NuDSTAna::CSSAna() to perform
	Donna's CSS study.  The second argument to FillEffPur is a boolean for
	wheter or not an event is selected -- thus the method is general.  To use
	it,

	   plots.fillEffPur(nu, nu.myID > 0.3);

	The CSSAna method can be modified in this one line to work for any of the
	variables.  FillEffPur will produce 6 plots in the output ntuple:

	Selected
	SelectedTrue
	AllTrue
	SelectedNC
	SelectedTrueNC
	AllTrueNC

	The names are self explanatory.  The NC variants have dpID > 0.4 cut applied.
	From these plots, the efficiency and purity plots as defined in doc 3548
	can be constructed (variable width bins already applied).

	   eff = SelectedTrue / Selected;
	   pur = SelectedTrue / AllTrue;

	Also, some small bug fixes for BRev functions.

2007-09-12 12:43  Nick West <n.west1@physics.oxford.ac.uk>

	* WebDocs/SnapshotRel.html:

	Add S07-09-06-R1-26

2007-09-12 12:26  ahimmel

	* NuMuBar/NuPlots.cxx:

	Fixed a bug causing plots not to be recreated for different BRev types.
	static vectors now append new plots to the end.

2007-09-12 11:06  ahimmel

	* NuMuBar/: NuDSTAna.cxx, NuPlots.cxx, NuPlots.h:

	Modified the BRev functions to allow truth, all selected, signal and
	contamination (NC, Wrong Sign) plots to be produced with the same
	method: NuPlots::FillBRev(NuEvent, TString, bool).  Thus, all selections,
	including truth selections, have been moved out of NuPlots into NuDSTAna.

2007-09-12 00:27  arms

	* Contrib/rhatcher/gminos_jobs/: md5check.sh, run_umn.sh,
	  umn_bulk_copy.sh:

	Make changes to allow umn scripts to run jobs with stdhep input from the commandline. Commit new version of md5check.sh that cleans up after itself if a file transfer corrupted a file. Alter umn bulk transfer script to not copy log files for corrupt gaf or reroot transfers.

2007-09-11 23:09  asousa

	* NCUtils/: Extrapolation/NCExtrapolationJK.cxx,
	  macros/nearFarExtrapolationSystExt.C:

	Fixing typo that prevented creation of summary output file. Also committing latest version of running macro

2007-09-11 22:03  Brian Rebel <brebel@fnal.gov>

	* NCUtils/NCType.h:

	need to change the NC background sigma from 50% to 25%

2007-09-11 21:25  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCType.h, Extrapolation/NCExtrapolationMQ.cxx,
	  Extrapolation/NCExtrapolationModule.cxx:

	NCType.h

	set default for normalization to 1

	MQ:

	make the values passed from the near detector the actual input values
	and not the change from the nominal - this was a major bug to be fixed
	sorry all

	Module:

	output to screen which parameters were changed in MC when used as data

2007-09-11 21:01  Sue Kasahara <schubert@hep.umn.edu>

	* CandNtupleSR/: NtpSREvent.cxx, NtpSREvent.h,
	  Module/NtpSRModule.cxx:

	Add new event variables:
	 Float_t* stpph0sigmap;//[nstrip] ph corrected for fiber attenuation (east)
	 Float_t* stpph0mip;   //[nstrip] ph in MIPs      (east)
	 Float_t* stpph0gev;   //[nstrip] ph in GeV       (east)
	 Float_t* stpph1sigmap;//[nstrip] ph corrected for fiber attenuation (west)
	 Float_t* stpph1mip;   //[nstrip] ph in MIPs      (west)
	 Float_t* stpph1gev;   //[nstrip] ph in GeV       (west)
	by request.
	These are the equivalent of the associated variables in the NtpSRShower
	and NtpSRTrack.  They will fatten the ntuple up a bit, but are for
	the convenience for the end-user and are filled from the CandEvent:
	            Float_t sigmap = event->GetStripCharge(eventstrip,
	                           CalStripType::kSigMapped,stripend);
	            Float_t mip = event->GetStripCharge(eventstrip,
	                             CalStripType::kMIP,stripend);
	            Float_t gev = event->GetStripCharge(eventstrip,
	                             CalStripType::kGeV,stripend);

2007-09-11 20:33  Robert Hatcher <rhatcher@fnal.gov>

	* Production/Cedar_phy/bfield.C:

	Use ASCII_DB_SET "bhcurvrev" if MC has a "4" as the appropriate character
	in the file name.

2007-09-11 20:28  Robert Hatcher <rhatcher@fnal.gov>

	* Production/asciidb/cedar_daikon/bhcurvrev/: BFLDDBIPLANEMAP.csv,
	  BFLDDBIPLANEMAPVLD.csv, catalogue.db:

	table entries for "bhcurv" maps scaled by -1 factor.  This will be needed
	if we generate any reverse bfield "bhcurv" MC.  Data is handled by additional
	VLD entries in the "bhcurv" directory.

2007-09-11 20:25  Robert Hatcher <rhatcher@fnal.gov>

	* Production/asciidb/cedar_daikon/bhcurv/: BFLDDBIPLANEMAP.csv,
	  BFLDDBIPLANEMAPVLD.csv:

	Add entries for periods when real detectors where reverse focussing
	(5 times for NearDet, once for FarDet) using SCALE=-1 multiplying the
	full, detail and gap maps.

2007-09-11 19:33  Robert Hatcher <rhatcher@fnal.gov>

	* Conventions/Munits.h:

	At the request of Justin Evans add "tonne" and "kilotonne" (and "kt") as units.

2007-09-11 17:54  Sue Kasahara <schubert@hep.umn.edu>

	* G3PTSim/TGeant3/TGeant3.cxx:

	Rewrote method TGeant3::ProdProcess, which is used to determine the
	secondary production mechanism for secondaries generated during the
	current step:
	//sk:begin
	//    Modified: S. Kasahara  2007/09/11 Method rewritten to make
	//    use of GCKING/KCASE variable for determining the production
	//    mechanism of the secondaries.  The old method was to pick the first
	//    active process from the current step's list of active processes
	//    that had the capability of generating secondaries.  This occasionally
	//    picked the wrong secondary production mechanism.
	...
	Will also let ROOT/VMC team know.

2007-09-11 17:43  hartnell

	* NuMuBar/NuPlots.cxx:

	Only fill truth plots if not data

2007-09-11 17:08  evans

	* NtupleUtils/: NuMatrixFitter.cxx, NuMatrixFitter.h,
	  NuMatrixMethod.cxx, macros/CombineMMHelpers.C:

	Bug fixes. Mainly memory management in CombineMMHelpers.C. Also a problem
	with units in the oscillation formulae in NuMatrixMethod. Got rid of unused
	parameters in NuMatrixFitter.

2007-09-11 16:31  hartnell

	* NtupleUtils/doc/cssSystematicsDSTs.html:

	Updated with NuDST file location. Also clarified other points.

2007-09-11 13:59  Brian Rebel <brebel@fnal.gov>

	* NCUtils/data/HessNewCorrections_LEall3_pME_pHE.root:

	add hessian file for running MQ extrapolation

2007-09-11 13:59  kordosky

	* CVSROOT/: check_access, modules:

	access rights for a new module

2007-09-11 13:43  evans

	* NtupleUtils/: NuMatrixFitter.cxx, NuMatrixFitter.h,
	  NuMatrixMethod.cxx, NuMatrixMethod.h, macros/CombineMMHelpers.C:

	Made more extrapolation parameters configurable. Ensured the correct cross-
	sections are picked up for each neutrino type. Other minor bug fixes.

2007-09-11 12:55  evans

	* NuMuBar/NuDSTAna.cxx:

	Forgot to uncomment the place where the truth histograms were written
	to the summary DST. Also a bug in the protection such that some of the
	helper histograms were never being created.

2007-09-11 12:11  asousa

	* NCUtils/: Extrapolation/NCExtrapolationJK.cxx,
	  Extrapolation/NCExtrapolationMQ.cxx,
	  Extrapolation/NCExtrapolationMQ.h,
	  macros/nearFarExtrapolationSystExt.C:

	Mods to JK extrapolation so that Syst. study can include x-section systematics. Changes to MQ extrapolation to output a result file.

2007-09-10 23:15  asousa

	* NCUtils/NCType.h:

	Setting default shift for relative Near/Far hadronic calibration to 0.03 instead of 0.02. Forgot to commit after running PID systematics study.

2007-09-10 17:20  arms

	* Contrib/rhatcher/gminos_jobs/gminos_cfg_CosmicMu_near_bhcurv.py:

	Preliminary new ND CosmicMu gminos_jobs cfg script, includes new Bfield maps, new rock material, line current Bfield in air gaps

2007-09-10 16:18  evans

	* NuMuBar/NuDSTAna.cxx:

	Uncommented the truth histograms required for the calculation of efficiency
	histograms: they're now being written out again. Added in individual
	protection against the case in which any one of them doesn't exist in an
	input file.

2007-09-10 16:00  hartnell

	* NuMuBar/NuAnalysis.cxx:

	Write out truth histos for data as well as MC so that they are there in
	the file as dummies.

2007-09-09 20:19  Brian Rebel <brebel@fnal.gov>

	* NCUtils/macros/nearFarExtrapolation.C:

	put a couple of lines of comments into macro to explain how to use it
	when changing systematic parameters in the fake data set.

2007-09-09 20:16  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolationMQ.cxx,
	  NumRec/MinosMinimization.cxx:

	MQ:

	Set the fit for the near detector beams.

	Base:

	get rid of some compiler warnings.  make sure to use preset values for
	DP and MQ extrapolation in near detector.

	MinosMinimization:

	in GetMCDistribution make sure to add in electrons and that the MC is the
	signal MC only, no backgrounds added in.

2007-09-07 23:10  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCAnalysisUtils.h, NCType.h,
	  Extrapolation/NCEnergyBin.cxx,
	  Extrapolation/NCExtrapolationMQ.cxx,
	  Extrapolation/NCExtrapolationModule.cxx,
	  NumRec/MinosMinimization.cxx:

	put the NC cross section and nubar cross section values at the end of the list
	so as not to mess up the MQ extrapolation.

	move the NCExtrapolationModule::FindEventWeight() method guts into
	NCAnalysisUtils.  now the module method calls the utils one.

	fix variable initialization in nc energy bin.

	minor bug fix in how MinosMinimization gets best fit for beam object
	histograms

2007-09-07 20:08  Robert Hatcher <rhatcher@fnal.gov>

	* CVSROOT/check_access:

	add Jason to numisoft/gnumi writers.

2007-09-07 20:02  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/docs/gbs.html:

	Start section on configuration

2007-09-07 18:23  Nathaniel Tagg <n.tagg1@physics.ox.ac.uk>

	* Contrib/tagg/TofAna/: AnaHeavyNu.cxx, AnaHeavyNu.h,
	  EnergyPenalty.cxx, EnergyPenalty.h, Minuit1Fit.cxx, Minuit1Fit.h,
	  test/GNUmakefile, test/LinkDef.h, test/main.cxx:

	Further tidy up.

	Includes code for heavy-neutrino tests, but these were stupid and so didn't get very far.

2007-09-07 18:21  Nathaniel Tagg <n.tagg1@physics.ox.ac.uk>

	* Contrib/tagg/TofAna/: FDEvent.cxx, FDEvent.h, GNUmakefile,
	  LinkDef.h, Systematics.cxx, TofAna.cxx, TofAna.h:

	Tidying up. Final commit of ToF code used to generate paper.

2007-09-07 15:34  Nick West <n.west1@physics.oxford.ac.uk>

	* WebDocs/WebDocs.html:

	Add link to DBS-LITE, and remove link to Oracle checksums

2007-09-07 15:31  Nick West <n.west1@physics.oxford.ac.uk>

	* DatabaseMaintenance/doc/: dbmauto_slave.html, dbs_lite.html:

	Add DBS-LITE, based on Alex's document

2007-09-06 23:48  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCAnalysisUtils.h, NCType.h:

	add method to compute weights for changing NC and nubar cross sections to
	NCAnalysisUtils.

	add appropriate constants to NCType to make that happen.  fix up some sigma values
	based on latest from calibration group

2007-09-06 23:46  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolationJK.cxx,
	  NCExtrapolationMQ.cxx, NCExtrapolationMQ.h,
	  NCExtrapolationModule.cxx, NCExtrapolationModule.h:

	MQ:

	remove methods to find event weights and do tweaking of systematics.  this is
	handled by the module.

	JK:

	comment out some MAXMSG calls as they are quite time consuming

	Module:

	make the determination of POT per file more intelligent to accomodate methods
	that use multiple beams.  now have a map of beam to pot/file for near and far
	detectors.  put pot/file for mock files in a data member.

	dont remove beams from index where no files were found - bug was happening where
	the near files would be there but no far and the near would get removed.  now
	test the entries in the chain in AddEventsToExtrapolation and simply return
	if the chain is empty.

	make the systematic studies a little easier to follow in FindEventWeight.

	add use of cross section uncertainties to FindEventWeight as well

2007-09-06 23:38  Brian Rebel <brebel@fnal.gov>

	* NCUtils/NumRec/MinosMinimization.cxx:

	add electrons, not the background again when including electrons in the fit

2007-09-06 22:34  George Irwin <gmieg@slac.stanford.edu>

	* WebDocs/macosx_instructions.txt:

	Add note about build and installation of BSD getopt
	command with long-option extension.

2007-09-06 20:56  Robert Hatcher <rhatcher@fnal.gov>

	* setup/packages-S07-09-06-R1-26:

	First commit

2007-09-06 20:34  Nick West <n.west1@physics.oxford.ac.uk>

	* HWDB/maintenance/: cmd_import_vfb_control_cable.pm, hdm.perl,
	  help.txt, vfb_control_cable_spreadsheet.dat:

	Add import_vfb_control + data to add VFB control cable from Doug's spreadsheet

2007-09-06 20:32  Nick West <n.west1@physics.oxford.ac.uk>

	* HWDB/maintenance/cmd_import_pulser.pm:

	Rename internal routine: process_group -> process_pulser_group.  Change FANOUTOFSERVICCE MOTID 1 -> 4

2007-09-06 20:08  Nathaniel Tagg <n.tagg1@physics.ox.ac.uk>

	* Contrib/tagg/NdMuons/: Makefile, chooser.f, main.cxx, prop_mu.f,
	  propmain.f, ran0.f:

	Added new working directory for muon propagation at ND.

2007-09-06 18:58  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/macro/PTSim_g3Config.C:

	Add an example use of SetUserDecayProductStableMinLifetime option.

2007-09-06 18:54  Sue Kasahara <schubert@hep.umn.edu>

	* G3PTSim/TGeant3/: TGeant3.cxx, TGeant3.h, TGeant3gu.cxx:

	Add TGeant3 configuration method:

	virtual void SetUserDecayProductStableMinLifetime(Double_t lifetime=1.E-15);

	and support code to allow the configuration of the user decay code
	(TGeant3gu::gudcay) to adjust the minimum lifetime by which decay products
	will be considered stable for kick back to the transport mechanism.
	If the lifetime of a decay product is less than the minimum, the particle
	will be decayed promptly and only if its decay products (if in turn stable)
	will be passed back to transport.
	Note: Only particle types previously defined to Geant3 can be kicked back.
	Args: lifetime (sec) (default = 1.E-15)

2007-09-06 17:32  George Irwin <gmieg@slac.stanford.edu>

	* IoModules/: IoDDSStreamItr.cxx, IoDDSStreamItr.h,
	  IoDataStreamFactory.cxx, IoDataStreamFactory.h,
	  IoInputModule.cxx, IoInputModule.h:

	Backport from development for dispatcher client ID from Sue.

2007-09-06 17:27  George Irwin <gmieg@slac.stanford.edu>

	* Dispatcher/: DDSClient.cxx, DDSClient.h, DDSClientId.cxx,
	  DDSClientId.h, test/DemoClient.cc:

	Backport from development for dispatcher client ID from Sue.

2007-09-06 17:22  George Irwin <gmieg@slac.stanford.edu>

	* Demo/dispatcher.C:

	Backport from development for dispatcher client ID from Sue.

2007-09-06 16:59  Brian Rebel <brebel@fnal.gov>

	* NCUtils/NumRec/: MinosMinimization.cxx, MinosMinimization.h:

	sync up with tom's latest code

2007-09-06 16:58  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCBeam.cxx, NCExtrapolationMQ.cxx,
	  NCExtrapolationMQ.h, NCExtrapolationModule.cxx:

	make changes to sync the MQ method with the rest of the methods.  remove debug
	output in NCBeam

2007-09-06 15:23  bckhouse

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h:

	Remove the last traces of single precision arithmetic in an attempt to appease Minuit.

2007-09-06 14:47  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/test/PTSimValidateInit.C:

	Update test script.

2007-09-06 14:37  bckhouse

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h:

	Use a better (quicker and more reliable) algorithm for contour-finding.

2007-09-06 13:20  evans

	* NtupleUtils/macros/CombineMMHelpers.C:

	A macro to combine helper histograms from various sources into one file and
	do all the divisions necessary for making the purity and efficiency plots.

2007-09-06 12:41  asousa

	* NCUtils/Extrapolation/NCExtrapolationJK.cxx:

	Previous bug fix did not completely squished the bug. Should be dead now.

2007-09-06 12:23  evans

	* NtupleUtils/: NuMatrixFitter.cxx, NuMatrixFitter.h:

	Matrix extrapolation updated to include a CPT antineutrino extrapolation.

	NuMatrixMethod extrapolates one ND data spectrum to the FD. NuMatrixFitter
	is a wrapper that creates as many NuMatrixMethod objects as necessary to
	extrapolate the required individual fluxes (e.g. numus and nubars
	independently). So far two CPT analysis methods are implemented: one
	performs the standard CC extrapolation on the numus and numubars separately
	with extra stages in the FD to oscillate the CC background. The other uses
	the CC numu extrapolation to calculate the CC numu background to the CC
	numubar prediction, and vice-versa.

	The code still requires testing.

2007-09-06 12:19  evans

	* NtupleUtils/: LinkDef.h, NuMatrixMethod.cxx, NuMatrixMethod.h:

	Matrix extrapolation updated to include a CPT antineutrino extrapolation.

	NuMatrixMethod extrapolates one ND data spectrum to the FD. NuMatrixFitter
	is a wrapper that creates as many NuMatrixMethod objects as necessary to
	extrapolate the required individual fluxes (e.g. numus and nubars
	independently). So far two CPT analysis methods are implemented: one
	performs the standard CC extrapolation on the numus and numubars separately
	with extra stages in the FD to oscillate the CC background. The other uses
	the CC numu extrapolation to calculate the CC numu background to the CC
	numubar prediction, and vice-versa.

	The code still requires testing.

2007-09-06 10:35  asousa

	* NCUtils/Extrapolation/: NCExtrapolationJK.cxx,
	  NCExtrapolationJK.h:

	When not fitting for systematics, systematics loop only takes one step, but this step was shifitng histograms by -1Sigma in studied systematic, now fixed. For the syst study, also added extraction name to best fit output file.

2007-09-05 19:20  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/macro/PTSim_decayConfig.C:

	Add K0L to the list of particles to be decayed by pythia6 instead of
	native Geant3 to preserve neutrino flavor.

	Add rho0,rho+,rho-,D+,D-,D0,D0bar to list of particles to be decayed by
	pythia6 instead of those modes defined to Geant3 via gsdk in
	TGeant3::DefineParticles.

	Set pi0 to be stable in pythia6 so that Geant3 can handle decay.
	The reason is described in PTSim_decayConfig.C as:
	 // In general, TGeant3 is set up through TGeant3gu::gudcay to pass
	 // all pythia6 decay products back to the G3 transport mechanism iff they
	 // have a lifetime > 1.E-15 sec for further transport.
	 // Since the pi0 lifetime is less than this, if pi0 is produced as a decay
	 // product in pythia6, e.g. KL0 -> pi0 pi+ pi-, the pi0 will be immediately
	 // decayed by pythia6 to 2 gammas, and the KL0 decay product list passed
	 // back to the transport mechanism will be "gamma gamma pi+ pi-", i.e.
	 // the pi0 will not be visible in the list of secondaries passed back to
	 // the transport mechanism and will not be pushed to the stack for possible
	 // storage to the stdhep output array.
	 // To avoid this, the pi0 is set to stable in pythia6, and its decay
	 // will be handled by Geant3.
	 pythia6.SetMDCY(pythia6.Pycomp(111),1,0);

2007-09-05 18:30  asousa

	* NCUtils/: Extrapolation/NCExtrapolationJK.cxx,
	  Extrapolation/NCExtrapolationJK.h,
	  macros/nearFarExtrapolationSyst.C:

	When doing syst study, write out a small output file with fit results. added protection against ND MC histogram having zero bins when low statistic samples are used. Fixed bug resulting in the systematic fitting still being done for one step with 1 sigma shift applied, even if systematic fitting was turned off.

2007-09-05 18:25  arms

	* Contrib/rhatcher/gminos_jobs/: gminos_cfg_L010185_far_osc0001.py,
	  gminos_cfg_L010185_far_osc0003.py,
	  gminos_cfg_L250200_far_osc0001.py,
	  gminos_cfg_L250200_far_osc0003.py:

	Add run 0001 and 0003 gminos cfg scripts, since these are open now. Run 0002 has yet to be revealed.

2007-09-05 17:27  arms

	* Contrib/rhatcher/gminos_jobs/setup_umn_bundle.sh:

	Update UMN default daikon version to daikon_03

2007-09-05 16:03  gallaghr

	* MCReweight/NeugenWeightCalculator.cxx:

	update to MODBYRS4

2007-09-05 16:00  gallaghr

	* NeugenInterface/: neugen_config.cxx, neugen_config.h,
	  neugen_wrapper.cxx:

	update to MODBYRS4

2007-09-05 15:28  Brian Rebel <brebel@fnal.gov>

	* AnalysisNtuples/Module/CondensedNtpModuleNC.cxx:

	return if no events in snarl before getting to the kNN initialization step.

	should speed things up quite a bit.

2007-09-05 14:02  bckhouse

	* NCUtils/Extrapolation/NCExtrapolation.cxx:

	Fix bug in Minuit contour finder.
	Physical limits weren't applied to the variables being minimized over - affecting the shape of the contours.

2007-09-05 11:29  bckhouse

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h:

	Add a version of the contour finding that uses Minuit.
	The large amount of duplicated code will be fixed when either one or the other method is removed, or both are kept and I merge the implementations.

2007-09-05 11:06  asousa

	* NCUtils/macros/nearFarExtrapolationSyst.C:

	Adding syst shift to name of output file
	.CVS: ----------------------------------------------------------------------

2007-09-05 11:02  hartnell

	* NuMuBar/: NuDSTAna.cxx, macros/FileListSpecial.C,
	  macros/dstAna.C:

	Commented out the hTrueEnergyTrueCC family of histograms in the DoIO()
	method. They appear not to exist and were causing segv's. I tried
	grepping in the code but couldn't find them. Maybe they are obsolete
	now?

2007-09-05 10:57  hartnell

	* NtupleUtils/NuInputEvents.cxx:

	Fixed massive memory leak. Each time a TFile was opened it wasn't
	closed.

	The fix seemed straightforward but for some reason the histograms cloned
	from histograms in the file were disappearing when the file was
	closed. I seem to recall a way to tell ROOT to separate histograms from
	files but I couldn't remember it. Anyway, my way round this problem was
	to just leave the first file open where the cloning was done from, but
	close all the others.

2007-09-05 09:08  evans

	* NtupleUtils/NuHistos.cxx, NuMuBar/NuDSTAna.cxx:

	Adding a new set of matrix method histograms: reco->true matrices for far
	detector oscillating impurities. To oscillate these correctly, one must
	perform reco->true->oscillate->reco.

2007-09-05 00:44  asousa

	* NCUtils/: Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationModule.h,
	  macros/nearFarExtrapolation.C, macros/nearFarExtrapolationSyst.C:

	Added flag to indicate if running in systematic study mode. If so, systematic parameters can be set individually to +-1sigma shifts from macro. Adjust functionality still works if not in syst study mode. Also modified Syst macro to take advantage of new functionality, with Jason's flag applied to prevent including systematics variation in fitting.

2007-09-04 22:06  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	handle MDC pot accounting correctly

2007-09-04 22:04  Robert Hatcher <rhatcher@fnal.gov>

	* CVSROOT/framework.list:

	add Jason Koskinen to the unfortunate souls who receive commit messages
	(per Brian's request, not pure spite on my part; maybe Brian's just
	being vindictive for some reason).

2007-09-04 21:58  Nick West <n.west1@physics.oxford.ac.uk>

	* HWDB/maintenance/: cmd_import_pulser.pm, hdm.perl, help.txt,
	  pulser_spreadsheet.dat:

	Add import_pulser command + data to add pulser power supply and timing board data from Doug's spreadsheet

2007-09-04 21:56  koskinen

	* NCUtils/Extrapolation/: NCExtrapolationJK.cxx,
	  NCExtrapolationJK.h:

	The predictspectrum() function in the F/N method no handles both systematic
	and non-systematic fitting depending solely on inputs to the
	nearFarExtrapolation.C macro, specifically the "FitSystematics" variable.
	The method was also updated to handle NearHadronic systematics, so the
	F/N method can no fit over CCBkg, NCBkg, Normalization, MuonEnergyScale
	NearHadronic and NearFarHadronic.

2007-09-04 21:53  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	a couple of more fixes - got the far detector exposure scaling working and
	got the file counting to print out correctly to the screen.  that last one
	was just cosmetic

2007-09-04 20:28  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	i think the problems with splitting the MC into 2 equal exposure sets is now
	fixed.  fixed up the way the total pot are calculated for the case with
	the filelimit < # entries in histogram and > # entries, made counting for
	MDC files more separate.  moved the scaling for the far exposure to a more
	appropriate location, but the macro still takes the value in # of pot x 10^20

2007-09-04 20:24  Robert Hatcher <rhatcher@fnal.gov>

	* CVSROOT/check_access:

	Add various aliases for Hugh to NeugenInterface and MCReweight.

2007-09-04 19:16  koskinen

	* NCUtils/macros/nearFarExtrapolation.C:

	NC run macro with the inclusion of the new "FitSystematics" variable

2007-09-04 19:10  koskinen

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	Added a new variable to be set in the macro "FitSystematics", which
	is used in the extrapolation method, currently only F/N, to signify
	whether to fit over the systematics.

2007-09-04 19:08  koskinen

	* NCUtils/: NCAnalysisUtils.cxx,
	  Extrapolation/NCExtrapolationJK.cxx:

	NCAnalysisUtils was updated to properly incorporate the NCBackground and
	CCBackground systematic shifts. The shift for the CCBackground was being
	applied to ALL reconstructed CC events with an event completeness <0.5,
	and now the flavor type is restricted to nu_mu and anti nu_mu, without
	the completeness cut. A bug was fixed in the NCExtrapolationJK method
	that set the CCBackground as the CC events in the NC sample.

2007-09-04 17:05  kordosky

	* NeugenInterface/: inuke_reweight.F, shower_ntuple.h:

	fix meaning of /shwr/ sp_idxpar. It now indexes into the init_* arrays as originally intended.

2007-09-04 16:57  kordosky

	* NeugenInterface/: inuke_reweight.F, shower_ntuple.cxx,
	  shower_ntuple.fi, shower_ntuple.h:

	add stdhep index to shower ntuple common

2007-09-04 15:25  bspeak

	* RunSummary/rate_plot.cc:

	Several changes in the plotter program.  Use rate_plot -h to see new options

2007-09-04 15:24  bspeak

	* RunSummary/UtilRSM.cxx:

	change 'new TFile' to 'TFile::Open'

2007-09-04 14:45  evans

	* NtupleUtils/: LinkDef.h, NuMatrixMethod.cxx, NuMatrixMethod.h,
	  macros/RunMMPrediction.C:

	Begun porting the matrix method extrapolation code into NtupleUtils.

	NuMatrixMethod is the new class that does the extrapolation.
	RunMMPrediction.C is an example of how to run it.

	At present, the code only runs the standard CC extrapolation on neutrinos.

2007-09-04 14:25  asousa

	* NCUtils/: Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationModule.h,
	  macros/nearFarExtrapolation.C, macros/nearFarExtrapolationSyst.C:

	Add functionality to set file limit separately for Near and Far detectors. Fix bug occurring when file limit is higher than number of files present in uDST. Far exposure scaling is now done in terms of POT and does need to be recalculated depending on file limit setting. Also committing necessary mods to running macros.

2007-09-04 14:17  niki

	* Contrib/niki/: ReducedNtuples/far/Load_Libs.C,
	  ReducedNtuples/far/copy_tree_far_cedardaikon.C,
	  ReducedNtuples/near/Load_Libs.C,
	  ReducedNtuples/near/copy_tree_near_cedardaikon.C,
	  ReducedNtuples/farnc/Load_Libs.C,
	  ReducedNtuples/farnc/copy_tree_far_cedardaikon.C,
	  ReducedNtuples/nearnc/Load_Libs.C,
	  ReducedNtuples/nearnc/copy_tree_near_cedardaikon.C,
	  correction_histos/near/norm_fix_near.C,
	  correction_histos/near/simple_chain_near.C,
	  correction_histos/far/norm_fix_far.C,
	  correction_histos/far/simple_chain_far.C:

	code for cedar-daikon

2007-09-04 14:14  niki

	* Contrib/niki/: Data/get_nearfar_spectra.C, FakeData/Load_Libs.C,
	  FakeData/RunMC.C, FakeData/get_nearfar_spectra_MC_CC2007.C,
	  FakeData/get_nearfar_spectra_MC_NC.C,
	  FakeData/get_nearfar_spectra_MC_NC_MDC.C,
	  NCana/Run_fit2_NDsyst_v313.C,
	  NCana/matrix_fit_br2norm_newmc_NDnew_fast_v3.C:

	code for cedar-daikon

2007-09-04 14:14  niki

	* Contrib/niki/CCana/: Run_fit2_NDsyst_v3.C,
	  Run_fit2_NDsyst_v3_noskzp.C, Run_fit2_NDsyst_v3_post.C,
	  Run_fit2_NDsyst_v3_post_noskzp.C, Run_fit2_NDsyst_v3_pre.C,
	  Run_fit2_NDsyst_v3_pre_noskzp.C, Run_fit2_NDsyst_v4.C,
	  Run_fit2_NDsyst_v4_noskzp.C, Run_fit2_NDsyst_v4_post.C,
	  Run_fit2_NDsyst_v4_post_noskzp.C, Run_fit2_NDsyst_v4_pre.C,
	  Run_fit2_NDsyst_v4_pre_noskzp.C,
	  matrix_fit_br2norm_newmc_NDnew_fast_v3.C,
	  matrix_fit_br2norm_newmc_NDnew_fast_v4.C:

	code for Cedar-Daikon

2007-09-04 14:13  niki

	* Contrib/niki/BeamMatrix/: Beam_ref_fin.C, Beam_ref_fin_neut.C,
	  RunBeam.C, RunBeam_dataw.C, RunBeam_dataw_phe.C,
	  RunBeam_datawo.C, RunBeam_datawp.C, RunBeam_datawp_phe.C,
	  RunBeam_neut.C, RunBeam_neut_dataw.C, RunBeam_neut_dataw_phe.C,
	  RunBeam_neut_datawo.C, RunBeam_neut_datawp.C,
	  RunBeam_neut_datawp_phe.C:

	Code for Daikon MC

2007-09-04 12:18  kordosky

	* Contrib/rhatcher/gminos_jobs/: acquire_sem.sh,
	  copy_flux_files_ral.sh, md5check.sh, run_ral.sh, submit_ral.sh,
	  submit_ral_stdin.sh:

	updates. in particular, run_ral now sets KRB5CCNAME so that each job has it's own ticket. This should fix a longstanding problem.

2007-09-04 09:31  asousa

	* NCUtils/macros/nearFarExtrapolationSyst.C:

	Changing file limit setting to 10000 for high statistics runs. Should use a much smaller number for test runs.

2007-09-03 17:55  koskinen

	* NCUtils/Extrapolation/NCExtrapolationJK.cxx:

	Fixed a bug that prevented the systematics search in the F/N from using
	zero as one of the test input parameters.

2007-09-02 21:38  asousa

	* NCUtils/macros/nearFarExtrapolationSyst.C:

	Adding macro used in NCUtils systematics runs at RAL.

2007-08-31 18:49  hartnell

	* NuMuBar/macros/microDst.C:

	New macro to make micro DSTs

2007-08-31 18:48  hartnell

	* NuMuBar/: NuDSTAna.cxx, NuDSTAna.h:

	Added MakeMicroDstForCSSSystematics()

2007-08-31 18:45  Robert Hatcher <rhatcher@fnal.gov>

	* RerootExodus/: RerootToTruthModule.cxx, RerootToTruthModule.h:

	Allow creation of DigiScintHit list to be an optional step (still on by
	default) so one can skip it when running ParticleTransportSim.

2007-08-31 18:45  hartnell

	* NuMuBar/NuAnalysis.cxx:

	Minor change to file naming and a print statement

2007-08-31 18:44  hartnell

	* NtupleUtils/doc/: NuDST.html, cssSystematicsDSTs.html:

	Nearly final documentation

2007-08-31 14:45  hartnell

	* NtupleUtils/doc/NuDST.html:

	Updated

2007-08-31 14:45  hartnell

	* NtupleUtils/NuCuts.cxx:

	Don't use the CC good beam cuts for nubars

2007-08-31 14:39  hartnell

	* NtupleUtils/doc/cssSystematicsDSTs.html:

	Bit more info, nearly finished.

2007-08-31 11:41  kordosky

	* Contrib/rhatcher/gminos_jobs/: acquire_sem.sh, release_sem.sh:

	new scripts implementing semaphore access via a shared network file

2007-08-31 11:23  asousa

	* NCUtils/macros/nearFarExtrapolation.C:

	Was missing declaration of extraction config string.

2007-08-30 21:46  Robert Hatcher <rhatcher@fnal.gov>

	*
	  Contrib/rhatcher/gminos_jobs/gminos_cfg_L010185_bhcurv_overlay.py:

	New nRockPerSnarl number for NDBEDROCK (down 18% compared to DOLOMITE).
	These *aren't* just rock muons but also the soft stuff coming from events
	near the HALL/LINR boundary.

2007-08-30 21:23  bspeak

	* OnlineEventDisplay/oedLive.C:

	Add the DDSClientType and DDSClientName options to the IoInputModule to identify
	online event display as:
	  DDSClientType = EventDisplay
	  DDSClientName = FarDetOnlineEventDisplay

	Also add the GifInBatch configuration line to the OnlineEventDisplay module.

2007-08-30 21:21  bspeak

	* OnlineEventDisplay/: OnlineEventDisplay.cxx,
	  OnlineEventDisplay.h:

	Added switch into Configuration "GifInBatch" to force the writing of gifs when
	the root client is in batch mode.

2007-08-30 21:18  hartnell

	* NtupleUtils/doc/cssSystematicsDSTs.html:

	Scribble down some basics on the DSTs for the charge separation
	selection systematics study. Nowhere near finished...

2007-08-30 16:32  asousa

	* NCUtils/macros/nearFarExtrapolation.C:

	Changing macro to take extraction being used as an argument

2007-08-30 16:11  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/fetch_and_build_overlays.py:

	tweak the printout info of what files have been found (include counts).

2007-08-30 16:10  Robert Hatcher <rhatcher@fnal.gov>

	*
	  Contrib/rhatcher/gminos_jobs/gminos_cfg_L010185_bhcurv_overlay.py:

	"bhcurv" files are Daikon_03, overlay needs to know that to find them.
	still need to update nRockPerSnarl due to new rock material.

2007-08-30 14:47  Nathaniel Tagg <n.tagg1@physics.ox.ac.uk>

	* setup/setup_minossoft_macfink.sh:

	Add my setup file for MINOS on a powermac using fink.

2007-08-30 11:42  asousa

	* NCUtils/: NCType.h, Extrapolation/NCExtrapolationJK.cxx,
	  Extrapolation/NCExtrapolationModule.cxx:

	Making sterile fit run from 0.0 to 1.0, commenting some lines used for testing and fixing a bug in custom code configuration.

2007-08-30 00:13  asousa

	* NCUtils/: NCAnalysisUtils.cxx, NCType.h,
	  Extrapolation/NCExtrapolationJK.cxx,
	  Extrapolation/NCExtrapolationJK.h,
	  Extrapolation/NCExtrapolationModule.cxx,
	  macros/nearFarExtrapolation.C:

	Committing Jason's updates to F/N extrapolation, necessary for evaluation of PID systematics. The JK extrapolation can now fit over individual systematic shifts, such as absolute and relative hadronic energy scale and normalization. The systematic shifts to fit over are selected via the nearFarExtrapolation.C macro.

2007-08-29 21:32  hartnell

	* NtupleUtils/doc/NuDST.html:

	More fleshing out... a few gaps still to fill in.

2007-08-29 16:46  kordosky

	* Contrib/rhatcher/gminos_jobs/submit_ral.sh:

	fix logical error in job throttling for 30 + 11 case

2007-08-29 16:04  hartnell

	* NtupleUtils/doc/NuDST.html:

	Flesh out a bit... still a work in progress.

2007-08-29 14:53  Nick West <n.west1@physics.oxford.ac.uk>

	* DatabaseMaintenance/scripts/make_priming_set.pm:

	Switch to assembling tar files on /data/tmp/nwest/db_priming_work
	(same disk as DB) as it has much more space but make sure that there
	is at least 40GB free so that there is no risk of causing DB problems.

	Reinstate exclusion of DCS_HV and PULSERGAIN tables as one already
	exceeds the ~ 4GB file size limit for

	  /afs/fnal.gov/files/data/minos/d210/database_dumps

	and the other is getting close.

2007-08-29 14:47  kordosky

	* Contrib/rhatcher/gminos_jobs/: copy_flux_files_ral.sh,
	  disk_checks.sh, gminos_cfg_short_test.py, run_ral.sh,
	  setup_ral_bundle.sh, submit_ral.sh, submit_ral_stdin.sh:

	updated production scripts for RAL

2007-08-29 11:52  hartnell

	* NtupleUtils/doc/NuDST.html:

	First commit of an outline for documentaion. Nowhere near finished.

2007-08-28 23:37  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/Gui/: PTGuiMainFrame.cxx,
	  PTGuiRollGMinos.cxx, PTGuiRollGMinos.h:

	Add some missing headers so the Gui package compiles again.

2007-08-28 23:35  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/macro/: PTSim_decayConfig.C, PTSim_testG3.C:

	PTSim_decayConfig.C is an example external decayer configuration script.
	It defines the use of TPythia6Decayer to the vmc as an external decayer,
	and activates the use of TPythia6Decayer in place of native Geant3 for
	handling the decays of mu+/-,pi+/-, and K+/-.  pythia6 is used in place
	of Geant3 for those particles because pythia6 will preserve
	the decay product neutrino flavors, and Geant3 will not.

	PTSim_testG3.C modified to include:
	jc.Path("Reco").Mod("PTSimModule").Set("DecayConfig=PTSim_decayConfig.C");

2007-08-28 22:55  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/: PTSimModule.cxx, PTSimModule.h:

	Add support for defining external decayer to be used to modify and/or
	define additional decay modes beyond those of the concrete monte carlo,
	e.g. Geant3.
	New configuration option "DecayConfig" is used to specify the name
	of the script that defines and configures the external decayer.
	For example:
	jc.Path("Reco").Mod("PTSimModule").Set("DecayConfig=PTSim_decayConfig.C");

2007-08-28 22:43  Sue Kasahara <schubert@hep.umn.edu>

	* MCApplication/: MCApplication.cxx, MCApplication.h,
	  test/GNUmakefile:

	Add support for defining an external "decayer", to be used to modify
	existing or add additional decay modes to those defined by the concrete
	Monte Carlo, e.g. Geant3.  An example of such an external decayer
	is TPythia6Decayer.

2007-08-28 22:34  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/test/PTSimValidate.cxx:

	Switch to using UtilIstHEP namespace over MCApp.

2007-08-28 22:33  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/PTSimStack.cxx:

	Switch to using UtilIstHEP namespace in place of MCApp.

2007-08-28 22:29  Sue Kasahara <schubert@hep.umn.edu>

	* MCApplication/test/MCAppValidate.cxx:

	Switch from MCApp namespace to UtilIstHEP

2007-08-28 22:27  Sue Kasahara <schubert@hep.umn.edu>

	* MCApplication/MCAppParticle.h:

	MCAppParticle::GetStatusCodeName() now invokes UtilIstHEP::AsString

2007-08-28 22:25  Sue Kasahara <schubert@hep.umn.edu>

	* MCApplication/: MCApp.cxx, MCApp.h:

	Remove methods and enumerated types now housed in Util/UtilIstHEP

2007-08-28 22:22  Sue Kasahara <schubert@hep.umn.edu>

	* MCNtuple/: NtpMCStdHep.cxx, Module/NtpMCModule.cxx:

	Update NtpMCStdHep print method to make use of UtilIstHEP::AsString(isthep)
	when printing status code.
	Fix comment in NtpMCModule.

2007-08-28 22:12  Sue Kasahara <schubert@hep.umn.edu>

	* Util/: UtilIstHEP.cxx, UtilIstHEP.h:

	New namespace to house utility methods and enumerated types for purposes
	of interpreting IstHEP codes used in the MINOS monte carlo.

2007-08-28 21:53  arms

	* RootUtil/TPSTest/TPSTest.h:

	Remove redundant include TClass.h in TPSTest.h

2007-08-28 18:47  tjyang

	* NueAna/macros/RunNueDisplay.C:

	forgot to load the libraries

2007-08-28 18:43  tjyang

	* PulserCalibration/tp.C:

	test

2007-08-28 18:42  tjyang

	* PulserCalibration/PulserDBModule.cxx:

	add protection to ND

2007-08-28 18:30  arms

	* RootUtil/TPSTest/: TPSTest.cxx, TPSTest.h:

	Add include for TClass

2007-08-28 18:28  arms

	* RootUtil/TPSTest/htmldoc/: TPSTest.h, TPSTest.html,
	  TPSTest_Tree.pdf, src/TPSTest.cxx.html:

	Really remove htmldoc directory

2007-08-28 17:32  bckhouse

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h:

	Tidy up additions to NCExtrapolation.

2007-08-28 13:47  asousa

	* CVSROOT/framework.list:

	Changing Chris's e-mail address for CVS sp... messages at his request.

2007-08-28 11:10  asousa

	* Contrib/asousa/NCStudy/: BatchScripts/makeScriptExt.csh,
	  BatchScripts/makeScriptExtTune.csh,
	  BatchScripts/nearFarExtrapolationCutTune.C,
	  BatchScripts/nearFarExtrapolationSense.C,
	  BatchScripts/runAllExt.csh, BatchScripts/runAllExtTune.csh,
	  BatchScripts/runAllExtTuneAS.csh,
	  BatchScripts/runAllExtTuneRO.csh,
	  BatchScripts/runAllExtTuneRPann.csh, BatchScripts/submitExt.csh,
	  BatchScripts/submitExtTune.csh, PIDTask/ExtSense.C,
	  PIDTask/ExtSenseDm2.C, PIDTask/ExtSenseSin22T.C,
	  PIDTask/ExtSenseTuneDm2.C, PIDTask/ExtSenseTuneEnergy.C:

	Committing running scripts and plotting macros used in NC studies of PID performance and tuning.

2007-08-27 21:55  arms

	* RootUtil/TPSTest/: TPSTest.cxx, TPSTest.h:

	Slight change in convention for combining significance values. Remove html dir

2007-08-27 20:37  kordosky

	* Contrib/kordosky/base_macros/: datathief_to_root.C,
	  datathief_to_root.h, move_stats.C, move_stats.h:

	updates for 5.16

2007-08-27 20:31  Nathaniel Tagg <n.tagg1@physics.ox.ac.uk>

	* TriD/: TridAnaglyphGLFrame.cxx, TridAnaglyphGLFrame.h,
	  TridGLFrame.h, TridPOV.cxx, TridPage.cxx, TridStereoGLFrame.cxx,
	  TridStereoGLFrame.h:

	Perform Sketch->SetDirty BEFORE deleting the associated GL view. This prevents the
	glList from being deleted twice (once for delete-on-context-change). I THINK this
	was causing the bug, anyway.

	Figure out how to do stereo views better: instead of rotating the view (causing some
	pretty severe headaches), instead I shift the view 1 meter laterally. This still has an
	unpleasant side-effect in anaglyph views, as the red and blue images are not stacked on top
	of each other.  I can't figure out a remedy for that without going back to OpenGL school.

	These updates spurred on by making TriD work at Soudan.

2007-08-27 19:38  Robert Hatcher <rhatcher@fnal.gov>

	* RerootExodus/: RerootToTruthModule.cxx, RerootToTruthModule.h:

	Move chunk of code out to new private method ModifyStdHep().  Add new
	StdHep modification "FixCharmDKStatus" which corrects for a GMINOS daikon
	bug where charm particles that generated a secondary (e.g. delta ray)
	before they decayed were marked as decayed (status=2) but the decay
	products weren't correctly flagged as "final state" (status=1).  This
	part of ModifyStdHep() is on by default.

	Also new configurable parameter "VldSimFlag" (default still at kReroot)
	controls what SimFlag_t value to use in creating the VldContext of
	the SimSnarlHeader in the SimSnarlRecord.  Sue requested this functionality
	and at some point we should switch the default over to kMC once we know
	the implications.

2007-08-27 19:32  Robert Hatcher <rhatcher@fnal.gov>

	* RerootExodus/: RerootExodus.cxx, RerootExodus.h:

	New method GetVldSimFlag() to mirror existing SetVldSimFlag().

2007-08-24 21:48  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/gminos_ffr.py:

	New field maps have a maximum of ~24 kGauss (was ~20) and we need to
	tell GEANT that for the materials it magnetizes.

2007-08-24 20:11  Robert Hatcher <rhatcher@fnal.gov>

	* Dispatcher/DDSClient.h:

	on gcc 4.0.1 there is no implicit "using namespace std" so one must use
	"std::string" rather than just "string"; this also matches other cases
	in this header.

2007-08-24 14:54  blake

	* CandMorgue/FillFarRunQuality.cxx:

	modify calculation of crate mask variable

2007-08-24 14:12  blake

	* RunQuality/DbuFarRunQuality.h:

	set an aggregate number (equal to the run number)

2007-08-24 12:11  Robert Hatcher <rhatcher@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolation.h:

	Call to assert() in inline version of GetChiSqrForMap() requires we have
	#include <cassert> under gcc 4.1.  Also compiler complains about not returning
	a value, not that it recognizes that it won't get there due to previously
	mentioned assert, so supply one to make it happy.

	NOTE: this assert is a run-time way of forcing the derived classes to
	override this function.  That is it doesn't show up until a derived
	class without the override tries to call it.  This is _not_ the best of
	practices.  If one really wants to force derived classes to implement
	their own version of a common interface the use the C++ language via:
	    virtual float GetChiSqrForMap(const CoordNDim&) = 0;
	Then if a derived classes doesn't implement the function then it can't
	be instantiated and this is caught at compile time.

	I won't do this at this time because the MQ, NS, DP, RS, and JK versions
	(that is, all of them) don't have this overridden.

2007-08-24 09:14  hartnell

	* NuMuBar/NuPlots.cxx:

	remove unused variable ‘containment’

2007-08-24 05:41  Sue Kasahara <schubert@hep.umn.edu>

	* Demo/dispatcher.C:

	Add example of setting the dds client name in job script.

2007-08-24 05:39  Sue Kasahara <schubert@hep.umn.edu>

	* Dispatcher/test/DemoClient.cc:

	Demonstrate use of client name.

2007-08-24 05:37  Sue Kasahara <schubert@hep.umn.edu>

	* IoModules/: IoDDSStreamItr.cxx, IoDDSStreamItr.h,
	  IoDataStreamFactory.cxx, IoDataStreamFactory.h,
	  IoInputModule.cxx, IoInputModule.h:

	Add support for optional dds client specified name, to be used in
	identification of client.
	For example:
	  JobC j;
	  j.Input.Set("Format=DDS");
	  j.Input.Set("DDSServer=minos-pc8.spa.umn.edu"); // dispatcher server host
	  j.Input.Set("DDSPort=9090");  // default dispatcher server port is 9090
	  j.Input.Set("DDSClientType=EventDisplay");  // clienttype used for id
	  j.Input.Set("DDSClientName='Control Room'");  // optional client name used for id

	is reported as:

	 2007/08/24 00:32:01 [-1|-1]> DDSParentServer Status: 1 active client.
	0) schubert "Sue Schubert" minos-pc8.spa.umn.edu Type: EventDisplay/Control Room
	   CS pid 25963 Start: 2007-08-24 05:32:01 UpTime(sec): 0.

2007-08-24 05:35  Robert Hatcher <rhatcher@fnal.gov>

	* CandMorgue/FillFarRunQuality.cxx:

	Add #include <cmath> so that the pow() function is available under gcc 4.x.

2007-08-24 05:23  Sue Kasahara <schubert@hep.umn.edu>

	* Dispatcher/: DDSClient.cxx, DDSClient.h, DDSClientId.cxx,
	  DDSClientId.h:

	Add optional client name string to be used as part of
	dispatcher client id.

2007-08-24 03:43  Robert Hatcher <rhatcher@fnal.gov>

	* setup/packages-development:

	Andy jumped the gun a bit and made CandMorgue dependent on RunQuality
	before it had a chance to be added to the package list.  Add it now so
	that base relases aren't broken.

2007-08-24 03:34  Robert Hatcher <rhatcher@fnal.gov>

	* AtNuAna/: AtNuHistogram.cxx, AtNuOscFit.cxx:

	ClassImp() is actually a c-pre-processor macro and not a function call;
	it is defined with a trailing semi-colon and so doesn't need one after it.
	gcc 4.x considers the a spurious ";" as an error.

2007-08-23 20:13  ahimmel

	* NuMuBar/: NuDSTAna.cxx, NuDSTAna.h, NuPlots.cxx, NuPlots.h:

	cvs commit NuDSTAna NuPlots

	NuDSTAna:
	    added BRevAna()
	    This method, based on JeffsTestAna, uses the function added to NuPlots
	    to perform reversed B-field acceptance and data-mc studies.

	NuPlots:
	    added FillBRev(NuEvent) and FillBRevTruth(NuEvent)
	    These methods fill the plots for the B-field data-mc and acceptance
	     studies.  Plots are broken down into positive and negative charge.
	    The former, to be used after selections have been applied, separates
	    events based on reconstructed charge.  The later, to be used before cuts,
	    separates based on inu.  Histograms are made of TrkEn, RecoY, and Theta.

	    added FormatPlots(TH1*, TString)
	    This is a utility function used by the above two.  It formats the plot
	    and its axes and was included purely as a convenience.

2007-08-23 18:35  blake

	* CandMorgue/: FillFarRunQuality.cxx, FillFarRunQuality.h,
	  LinkDef.h, fillfarrunquality.C:

	A module and macro to fill the new DbuFarRunQuality database table.

2007-08-23 18:34  blake

	* RunQuality/: DbuFarRunQuality.cxx, DbuFarRunQuality.h,
	  GNUmakefile, LinkDef.h:

	a database table to hold my run selection variables.

2007-08-23 17:04  arms

	* Contrib/rhatcher/gminos_jobs/gminos_cfg_L010185_far_rock.py:

	Preliminary cfg script for gminos_jobs to produce FD rock events

2007-08-23 16:55  bspeak

	* Monitoring/Producer_dispatcher.cc:

	Add ClientType = DDS::kOnlineMonitoring to DDSClient

2007-08-23 16:50  Robert Hatcher <rhatcher@fnal.gov>

	* CVSROOT/check_access:

	Start of Andy Blake's RunQuality package.
	Add Ben Speakman to Monitoring, Caryatid, OnlineEventDisplay, ControlRoomSoftware per his request.

2007-08-23 16:49  kordosky

	* NeugenInterface/: shower_ntuple.cxx, shower_ntuple.h:

	document code, fix a missing :

2007-08-23 16:49  Robert Hatcher <rhatcher@fnal.gov>

	* CVSROOT/modules:

	Start of Andy Blake's RunQuality package.

2007-08-23 16:42  Robert Hatcher <rhatcher@fnal.gov>

	* RunQuality/.cvsignore:

	Start of RunQuality package for Andy Blake.

2007-08-23 16:30  kordosky

	* NeugenInterface/shower_ntuple.cxx:

	forgot to commit this one

2007-08-23 16:19  kordosky

	* NeugenInterface/shower_ntuple.h:

	add feature to dump out the intranuke fates and weights block to a ttree

2007-08-23 15:58  kordosky

	* Mad/: MadMKAnalysis.cxx, MadMKAnalysis.h, macros/MakePanMK.C:

	small updates, not committed before

2007-08-23 15:56  kordosky

	* NeugenInterface/: inuke_reweight.F, inuke_rw.cxx, inuke_rw.h:

	small updates, not committed earlier

2007-08-23 15:19  Robert Hatcher <rhatcher@fnal.gov>

	* DatabaseUpdater/dbu_dds.C:

	backport setting of DDSClientType to R1.26 branch.

2007-08-23 15:17  Robert Hatcher <rhatcher@fnal.gov>

	* DatabaseUpdater/dbu_dds.C:

	set DDDSClientType identifier.

2007-08-23 14:37  niki

	* NCUtils/Extrapolation/NCExtrapolationNS.cxx:

	Fix ND Fiducial mass with NC fiducial mass definition

2007-08-23 14:09  blake

	* AtNuAna/: AtNuHistogram.cxx, AtNuHistogram.h, AtNuOscFit.cxx,
	  AtNuOscFit.h, Fitter.C, LinkDef.h:

	adding some code for oscillation fitting.

2007-08-22 20:43  bspeak

	* setup/: setup_minossoft_soudan.csh, setup_minossoft_soudan.sh,
	  setup_minossoft_umn.csh, setup_minossoft_umn.sh:

	Update minossoft setup scripts for soudan and umn.
	These scripts may be called with the following options:
	  -h: help, returns this usage statement
	  -q: quiet down setup script
	  -v: louden up setup script
	  -m [minossoft release]: Use this minossoft release
	  -r [root release]: Use this root release
	  -t [test release dir]: Use this test release directory
	  -O: use optmized build
	  -f: force using this release combination, for building

	The umn scripts are by default loud while the soudan scripts are by default
	quiet.

2007-08-22 19:31  Robert Hatcher <rhatcher@fnal.gov>

	* Production/Cedar_phy/bfield.C:

	MC bfield char "3" means use the "bhcurv" ASCII_DB_SET.

2007-08-22 18:31  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: Extrapolation/NCExtrapolationModule.cxx,
	  macros/nearFarExtrapolation.C:

	fix file counting for MDC files to get right POT value

	fix TMath::Format to be TString::Format in macro and use correct variable
	names

2007-08-22 16:54  bspeak

	* setup/: setup_minossoft_umn.csh, setup_minossoft_umn.sh:

	Updated setup for UMNTC machines

2007-08-22 16:52  pittam

	* NCUtils/Extraction/NCExtractionRPann.cxx:

	tidied up how the NC/CC seperation cut value is set in RPann to use the cuts->GetExtractionCut() method

2007-08-22 16:44  asousa

	* CVSROOT/check_access:

	Giving Chris write permissions to NCUtils.

2007-08-22 16:42  asousa

	* CVSROOT/framework.list:

	Adding Chris Backhouse to the congregation of enlightened ones who willingly receive minoscvs spam.

2007-08-22 16:28  asousa

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h:

	Commiting Chris's fix for hash_map compile failure.

2007-08-22 14:31  Brian Rebel <brebel@fnal.gov>

	* NCUtils/NCAnalysisUtils.cxx:

	make the call to FindMODBYRSWeight in FindMEGAFitWeight only if using
	carrot MC.  this should save a lot of time in making mc uDSTs

2007-08-22 14:05  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolation.cxx, NCExtrapolation.h:

	add fitting code from Chris Backhouse

2007-08-22 12:42  hartnell

	* NuMuBar/: NuAnalysis.cxx, NuPlots.cxx:

	Use jPID not jeID.

	Extract the new fid vol variables.

2007-08-22 12:40  hartnell

	* NtupleUtils/: NuExtraction.cxx, NuExtraction.h:

	Calculate the fvXXX variables.

	Copy the new weights across to NuMCEvent

2007-08-22 12:39  hartnell

	* NtupleUtils/: NuCuts.cxx, NuCuts.h, NuReco.cxx:

	For nubar selection pass ntrks>=1 and do LI cut on MC as well as data.

	Change horn current initialisation check to nu.hornCur!=-999999

	Implement a "numubar" fiducial volume and use it.

2007-08-22 12:36  hartnell

	* NtupleUtils/: NuMCEvent.cxx, NuMCEvent.h:

	Added:

	  //weights for RunI (2005-2006), e.g. LE-10
	  Float_t trkEnWeightRunI;//as above
	  Float_t shwEnWeightRunI;//as above
	  Float_t beamWeightRunI;//as above
	  Float_t detectorWeightRunI;//as above

	  //weights for RunII (2006-2007), e.g. LE-09
	  Float_t trkEnWeightRunII;//as above
	  Float_t shwEnWeightRunII;//as above
	  Float_t beamWeightRunII;//as above
	  Float_t detectorWeightRunII;//as above

	Removed:

	  Int_t chargeMC;//this is +1 for antiparticles and -1 for particles

2007-08-22 12:34  hartnell

	* NtupleUtils/: NuEvent.cxx, NuEvent.h:

	Added:

	  Bool_t fvnmb;//true if in NuMuBar fiducial volume
	  Bool_t fvpitt;//true if in Pittsburgh fiducial volume
	  Bool_t fvcc;//true if in latest CC fiducial volume, e.g. 2.5e20 anal.

	Removed:

	  Float_t jeID;//JE's PID variable (use jPID instead)
	  Int_t pittContainmentFlagMC; (not actually implemented)
	  Int_t chargeMC; (pretty pointless)

2007-08-22 05:50  Sue Kasahara <schubert@hep.umn.edu>

	* G3PTSim/TGeant3/TGeant3gu.cxx:

	Activate push of neutrinos to stack so that they can be recorded as
	products of a decay.

2007-08-22 05:03  Sue Kasahara <schubert@hep.umn.edu>

	* MCApplication/MCAppStack.cxx,
	  ParticleTransportSim/PTSimStack.cxx:

	Bug fix to push to stack in the case of a decay product.

2007-08-22 02:30  asousa

	* NCUtils/macros/nearFarExtrapolation.C:

	Deactivating PIDCustomCut setting in macro, should only be used for special studies.

2007-08-21 23:22  asousa

	* NCUtils/: Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationModule.h,
	  macros/nearFarExtrapolation.C:

	Adding option to define a custom PID cut value for extrapolation running, potentially useful for PID sensitivity and systematics studies.

2007-08-21 20:07  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationNS.cxx:

	use NC fiducial mass for near detector

2007-08-21 17:39  hartnell

	* NuMuBar/macros/: FileListSpecial.C, chargeSeparation.C, dstAna.C,
	  mEffPur.C, mEnergy.C, mTrueEnergy.C, mXYZ.C:

	Add a bunch of macros used to run the code or make plots.

2007-08-21 17:36  hartnell

	* NuMuBar/NuDSTAna.cxx:

	Minor changes

2007-08-21 17:35  hartnell

	* NtupleUtils/NuInputEvents.cxx:

	Just return 0 entries in tree if no NuMCEvent tree.

	Change messages from Fatal to Error since the message doesn't print when
	Fatal anymore.

2007-08-21 17:01  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/docs/gbs.html:

	Start the Programmer Manual section

2007-08-21 15:32  Robert Hatcher <rhatcher@fnal.gov>

	* NuMuBar/NuBase.h:

	some versions of gcc need the explicit #include <vector>, for others it
	seems to be implicitly included by some other header.

2007-08-21 13:36  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/register_models.py:

	Add GBSTaskManager to the default model

2007-08-21 13:36  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/bootstrap.py:

	Respond to changed GBSTaskMaster initialiser call sequence.

2007-08-21 13:36  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/GBSTaskMaster.py:

	Initialiser no longer takes creationMode (now inferred from existence
	of state file) or storeLocation (now obtained from config file).

	Add I/O.

	Add ability to create and access TaskManagers.

2007-08-21 13:36  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/GBSTaskManager.py:

	Add a default TaskManager, dummy so far.

2007-08-21 13:36  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/GBSObject.py:

	Add ability to store on disk.

	Remove creationMode, instead, on creation if state file already exists,
	restore from it, otherwise create and write out to it.

2007-08-21 13:36  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/: GBSModel.py, GBSModelRegistry.py:

	Add debug printout.

2007-08-21 13:36  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/GBSIOHelper.py:

	I/O helper class.

2007-08-20 21:54  hartnell

	* NuMuBar/macros/makeDst.C:

	Macro to run over sntp files and create DST.

2007-08-20 21:49  hartnell

	* NuMuBar/tools/farm.pl:

	First commit

2007-08-20 21:45  hartnell

	* NuMuBar/: GNUmakefile, LinkDef.h, NuAnalysis.cxx, NuAnalysis.h,
	  NuBase.cxx, NuBase.h, NuBeam.cxx, NuBeam.h, NuConfig.cxx,
	  NuConfig.h, NuDSTAna.cxx, NuDSTAna.h, NuMadAnalysis.cxx,
	  NuMadAnalysis.h, NuModule.cxx, NuModule.h, NuOutputWriter.cxx,
	  NuOutputWriter.h, NuPIDInterface.cxx, NuPIDInterface.h,
	  NuPlots.cxx, NuPlots.h, NuTime.cxx, NuTime.h:

	First commit of NuMuBar code to minoscvs

2007-08-20 21:30  hartnell

	* NtupleUtils/NuZBeamReweight.cxx:

	Check MC type before applying generator weights (e.g. MODBYRS).

2007-08-20 18:36  Robert Hatcher <rhatcher@fnal.gov>

	*
	  Contrib/rhatcher/gminos_jobs/gminos_cfg_L010185_bhcurv_overlay.py:

	*preliminary* config for "bhcurv" NearDet L010185 overlay.
	Rock #'s might change due to DOLOMITE -> NDBEDROCK change.

2007-08-20 18:22  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/gminos_cfg_L010185_rock_bhcurv.py:

	NearDet rock config for "bhcurv" (new field maps, daikon_03, spectrometer
	segments, field in the gaps, MARS,LINR TMED = NDBEDROCK).

2007-08-20 17:05  hartnell

	* NtupleUtils/: NuCuts.cxx, NuCuts.h, NuInputEvents.cxx,
	  NuInputEvents.h:

	NuInputEvents now reads in NuMCEvent trees too.

2007-08-20 16:56  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Cuts/NCAnalysisCuts.cxx:

	rustem wants his cut at 0.3 instead of 0.5 for the kNN method

2007-08-20 16:23  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationModule.h,
	  macros/nearFarExtrapolation.C:

	make it possible to look at only a subset of the MDC files.  to do so,
	run the macro as

	loon nearFarExtrapolation.C("dir/", 0, start, end)

	where start is the first file you want to look at and end is the last one.

2007-08-17 22:25  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/gminos_cfg_L010185_near_bhcurv.py:

	Config for L010185 NearDet running with the new field maps
	Also includes spectrometer coil segments, field in the air gaps and
	using NDBEDROCK for MARS,LINR volumes.

2007-08-17 22:20  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/gminos_ffr.py:

	'BField' can now be one of:
	    Normal/Forward, Reverse, Zero/Off, BHCurv, BHCurvRev
	the BHCurv modes set the new maps 170/171/172 and 218/219/220

	new 'bfldgap' (default False) if True turns on the field in the air gaps
	using GHELIX to swim -- sets both BSWM and KATURN cards.

2007-08-17 20:48  llhsu

	* NCUtils/NCAnalysisUtils.cxx:

	Fix to make modbyrs override work properly with newest base releases

2007-08-17 19:58  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extraction/NCAnalysisModule.cxx:

	get SKZP weight for all events, not just those in the fiducial volume

2007-08-17 17:07  hartnell

	* NtupleUtils/: NuCounter.cxx, NuCounter.h:

	Added: goodCoilCurrentSpillCounter.

	Also changed printout format

2007-08-17 17:07  hartnell

	* NtupleUtils/NuCuts.cxx:

	Add different coil cuts for different analysis versions.

2007-08-17 17:06  hartnell

	* NtupleUtils/NuExtraction.cxx:

	Deal with the case that there is no coil current information in the
	database.

2007-08-17 17:05  hartnell

	* NtupleUtils/NuZBeamReweight.cxx:

	Use beamType determined from files rather than a hard coded value.

2007-08-17 15:09  evans

	* NtupleUtils/NuHistos.cxx:

	New histograms to keep track of the wrong-sign CC contamination and NC
	contamination separately: needed for a matrix method CPT extrapolation
	where the wrong-sign CC background needs to be oscillated independently.

	Also added code that can put oscillations into the FD data histograms to
	enable the creation of fake data. This is hard-coded to be off by default.

2007-08-17 14:58  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: Extraction/NCAnalysisModule.cxx,
	  Extrapolation/NCExtrapolationModule.cxx,
	  macros/nearFarExtrapolation.C:

	changes to the extrapolation macro to handle mdc
	change extrapolation module to handle scaling down from high statistics
	change analysis module to put one entry for each run/subrun in the pot
	histograms

2007-08-17 14:19  hartnell

	* NtupleUtils/: NuEvent.cxx, NuEvent.h, NuZBeamReweight.cxx:

	Added:

	//weights for RunI (2005-2006), e.g. LE-10
	Float_t trkEnWeightRunI;//as above
	Float_t shwEnWeightRunI;//as above
	Float_t beamWeightRunI;//as above
	Float_t detectorWeightRunI;//as above

	//weights for RunII (2006-2007), e.g. LE-09
	Float_t trkEnWeightRunII;//as above
	Float_t shwEnWeightRunII;//as above
	Float_t beamWeightRunII;//as above
	Float_t detectorWeightRunII;//as above

	The original variables are now the average weight of the run periods,
	which is returned by GetRFWWeights.

	Can add further run periods as required...

2007-08-17 14:11  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCEnergyBin.cxx:

	make sure to scale the MC weights given back in the GetMCInformation methods
	by the appropriate exposure scaling for the data to mc pot ratio

2007-08-17 14:11  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolationJK.cxx,
	  NCExtrapolationJK.h, NCExtrapolationModule.cxx,
	  NCExtrapolationModule.h:

	fixes to do the plotting of the best fits correctly for the JK method and
	to handle MDC files correctly in NCExtrapolationModule

2007-08-17 01:31  Robert Hatcher <rhatcher@fnal.gov>

	* JobControl/JobCEnv.cxx:

	Sending the USR1 signal (ala "kill -USR1 <pid>") to a loon process
	running a job script now immediately signals it's current state:

	  JobCEnv: Process 21684 received SIGUSR1 after 143 record sets,
	    last processed run 14011011 snarl 142
	    CPU: user 12.8092s, sys 0.657842s,  Mem: res 52800k, virtual 1050888k

	Sending HUP signal still give a clean shutdown on the next record set.

2007-08-16 22:45  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/test/file1:

	another attempt at the name blame assignment -- was running /usr/bin/cvs
	rather than modified cvs, now in /home/minoscvs/bin/cvs[_v1_11_17]

2007-08-16 22:33  Minos CVS group account.  Do not commit from here!

	* DocBuilder/GNUmakefile:

	Remove Islands, USER_Classes, TOOL_Classes.  BubbleSpeak already gone.

2007-08-16 22:05  Minos CVS group account.  Do not commit from here!

	* Contrib/rhatcher/test/file1:

	yet another test.

2007-08-16 20:22  Minos CVS group account.  Do not commit from here!

	* Contrib/rhatcher/test/file1:

	tsest ... is this assigned to rhatcher or minoscvs?

2007-08-16 20:09  Minos CVS group account.  Do not commit from here!

	* NtupleUtils/: NuEvent.cxx, NuEvent.h:

	Added:
	Float_t relativeAngle;//RO's track angle relative to muon dir.

2007-08-16 19:48  Minos CVS group account.  Do not commit from here!

	* Contrib/rhatcher/test/file1:

	A test to see that CVS is picking up user name.

2007-08-16 19:38  Minos CVS group account.  Do not commit from here!

	* IoModules/IoInputModule.cxx:

	Change verbosity of GetCurrentFile() "I'm here" message to Debug from Info -- why was this ever set to Info?

2007-08-16 17:10  Minos CVS group account.  Do not commit from here!

	* NCUtils/data/: Mda_Coeff_Far_L010z185i_CedarDaikon.dat,
	  Mda_HistDef_Far_L010z185i_CedarDaikon.dat:

	FD Discriminant based on discriminator variables used for ND discriminant. Selection figures-of-merit are very similar to previous descriminant while ensuring Data/MC agreement is as good as possible given information from the Near Detector.

2007-08-16 16:44  Minos CVS group account.  Do not commit from here!

	* AnalysisNtuples/Module/CondensedNtpModuleNC.cxx:

	remove test for file.IsOpen() as it fails if the file already exists

2007-08-16 07:45  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/GBSObject.py:

	Cosmetic

2007-08-16 07:45  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/: GBSModel.py, GBSModelRegistry.py:

	Add a logger message

2007-08-16 07:33  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/bootstrap.py:

	Drop leading GBS from DataDirectory

2007-08-16 07:32  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/GBSConfig.py:

	Resource file is now called ~/.gbsrc

2007-08-16 07:32  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/: GBSLogger.py, GBSObject.py:

	Add a very primitive logger

2007-08-16 06:25  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/python/: .cvsignore, GBSConfig.py,
	  GBSModel.py, GBSModelRegistry.py, GBSObject.py, GBSTaskMaster.py,
	  __init__.py, bootstrap.py, register_models.py:

	Start to rough out the basics of object construction.

2007-08-16 06:18  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/GBS/docs/gbs.html:

	Rename Master to TaskMaster

2007-08-16 06:17  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/docs/index.html:

	Add link to GBS

2007-08-16 05:12  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/DataCacheManager/docs/help_summary.txt:

	Fix typo in help message

2007-08-16 04:29  Nick West <n.west1@physics.oxford.ac.uk>

	* DatabaseMaintenance/scripts/logentry_mail_list:

	Remove Phil; his email account has closed

2007-08-15 20:36  jpochoa

	* NuBarPID/files/: POpdf_birch_carrot.root,
	  POpdf_birch_carrot_FD.root, POpdf_birch_pre-daikon.root,
	  POpdf_cedar_carrot.root, POpdf_cedar_carrot_FD.root:

	Removed obsolete PDF files for NuBarPID

2007-08-15 20:35  Robert Hatcher <rhatcher@fnal.gov>

	* Production/asciidb/cedar_daikon/bhcurv/: BFLDDBIPLANEMAP.csv,
	  BFLDDBIPLANEMAPVLD.csv, catalogue.db:

	New ASCIIDB files for BFLDDBIPLANEMAP table to pick up new map files.
	NearDet uses maps 170,171,172 for full,detail,gap maps.   FarDet
	anticipates maps 218,219,220 (subject to change).  Both are in the
	forward field configuration.

2007-08-15 20:32  jpochoa

	* NuBarPID/files/POpdf_cedar_daikon_ND.root:

	New PDFs for NuBarPID that use trklength instead of trk_nplanes.
	NuBarPID also designed to now take events with two more cuts in preselection:
	trklength>25 and andy_cc_pid>0.85

2007-08-15 18:03  hartnell

	* NtupleUtils/: NuCounter.cxx, NuCounter.h:

	Added "entry" to count the number of snarls processed

2007-08-15 15:12  Robert Hatcher <rhatcher@fnal.gov>

	* CVSROOT/framework.list:

	add Alex Himmel to the unfortunate souls who receive commit messages
	(per his request, not pure spite on my part).

2007-08-15 12:40  hartnell

	* NtupleUtils/: NuEvent.cxx, NuEvent.h:

	Added flag: calcMajCurv, which is used as a switch.

2007-08-15 12:39  hartnell

	* NtupleUtils/: NuMCEvent.cxx, NuMCEvent.h:

	Need the beam weights in the truth ntuple as well:

	Float_t rw;//weight=1 or the MC reweight value as required
	Float_t rwActual;//beam reweight factor actually used
	Float_t trkEnWeight;//SKZP weight applied to trkEn (number close to
	1)
	Float_t shwEnWeight;//SKZP weight applied to shwEn (number close to
	1)
	Float_t generatorWeight;//weight factor from generator
	Float_t beamWeight;//SKZP weight applied to beam (e.g. hadron prod.)
	Float_t detectorWeight;//SKZP weight applied to detector (e.g. xsec)

2007-08-15 12:37  hartnell

	* NtupleUtils/: NuExtraction.cxx, NuExtraction.h, NuReco.cxx,
	  NuReco.h:

	Change where the Majority Curvature is calculated. It has been moved to
	its own function. This allows it to be calculated after pre-selection,
	which speeds up the code.

2007-08-15 04:01  tjyang

	* MiniBooNEAna/: MNtp.cxx, MNtp.h, MNtpModule.cxx:

	add true shower energy and muon momentum

2007-08-14 23:01  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolationModule.cxx,
	  NCExtrapolationModule.h:

	convert to using # of files to limit size of input data/mc sets when doing
	tests.  beware, the EventLimit is really the FileLimit now, i left in the
	key for the registry so as not to break too many macros out there.

2007-08-14 22:51  llhsu

	* NCUtils/: NCAnalysisUtils.cxx, NCAnalysisUtils.h:

	Adding MODBYRS override variable to FindNeugenWeight

2007-08-14 22:12  George Irwin <gmieg@slac.stanford.edu>

	* NtupleUtils/NuInputEvents.cxx:

	Add ' #include <cassert> ' for GCC 3.3.4.

2007-08-14 21:17  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	fix bug in tau file scaling

2007-08-14 20:52  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationMQ.cxx:

	forgot to commit change for NCAnalysisUtils

2007-08-14 20:44  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extraction/NCAnalysisModule.cxx:

	make the data files have "data" in the file name

2007-08-14 20:44  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCAnalysisUtils.h:

	remove baseline argument from FindSurvivalProbability because we
	never used it

2007-08-14 20:31  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolationJK.cxx,
	  NCExtrapolationJK.h, NCExtrapolationNS.cxx:

	major speed improvement in JK method.  now takes about 0.1s/loop over
	delta m^2, sin^2 2theta and fsterile.

	fix scaling bug in NCExtrapolationNS

2007-08-14 20:01  Robert Hatcher <rhatcher@fnal.gov>

	* DataUtil/DataQualDB.cxx:

	Use HvStatusFinder as a singleton as it was intended (required now since
	the ctor was made private) -- this will speed things up because caching
	will actually work.

2007-08-14 19:57  Robert Hatcher <rhatcher@fnal.gov>

	* AnalysisNtuples/Module/ANtpInfoObjectFiller.cxx:

	Use HvStatusFinder as a singleton as it was intended (required now since
	the ctor was made private) -- this will speed things up because caching
	will actually work.

2007-08-14 18:55  arms

	* Contrib/rhatcher/gminos_jobs/: umn_bulk_copy.sh,
	  umn_list_wrkdirs.sh:

	Updated UMN farm scripts for ND running already used for L010185 ND rev Bfield

2007-08-14 18:28  blake

	* DcsUser/HvStatusFinder.h:

	make HvStatusFinder constructor private

2007-08-14 18:25  hartnell

	* NtupleUtils/: NuReco.cxx, NuReco.h:

	Added CalcExtraTruthVariables to fill the new variables

2007-08-14 18:24  hartnell

	* NtupleUtils/: NuMCEvent.cxx, NuMCEvent.h:

	New variables

2007-08-14 18:24  hartnell

	* NtupleUtils/: NuEvent.cxx, NuEvent.h:

	Added more variables:

	   Float_t sigma;//mc.sigma=cross-section
	   Float_t vtxuMC;//vtx u, calculated from x&y
	   Float_t vtxvMC;//vtx v, calculated from x&y
	   Int_t planeTrkVtxMC;//calculated from z
	   Float_t rTrkVtxMC;//calculated from x&y

2007-08-14 18:23  hartnell

	* NtupleUtils/: NuExtraction.cxx, NuExtraction.h:

	Added: NuMCEventFromNuEvent, which copies information from the NuEvent
	across to the NuMCEvent

2007-08-14 18:21  hartnell

	* NtupleUtils/: NuCuts.cxx, NuCuts.h:

	Added: IsInFidVolLoose for writing out a more general DST

2007-08-14 18:04  blake

	* Mad/MadPIDAnalysis.cxx:

	use singleton version of HvStatusFinder to look up HV status

2007-08-14 17:31  blake

	* DcsUser/: HvStatusFinder.cxx, HvStatusFinder.h:

	add Cleaner struct to call HvStatusFinder destructor at end of job.

2007-08-14 16:48  blake

	* SpillTiming/: SpillServerMonFinder.cxx, SpillServerMonFinder.h:

	making SpillServerMonFinder constructor private to force singleton use;
	adding Cleaner to call SpillServerMonFinder destructor at end of job.

2007-08-14 16:04  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolationModule.cxx,
	  NCExtrapolationModule.h:

	make separate vector to hold tau file pot information.  the change is tested
	and appears to work.  have to uncomment line 802 to pick up the scaling,
	right now it is taken out so as not to mess up people only looking at a
	subset of the data.

2007-08-14 12:18  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Ganga/: GBS/docs/gbs.html, docs/ganga.html:

	Commit first part (Requirements and Design) of  doc for GBS: Ganga-based Batch Submission

2007-08-14 12:04  evans

	* NtupleUtils/MajorityCurvature.cxx:

	Changing the calulation of the smoothMajC variable to be the most up to
	date.

2007-08-13 23:18  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolationJK.cxx,
	  NCExtrapolationJK.h, NCExtrapolationNS.cxx, NCExtrapolationNS.h:

	add some debugging to NS method.

	JK method now works.  had to add taus to the NC spectrum.  put some of the
	code into methods in order to increase readability.

2007-08-13 21:00  Nathaniel Tagg <n.tagg1@physics.ox.ac.uk>

	* SpillTiming/: SpillTimeFinder.cxx, looter/lootSpillFiles.cxx:

	Attempts to fix recent infinite-loop:
	Mod the looter so it tries to always create at least 1-second intervals.
	Mod the SpillTimeFinder so that it tries to advance the 'next' and 'prev' context
	finders by at least one second.

	Neither of these mods has been tested.

2007-08-13 19:46  Robert Hatcher <rhatcher@fnal.gov>

	* CVSROOT/check_access:

	not sure whether Alex Himmel needs "himmel" or "ahimmel" so add both.

2007-08-13 18:38  koskinen

	* NCUtils/Extrapolation/: NCExtrapolationJK.cxx,
	  NCExtrapolationJK.h:

	Updated the NCExtrapolationJK method, which is the NC F/N, to now include
	the tau background in the analysis.

2007-08-13 16:42  hartnell

	* NtupleUtils/: LinkDef.h, NuMCEvent.cxx, NuMCEvent.h:

	A new lightweight class to hold the MC truth information.

2007-08-13 16:14  Robert Hatcher <rhatcher@fnal.gov>

	* CVSROOT/: check_access, modules:

	Start NuMuBar package for Jeff Hartnell &co.

2007-08-13 15:59  Robert Hatcher <rhatcher@fnal.gov>

	* NuMuBar/.cvsignore:

	Start NuMuBar package for Jeff Hartnell.

2007-08-13 12:51  hartnell

	* NtupleUtils/: NuEvent.cxx, NuEvent.h, NuExtraction.cxx,
	  NuReco.cxx:

	Add and fill the MajorityCurvature variables:

	  Double_t jitter;//from MajCInfo
	  Double_t jPID;//from MajCInfo
	  Double_t majC;//from MajCInfo
	  Double_t majCRatio;//from MajCInfo
	  Double_t rms;//from MajCInfo
	  Double_t simpleMajC;//from MajCInfo
	  Double_t smoothMajC;//from MajCInfo
	  Double_t sqJitter;//from MajCInfo
	  Double_t totWidth;//from MajCInfo

2007-08-13 12:50  hartnell

	* NtupleUtils/LinkDef.h:

	Forgot to commit this with the new NuInputEvents class.

2007-08-13 12:48  hartnell

	* NtupleUtils/NuLibrary.h:

	Add a majority curvature object so that it can be easily accessed.

2007-08-13 12:47  hartnell

	* NtupleUtils/MajorityCurvature.cxx:

	Set the gDirectory back to what it was before opening the PID file.

2007-08-12 09:14  hartnell

	* NtupleUtils/: NuInputEvents.cxx, NuInputEvents.h:

	This class reads in ntuples of NuEvents. A subset of events can be
	stored in a cache for faster looping over events.

2007-08-11 19:26  mskim

	* LISummary/mskim/: README, offline0.dat, offline1.dat:

	Update gain calibration package. It includes README and log files

2007-08-11 19:09  Sue Kasahara <schubert@hep.umn.edu>

	* Dispatcher/doc/detectorSiteSWInstallations.log:

	Update with instructions to identify client type.

2007-08-11 18:47  mskim

	* LISummary/mskim/: LIAna2.C, MakeCalAdcToPe2.C, ReadDbGains2.C,
	  check_calib.C, check_calibType.C, check_led.C, check_run.C,
	  check_spot.C, check_stat.C, gain.csh, reco.csh:

	Package for gain calibrations

2007-08-11 18:37  Sue Kasahara <schubert@hep.umn.edu>

	* Dispatcher/doc/: detectorSiteSWInstallations.log,
	  dispatcherTests.log:

	Begin log of dispatcher test results according to release.  Update
	log of detector site dispatcher installation.

2007-08-10 18:06  tinti

	* Contrib/barr/na49an/na49an.cxx:

	last updates

2007-08-10 16:46  Robert Hatcher <rhatcher@fnal.gov>

	* Contrib/rhatcher/gminos_jobs/gminos_ffr.py:

	Add Vegetable 'X' for non-official releases.

2007-08-10 15:25  tjyang

	* NueAna/: AnnAna.cxx, macros/RunNueDisplay.C:

	fixing a typo, change the way to load libraries

2007-08-10 15:00  Robert Hatcher <rhatcher@fnal.gov>

	* CVSROOT/check_access:

	Add Andy Blake to DcsUser (so he can edit HvStatusFinder).

2007-08-10 05:54  George Irwin <gmieg@slac.stanford.edu>

	* Dispatcher/DDSChildServer.cxx:

	Backport Sue's mod to update TNetFile usage for ROOT 5.16/00.

2007-08-10 05:14  Sue Kasahara <schubert@hep.umn.edu>

	* Dispatcher/DDSChildServer.cxx:

	Change implemented beginning with root v5.10/00 to
	enforce use of rootd over xrootd is no longer a good idea with
	root v5.16/00.  Block it out when using v5.16/00 or higher:
	   if ( gROOT -> GetVersionInt() < 51600 )
	      gROOT -> GetPluginManager() -> RemoveHandler("TFile","^root:");

2007-08-09 22:52  tjyang

	* MiniBooNEAna/macros/makemntp.C:

	turn the trigger off by default

2007-08-09 22:48  tjyang

	* MiniBooNEAna/MNtpModule.cxx:

	update shower energy correction based on reconstruction release

2007-08-09 09:36  evans

	* NtupleUtils/: NuHistos.cxx, macros/MakeMMFluxHelpers.C:

	Fixing a memory leak: two histograms were being created twice.

2007-08-09 07:10  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Scripts/docs/Scripts.html:

	Cosmetic change

2007-08-08 19:37  George Irwin <gmieg@slac.stanford.edu>

	* PhysicsNtuple/: Event.cxx, Plot/PlotData.cxx:

	Add ' #include <cassert> ' for GCC 3.3.4

2007-08-08 16:05  Robert Hatcher <rhatcher@fnal.gov>

	* GridTools/RemoteSoftwareDeployment/libs_and_builds/build_lund.sh:

	build_lund.sh script has been replaced by build_pythia6.sh.

2007-08-08 12:09  hartnell

	* NtupleUtils/NuReco.cxx:

	When determining whether an event stops in the calorimeter or
	spectrometer use z=7 m everywhere.

2007-08-08 12:07  hartnell

	* NtupleUtils/NuGeneral.cxx:

	Make less verbose

2007-08-08 11:25  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/install_pythia.sh:

	Switch from build_lund.sh to its replacement build_pythia6.sh

2007-08-08 04:55  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/DataCacheManager/config/sno.site_oxford_sno.local_disks:

	Add resource lock

2007-08-07 21:28  Robert Hatcher <rhatcher@fnal.gov>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/build_pythia6.sh:

	revised (and renamed) version of what used to be build_lund.sh
	this version can handle different version # specification formats and
	new location of files (6.4.11 and beyond).

2007-08-07 16:54  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationModule.h,
	  macros/nearFarExtrapolation.C:

	fix the mc pot map to hold the MC values, not data values
	add functionality to module to all for scaling near and far detector data
	exposures.  useful for ND fit style methods that want to have similar
	statistical power for all beams used (simply scales to lowest pot value now)
	and MC/MDC studies in far detector that want to scale large exposures down
	in order to remove statistical fluctuations.

	scales are only applied to data samples, not mc

2007-08-07 16:42  evans

	* NtupleUtils/: NuFluxHelper.cxx, NuFluxHelper.h,
	  macros/MakeMMFluxHelpers.C:

	Beam matrices can now be made for any ND fiducial volume (needn't be
	cylindrical).

	This involved altering the ND co-ordinate to be the real ND co-ordinate
	system (no longer centered on the beam spot), and making the ND fiducial
	volume and position of the beam spot centre more easily configurable. At
	present the old beam spot center is still hard coded in, but can easily be
	changed.

2007-08-07 04:34  Robert Hatcher <rhatcher@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationNS.cxx:

	fBeams is a vector<NCBeam> and so one needs fBeams[nearBeamI].GetDataPOT()
	not -> (i.e. it's not a vector of pointers).  Code now compiles, but still
	the potNear/potFar on lines 690,691 are unused.

2007-08-06 21:41  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCEnergyBin.cxx:

	fix problem with electrons - removing evolutionary dead end.

2007-08-06 21:13  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCAnalysisUtils.h,
	  Extrapolation/NCBeam.cxx, Extrapolation/NCBeam.h,
	  Extrapolation/NCEnergyBin.cxx, Extrapolation/NCEnergyBin.h,
	  Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolation.h,
	  Extrapolation/NCExtrapolationDP.cxx,
	  Extrapolation/NCExtrapolationDP.h,
	  Extrapolation/NCExtrapolationJK.cxx,
	  Extrapolation/NCExtrapolationJK.h,
	  Extrapolation/NCExtrapolationMQ.cxx,
	  Extrapolation/NCExtrapolationMQ.h,
	  Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationModule.h,
	  Extrapolation/NCExtrapolationNS.cxx,
	  Extrapolation/NCExtrapolationNS.h,
	  Extrapolation/NCExtrapolationRS.cxx,
	  Extrapolation/NCExtrapolationRS.h, macros/nearFarExtrapolation.C:

	change extrapolation methods to hold maps of beam type number to total pot
	for data and mc, rather than scale factors.  the reason for this is that
	the beam matrix needs to know pot in near and far.  alter the constructors
	and remaining methods to handle the change.

	also make NCExtrapolation::AddNearEvent() --> NCExtrapolation::AddEvent()
	because it can be more general.  now all methods call this one from within
	their AddNear/FarEvent methods.  everyone does exactly the same thing.

	fill NCBeam::fDefaultMCHistogramNC(CC) from within NCBeam::AddEvent so
	it is filled for all methods.

	also, NCBeam objects now know how many pot there are for the data and
	mc in them.  the NCEnergyBin objects still only know about the scaling
	for data to mc

2007-08-06 19:38  ishi

	* Contrib/ishi/GeoSwimmer/: GeoSwimParticle.cxx, GeoSwimmer.cxx:

	PID is properly set for backward tracking.

2007-08-06 18:54  boehm

	* NueAna/macros/RunTrimmer.C:

	Fixing the name of the macro

2007-08-06 16:15  evans

	* NtupleUtils/: NuFluxHelper.cxx, NuFluxHelper.h,
	  macros/MakeMMFluxHelpers.C:

	Allowing more than one type of neutrino to be extrapolated at once. Only
	CC numus and CC numubars are supported at the moment.

	The macro MakeMMFluxHelpers.C must now be compiled as the use of the
	NuParticle enum doesn't work in interpreted mode.

2007-08-06 15:48  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	only find the weights for MCAsData if the parameters are turned on.
	should speed up loading events

2007-08-06 14:28  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationNS.cxx:

	some more debug statements

2007-08-06 13:43  evans

	* NtupleUtils/: NuHistos.cxx, macros/MakeMMFluxHelpers.C:

	Adding code to make Matrix Method histograms for CC numubars and for CC
	(numus + numubars).

2007-08-05 21:18  rustem

	* PhysicsNtuple/: Event.cxx, RecoNu.cxx, RecoNu.h, RunAlgEvent.cxx,
	  Config/PlotBasic.xml, Config/PlotBeam.xml, Config/PlotEvent.xml,
	  Config/PlotKinem.xml, Config/PlotkNN.xml, Draw/DrawSnarl.cxx,
	  Draw/DrawSnarl.h, Draw/RecordStore.cxx, Fill/FillMuonId.cxx,
	  Hist/HistMan.cxx, Plot/Data.cxx, Plot/Plot.cxx,
	  Plot/PlotData.cxx, Plot/PlotData.h, Plot/PlotEvent.cxx,
	  Plot/PlotEvent.h, Plot/PlotSelect.cxx, Plot/PlotSelect.h,
	  Select/SelectNeutrino.cxx, Select/SelectNeutrino.h,
	  kNNAlg/FillkNN.cxx, kNNAlg/FillkNN.h:

	A snapshot of the development.

2007-08-03 21:07  llhsu

	* NCUtils/NCAnalysisUtils.cxx:

	Updated GetEventVertex to use the same vertex that is being cut on in NCAnalysisCuts::InBeamFiducialVolumeOx()

2007-08-03 20:26  koskinen

	* NCUtils/: NCAnalysisUtils.cxx, NCAnalysisUtils.h:

	Overload the FindSurvivalProbability fucntion in order to return
	probabilities that do not rely on the truth info beam object, but instead
	rely on passed oscillation parameters and individual particle info.

2007-08-03 18:52  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolationDP.cxx,
	  NCExtrapolationModule.cxx, NCExtrapolationModule.h,
	  NCExtrapolationNS.cxx:

	add debugging stuff into NS method.

	change how chains for data/MC are handled in NCExtrapolationModule.  created
	maps for each combo of data/mc, near/far to give a separate chain for each
	beam.  pass each chain to the AddEventsToExtrapolation method so that
	extrapolations that need multiple beams will get them correctly, even if you
	only want some number < total from each beam.

2007-08-03 14:48  kordosky

	* CVSROOT/: check_access, modules:

	new module in minospub

2007-08-03 10:16  evans

	* NtupleUtils/: NuFluxChain.cxx, NuFluxHelper.cxx, NuFluxHelper.h,
	  macros/MakeMMFluxHelpers.C:

	Fixing a bug in the setting of branch addresses in NuFluxChain.

	Fixing a bug in how one of the matrices was normalised in NuFluxHelper.

	Fixing the units where NuFluxChain (which uses Munits) interacts with the
	matrix method code in NuFluxHelper (which doesn't use Munits).

	Now making only one TRandom3 object as a member variable of NuFluxHelper so
	that the random neutrino interaction point in the near detector really is
	random.

2007-08-02 21:39  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCType.h, Extrapolation/NCBeam.cxx,
	  Extrapolation/NCBeam.h, Extrapolation/NCEnergyBin.cxx,
	  Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolationDP.cxx,
	  Extrapolation/NCExtrapolationNS.cxx,
	  macros/nearFarExtrapolation.C:

	pass in argument whether to use preset values or recompute them for
	NCBeam::MakeResultPlots()  useful for NDFit style methods when you want
	to see how the fit changes the nominal case.

	remove commented out legacy code from NCType.h

	debug a bit with NDFit method.

	add debugging statements to BeamMatrix method and clean up filling of
	arrays in PredictSpectrum

	make sure canvases are named by run type as well in NCExtrapolation

2007-08-02 20:52  Robert Hatcher <rhatcher@fnal.gov>

	* G3PTSim/GNUmakefile:

	Add some magic so that the fortran runtime libraries get linked in as
	necessary.  Not quite sure how this worked without it, various loaders
	must take it upon themselves to "do the right thing".

2007-08-02 20:23  hartnell

	* NtupleUtils/NuHistos.cxx:

	Fix memory leak (discovered when all my jobs bombed on the farm!)

2007-08-02 19:26  Brian Rebel <brebel@fnal.gov>

	* AnalysisNtuples/: Module/ANtpInfoObjectFiller.cxx,
	  Module/ANtpInfoObjectFiller.h,
	  Module/ANtpInfoObjectFillerBeam.cxx,
	  Module/ANtpInfoObjectFillerNC.cxx,
	  Module/CondensedNtpModuleNC.cxx, macros/makeCondensedNtupleNC.C:

	fix the filling of vtxMetersToCloseEdge.  there was a bug where it would
	use the vertex in the NtpSREvent object rather than the vertex finder one.

	also include filling of the parents for the neutrinos

2007-08-02 19:16  Robert Hatcher <rhatcher@fnal.gov>

	* RerootExodus/: RerootToTruthModule.cxx, RerootToTruthModule.h:

	Now configurable to:
	 - convert ions to either kStdHep or kPDG2006 numbering scheme
	     (default leave unchanged)
	 - edit out entries from StdHep list
	    + those added by GMINOS during GEANT propagation (unrelated to charm/tau)
	    + charm/tau additions (including decay point and decay products)
	    + status code 999 line
	    + user defined criteria (DANGER: thar be dragons).

2007-08-02 19:02  Robert Hatcher <rhatcher@fnal.gov>

	* RerootExodus/WriteStdHepFileModule.cxx:

	Print ion scheme message only if the value has changed from previous.

2007-08-02 18:59  Nick West <n.west1@physics.oxford.ac.uk>

	* DatabaseMaintenance/tools/load_tables.sh:

	In table creation SQL force dates whose default is 0000-00-00 to have
	time 00:00:00 as well as some flavours of version 5 take exception to
	default like '0000-00-00 23:30:00'.  At the same time remove
	code that tests for --server_v3 as it's hardwired on anyway.

2007-08-02 18:49  Robert Hatcher <rhatcher@fnal.gov>

	* Util/: UtilHepevt.cxx, UtilHepevt.h:

	squeezeStdHep() removes entries from StdHep list that have a particular
	status code -- attempts to adjust mother/daughter links accordingly (but
	might not work in all general cases).

	modStatusStdHep() gives entries a new status code based on a interpreted
	conditional string.  Contitional string has access to particle's pointer
	and some extracted info (indx,ist,ipdg,mo0,mo1,da0,da1,ischarm,istau,
	fromcharm,fromtau).  Examples include:
	  flag non-tau, non-charm entries added by GMINOS in GEANT propagation phase:
	     "(  (ist> 200 && ist< 231) || (ist> 300 && ist< 310) ||
	         (ist>1200 && ist<1231) || (ist>1300 && ist<1310)    )
	      && !ischarm && !istau "
	  flag tau decay point entry and decay daughters
	     "(istau && ist==1205) || (fromtau && ist==1)"
	  flag decayed tau (after daughters have been removed)
	     "istau && ist==2 && da0==-1"
	By default the new status code is 0xdead, but for the last case one would
	want to set it to 1 to make it active again.

2007-08-02 18:39  Robert Hatcher <rhatcher@fnal.gov>

	* Util/: UtilPDG.cxx, UtilPDG.h:

	Add function for testing whether pdg code contains quark of a given flavor
	and an isCharm() function.

	Variants for getIonAZJ() and makeIonPDG() in fancy-shmancy case of ions
	with lambdas (mostly just for test purposes).

2007-08-02 17:58  hartnell

	* NtupleUtils/NuEvent.h:

	Increment classdef

2007-08-02 17:51  hartnell

	* NtupleUtils/: NuEvent.cxx, NuEvent.h, NuExtraction.cxx,
	  NuExtraction.h, NuReco.cxx:

	Added:

	Float_t vtxxMC;//vtxx: x vtx of neutrino interaction
	Float_t vtxyMC;//vtxy: y vtx of neutrino interaction
	Float_t vtxzMC;//vtxz: z vtx of neutrino interaction

2007-08-02 15:19  evans

	* NtupleUtils/: NuFluxHelper.cxx, NuFluxHelper.h, NuHistos.cxx,
	  macros/MakeMMFluxHelpers.C:

	In NuHistos: filling the data histograms (RecoEnergy_ND & _FD) for both
	data and MC, so that mock data can be used.

	Improving the memory management in NuFluxHelper: primarily removing the
	memory leak whereby ten new TRandom3 objects were created for each fluka
	entry and never deleted.

2007-08-02 14:41  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCEnergyBin.cxx:

	account for tobi's changes for the nu_e survival probability

2007-08-02 09:27  raufer

	* NCUtils/NCAnalysisUtils.cxx:

	Re-correct Oscillation probability in NCAnalysisUtils. If nu_e don't oscillate due to U_e3 being zero, it makes no difference whether they interact as CC or NC. Their survival probability is 1.

	In the nu_mu case, there is a difference between CC and NC because the NC events distinguish between two different final states, nu_tau and nu_sterile, whereas CC events don't. For the CC it's all just disappearance.

	In any case, if the survival probability is 1, nothing oscillates and there can't be a difference between NC and CC.

2007-08-02 07:29  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/docs/ChangeLog:

	Press 'Save' in editor before committing

2007-08-02 07:23  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/docs/ChangeLog:

	RSD     - Remote directory restructure
	DCM     - Minor bug fixes.
	Scripts - Work in progress on LCG equivalent of the daikon_scripts run_xxx.sh

2007-08-02 07:23  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Scripts/jobs/run_lcg.sh:

	Begin development of the LCG equivalent of the daikon_scripts run_xxx.sh.
	Very much work in progress.  When stable may move to daikon_scripts.

2007-08-02 07:23  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Scripts/jobs/copy_flux_files_lcg.sh:

	Utility to use DCM to copy flux files.

2007-08-02 07:23  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/install_minossoft.sh:

	Attempt to remove SRT before installing.  Again make dependent on
	daikon_versions so that it can build rerootjob.

2007-08-02 07:23  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/install_hello_world.sh:

	Add more tests for new remote directory structure.

2007-08-02 07:23  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/install_daikon_scripts.sh:

	Change library version from daikon_nn to nn, so tar file now named
	daikon_versions_nn.  Use libs/ (not apps/) path to define LABYRINTH.

2007-08-02 07:22  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/libs_and_builds/:
	  install_GENIE.sh, install_cernlib.sh, install_neugen3.sh,
	  install_pythia.sh, install_root.sh:

	Adapt to the new definition of RSD_LIB_BUILD_DIR (brought about by new
	remote directory structure).

2007-08-02 07:22  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/build_config_table.dat:

	Replace Application:CedarDaikon:0-build_0 by CedarDaikon:03-build_0 which has
	the latest daikon libraries: daikon_versions:03 and daikon_scripts:070711

2007-08-02 07:22  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/libs_and_builds/:
	  assemble_daikon_versions.sh, install_daikon_versions.sh:

	Change library version from daikon_nn to nn, so tar file now named
	daikon_versions_nn.

2007-08-02 07:22  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/driver/survey_and_clean_up.pm:

	Adapt to new remote directory structure.
	Produce more compact summary.

2007-08-02 07:22  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/driver/cmd_launch.pm:

	At job end move back to original directory so that Ganga can return
	install logs.

2007-08-02 07:22  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/driver/: cmd_install.pm,
	  get_lib_info.pm, initialise_globals.pm, lss_connect_library.pm,
	  lss_harvest_build.pm, lss_is_lib_soft_link.pm,
	  lss_process_file.pm, lss_share_library.pm, terminate_install.pm:

	Adapt to new remote directory structure.

2007-08-02 07:22  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/doc/rsd.html:

	Major reorganisation of remote directory structure:-
	  1)  Removal of the libs/ build directory level.  Now installed
	      libraries are placed directly under libs/
	  2)  Creation of parallel rsd/ structure to hold external build products
	      and admin info.
	The driver for the change is to make much shorter library paths (up to
	30 characters short) as previous paths caused gcc 3.2.3 to SegV and
	Rerootjob to fail (path overflowed internal buffer in CALINI). As
	a cosmetic by product the new structure is easier to read.

2007-08-02 07:22  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/DataCacheManager/resource_set_lock.pm:

	Fix typo in comment.

2007-08-02 07:22  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/DataCacheManager/init_local_disks.pm:

	Bug fix: Was not setting $DSK::DCM_catalogue or $DSK::resource_lock_dir
	correctly in WN mode.

2007-08-02 07:22  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/: DataCacheManager/init.pm,
	  DataCacheManager/docs/dcm.html,
	  Scripts/maintenance/version_number:

	Update to version V00-07-30

2007-08-01 21:49  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, Extraction/NCAnalysisModule.cxx:

	NCAnalysisModule::FindSurvivalProbability() didnt treat nu_e NC events
	correctly, it just gave every nu_e event a survival probability of 1

2007-08-01 21:45  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCEnergyBin.cxx, NCEnergyBin.h,
	  NCExtrapolationDP.cxx, NCExtrapolationNS.cxx,
	  NCExtrapolationRS.cxx:

	add vectors, variables, and such to NCEnergyBin to handle beam nu_e events
	that are in the MC.  the background now consists of explicit arrays for
	nc/nu_mu cc, nu_tau cc, and nu_e cc in each bin.

	fix a couple of lines in RS extrapolation to account for the change in
	ncenergy bin, namely lines 1476 and 1499...it just adds the electrons to
	the sum of backgrounds

	fix up DP object code formatting.

	make far and near masses constants in NS object, some debugging changes

2007-08-01 21:29  koskinen

	* NCUtils/Extrapolation/NCExtrapolationJK.h:

	A nefarious MakeRecoChangeHistos function made it's way into the header
	file, while it was unsupported by source file.

2007-08-01 21:15  koskinen

	* NCUtils/Extrapolation/: NCExtrapolationJK.cxx,
	  NCExtrapolationJK.h:

	The F/N method has been updated to use the NCEnergyBin object for loading
	and Monte Carlo. All important histograms have been converted to vectors of
	histograms. A memory leak resulting from the numerous instances of cloned
	histograms has also been resolved. Fitting for the CC sample has also been
	implemented.

2007-08-01 21:00  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationModule.cxx:

	dont pass through events from tau files that were originally nu_e before
	being oscillated.

2007-08-01 20:43  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCBeam.cxx:

	handle case where energy of event is > max energy allowed to look at.  in
	that case just dont use the event, ie it doesnt get passed on to the
	NCEnergyBin objects.  before the events were put into the largest energy
	bin which isnt correct

2007-08-01 18:21  rustem

	* PhysicsNtuple/Config/PlotKinem.xml:

	New histogram definitions.

2007-08-01 18:20  rustem

	* PhysicsNtuple/: BeamData.h, DataItem.h, RunAlgEvent.cxx,
	  RunAlgEvent.h, RunAlgSnarl.cxx, RunAlgSnarl.h,
	  Config/PlotBasic.xml, Config/PlotBeam.xml, Config/PlotEvent.xml,
	  Config/PlotEventPid.xml, Config/PlotMuonId.xml,
	  Config/PlotkNN.xml, Fill/FillMuonId.cxx, Fill/FillMuonId.h,
	  Hist/HistMan.h, Plot/Data.cxx, Plot/Data.h, Plot/LinkDef.h,
	  Plot/Plot.cxx, Plot/Plot.h, Plot/PlotBasic.cxx, Plot/PlotBasic.h,
	  Plot/PlotBeam.cxx, Plot/PlotData.cxx, Plot/PlotData.h,
	  Plot/PlotEff.cxx, Plot/PlotPur.cxx, Plot/PlotSelect.cxx,
	  Plot/PlotSelect.h, Plot/PlotTruth.cxx, Select/SelectNeutrino.cxx,
	  Select/SelectNeutrino.h, kNNAlg/FillkNN.cxx, kNNAlg/FillkNN.h,
	  macros/make_data.C, macros/make_mc.C:

	A development snapshot:

	1) Change FillkNN algorithm to retrieve truth using a key, add an
	option to read input variables from track or event data array,

	2) Upgrade PlotData to ease the addition of the new truth categories,

	3) Change FillMuonId to add a truth key; make IsStudy a default option;
	add truth key,

	4) Add selection based on kinematic distributions.

	5) Add time span histogram to PlotBasic algorithm

	Lots of other small changes.

2007-08-01 13:55  raufer

	* NCUtils/Extrapolation/NCExtrapolationRS.cxx:

	Small updates. The default MC histos are now scaled by bin width to be able to overlay them with the other ones.

	I don't understand why they don't look the same if all my factors are set to 1. Need to investigate.

2007-08-01 13:10  raufer

	* NCUtils/Extrapolation/: NCExtrapolationModule.cxx,
	  NCExtrapolationModule.h:

	Add registry switch "FillChangeHistos"; default is true.

	If this is set to false in the job macro, histograms showing how shower and track energy changes affect the bin contents are not filled. This speeds up execution immensely for debugging.

2007-08-01 04:46  Robert Hatcher <rhatcher@fnal.gov>

	* NtupleUtils/NuGeneral.cxx:

	need #include <cassert> for assert() under gcc 4.1.

2007-08-01 04:43  Robert Hatcher <rhatcher@fnal.gov>

	* NtupleUtils/NuFluxHelper.cxx:

	need #include <cmath> for fabs() on gcc 4.0.1.

2007-07-31 18:30  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCExtrapolationJK.cxx,
	  NCExtrapolationJK.h:

	begin making adjustments to get CC spectrum into fit

2007-07-31 18:12  hartnell

	* NtupleUtils/NuGeneral.cxx:

	Change to MSG

2007-07-31 17:03  hartnell

	* NtupleUtils/: NuGeneral.cxx, NuGeneral.h:

	Added:

	std::string NuGeneral::GetReleaseDirToUse(std::string sPackageDir) const
	  ///this returns the location of either the test or base release
	  ///directory e.g. /home/hartnell/minos/minossoft/releases/development
	  ///which one depends on whether the package exists
	  ///the test release is returned if it exists
	  ///
	  ///sPackageDir should be say "Mad" or other package name
	  ///it also works if you give say "Mad/data"

2007-07-31 16:28  raufer

	* NCUtils/NCAnalysisUtils.cxx:

	Changed FindSurvivalProbability() to:

	- be more pedestrian so that Tobi can understand the boolean logic
	- take care of nu_e events (U_e3 is assumed to be 0)
	- not add nu_tau CC events which came from a beam nu_e
	- not add nu_tau NC events

2007-07-31 14:52  hartnell

	* NtupleUtils/NuHistos.cxx:

	Sanity check was in the wrong place

2007-07-31 14:51  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, Extrapolation/NCBeam.cxx,
	  Extrapolation/NCEnergyBin.cxx,
	  Extrapolation/NCExtrapolationDP.cxx,
	  Extrapolation/NCExtrapolationDP.h,
	  Extrapolation/NCExtrapolationModule.cxx,
	  macros/nearFarExtrapolation.C:

	debugging changes, nothing structural

2007-07-31 14:10  hartnell

	* NtupleUtils/: NuCounter.cxx, NuCuts.cxx, NuCuts.h,
	  NuDemoModule.cxx, NuExtraction.cxx, NuReco.cxx:

	Switch to using NuLibrary.

	Also, change the order in which variables are tested to determine
	whether to cut or extract data

2007-07-30 16:52  hartnell

	* NtupleUtils/: LinkDef.h, NuHistos.cxx, NuLibrary.cxx,
	  NuLibrary.h:

	NuLibrary is a singleton that allows access to all the other objects
	such as NuCuts, NuReco, etc.

	It's basically just a simpler interface to the code so that static
	objects don't have to be created throughout the code.

2007-07-30 16:24  llhsu

	* NCUtils/NCAnalysisUtils.cxx:

	Modifications to make FindNeugen weights explicitly pick up Carrot defaults when mcType is Carrot

2007-07-30 16:19  llhsu

	* NCUtils/NCType.h:

	Added Carrot Neugen parameters - LLH

2007-07-30 13:24  evans

	* NtupleUtils/NuHistos.cxx:

	Fixing the titles of the ND matrix method histograms so they now say
	'NearDet' rather than 'FarDet'.

2007-07-30 11:14  blake

	* AtNuAna/: AtNuEventNtuple.cxx, AtNuEventNtuple.h,
	  AtNuEventSelectionAB.cxx, AtNuEventSelectionAB.h,
	  AtNuEventType.h, AtNuEventViewer.cxx:

	modifications to AtNuEventSelectionAB.cxx class:
	 o introduced selection criteria for 'good' energy
	 o added horizontal muons to upward muons
	 o fix containment bug - now require DistToEdge>20cm AND TraceZ>15cm
	 o modified primary track/shower selection

2007-07-30 04:56  Nick West <n.west1@physics.oxford.ac.uk>

	* WebDocs/SnapshotRel.html:

	Add S07-07-27-R1-26

2007-07-27 22:33  George Irwin <gmieg@slac.stanford.edu>

	* setup/packages-S07-07-27-R1-26:

	First commit

2007-07-27 22:25  George Irwin <gmieg@slac.stanford.edu>

	* PhysicsNtuple/Plot/Plot.cxx:

	Add ' #include <cassert> ' for GCC 3.3.4

2007-07-27 20:02  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/: NCBeam.cxx, NCBeam.h,
	  NCExtrapolationDP.cxx, NCExtrapolationRS.cxx:

	make fDefaultMCHistogramCC(NC) private and provide a getter to access them.
	change NCExtrapolationRS to use the getter.

2007-07-27 19:41  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCType.h,
	  Extraction/NCAnalysisModule.cxx, Extrapolation/NCBeam.cxx,
	  Extrapolation/NCEnergyBin.cxx, Extrapolation/NCEnergyBin.h,
	  Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolation.h,
	  Extrapolation/NCExtrapolationDP.cxx,
	  Extrapolation/NCExtrapolationJK.cxx,
	  Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationModule.h,
	  Extrapolation/NCExtrapolationNS.cxx,
	  Extrapolation/NCExtrapolationNS.h, macros/nearFarExtrapolation.C:

	NCAnalysisUtils - more changes for using the correct run types with the
	SKZP reweighting.  make the survival probability return the correct values
	for nutaus

	NCType - add in run types

	NCAnalysisModule - same as NCAnalysisUtils

	NCBeam - changes to deug statements

	NCEnergyBin - use the correct weight based on runtype, add weights for
	data events, which is useful when using mc as data.  Change GetDataEnergy
	to GetDataInformation and get the weight as well as energy for each
	data event.  return the vector sizes for the weight vectors, make sure
	to fill the vectors for ND events as well.

	NCExtrapolation - add code to determine run type.  also add code to
	loop over chi^2 values in 3d parameter space to fill the 2D delta chi^2
	plots

	NCExtrapolationDP - remove a few bugs, such as not adding chi^2 penalty
	term for ma_res and make sure to apply nd shifts to FD even if those
	parameters are not explicitly turned on by the job macro

	NCExtrapolationJK - make it use NCEnergyBins and a few of the new functions
	in the base class.  also put the writing out of histograms into the
	WriteResources method.

	NCExtrapolationNS - some more debugging

	NCExtrapolationModule - add method to return the run type based on
	the run of an event

2007-07-27 18:16  raufer

	* NCUtils/Extrapolation/NCExtrapolationRS.cxx:

	Use GetTotalMC() in order to obtain the oscillated monte carlo prediction. This makes the fit return the correct values. That's quite a step forward!

2007-07-27 16:22  boehm

	* NueAna/NueHeader.h:

	Incrementing the classdef

2007-07-27 16:21  boehm

	* NueAna/macros/LoadLibs.C:

	Cleaning up some library loading

2007-07-27 16:16  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/install_daikon_scripts.sh:

	Bug fix: DAIKON_VERSION not DAIKON_VERISON

2007-07-27 16:13  kordosky

	* Contrib/kordosky/neugen_4vec/: Makefile, access_inuke_xsecs.cc,
	  compare_escale_response.C, do_plot_neugen.C,
	  hadronic_state_summary.fi, inuke_reweight.F, inuke_reweight.fi,
	  miketest4.F, plot_neugen.C, response_model.F, shower_ntuple.fi,
	  summarise_hadronic_system.F:

	updates

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/docs/ChangeLog:

	Minor updates to DCM, RSD and scripts.

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Scripts/setup/setup_wn.sh:

	Don"t attempt to source an application setup script for the very good
	reason that isn"t one.

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Scripts/setup/locate_and_run_setup_wn.sh:

	Switch to "Simulated GRID Mode" on basis of $MOG_SIMULATE_GRID, not $PBS_JOBNAME.

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Scripts/maintenance/version_number:

	Update to version V00-07-26

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Scripts/docs/Scripts.html:

	Major rewrite of section: Setting up the Environment on a Worker Node
	Simplify section: Simulated GRID Mode

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/install_minossoft.sh:

	Document according to new recommendation.

	Don"t check for presence of daikon_versions (minossoft is now
	the supporting library).

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/install_daikon_versions.sh:

	Document according to new recommendation.

	Create new non-(RSD)-standard link $RSD_TOP_DIR/$RSD_LIBRARY_VERSION

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/install_daikon_scripts.sh:

	Document according to new recommendation.

	Use new non-(RSD)-standard link $RSD_TOP_DIR/$RSD_LIBRARY_VERSION
	produced by install_daikon_versions.sh so that $DAIKON_VERISON
	can be e.g. daikon_02 and not the clumsy daikon_versions-daikon_02

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/libs_and_builds/:
	  install_GridTools.sh, install_MyODBC.sh, install_bfieldmap.sh,
	  install_cernlib.sh, install_dcap.sh, install_mysql.sh,
	  install_neugen3.sh, install_pythia.sh, install_root.sh,
	  install_unixODBC.sh:

	Document according to new recommendation.

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/install_GENIE.sh:

	Document according to new recommendation.

	C. Andreopoulos:

	  GENIE now requires XML2.
	  Check that all supporting libraries are present
	  Generate setup scripts.

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/build_config_table.dat:

	C. Andreopoulos: GENIE now requires XML2.

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/libs_and_builds/:
	  assemble_libxml2.sh, install_libxml2.sh:

	C. Andreopoulos: Add support for XML2.

2007-07-27 15:42  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/assemble_daikon_scripts.sh:

	Remove compiled python code before making tar.

2007-07-27 15:41  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/driver/cmd_remove.pm:

	Bug fix: define  $SYS::RSD_SW_DIR

	Do not do software surveys: remove is often called internally from an
	install job to remove unwanted libraries and the calling job will do a
	final survey.

2007-07-27 15:41  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/RemoteSoftwareDeployment/doc/rsd.html:

	Add warning that --build_config_table is not forwarded to remote installs.

	Add recommendation on documenting install scripts describing the setup
	scripts they produce and libraries that they require.

2007-07-27 15:41  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/DataCacheManager/docs/dcm.html:

	WN mode now assumes that it will access to full catalogues, even if
	the system is not in place yet.

2007-07-27 13:59  hartnell

	* NtupleUtils/NuHistos.cxx:

	Fill matrix method data histos as well

2007-07-27 13:45  raufer

	* NCUtils/macros/nearFarExtrapolation.C:

	Revert accidental cvs commit.

2007-07-27 13:42  raufer

	* NCUtils/NCType.h:

	Revert accidental commit

2007-07-27 13:35  raufer

	* NCUtils/: NCType.h, Extrapolation/NCExtrapolationRS.cxx,
	  macros/ncccSeparation.C, macros/nearFarExtrapolation.C:

	[no log message]

2007-07-27 13:33  raufer

	* NCUtils/Extrapolation/NCExtrapolation.cxx:

	Add a leg->Draw() command to fraw legend on contour plots.

2007-07-27 13:31  raufer

	* NCUtils/Extrapolation/: NCBeam.cxx, NCBeam.h:

	Add a histogram for "vanilla" monte carlo.

2007-07-26 23:01  rustem

	* PhysicsNtuple/Config/: PlotEff.xml, PlotPur.xml:

	Histogram definitions for purity andd efficiency algorithms.

2007-07-26 22:59  rustem

	* PhysicsNtuple/: Hist1d.h, RecoNu.h, Config/PlotEvent.xml,
	  Config/PlotEventPid.xml, Fill/FillMuonId.cxx, Fill/FillMuonId.h,
	  Plot/CountHist.cxx, Plot/CountHist.h, Plot/LinkDef.h,
	  Plot/Plot.cxx, Plot/Plot.h, Plot/PlotData.cxx, Plot/PlotEff.cxx,
	  Plot/PlotEff.h, Plot/PlotEvent.cxx, Plot/PlotEvent.h,
	  Plot/PlotPur.cxx, Plot/PlotPur.h, Plot/PlotSelect.cxx,
	  Plot/PlotSelect.h, Store/FillBeam.cxx, macros/make_data.C,
	  macros/make_mc.C:

	Take a snapshot of the develpment. Some of the majot changes: Hist1d<T> is now fully
	functional histogram template which has couple convinient functions that convert
	to/from TH1 classes; PlotEff uses Hist1d to merge bins that have less than a minimum
	number of entries; PlotSelect has more options for bins; etc.

2007-07-26 13:44  ishi

	* Contrib/ishi/2DFit/: FDFit.cxx, FDFit.h, NDFit.cxx, NDFit.h,
	  RunFDFit.C, RunNDFit.C:

	Analysis codes used for 2.5e20POT data.

2007-07-26 10:32  evans

	* NtupleUtils/: LinkDef.h, MajorityCurvature.cxx, NuFluxChain.cxx,
	  NuFluxChain.h, NuFluxHelper.cxx, NuFluxHelper.h,
	  macros/MakeMMFluxHelpers.C:

	Adding an implementation of code to make a beam matrix for extrapolation.

	NuFluxHelper makes the beam matrix. It's configurable to make the matrix
	for either numus or numubars, and even to make a non-square beam matrix if
	the mood takes you.

	NuFluxChain is a wrapper around a fluka file to give the interface required
	by NuFluxHelper.

	macros/MakeMMFluxHelpers.C is an example macro of how to make the beam
	matrix.

2007-07-26 10:29  tinti

	* Contrib/barr/na49an/makefile:

	add lMinuit to the makefile

2007-07-26 10:28  tinti

	* Contrib/barr/na49an/na49an.cxx:

	implemented minuit minimization

2007-07-25 22:16  George Irwin <gmieg@slac.stanford.edu>

	* setup/: packages-development, setup_minossoft_SLAC:

	Remove first set of obsolete and unused packages from development release.
	Edit BubbleSpeak, Islands, TOOL_Classes, USER_Classes out of development
	list.  Users can type "rmpkg <package_name>" in $SRT_PUBLIC_CONTEXT to
	delete these packages from their base release.

2007-07-25 18:45  litchfld

	* NCUtils/Extraction/NCExtractionDP.cxx:

	Add calls to Make2DHistograms() so these histograms can be filled later.

2007-07-25 16:07  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: Extrapolation/NCExtrapolationNS.cxx,
	  macros/nearFarExtrapolation.C:

	fix bugs in NS method

2007-07-25 16:02  Nick West <n.west1@physics.oxford.ac.uk>

	* Contrib/rhatcher/gminos_jobs/run_ral.sh:

	Fix bug calling rerootjob: input file is $GAFNAME not $name

2007-07-25 14:27  litchfld

	* NCUtils/Extraction/NCExtractionPL.cxx:

	Remove profanity from comments.

2007-07-25 14:15  litchfld

	* NCUtils/Extraction/: NCAnalysisModule.cxx, NCAnalysisModule.h,
	  NCExtractionPL.cxx, NCExtractionPL.h:

	Updated NCExtractionPL so that it implements more of the peripheral stuff, 'pdf' plots and the like.

	Some things still don't work right.  The calls to PrintEfficeiencytAndPurity() that i see in other objects WriteResources() methods cause segvs and i can't work out why.

	Thankfully these calls don't seem to be nessecary for the running of the extrapolation so can be commented out.

2007-07-25 14:10  litchfld

	* NCUtils/NCType.h:

	Put in algorithm designators for NCExtractionPL. Displaced Unknown extraction back one, so it is still the last one defined. Is this the correct thing to do?

2007-07-25 06:55  Sue Kasahara <schubert@hep.umn.edu>

	* ParticleTransportSim/PTSimApplication.cxx:

	Modify print statements.

2007-07-25 06:53  Sue Kasahara <schubert@hep.umn.edu>

	* MCApplication/: MCApplication.cxx, MCApplication.h:

	New methods:
	1)AddParticles, called by TVirtualMC::Init during initialization.
	2)AddIons, called by AddParticles.  Used to defined MINOS required ion
	types. Ions are defined according to ion particle definitions in
	TDatabasePDG, as filled by LoadMinosPDG, for all ions in table
	up to Z=28.

2007-07-25 06:46  Sue Kasahara <schubert@hep.umn.edu>

	* G3PTSim/TGeant3/TGeant3.cxx:

	Change ion codes of 4 ion types defined by TGeant3 to conform to
	pdg 2006 standard.  (This change has also been requested of the vmc team.)
	Only add ions to database if not already present.

2007-07-25 04:24  Robert Hatcher <rhatcher@fnal.gov>

	* NtupleUtils/NuHistos.cxx:

	fabs() needs #include <cmath> on gcc 3.4.3 and later.

2007-07-25 02:38  Sue Kasahara <schubert@hep.umn.edu>

	* G3PTSim/gtrak/gthion.F:

	Add protection during ion transport:
	C sk:begin
	C Modified 2007/07/24 S. Kasahara to protect against case where IKF=0
	C This may occur when EKF is nearly equal to or equal to ELOW(1)
	          IKF=MAX(IKF,1)
	C sk:end

2007-07-24 23:37  tjyang

	* MiniBooNEAna/: GNUMakefile, GNUmakefile:

	rename GNUMakefile to GNUmakefile

2007-07-24 19:47  Sue Kasahara <schubert@hep.umn.edu>

	* G3PTSim/TGeant3/: TGeant3.cxx, TGeant3.h:

	Changes to support addition and debugging of ion particles:
	1)Inncrease kMaxParticles, used to define a fixed size array
	  of particles pdg codes:
	    Int_t fPDGCode[kMaxParticles];  // Translation table of PDG codes
	  ,from 100 to 300.
	2)Add protection to TGeant3::DefineParticle to check if fixed
	  size array limit has been reached before adding new particle.
	3)Add print method Gppart to invoke G3 fortran routine gppart.
	1 & 2 have also been brought to vmc team attention.

2007-07-24 18:10  hartnell

	* NtupleUtils/: LinkDef.h, NuHistos.cxx, NuHistos.h:

	New class for making histograms

2007-07-24 18:02  hartnell

	* NtupleUtils/: NuReco.cxx, NuReco.h:

	Use new beam centre to calc radius.

	Move GetTruthInfo code into two separate functions.

2007-07-24 17:28  Sue Kasahara <schubert@hep.umn.edu>

	* Persistency/: PerInputStream.cxx, PerInputStream.h:

	Make use of root development fix of yesterday to improve dcache
	performance.  On a read of an NtpSt file with 1235 entries, latest
	benchmarks:
	1)Dcache 35 sec real, 11 sec cpu.
	2)xrootd 12 sec real, 11 sec cpu.
	This is on minos01.fnal.gov.
	The dcache performance is improved by a factor of 5 from what it
	was a couple days ago (165 sec real, 11 sec cpu), but still can't compete
	with either xrootd, or root dcache performance circa v5.10/00.

2007-07-24 17:16  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: Extrapolation/LinkDef.h,
	  Extrapolation/NCExtrapolationJK.cxx,
	  Extrapolation/NCExtrapolationJK.h, macros/nearFarExtrapolation.C:

	add JK method to link def.  comment out some unused variables in JK method,
	also convert to using NCExtrapolation::FindBeamIndex in AddEvent method.

2007-07-24 16:52  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCType.h,
	  Extrapolation/NCBeam.cxx, Extrapolation/NCBeam.h,
	  Extrapolation/NCEnergyBin.cxx, Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolationDP.cxx,
	  Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationNS.cxx:

	change the NCAnalysisUtils::FindSurvivalProbability method to actually return
	the oscillation probability in the case of nutau events.

	fix the plotting of the tau events and the calculation of their contribution
	in NCEnergyBin and NCBeam

	more corrections to NCExtrapolationNS to account for using different runs.

2007-07-24 16:47  koskinen

	* NCUtils/NCType.h:

	Comitting the edit made to NCType.h

2007-07-24 14:50  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/docs/ChangeLog:

	Minor updates to DCM, RSD and Scripts

2007-07-24 14:50  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/Scripts/docs/Scripts.html:

	Document WN environment.
	Describe Simulated GRID Mode

2007-07-24 14:50  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/build_config_table.dat:

	Use Robert"s pythia version number convention.

	C. Andreopoulos: Get log4cpp from downloads instead of CVS.

2007-07-24 14:50  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/RemoteSoftwareDeployment/libs_and_builds/assemble_log4cpp.sh:

	C. Andreopoulos: Side step problems with libtools (not present on PBS
	back-end). Rather than getting the code from cvs, get a tarball from
	http://downloads.sourceforge.net. The code in this tarball has a
	"configure" script; there is no need to run "autogen.sh".

2007-07-24 14:49  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/: DataCacheManager/init.pm,
	  RemoteSoftwareDeployment/doc/rsd.html,
	  RemoteSoftwareDeployment/driver/initialise_globals.pm,
	  Scripts/maintenance/version_number:

	Update to version V00-07-25

2007-07-24 14:49  Nick West <n.west1@physics.oxford.ac.uk>

	* GridTools/DataCacheManager/: frs_collect_file_list.pm,
	  frs_get_local_dest_dir.pm, frs_retrieve_all_files.pm,
	  frs_retrieve_next_batch.pm, get_cmd_options.pm, main.pm,
	  docs/dcm.html, docs/help_summary.txt:

	Introduce get option --preserve_rel_dir to preserve relative directory
	structure.  Useful when copying flux files.

2007-07-24 14:49  Nick West <n.west1@physics.oxford.ac.uk>

	*
	  GridTools/DataCacheManager/config/minos.site_ral_t1_wn.local_disks:

	Short term hack, until system in place to propagate catalogues: use UI
	catlogue.

2007-07-24 13:50  koskinen

	* NCUtils/Extrapolation/: NCExtrapolationJK.cxx,
	  NCExtrapolationJK.h, NCExtrapolationModule.cxx,
	  NCExtrapolationModule.h:

	Adds the Far/Near extrapolation method to the NCUtils package.

2007-07-24 10:45  Nick West <n.west1@physics.oxford.ac.uk>

	* DatabaseMaintenance/tools/expire_duplicate_rows.perl:

	Add --delete_and_fixup

2007-07-23 15:56  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolation.h,
	  Extrapolation/NCExtrapolationDP.cxx,
	  Extrapolation/NCExtrapolationNS.cxx,
	  Extrapolation/NCExtrapolationRS.cxx,
	  macros/nearFarExtrapolation.C:

	make NCExtrapolation::FindBeamIndex() a bit more intelligent.  give it
	2 additional arguments, a bool and a double.  if the bool is true and
	the beam isnt found in the vector, then that beam will be added to the
	vector.  otherwise it still returns a nonsense index. the default is for
	the bool to be false.  it should only be set to true in the Add*Event
	methods.

2007-07-23 15:27  Brian Rebel <brebel@fnal.gov>

	* NCUtils/Extrapolation/NCExtrapolationNS.cxx:

	finish making NS method account for different run types

2007-07-23 13:19  raufer

	* NCUtils/Extrapolation/NCExtrapolation.cxx:

	Fix some MSG("NCEXtrapolation") typos.

2007-07-23 13:18  raufer

	* NCUtils/Extrapolation/: NCExtrapolationRS.cxx,
	  NCExtrapolationRS.h:

	Change beam loop to new FindBeamIndex() method

2007-07-23 13:15  raufer

	* AnalysisNtuples/ANtpRecoInfo.h:

	Increment ClassDef number. Brian recently added a new data member.

2007-07-22 01:18  Brian Rebel <brebel@fnal.gov>

	* AnalysisNtuples/: ANtpRecoInfo.cxx, ANtpRecoInfo.h:

	add new weight variable for run II skzp weights

2007-07-22 01:12  Brian Rebel <brebel@fnal.gov>

	* NCUtils/: NCAnalysisUtils.cxx, NCAnalysisUtils.h,
	  Extraction/NCAnalysisModule.cxx, Extrapolation/NCBeam.cxx,
	  Extrapolation/NCBeam.h, Extrapolation/NCEnergyBin.cxx,
	  Extrapolation/NCEnergyBin.h,
	  Extrapolation/NCEnergyBinGradients.cxx,
	  Extrapolation/NCEnergyBinGradients.h,
	  Extrapolation/NCExtrapolation.cxx,
	  Extrapolation/NCExtrapolation.h,
	  Extrapolation/NCExtrapolationDP.cxx,
	  Extrapolation/NCExtrapolationDP.h,
	  Extrapolation/NCExtrapolationMQ.cxx,
	  Extrapolation/NCExtrapolationMQ.h,
	  Extrapolation/NCExtrapolationModule.cxx,
	  Extrapolation/NCExtrapolationModule.h,
	  Extrapolation/NCExtrapolationNS.cxx,
	  Extrapolation/NCExtrapolationNS.h,
	  Extrapolation/NCExtrapolationRS.cxx,
	  Extrapolation/NCExtrapolationRS.h:

	prepare for using the post shutdown data.  run type is designated by a
	placeholder int for now, but will change to RunType::RunType_t when it is
	available.

	also change many instances of loops to look for a beam index to calls to
	NCExtrapolation::FindBeamIndex() method in the extrapolation methods.

2007-07-21 17:40  Ed Larty <lartey@hepr0.physics.tamu.edu>

	* setup/packages-R1.24.3:

	# Added missen packages

2007-07-21 17:19  Ed Larty <lartey@hepr0.physics.tamu.edu>

	* setup/packages-development:

	# modified package development for missing package MiniBooNEAna